diff options
4605 files changed, 41208 insertions, 15742 deletions
diff --git a/.codecov.yml b/.codecov.yml index 4072fa8974..a70b19c39c 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -4,13 +4,13 @@ coverage: range: 60...90 status: project: - default: yes + default: + threshold: 0.3% ignore: - lib/spack/spack/test/.* - lib/spack/docs/.* - lib/spack/external/.* - share/spack/qa/.* - - share/spack/spack-completion.bash comment: off diff --git a/.coveragerc b/.coveragerc index c0c5f76688..7292badff5 100644 --- a/.coveragerc +++ b/.coveragerc @@ -9,6 +9,7 @@ omit = lib/spack/spack/test/* lib/spack/docs/* lib/spack/external/* + share/spack/qa/* [report] # Regexes for lines to exclude from consideration diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000000..95105a3731 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +*.py diff=python diff --git a/.github/actions/add-maintainers-as-reviewers/entrypoint.py b/.github/actions/add-maintainers-as-reviewers/entrypoint.py index 53f7318f82..aa89fcd468 100755 --- a/.github/actions/add-maintainers-as-reviewers/entrypoint.py +++ b/.github/actions/add-maintainers-as-reviewers/entrypoint.py @@ -1,6 +1,6 @@ #!/usr/bin/env python # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/.github/workflows/linux_build_tests.yaml b/.github/workflows/linux_build_tests.yaml new file mode 100644 index 0000000000..27be6c3c18 --- /dev/null +++ b/.github/workflows/linux_build_tests.yaml @@ -0,0 +1,57 @@ +name: linux builds + +on: + push: + branches: + - master + - develop + pull_request: + branches: + - master + - develop + paths-ignore: + # Don't run if we only modified packages in the built-in repository + - 'var/spack/repos/builtin/**' + - '!var/spack/repos/builtin/packages/lz4/**' + - '!var/spack/repos/builtin/packages/mpich/**' + - '!var/spack/repos/builtin/packages/tut/**' + - '!var/spack/repos/builtin/packages/py-setuptools/**' + - '!var/spack/repos/builtin/packages/openjpeg/**' + - '!var/spack/repos/builtin/packages/r-rcpp/**' + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + max-parallel: 4 + matrix: + package: [lz4, mpich, tut, py-setuptools, openjpeg, r-rcpp] + steps: + - uses: actions/checkout@v1 + - name: Cache ccache's store + uses: actions/cache@v1 + with: + path: ~/.ccache + key: ccache-build-${{ matrix.package }} + restore-keys: | + ccache-build-${{ matrix.package }} + - name: Setup Python + uses: actions/setup-python@v1 + with: + python-version: 3.8 + - name: Install System Packages + run: | + sudo apt-get -yqq install ccache gfortran perl perl-base r-base r-base-core r-base-dev findutils openssl libssl-dev libpciaccess-dev + R --version + perl --version + - name: Copy Configuration + run: | + ccache -M 300M && ccache -z + # Set up external deps for build tests, b/c they take too long to compile + cp share/spack/qa/configuration/*.yaml etc/spack/ + - name: Run the build test + run: | + . share/spack/setup-env.sh + SPEC=${{ matrix.package }} share/spack/qa/run-build-tests + ccache -s diff --git a/.github/workflows/minimum_python_versions.yaml b/.github/workflows/minimum_python_versions.yaml new file mode 100644 index 0000000000..c55042ffa1 --- /dev/null +++ b/.github/workflows/minimum_python_versions.yaml @@ -0,0 +1,30 @@ +name: python version check + +on: + push: + branches: + - master + - develop + pull_request: + branches: + - master + - develop +jobs: + validate: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v1 + - name: Setup Python + uses: actions/setup-python@v1 + with: + python-version: 3.7 + - name: Install Python Packages + run: | + pip install --upgrade pip + pip install --upgrade vermin + - name: Minimum Version (Spack's Core) + run: vermin --backport argparse -t=2.6- -t=3.5- -v lib/spack/spack/ lib/spack/llnl/ bin/ + - name: Minimum Version (Repositories) + run: vermin --backport argparse -t=2.6- -t=3.5- -v var/spack/repos diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml deleted file mode 100644 index f0cfd456ff..0000000000 --- a/.gitlab-ci.yml +++ /dev/null @@ -1,14 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -generate ci jobs: - script: - - "./bin/generate-gitlab-ci-yml.sh" - tags: - - "spack-pre-ci" - artifacts: - paths: - - ci-generation - when: always diff --git a/.travis.yml b/.travis.yml index c9d442ee8e..86b9f4d3db 100644 --- a/.travis.yml +++ b/.travis.yml @@ -61,61 +61,10 @@ jobs: language: generic env: [ TEST_SUITE=unit, PYTHON_VERSION=2.7, COVERAGE=true ] if: type != pull_request -# mpich (AutotoolsPackage) - - stage: 'build tests' - python: '2.7' - os: linux - language: python - env: [ TEST_SUITE=build, 'SPEC=mpich' ] -# astyle (MakefilePackage) - - python: '3.8' - os: linux - language: python - env: [ TEST_SUITE=build, 'SPEC=astyle' ] -# tut (WafPackage) - - python: '3.8' - os: linux - language: python - env: [ TEST_SUITE=build, 'SPEC=tut' ] -# py-setuptools (PythonPackage) - - python: '3.8' - os: linux - language: python - env: [ TEST_SUITE=build, 'SPEC=py-setuptools' ] -# perl-dbi (PerlPackage) -# - python: '3.8' -# os: linux -# language: python -# env: [ TEST_SUITE=build, 'SPEC=perl-dbi' ] -# openjpeg (CMakePackage + external cmake) - - python: '3.8' - os: linux - language: python - env: [ TEST_SUITE=build, 'SPEC=openjpeg' ] -# r-rcpp (RPackage + external R) - - python: '3.8' - os: linux - language: python - env: [ TEST_SUITE=build, 'SPEC=r-rcpp' ] -# mpich (AutotoolsPackage) - - python: '3.8' - os: linux - language: python - env: [ TEST_SUITE=build, 'SPEC=mpich' ] - - python: '3.8' - stage: 'docker build' - os: linux - language: python - env: TEST_SUITE=docker - allow_failures: - - env: TEST_SUITE=docker stages: - 'style checks' - 'unit tests + documentation' - - 'build tests' - - name: 'docker build' - if: type = push AND branch IN (develop, master) #============================================================================= @@ -159,7 +108,6 @@ cache: pip: true ccache: true directories: - - ~/.mirror - ~/.ccache # Work around Travis's lack of support for Python on OSX @@ -192,17 +140,9 @@ before_script: # Need this to be able to compute the list of changed files - git fetch origin ${TRAVIS_BRANCH}:${TRAVIS_BRANCH} - # Set up external deps for build tests, b/c they take too long to compile - - if [[ "$TEST_SUITE" == "build" ]]; then - cp share/spack/qa/configuration/*.yaml etc/spack/; - fi - #============================================================================= # Building #============================================================================= -services: - - docker - script: - share/spack/qa/run-$TEST_SUITE-tests @@ -68,10 +68,6 @@ PackageName: py PackageHomePage: https://pypi.python.org/pypi/py PackageLicenseDeclared: MIT -PackageName: pyqver -PackageHomePage: https://github.com/ghewgill/pyqver -PackageLicenseDeclared: BSD-3-Clause - PackageName: pytest PackageHomePage: https://pypi.python.org/pypi/pytest PackageLicenseDeclared: MIT diff --git a/LICENSE-MIT b/LICENSE-MIT index 7ddb1a64ee..4f8ce2fc44 100644 --- a/LICENSE-MIT +++ b/LICENSE-MIT @@ -1,4 +1,4 @@ -Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. Permission is hereby granted, free of charge, to any person obtaining a @@ -1,6 +1,7 @@ # <img src="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo.svg" width="64" valign="middle" alt="Spack"/> Spack [](https://travis-ci.org/spack/spack) +[](https://github.com/spack/spack/actions) [](https://codecov.io/gh/spack/spack) [](https://spack.readthedocs.io) [](https://spackpm.herokuapp.com) diff --git a/bin/generate-gitlab-ci-yml.sh b/bin/generate-gitlab-ci-yml.sh deleted file mode 100755 index bb59199cf2..0000000000 --- a/bin/generate-gitlab-ci-yml.sh +++ /dev/null @@ -1,91 +0,0 @@ -#! /usr/bin/env bash - -# Remember where we are initially, it's the repo cloned by gitlab-ci -original_directory=$(pwd) -. "${original_directory}/share/spack/setup-env.sh" - -# Create a temporary working directory -temp_dir=$(mktemp -d) -trap 'rm -rf "$temp_dir"' INT TERM QUIT EXIT - -if [ -z "${DOWNSTREAM_CI_REPO}" ] ; then - echo "ERROR: missing variable: DOWNSTREAM_CI_REPO" >&2 - exit 1 -fi - -if [ -z "${SPACK_RELEASE_ENVIRONMENT_PATH}" ] ; then - echo "ERROR: missing variable: SPACK_RELEASE_ENVIRONMENT_PATH" >&2 - exit 1 -fi - -if [ -z "${CDASH_AUTH_TOKEN}" ] ; then - echo "WARNING: missing variable: CDASH_AUTH_TOKEN" >&2 -else - token_file="${temp_dir}/cdash_auth_token" - echo ${CDASH_AUTH_TOKEN} > ${token_file} -fi - -if [ -z "${SPACK_RELEASE_ENVIRONMENT_REPO}" ] ; then - echo "Assuming spack repo contains environment" >&2 - env_repo_dir=${original_directory} -else - echo "Cloning ${SPACK_RELEASE_ENVIRONMENT_REPO} into ${temp_dir}/envrepo" >&2 - cd ${temp_dir} - git clone ${SPACK_RELEASE_ENVIRONMENT_REPO} envrepo - cd envrepo - env_repo_dir=$(pwd) -fi - -current_branch="$CI_COMMIT_REF_NAME" - -# Because want to see generated gitlab-ci file as an artifact, -# we need to write it within the spack repo cloned by gitlab-ci. -gen_ci_dir="${original_directory}/ci-generation" -gen_ci_file="${gen_ci_dir}/.gitlab-ci.yml" -mkdir -p ${gen_ci_dir} - -env_dir="${env_repo_dir}/${SPACK_RELEASE_ENVIRONMENT_PATH}" - -if [ ! -f "${env_dir}/spack.yaml" ] ; then - echo "ERROR: Cannot find spack environment file in ${env_dir}" - exit 1 -fi - -cd $env_dir - -# The next commands generates the .gitlab-ci.yml (and optionally creates a -# buildgroup in cdash) -RELEASE_JOBS_ARGS=("--output-file" "${gen_ci_file}") -if [ ! -z "${token_file}" ]; then - RELEASE_JOBS_ARGS+=("--cdash-credentials" "${token_file}") -fi - -spack release-jobs "${RELEASE_JOBS_ARGS[@]}" - -if [[ $? -ne 0 ]]; then - echo "spack release-jobs command failed" - exit 1 -fi - -cd "$original_directory" -mv .git "$temp_dir/original-git-dir" -git init . - -git config user.email "robot@spack.io" -git config user.name "Spack Build Bot" - -cp ${gen_ci_file} "${original_directory}/.gitlab-ci.yml" -git add . - -echo "git commit" -commit_message="Auto-generated commit testing" -commit_message="${commit_message} ${current_branch} (${CI_COMMIT_SHA})" -git commit --message="${commit_message}" - -echo "git push" -git remote add origin "$DOWNSTREAM_CI_REPO" -git push --force origin "master:multi-ci-${current_branch}" - -rm -rf .git -mv "$temp_dir/original-git-dir" .git -git reset --hard HEAD diff --git a/bin/rebuild-index.sh b/bin/rebuild-index.sh deleted file mode 100755 index 009010baf1..0000000000 --- a/bin/rebuild-index.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash - -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -set -x - -SPACK_BIN_DIR="${CI_PROJECT_DIR}/bin" -export PATH="${SPACK_BIN_DIR}:${PATH}" - -spack buildcache update-index -d "$MIRROR_URL" diff --git a/bin/rebuild-package.sh b/bin/rebuild-package.sh deleted file mode 100755 index 657e431052..0000000000 --- a/bin/rebuild-package.sh +++ /dev/null @@ -1,399 +0,0 @@ -#!/bin/bash - -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -### -### This script represents a gitlab-ci job, corresponding to a single release -### spec. As such this script must first decide whether or not the spec it -### has been assigned is up to date on the remote binary mirror. If it is -### not (i.e. the source code has changed in a way that caused a change in the -### full_hash of the spec), this script will build the package, create a -### binary cache for it, and then push all related files to the remote binary -### mirror. This script also optionally communicates with a remote CDash -### instance to share status on the package build process. -### -### The following environment variables are (possibly) used within this script -### in order for the various elements function properly. -### -### First are two defaults we rely on from gitlab: -### -### CI_PROJECT_DIR -### CI_JOB_NAME -### -### The following must be set up in the variables section of gitlab: -### -### AWS_ACCESS_KEY_ID -### AWS_SECRET_ACCESS_KEY -### SPACK_SIGNING_KEY -### -### SPACK_S3_UPLOAD_MIRROR_URL // only required in the short term for the cloud case -### -### The following variabes are defined by the ci generation process and are -### required: -### -### SPACK_ENABLE_CDASH -### SPACK_ROOT_SPEC -### SPACK_MIRROR_URL -### SPACK_JOB_SPEC_PKG_NAME -### SPACK_COMPILER_ACTION -### -### Finally, these variables are optionally defined by the ci generation -### process, and may or may not be present: -### -### SPACK_CDASH_BASE_URL -### SPACK_CDASH_PROJECT -### SPACK_CDASH_PROJECT_ENC -### SPACK_CDASH_BUILD_NAME -### SPACK_CDASH_SITE -### SPACK_RELATED_BUILDS -### SPACK_JOB_SPEC_BUILDGROUP -### - -shopt -s expand_aliases - -export FORCE_UNSAFE_CONFIGURE=1 - -TEMP_DIR="${CI_PROJECT_DIR}/jobs_scratch_dir" - -JOB_LOG_DIR="${TEMP_DIR}/logs" -SPEC_DIR="${TEMP_DIR}/specs" -LOCAL_MIRROR="${CI_PROJECT_DIR}/local_mirror" -BUILD_CACHE_DIR="${LOCAL_MIRROR}/build_cache" -SPACK_BIN_DIR="${CI_PROJECT_DIR}/bin" - -if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then - CDASH_UPLOAD_URL="${SPACK_CDASH_BASE_URL}/submit.php?project=${SPACK_CDASH_PROJECT_ENC}" - DEP_JOB_RELATEBUILDS_URL="${SPACK_CDASH_BASE_URL}/api/v1/relateBuilds.php" - declare -a JOB_DEPS_PKG_NAMES -fi - -export SPACK_ROOT=${CI_PROJECT_DIR} -# export PATH="${SPACK_BIN_DIR}:${PATH}" -export GNUPGHOME="${CI_PROJECT_DIR}/opt/spack/gpg" - -. "${CI_PROJECT_DIR}/share/spack/setup-env.sh" - -mkdir -p ${JOB_LOG_DIR} -mkdir -p ${SPEC_DIR} - -cleanup() { - set +x - - if [ -z "$exit_code" ] ; then - - exit_code=$1 - if [ -z "$exit_code" ] ; then - exit_code=0 - fi - - restore_io - - if [ "$( type -t finalize )" '=' 'function' ] ; then - finalize "$JOB_LOG_DIR/cdash_log.txt" - fi - - # We can clean these out later on, once we have a good sense for - # how the logging infrastructure is working - # rm -rf "$JOB_LOG_DIR" - fi - - \exit $exit_code -} - -alias exit='cleanup' - -begin_logging() { - trap "cleanup 1; \\exit \$exit_code" INT TERM QUIT - trap "cleanup 0; \\exit \$exit_code" EXIT - - rm -rf "$JOB_LOG_DIR/cdash_log.txt" - - # NOTE: Here, some redirects are set up - exec 3>&1 # fd 3 is now a dup of stdout - exec 4>&2 # fd 4 is now a dup of stderr - - # stdout and stderr are joined and redirected to the log - exec &> "$JOB_LOG_DIR/cdash_log.txt" - - set -x -} - -restore_io() { - exec >&- - exec 2>&- - - exec >&3 - exec 2>&4 - - exec 3>&- - exec 4>&- -} - -finalize() { - # If you define a finalize function: - # - it will always be called at the very end of the script - # - the log file will be passed in as the first argument, and - # - the code in this function will not be logged. - echo "The full log file is located at $1" - # TODO: send this log data to cdash! -} - -check_error() -{ - local last_exit_code=$1 - local last_cmd=$2 - if [[ ${last_exit_code} -ne 0 ]]; then - echo "${last_cmd} exited with code ${last_exit_code}" - echo "TERMINATING JOB" - exit 1 - else - echo "${last_cmd} completed successfully" - fi -} - -extract_build_id() -{ - LINES_TO_SEARCH=$1 - regex="buildSummary\.php\?buildid=([[:digit:]]+)" - SINGLE_LINE_OUTPUT=$(echo ${LINES_TO_SEARCH} | tr -d '\n') - - if [[ ${SINGLE_LINE_OUTPUT} =~ ${regex} ]]; then - echo "${BASH_REMATCH[1]}" - else - echo "NONE" - fi -} - -get_relate_builds_post_data() -{ - cat <<EOF -{ - "project": "${1}", - "buildid": ${2}, - "relatedid": ${3}, - "relationship": "depends on" -} -EOF -} - -gen_full_specs_for_job_and_deps() { - SPEC_YAML_PATH="${SPEC_DIR}/${SPACK_JOB_SPEC_PKG_NAME}.yaml" - local spec_names_to_save="${SPACK_JOB_SPEC_PKG_NAME}" - - if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then - IFS=';' read -ra DEPS <<< "${SPACK_RELATED_BUILDS}" - for i in "${DEPS[@]}"; do - depPkgName="${i}" - spec_names_to_save="${spec_names_to_save} ${depPkgName}" - JOB_DEPS_PKG_NAMES+=("${depPkgName}") - done - fi - - if [ "${SPACK_COMPILER_ACTION}" == "FIND_ANY" ]; then - # This corresponds to a bootstrapping phase where we need to - # rely on any available compiler to build the package (i.e. the - # compiler needed to be stripped from the spec), and thus we need - # to concretize the root spec again. - spack -d buildcache save-yaml --specs "${spec_names_to_save}" --root-spec "${SPACK_ROOT_SPEC}" --yaml-dir "${SPEC_DIR}" - else - # in this case, either we're relying on Spack to install missing compiler - # bootstrapped in a previous phase, or else we only had one phase (like a - # site which already knows what compilers are available on it's runners), - # so we don't want to concretize that root spec again. The reason we need - # this in the first case (bootstrapped compiler), is that we can't concretize - # a spec at this point if we're going to ask spack to "install_missing_compilers". - tmp_dir=$(mktemp -d) - TMP_YAML_PATH="${tmp_dir}/root.yaml" - ROOT_SPEC_YAML=$(spack python -c "import base64 ; import zlib ; print(str(zlib.decompress(base64.b64decode('${SPACK_ROOT_SPEC}')).decode('utf-8')))") - echo "${ROOT_SPEC_YAML}" > "${TMP_YAML_PATH}" - spack -d buildcache save-yaml --specs "${spec_names_to_save}" --root-spec-yaml "${TMP_YAML_PATH}" --yaml-dir "${SPEC_DIR}" - rm -rf ${tmp_dir} - fi -} - -begin_logging - -echo "Running job for spec: ${CI_JOB_NAME}" - -# This should create the directory we referred to as GNUPGHOME earlier -spack gpg list - -# Importing the secret key using gpg2 directly should allow to -# sign and verify both -set +x -KEY_IMPORT_RESULT=`echo ${SPACK_SIGNING_KEY} | base64 --decode | gpg2 --import` -check_error $? "gpg2 --import" -set -x - -spack gpg list --trusted -spack gpg list --signing - -# To have spack install missing compilers, we need to add a custom -# configuration scope, then we pass that to the package installation -# command -CUSTOM_CONFIG_SCOPE_DIR="${TEMP_DIR}/config_scope" -mkdir -p "${CUSTOM_CONFIG_SCOPE_DIR}" -CUSTOM_CONFIG_SCOPE_ARG="" - -if [ "${SPACK_COMPILER_ACTION}" == "INSTALL_MISSING" ]; then - echo "Make sure bootstrapped compiler will be installed" - custom_config_file_path="${CUSTOM_CONFIG_SCOPE_DIR}/config.yaml" - cat <<CONFIG_STUFF > "${custom_config_file_path}" -config: - install_missing_compilers: true -CONFIG_STUFF - CUSTOM_CONFIG_SCOPE_ARG="-C ${CUSTOM_CONFIG_SCOPE_DIR}" - # Configure the binary mirror where, if needed, this jobs compiler - # was installed in binary pacakge form, then tell spack to - # install_missing_compilers. -elif [ "${SPACK_COMPILER_ACTION}" == "FIND_ANY" ]; then - echo "Just find any available compiler" - spack compiler find -else - echo "No compiler action to be taken" -fi - -# Finally, list the compilers spack knows about -echo "Compiler Configurations:" -spack config get compilers - -# Write full-deps yamls for this job spec and its dependencies -gen_full_specs_for_job_and_deps - -# Make the build_cache directory if it doesn't exist -mkdir -p "${BUILD_CACHE_DIR}" - -# Get buildcache name so we can write a CDash build id file in the right place. -# If we're unable to get the buildcache name, we may have encountered a problem -# concretizing the spec, or some other issue that will eventually cause the job -# to fail. -JOB_BUILD_CACHE_ENTRY_NAME=`spack -d buildcache get-buildcache-name --spec-yaml "${SPEC_YAML_PATH}"` -if [[ $? -ne 0 ]]; then - echo "ERROR, unable to get buildcache entry name for job ${CI_JOB_NAME}" - exit 1 -fi - -if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then - # Whether we have to build the spec or download it pre-built, we expect to find - # the cdash build id file sitting in this location afterwards. - JOB_CDASH_ID_FILE="${BUILD_CACHE_DIR}/${JOB_BUILD_CACHE_ENTRY_NAME}.cdashid" -fi - -# Finally, we can check the spec we have been tasked with build against -# the built binary on the remote mirror to see if it needs to be rebuilt -spack -d buildcache check --spec-yaml "${SPEC_YAML_PATH}" --mirror-url "${SPACK_MIRROR_URL}" --rebuild-on-error - -if [[ $? -ne 0 ]]; then - # Configure mirror - spack mirror add local_artifact_mirror "file://${LOCAL_MIRROR}" - - if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then - JOB_CDASH_ID="NONE" - - # Install package, using the buildcache from the local mirror to - # satisfy dependencies. - BUILD_ID_LINE=`spack -d -k -v "${CUSTOM_CONFIG_SCOPE_ARG}" install --keep-stage --cdash-upload-url "${CDASH_UPLOAD_URL}" --cdash-build "${SPACK_CDASH_BUILD_NAME}" --cdash-site "${SPACK_CDASH_SITE}" --cdash-track "${SPACK_JOB_SPEC_BUILDGROUP}" -f "${SPEC_YAML_PATH}" | grep "buildSummary\\.php"` - check_error $? "spack install" - - # By parsing the output of the "spack install" command, we can get the - # buildid generated for us by CDash - JOB_CDASH_ID=$(extract_build_id "${BUILD_ID_LINE}") - - # Write the .cdashid file to the buildcache as well - echo "${JOB_CDASH_ID}" >> ${JOB_CDASH_ID_FILE} - else - spack -d -k -v "${CUSTOM_CONFIG_SCOPE_ARG}" install --keep-stage -f "${SPEC_YAML_PATH}" - fi - - # Copy some log files into an artifact location, once we have a way - # to provide a spec.yaml file to more spack commands (e.g. "location") - # stage_dir=$(spack location --stage-dir -f "${SPEC_YAML_PATH}") - # build_log_file=$(find -L "${stage_dir}" | grep "spack-build\\.out") - # config_log_file=$(find -L "${stage_dir}" | grep "config\\.log") - # cp "${build_log_file}" "${JOB_LOG_DIR}/" - # cp "${config_log_file}" "${JOB_LOG_DIR}/" - - # Create buildcache entry for this package, reading the spec from the yaml - # file. - spack -d buildcache create --spec-yaml "${SPEC_YAML_PATH}" -a -f -d "${LOCAL_MIRROR}" --no-rebuild-index - check_error $? "spack buildcache create" - - # TODO: The upload-s3 command should eventually be replaced with something - # like: "spack buildcache put <mirror> <spec>", when that subcommand is - # properly implemented. - if [ ! -z "${SPACK_S3_UPLOAD_MIRROR_URL}" ] ; then - spack -d upload-s3 spec --base-dir "${LOCAL_MIRROR}" --spec-yaml "${SPEC_YAML_PATH}" --endpoint-url "${SPACK_S3_UPLOAD_MIRROR_URL}" - check_error $? "spack upload-s3 spec" - else - spack -d buildcache copy --base-dir "${LOCAL_MIRROR}" --spec-yaml "${SPEC_YAML_PATH}" --destination-url "${SPACK_MIRROR_URL}" - fi -else - echo "spec ${CI_JOB_NAME} is already up to date on remote mirror, downloading it" - - # Configure remote mirror so we can download buildcache entry - spack mirror add remote_binary_mirror ${SPACK_MIRROR_URL} - - # Now download it - BUILDCACHE_DL_ARGS=("--spec-yaml" "${SPEC_YAML_PATH}" "--path" "${BUILD_CACHE_DIR}/" ) - if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then - BUILDCACHE_DL_ARGS+=( "--require-cdashid" ) - fi - spack -d buildcache download "${BUILDCACHE_DL_ARGS[@]}" - check_error $? "spack buildcache download" -fi - -# The next step is to relate this job to the jobs it depends on -if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then - if [ -f "${JOB_CDASH_ID_FILE}" ]; then - JOB_CDASH_BUILD_ID=$(<${JOB_CDASH_ID_FILE}) - - if [ "${JOB_CDASH_BUILD_ID}" == "NONE" ]; then - echo "ERROR: unable to read this jobs id from ${JOB_CDASH_ID_FILE}" - exit 1 - fi - - # Now get CDash ids for dependencies and "relate" each dependency build - # with this jobs build - for DEP_PKG_NAME in "${JOB_DEPS_PKG_NAMES[@]}"; do - echo "Getting cdash id for dependency --> ${DEP_PKG_NAME} <--" - DEP_SPEC_YAML_PATH="${SPEC_DIR}/${DEP_PKG_NAME}.yaml" - DEP_JOB_BUILDCACHE_NAME=`spack -d buildcache get-buildcache-name --spec-yaml "${DEP_SPEC_YAML_PATH}"` - - if [[ $? -eq 0 ]]; then - DEP_JOB_ID_FILE="${BUILD_CACHE_DIR}/${DEP_JOB_BUILDCACHE_NAME}.cdashid" - echo "DEP_JOB_ID_FILE path = ${DEP_JOB_ID_FILE}" - - if [ -f "${DEP_JOB_ID_FILE}" ]; then - DEP_JOB_CDASH_BUILD_ID=$(<${DEP_JOB_ID_FILE}) - echo "File ${DEP_JOB_ID_FILE} contained value ${DEP_JOB_CDASH_BUILD_ID}" - echo "Relating builds -> ${SPACK_CDASH_BUILD_NAME} (buildid=${JOB_CDASH_BUILD_ID}) depends on ${DEP_PKG_NAME} (buildid=${DEP_JOB_CDASH_BUILD_ID})" - relateBuildsPostBody="$(get_relate_builds_post_data "${SPACK_CDASH_PROJECT}" ${JOB_CDASH_BUILD_ID} ${DEP_JOB_CDASH_BUILD_ID})" - relateBuildsResult=`curl "${DEP_JOB_RELATEBUILDS_URL}" -H "Content-Type: application/json" -H "Accept: application/json" -d "${relateBuildsPostBody}"` - echo "Result of curl request: ${relateBuildsResult}" - else - echo "ERROR: Did not find expected .cdashid file for dependency: ${DEP_JOB_ID_FILE}" - exit 1 - fi - else - echo "ERROR: Unable to get buildcache entry name for ${DEP_SPEC_NAME}" - exit 1 - fi - done - else - echo "ERROR: Did not find expected .cdashid file ${JOB_CDASH_ID_FILE}" - exit 1 - fi -fi - -# Show the size of the buildcache and a list of what's in it, directly -# in the gitlab log output -( - restore_io - du -sh ${BUILD_CACHE_DIR} - find ${BUILD_CACHE_DIR} -maxdepth 3 -type d -ls -) - -echo "End of rebuild package script" @@ -1,6 +1,6 @@ #!/bin/bash # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -103,10 +103,10 @@ interpreter_f="${interpreter_v[0]}" # Invoke any interpreter found, or raise an error if none was found. if [[ -n "$interpreter_f" ]]; then - if [[ "${interpreter_f##*/}" = "perl" ]]; then - exec $interpreter_v -x "$@" + if [[ "${interpreter_f##*/}" = "perl"* ]]; then + exec $interpreter -x "$@" else - exec $interpreter_v "$@" + exec $interpreter "$@" fi else echo "error: sbang found no interpreter in $script" @@ -1,7 +1,7 @@ #!/bin/sh # -*- python -*- # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/bin/spack-python b/bin/spack-python index 562b633c70..b81c8b7dbb 100755 --- a/bin/spack-python +++ b/bin/spack-python @@ -1,6 +1,6 @@ #!/bin/sh # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index 0d2d74b43f..56d60a29da 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -232,6 +232,50 @@ remove dependent packages *before* removing their dependencies or use the .. _nondownloadable: +^^^^^^^^^^^^^^^^^^ +Garbage collection +^^^^^^^^^^^^^^^^^^ + +When Spack builds software from sources, if often installs tools that are needed +just to build or test other software. These are not necessary at runtime. +To support cases where removing these tools can be a benefit Spack provides +the ``spack gc`` ("garbage collector") command, which will uninstall all unneeded packages: + +.. code-block:: console + + $ spack find + ==> 24 installed packages + -- linux-ubuntu18.04-broadwell / gcc@9.0.1 ---------------------- + autoconf@2.69 findutils@4.6.0 libiconv@1.16 libszip@2.1.1 m4@1.4.18 openjpeg@2.3.1 pkgconf@1.6.3 util-macros@1.19.1 + automake@1.16.1 gdbm@1.18.1 libpciaccess@0.13.5 libtool@2.4.6 mpich@3.3.2 openssl@1.1.1d readline@8.0 xz@5.2.4 + cmake@3.16.1 hdf5@1.10.5 libsigsegv@2.12 libxml2@2.9.9 ncurses@6.1 perl@5.30.0 texinfo@6.5 zlib@1.2.11 + + $ spack gc + ==> The following packages will be uninstalled: + + -- linux-ubuntu18.04-broadwell / gcc@9.0.1 ---------------------- + vn47edz autoconf@2.69 6m3f2qn findutils@4.6.0 ubl6bgk libtool@2.4.6 pksawhz openssl@1.1.1d urdw22a readline@8.0 + ki6nfw5 automake@1.16.1 fklde6b gdbm@1.18.1 b6pswuo m4@1.4.18 k3s2csy perl@5.30.0 lp5ya3t texinfo@6.5 + ylvgsov cmake@3.16.1 5omotir libsigsegv@2.12 leuzbbh ncurses@6.1 5vmfbrq pkgconf@1.6.3 5bmv4tg util-macros@1.19.1 + + ==> Do you want to proceed? [y/N] y + + [ ... ] + + $ spack find + ==> 9 installed packages + -- linux-ubuntu18.04-broadwell / gcc@9.0.1 ---------------------- + hdf5@1.10.5 libiconv@1.16 libpciaccess@0.13.5 libszip@2.1.1 libxml2@2.9.9 mpich@3.3.2 openjpeg@2.3.1 xz@5.2.4 zlib@1.2.11 + +In the example above Spack went through all the packages in the DB +and removed everything that is not either: + +1. A package installed upon explicit request of the user +2. A ``link`` or ``run`` dependency, even transitive, of one of the packages at point 1. + +You can check :ref:`cmd-spack-find-metadata` to see how to query for explicitly installed packages +or :ref:`dependency-types` for a more thorough treatment of dependency types. + ^^^^^^^^^^^^^^^^^^^^^^^^^ Non-Downloadable Tarballs ^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -414,6 +458,8 @@ Packages are divided into groups according to their architecture and compiler. Within each group, Spack tries to keep the view simple, and only shows the version of installed packages. +.. _cmd-spack-find-metadata: + """""""""""""""""""""""""""""""" Viewing more metadata """""""""""""""""""""""""""""""" @@ -883,11 +929,13 @@ in GNU Autotools. If all flags are set, the order is Compiler environment variables and additional RPATHs ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -In the exceptional case a compiler requires setting special environment -variables, like an explicit library load path. These can bet set in an -extra section in the compiler configuration (the supported environment -modification commands are: ``set``, ``unset``, ``append-path``, and -``prepend-path``). The user can also specify additional ``RPATHs`` that the +Sometimes compilers require setting special environment variables to +operate correctly. Spack handles these cases by allowing custom environment +modifications in the ``environment`` attribute of the compiler configuration +section. See also the :ref:`configuration_environment_variables` section +of the configuration files docs for more information. + +It is also possible to specify additional ``RPATHs`` that the compiler will add to all executables generated by that compiler. This is useful for forcing certain compilers to RPATH their own runtime libraries, so that executables will run without the need to set ``LD_LIBRARY_PATH``. @@ -904,28 +952,19 @@ that executables will run without the need to set ``LD_LIBRARY_PATH``. fc: /opt/gcc/bin/gfortran environment: unset: - BAD_VARIABLE: # The colon is required but the value must be empty + - BAD_VARIABLE set: GOOD_VARIABLE_NUM: 1 GOOD_VARIABLE_STR: good - prepend-path: + prepend_path: PATH: /path/to/binutils - append-path: + append_path: LD_LIBRARY_PATH: /opt/gcc/lib extra_rpaths: - /path/to/some/compiler/runtime/directory - /path/to/some/other/compiler/runtime/directory -.. note:: - - The section `environment` is interpreted as an ordered dictionary, which - means two things. First, environment modification are applied in the order - they are specified in the configuration file. Second, you cannot express - environment modifications that require mixing different commands, i.e. you - cannot `set` one variable, than `prepend-path` to another one, and than - again `set` a third one. - ^^^^^^^^^^^^^^^^^^^^^^^ Architecture specifiers ^^^^^^^^^^^^^^^^^^^^^^^ @@ -1271,10 +1310,9 @@ directly when you run ``python``: Using Extensions ^^^^^^^^^^^^^^^^ -There are three ways to get ``numpy`` working in Python. The first is -to use :ref:`shell-support`. You can simply ``load`` the -module for the extension, and it will be added to the ``PYTHONPATH`` -in your current shell: +There are four ways to get ``numpy`` working in Python. The first is +to use :ref:`shell-support`. You can simply ``load`` the extension, +and it will be added to the ``PYTHONPATH`` in your current shell: .. code-block:: console @@ -1284,11 +1322,29 @@ in your current shell: Now ``import numpy`` will succeed for as long as you keep your current session open. +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Loading Extensions via Modules +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Instead of using Spack's environment modification capabilities through +the ``spack load`` command, you can load numpy through your +environment modules (using ``environment-modules`` or ``lmod``). This +will also add the extension to the ``PYTHONPATH`` in your current +shell. + +.. code-block:: console + + $ module load <name of numpy module> + +If you do not know the name of the specific numpy module you wish to +load, you can use the ``spack module tcl|lmod loads`` command to get +the name of the module from the Spack spec. + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Activating Extensions in a View ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The second way to use extensions is to create a view, which merges the +Another way to use extensions is to create a view, which merges the python installation along with the extensions into a single prefix. See :ref:`filesystem-views` for a more in-depth description of views and :ref:`cmd-spack-view` for usage of the ``spack view`` command. diff --git a/lib/spack/docs/binary_caches.rst b/lib/spack/docs/binary_caches.rst index a54c0541c2..614ad2864c 100644 --- a/lib/spack/docs/binary_caches.rst +++ b/lib/spack/docs/binary_caches.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_settings.rst b/lib/spack/docs/build_settings.rst index fbd73d7a52..45f54084ae 100644 --- a/lib/spack/docs/build_settings.rst +++ b/lib/spack/docs/build_settings.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems.rst b/lib/spack/docs/build_systems.rst index 93b8e5c7a8..a68dd99911 100644 --- a/lib/spack/docs/build_systems.rst +++ b/lib/spack/docs/build_systems.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -56,6 +56,7 @@ on these ideas for each distinct build system that Spack supports: :maxdepth: 1 :caption: Other + build_systems/bundlepackage build_systems/cudapackage build_systems/intelpackage build_systems/custompackage diff --git a/lib/spack/docs/build_systems/autotoolspackage.rst b/lib/spack/docs/build_systems/autotoolspackage.rst index 4b6ea68726..a2baedd576 100644 --- a/lib/spack/docs/build_systems/autotoolspackage.rst +++ b/lib/spack/docs/build_systems/autotoolspackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/bundlepackage.rst b/lib/spack/docs/build_systems/bundlepackage.rst new file mode 100644 index 0000000000..e22e4b26be --- /dev/null +++ b/lib/spack/docs/build_systems/bundlepackage.rst @@ -0,0 +1,52 @@ +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other + Spack Project Developers. See the top-level COPYRIGHT file for details. + + SPDX-License-Identifier: (Apache-2.0 OR MIT) + +.. _bundlepackage: + +------------- +BundlePackage +------------- + +``BundlePackage`` represents a set of packages that are expected to work well +together, such as a collection of commonly used software libraries. The +associated software is specified as bundle dependencies. + + +^^^^^^^^ +Creation +^^^^^^^^ + +Be sure to specify the ``bundle`` template if you are using ``spack create`` +to generate a package from the template. For example, use the following +command to create a bundle package whose class name will be ``Mybundle``: + +.. code-block:: console + + $ spack create --template bundle --name mybundle + + + +^^^^^^ +Phases +^^^^^^ + +The ``BundlePackage`` base class does not provide any phases by default +since the bundle does not represent a build system. + + +^^^ +URL +^^^ + +The ``url`` property does not have meaning since there is no package-specific +code to fetch. + + +^^^^^^^ +Version +^^^^^^^ + +At least one ``version`` must be specified in order for the package to +build. diff --git a/lib/spack/docs/build_systems/cmakepackage.rst b/lib/spack/docs/build_systems/cmakepackage.rst index 7e246b11a1..0a771edad3 100644 --- a/lib/spack/docs/build_systems/cmakepackage.rst +++ b/lib/spack/docs/build_systems/cmakepackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/cudapackage.rst b/lib/spack/docs/build_systems/cudapackage.rst index d2097ac5ec..b4561c69ed 100644 --- a/lib/spack/docs/build_systems/cudapackage.rst +++ b/lib/spack/docs/build_systems/cudapackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/custompackage.rst b/lib/spack/docs/build_systems/custompackage.rst index 611ead22d4..8a20dada92 100644 --- a/lib/spack/docs/build_systems/custompackage.rst +++ b/lib/spack/docs/build_systems/custompackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/intelpackage.rst b/lib/spack/docs/build_systems/intelpackage.rst index f7d975899e..c14fc34f51 100644 --- a/lib/spack/docs/build_systems/intelpackage.rst +++ b/lib/spack/docs/build_systems/intelpackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/makefilepackage.rst b/lib/spack/docs/build_systems/makefilepackage.rst index 41a66a8137..406ec8ce89 100644 --- a/lib/spack/docs/build_systems/makefilepackage.rst +++ b/lib/spack/docs/build_systems/makefilepackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/mesonpackage.rst b/lib/spack/docs/build_systems/mesonpackage.rst index 22fc8d3e11..75b0e1caae 100644 --- a/lib/spack/docs/build_systems/mesonpackage.rst +++ b/lib/spack/docs/build_systems/mesonpackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/octavepackage.rst b/lib/spack/docs/build_systems/octavepackage.rst index 2405dbb387..90e582e36c 100644 --- a/lib/spack/docs/build_systems/octavepackage.rst +++ b/lib/spack/docs/build_systems/octavepackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/perlpackage.rst b/lib/spack/docs/build_systems/perlpackage.rst index 4eafe1248e..11968e1560 100644 --- a/lib/spack/docs/build_systems/perlpackage.rst +++ b/lib/spack/docs/build_systems/perlpackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/pythonpackage.rst b/lib/spack/docs/build_systems/pythonpackage.rst index 595f905e4a..3021f5b6dc 100644 --- a/lib/spack/docs/build_systems/pythonpackage.rst +++ b/lib/spack/docs/build_systems/pythonpackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/qmakepackage.rst b/lib/spack/docs/build_systems/qmakepackage.rst index 051ff1fe0b..81d0f7f798 100644 --- a/lib/spack/docs/build_systems/qmakepackage.rst +++ b/lib/spack/docs/build_systems/qmakepackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/rpackage.rst b/lib/spack/docs/build_systems/rpackage.rst index 5533792541..60c76816c5 100644 --- a/lib/spack/docs/build_systems/rpackage.rst +++ b/lib/spack/docs/build_systems/rpackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/rubypackage.rst b/lib/spack/docs/build_systems/rubypackage.rst index 44667257d3..6310507809 100644 --- a/lib/spack/docs/build_systems/rubypackage.rst +++ b/lib/spack/docs/build_systems/rubypackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/sconspackage.rst b/lib/spack/docs/build_systems/sconspackage.rst index fa0c190e6d..f29d6c5f45 100644 --- a/lib/spack/docs/build_systems/sconspackage.rst +++ b/lib/spack/docs/build_systems/sconspackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/sippackage.rst b/lib/spack/docs/build_systems/sippackage.rst index 1f0fb7b426..b8c08ec513 100644 --- a/lib/spack/docs/build_systems/sippackage.rst +++ b/lib/spack/docs/build_systems/sippackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/build_systems/wafpackage.rst b/lib/spack/docs/build_systems/wafpackage.rst index 9876106468..1916630f4c 100644 --- a/lib/spack/docs/build_systems/wafpackage.rst +++ b/lib/spack/docs/build_systems/wafpackage.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/chain.rst b/lib/spack/docs/chain.rst index ca6d0d4779..d84db87ff3 100644 --- a/lib/spack/docs/chain.rst +++ b/lib/spack/docs/chain.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/conf.py b/lib/spack/docs/conf.py index e5305a9317..e19dd05511 100644 --- a/lib/spack/docs/conf.py +++ b/lib/spack/docs/conf.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -176,7 +176,25 @@ exclude_patterns = ['_build', '_spack_root', '.spack-env'] #show_authors = False # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +# We use our own extension of the default style with a few modifications +from pygments.style import Style +from pygments.styles.default import DefaultStyle +from pygments.token import Generic, Comment, Text + +class SpackStyle(DefaultStyle): + styles = DefaultStyle.styles.copy() + background_color = "#f4f4f8" + styles[Generic.Output] = "#355" + styles[Generic.Prompt] = "bold #346ec9" + +import pkg_resources +dist = pkg_resources.Distribution(__file__) +sys.path.append('.') # make 'conf' module findable +ep = pkg_resources.EntryPoint.parse('spack = conf:SpackStyle', dist=dist) +dist._ep_map = {'pygments.styles': {'plugin1': ep}} +pkg_resources.working_set.add(dist) + +pygments_style = 'spack' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] diff --git a/lib/spack/docs/config_yaml.rst b/lib/spack/docs/config_yaml.rst index d8d07b505a..865845b274 100644 --- a/lib/spack/docs/config_yaml.rst +++ b/lib/spack/docs/config_yaml.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,11 +30,21 @@ Default is ``$spack/opt/spack``. ``install_hash_length`` and ``install_path_scheme`` --------------------------------------------------- -The default Spack installation path can be very long and can create -problems for scripts with hardcoded shebangs. There are two parameters -to help with that. Firstly, the ``install_hash_length`` parameter can -set the length of the hash in the installation path from 1 to 32. The -default path uses the full 32 characters. +The default Spack installation path can be very long and can create problems +for scripts with hardcoded shebangs. Additionally, when using the Intel +compiler, and if there is also a long list of dependencies, the compiler may +segfault. If you see the following: + + .. code-block:: console + + : internal error: ** The compiler has encountered an unexpected problem. + ** Segmentation violation signal raised. ** + Access violation or stack overflow. Please contact Intel Support for assistance. + +it may be because variables containing dependency specs may be too long. There +are two parameters to help with long path names. Firstly, the +``install_hash_length`` parameter can set the length of the hash in the +installation path from 1 to 32. The default path uses the full 32 characters. Secondly, it is also possible to modify the entire installation scheme. By default Spack uses diff --git a/lib/spack/docs/configuration.rst b/lib/spack/docs/configuration.rst index 7721c07a8e..41c9de79f9 100644 --- a/lib/spack/docs/configuration.rst +++ b/lib/spack/docs/configuration.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -427,6 +427,33 @@ home directory, and ``~user`` will expand to a specified user's home directory. The ``~`` must appear at the beginning of the path, or Spack will not expand it. +.. _configuration_environment_variables: + +------------------------- +Environment Modifications +------------------------- + +Spack allows to prescribe custom environment modifications in a few places +within its configuration files. Every time these modifications are allowed +they are specified as a dictionary, like in the following example: + +.. code-block:: yaml + + environment: + set: + LICENSE_FILE: '/path/to/license' + unset: + - CPATH + - LIBRARY_PATH + append_path: + PATH: '/new/bin/dir' + +The possible actions that are permitted are ``set``, ``unset``, ``append_path``, +``prepend_path`` and finally ``remove_path``. They all require a dictionary +of variable names mapped to the values used for the modification. +The only exception is ``unset`` that requires just a list of variable names. +No particular order is ensured on the execution of each of these modifications. + ---------------------------- Seeing Spack's Configuration ---------------------------- diff --git a/lib/spack/docs/containers.rst b/lib/spack/docs/containers.rst new file mode 100644 index 0000000000..bbb21a2e00 --- /dev/null +++ b/lib/spack/docs/containers.rst @@ -0,0 +1,307 @@ +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other + Spack Project Developers. See the top-level COPYRIGHT file for details. + + SPDX-License-Identifier: (Apache-2.0 OR MIT) + +.. _containers: + +================ +Container Images +================ + +Spack can be an ideal tool to setup images for containers since all the +features discussed in :ref:`environments` can greatly help to manage +the installation of software during the image build process. Nonetheless, +building a production image from scratch still requires a lot of +boilerplate to: + +- Get Spack working within the image, possibly running as root +- Minimize the physical size of the software installed +- Properly update the system software in the base image + +To facilitate users with these tedious tasks, Spack provides a command +to automatically generate recipes for container images based on +Environments: + +.. code-block:: console + + $ ls + spack.yaml + + $ spack containerize + # Build stage with Spack pre-installed and ready to be used + FROM spack/centos7:latest as builder + + # What we want to install and how we want to install it + # is specified in a manifest file (spack.yaml) + RUN mkdir /opt/spack-environment \ + && (echo "spack:" \ + && echo " specs:" \ + && echo " - gromacs+mpi" \ + && echo " - mpich" \ + && echo " concretization: together" \ + && echo " config:" \ + && echo " install_tree: /opt/software" \ + && echo " view: /opt/view") > /opt/spack-environment/spack.yaml + + # Install the software, remove unecessary deps + RUN cd /opt/spack-environment && spack install && spack gc -y + + # Strip all the binaries + RUN find -L /opt/view/* -type f -exec readlink -f '{}' \; | \ + xargs file -i | \ + grep 'charset=binary' | \ + grep 'x-executable\|x-archive\|x-sharedlib' | \ + awk -F: '{print $1}' | xargs strip -s + + # Modifications to the environment that are necessary to run + RUN cd /opt/spack-environment && \ + spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh + + + # Bare OS image to run the installed executables + FROM centos:7 + + COPY --from=builder /opt/spack-environment /opt/spack-environment + COPY --from=builder /opt/software /opt/software + COPY --from=builder /opt/view /opt/view + COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh + + RUN yum update -y && yum install -y epel-release && yum update -y \ + && yum install -y libgomp \ + && rm -rf /var/cache/yum && yum clean all + + RUN echo 'export PS1="\[$(tput bold)\]\[$(tput setaf 1)\][gromacs]\[$(tput setaf 2)\]\u\[$(tput sgr0)\]:\w $ \[$(tput sgr0)\]"' >> ~/.bashrc + + + LABEL "app"="gromacs" + LABEL "mpi"="mpich" + + ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"] + + +The bits that make this automation possible are discussed in details +below. All the images generated in this way will be based on +multi-stage builds with: + +- A fat ``build`` stage containing common build tools and Spack itself +- A minimal ``final`` stage containing only the software requested by the user + +----------------- +Spack Base Images +----------------- + +Docker images with Spack preinstalled and ready to be used are +built on `Docker Hub <https://hub.docker.com/u/spack>`_ +at every push to ``develop`` or to a release branch. The OS that +are currently supported are summarized in the table below: + +.. _containers-supported-os: + +.. list-table:: Supported operating systems + :header-rows: 1 + + * - Operating System + - Base Image + - Spack Image + * - Ubuntu 16.04 + - ``ubuntu:16.04`` + - ``spack/ubuntu-xenial`` + * - Ubuntu 18.04 + - ``ubuntu:16.04`` + - ``spack/ubuntu-bionic`` + * - CentOS 6 + - ``centos:6`` + - ``spack/centos6`` + * - CentOS 7 + - ``centos:7`` + - ``spack/centos7`` + +All the images are tagged with the corresponding release of Spack: + +.. image:: dockerhub_spack.png + +with the exception of the ``latest`` tag that points to the HEAD +of the ``develop`` branch. These images are available for anyone +to use and take care of all the repetitive tasks that are necessary +to setup Spack within a container. All the container recipes generated +automatically by Spack use them as base images for their ``build`` stage. + + +------------------------- +Environment Configuration +------------------------- + +Any Spack Environment can be used for the automatic generation of container +recipes. Sensible defaults are provided for things like the base image or the +version of Spack used in the image. If a finer tuning is needed it can be +obtained by adding the relevant metadata under the ``container`` attribute +of environments: + +.. code-block:: yaml + + spack: + specs: + - gromacs+mpi + - mpich + + container: + # Select the format of the recipe e.g. docker, + # singularity or anything else that is currently supported + format: docker + + # Select from a valid list of images + base: + image: "centos:7" + spack: develop + + # Whether or not to strip binaries + strip: true + + # Additional system packages that are needed at runtime + os_packages: + - libgomp + + # Extra instructions + extra_instructions: + final: | + RUN echo 'export PS1="\[$(tput bold)\]\[$(tput setaf 1)\][gromacs]\[$(tput setaf 2)\]\u\[$(tput sgr0)\]:\w $ \[$(tput sgr0)\]"' >> ~/.bashrc + + # Labels for the image + labels: + app: "gromacs" + mpi: "mpich" + +The tables below describe the configuration options that are currently supported: + +.. list-table:: General configuration options for the ``container`` section of ``spack.yaml`` + :header-rows: 1 + + * - Option Name + - Description + - Allowed Values + - Required + * - ``format`` + - The format of the recipe + - ``docker`` or ``singularity`` + - Yes + * - ``base:image`` + - Base image for ``final`` stage + - See :ref:`containers-supported-os` + - Yes + * - ``base:spack`` + - Version of Spack + - Valid tags for ``base:image`` + - Yes + * - ``strip`` + - Whether to strip binaries + - ``true`` (default) or ``false`` + - No + * - ``os_packages`` + - System packages to be installed + - Valid packages for the ``final`` OS + - No + * - ``extra_instructions:build`` + - Extra instructions (e.g. `RUN`, `COPY`, etc.) at the end of the ``build`` stage + - Anything understood by the current ``format`` + - No + * - ``extra_instructions:final`` + - Extra instructions (e.g. `RUN`, `COPY`, etc.) at the end of the ``final`` stage + - Anything understood by the current ``format`` + - No + * - ``labels`` + - Labels to tag the image + - Pairs of key-value strings + - No + +.. list-table:: Configuration options specific to Singularity + :header-rows: 1 + + * - Option Name + - Description + - Allowed Values + - Required + * - ``singularity:runscript`` + - Content of ``%runscript`` + - Any valid script + - No + * - ``singularity:startscript`` + - Content of ``%startscript`` + - Any valid script + - No + * - ``singularity:test`` + - Content of ``%test`` + - Any valid script + - No + * - ``singularity:help`` + - Description of the image + - Description string + - No + +Once the Environment is properly configured a recipe for a container +image can be printed to standard output by issuing the following +command from the directory where the ``spack.yaml`` resides: + +.. code-block:: console + + $ spack containerize + +The example ``spack.yaml`` above would produce for instance the +following ``Dockerfile``: + +.. code-block:: docker + + # Build stage with Spack pre-installed and ready to be used + FROM spack/centos7:latest as builder + + # What we want to install and how we want to install it + # is specified in a manifest file (spack.yaml) + RUN mkdir /opt/spack-environment \ + && (echo "spack:" \ + && echo " specs:" \ + && echo " - gromacs+mpi" \ + && echo " - mpich" \ + && echo " concretization: together" \ + && echo " config:" \ + && echo " install_tree: /opt/software" \ + && echo " view: /opt/view") > /opt/spack-environment/spack.yaml + + # Install the software, remove unecessary deps + RUN cd /opt/spack-environment && spack install && spack gc -y + + # Strip all the binaries + RUN find -L /opt/view/* -type f -exec readlink -f '{}' \; | \ + xargs file -i | \ + grep 'charset=binary' | \ + grep 'x-executable\|x-archive\|x-sharedlib' | \ + awk -F: '{print $1}' | xargs strip -s + + # Modifications to the environment that are necessary to run + RUN cd /opt/spack-environment && \ + spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh + + + # Bare OS image to run the installed executables + FROM centos:7 + + COPY --from=builder /opt/spack-environment /opt/spack-environment + COPY --from=builder /opt/software /opt/software + COPY --from=builder /opt/view /opt/view + COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh + + RUN yum update -y && yum install -y epel-release && yum update -y \ + && yum install -y libgomp \ + && rm -rf /var/cache/yum && yum clean all + + RUN echo 'export PS1="\[$(tput bold)\]\[$(tput setaf 1)\][gromacs]\[$(tput setaf 2)\]\u\[$(tput sgr0)\]:\w $ \[$(tput sgr0)\]"' >> ~/.bashrc + + + LABEL "app"="gromacs" + LABEL "mpi"="mpich" + + ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"] + +.. note:: + Spack can also produce Singularity definition files to build the image. The + minimum version of Singularity required to build a SIF (Singularity Image Format) + from them is ``3.5.3``.
\ No newline at end of file diff --git a/lib/spack/docs/contribution_guide.rst b/lib/spack/docs/contribution_guide.rst index 73f25c6f03..0b79141ee3 100644 --- a/lib/spack/docs/contribution_guide.rst +++ b/lib/spack/docs/contribution_guide.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -64,6 +64,8 @@ If you take a look in ``$SPACK_ROOT/.travis.yml``, you'll notice that we test against Python 2.6, 2.7, and 3.4-3.7 on both macOS and Linux. We currently perform 3 types of tests: +.. _cmd-spack-test: + ^^^^^^^^^^ Unit Tests ^^^^^^^^^^ @@ -86,40 +88,83 @@ To run *all* of the unit tests, use: $ spack test -These tests may take several minutes to complete. If you know you are only -modifying a single Spack feature, you can run a single unit test at a time: +These tests may take several minutes to complete. If you know you are +only modifying a single Spack feature, you can run subsets of tests at a +time. For example, this would run all the tests in +``lib/spack/spack/test/architecture.py``: + +.. code-block:: console + + $ spack test architecture.py + +And this would run the ``test_platform`` test from that file: .. code-block:: console - $ spack test architecture + $ spack test architecture.py::test_platform -This allows you to develop iteratively: make a change, test that change, make -another change, test that change, etc. To get a list of all available unit -tests, run: +This allows you to develop iteratively: make a change, test that change, +make another change, test that change, etc. We use `pytest +<http://pytest.org/>`_ as our tests fromework, and these types of +arguments are just passed to the ``pytest`` command underneath. See `the +pytest docs +<http://doc.pytest.org/en/latest/usage.html#specifying-tests-selecting-tests>`_ +for more details on test selection syntax. + +``spack test`` has a few special options that can help you understand +what tests are available. To get a list of all available unit test +files, run: .. command-output:: spack test --list + :ellipsis: 5 + +To see a more detailed list of available unit tests, use ``spack test +--list-long``: + +.. command-output:: spack test --list-long + :ellipsis: 10 + +And to see the fully qualified names of all tests, use ``--list-names``: -A more detailed list of available unit tests can be found by running -``spack test --long-list``. +.. command-output:: spack test --list-names + :ellipsis: 5 -By default, ``pytest`` captures the output of all unit tests. If you add print -statements to a unit test and want to see the output, simply run: +You can combine these with ``pytest`` arguments to restrict which tests +you want to know about. For example, to see just the tests in +``architecture.py``: + +.. command-output:: spack test --list-long architecture.py + +You can also combine any of these options with a ``pytest`` keyword +search. For example, to see the names of all tests that have "spec" +or "concretize" somewhere in their names: + +.. command-output:: spack test --list-names -k "spec and concretize" + +By default, ``pytest`` captures the output of all unit tests, and it will +print any captured output for failed tests. Sometimes it's helpful to see +your output interactively, while the tests run (e.g., if you add print +statements to a unit tests). To see the output *live*, use the ``-s`` +argument to ``pytest``: .. code-block:: console - $ spack test -s -k architecture + $ spack test -s architecture.py::test_platform -Unit tests are crucial to making sure bugs aren't introduced into Spack. If you -are modifying core Spack libraries or adding new functionality, please consider -adding new unit tests or strengthening existing tests. +Unit tests are crucial to making sure bugs aren't introduced into +Spack. If you are modifying core Spack libraries or adding new +functionality, please add new unit tests for your feature, and consider +strengthening existing tests. You will likely be asked to do this if you +submit a pull request to the Spack project on GitHub. Check out the +`pytest docs <http://pytest.org/>`_ and feel free to ask for guidance on +how to write tests! .. note:: - There is also a ``run-unit-tests`` script in ``share/spack/qa`` that - runs the unit tests. Afterwards, it reports back to Codecov with the - percentage of Spack that is covered by unit tests. This script is - designed for Travis CI. If you want to run the unit tests yourself, we - suggest you use ``spack test``. + You may notice the ``share/spack/qa/run-unit-tests`` script in the + repository. This script is designed for Travis CI. It runs the unit + tests and reports coverage statistics back to Codecov. If you want to + run the unit tests yourself, we suggest you use ``spack test``. ^^^^^^^^^^^^ Flake8 Tests @@ -223,8 +268,7 @@ documentation. In order to prevent things like broken links and missing imports, we added documentation tests that build the documentation and fail if there are any warning or error messages. -Building the documentation requires several dependencies, all of which can be -installed with Spack: +Building the documentation requires several dependencies: * sphinx * sphinxcontrib-programoutput @@ -234,11 +278,18 @@ installed with Spack: * mercurial * subversion +All of these can be installed with Spack, e.g. + +.. code-block:: console + + $ spack install py-sphinx py-sphinxcontrib-programoutput py-sphinx-rtd-theme graphviz git mercurial subversion + .. warning:: Sphinx has `several required dependencies <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-sphinx/package.py>`_. - If you installed ``py-sphinx`` with Spack, make sure to add all of these - dependencies to your ``PYTHONPATH``. The easiest way to do this is to run: + If you're using a ``python`` from Spack and you installed + ``py-sphinx`` and friends, you need to make them available to your + ``python``. The easiest way to do this is to run: .. code-block:: console @@ -246,8 +297,10 @@ installed with Spack: $ spack activate py-sphinx-rtd-theme $ spack activate py-sphinxcontrib-programoutput - so that all of the dependencies are symlinked to a central location. - If you see an error message like: + so that all of the dependencies are symlinked into that Python's + tree. Alternatively, you could arrange for their library + directories to be added to PYTHONPATH. If you see an error message + like: .. code-block:: console diff --git a/lib/spack/docs/developer_guide.rst b/lib/spack/docs/developer_guide.rst index d25b40e45a..de2fe80f85 100644 --- a/lib/spack/docs/developer_guide.rst +++ b/lib/spack/docs/developer_guide.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -363,12 +363,12 @@ Developer commands ``spack doc`` ^^^^^^^^^^^^^ -.. _cmd-spack-test: - ^^^^^^^^^^^^^^ ``spack test`` ^^^^^^^^^^^^^^ +See the :ref:`contributor guide section <cmd-spack-test>` on ``spack test``. + .. _cmd-spack-python: ^^^^^^^^^^^^^^^^ diff --git a/lib/spack/docs/docker_for_developers.rst b/lib/spack/docs/docker_for_developers.rst index f60c648b8c..2b489cdec4 100644 --- a/lib/spack/docs/docker_for_developers.rst +++ b/lib/spack/docs/docker_for_developers.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/dockerhub_spack.png b/lib/spack/docs/dockerhub_spack.png Binary files differnew file mode 100644 index 0000000000..44ff0ed7ed --- /dev/null +++ b/lib/spack/docs/dockerhub_spack.png diff --git a/lib/spack/docs/environments.rst b/lib/spack/docs/environments.rst index 1ce765210f..5ec1ec9032 100644 --- a/lib/spack/docs/environments.rst +++ b/lib/spack/docs/environments.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -49,6 +49,8 @@ Spack uses a "manifest and lock" model similar to `Bundler gemfiles managers. The user input file is named ``spack.yaml`` and the lock file is named ``spack.lock`` +.. _environments-using: + ------------------ Using Environments ------------------ @@ -382,11 +384,12 @@ the Environment. Loading ^^^^^^^ -Once an environment has been installed, the following creates a load script for it: +Once an environment has been installed, the following creates a load +script for it: .. code-block:: console - $ spack env myenv loads -r + $ spack env loads -r This creates a file called ``loads`` in the environment directory. Sourcing that file in Bash will make the environment available to the diff --git a/lib/spack/docs/extensions.rst b/lib/spack/docs/extensions.rst index 8f4c54b435..c71a6511ed 100644 --- a/lib/spack/docs/extensions.rst +++ b/lib/spack/docs/extensions.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,12 +9,6 @@ Custom Extensions ================= -.. warning:: - - The support for extending Spack with custom commands is still experimental. - Users should expect APIs or prescribed directory structures to - change at any time. - *Spack extensions* permit you to extend Spack capabilities by deploying your own custom commands or logic in an arbitrary location on your filesystem. This might be extremely useful e.g. to develop and maintain a command whose purpose is diff --git a/lib/spack/docs/features.rst b/lib/spack/docs/features.rst index a242eab595..cd7d3a083f 100644 --- a/lib/spack/docs/features.rst +++ b/lib/spack/docs/features.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst index 7f3a34b62b..3a9b2d42b2 100644 --- a/lib/spack/docs/getting_started.rst +++ b/lib/spack/docs/getting_started.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -97,7 +97,7 @@ Check Installation With Spack installed, you should be able to run some basic Spack commands. For example: -.. command-output:: spack spec netcdf +.. command-output:: spack spec netcdf-c ^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/lib/spack/docs/index.rst b/lib/spack/docs/index.rst index 48af67982a..8170f152a4 100644 --- a/lib/spack/docs/index.rst +++ b/lib/spack/docs/index.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -66,6 +66,7 @@ or refer to the full manual below. config_yaml build_settings environments + containers mirrors module_file_support repositories @@ -74,6 +75,7 @@ or refer to the full manual below. package_list chain extensions + pipelines .. toctree:: :maxdepth: 2 diff --git a/lib/spack/docs/known_issues.rst b/lib/spack/docs/known_issues.rst index bdd8db2f4c..7d47137392 100644 --- a/lib/spack/docs/known_issues.rst +++ b/lib/spack/docs/known_issues.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/mirrors.rst b/lib/spack/docs/mirrors.rst index b161682374..5268c87067 100644 --- a/lib/spack/docs/mirrors.rst +++ b/lib/spack/docs/mirrors.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/module_file_support.rst b/lib/spack/docs/module_file_support.rst index 1b5de3a0e8..aa7eb57653 100644 --- a/lib/spack/docs/module_file_support.rst +++ b/lib/spack/docs/module_file_support.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -119,7 +119,7 @@ For example this will add the ``mpich`` package built with ``gcc`` to your path: # ... wait for install ... - $ spack load mpich %gcc@4.4.7 # modules + $ spack load mpich %gcc@4.4.7 $ which mpicc ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4/bin/mpicc @@ -129,27 +129,29 @@ want to use a package, you can type unload or unuse similarly: .. code-block:: console - $ spack unload mpich %gcc@4.4.7 # modules + $ spack unload mpich %gcc@4.4.7 .. note:: - The ``load`` and ``unload`` subcommands are - only available if you have enabled Spack's shell support *and* you - have environment-modules installed on your machine. + The ``load`` and ``unload`` subcommands are only available if you + have enabled Spack's shell support. These command DO NOT use the + underlying Spack-generated module files. -^^^^^^^^^^^^^^^^^^^^^^ -Ambiguous module names -^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^ +Ambiguous specs +^^^^^^^^^^^^^^^ -If a spec used with load/unload or use/unuse is ambiguous (i.e. more -than one installed package matches it), then Spack will warn you: +If a spec used with load/unload or is ambiguous (i.e. more than one +installed package matches it), then Spack will warn you: .. code-block:: console $ spack load libelf - ==> Error: Multiple matches for spec libelf. Choose one: - libelf@0.8.13%gcc@4.4.7 arch=linux-debian7-x86_64 - libelf@0.8.13%intel@15.0.0 arch=linux-debian7-x86_64 + ==> Error: libelf matches multiple packages. + Matching packages: + libelf@0.8.13%gcc@4.4.7 arch=linux-debian7-x86_64 + libelf@0.8.13%intel@15.0.0 arch=linux-debian7-x86_64 + Use a more specific spec You can either type the ``spack load`` command again with a fully qualified argument, or you can add just enough extra constraints to @@ -171,8 +173,15 @@ To identify just the one built with the Intel compiler. ``spack module tcl loads`` ^^^^^^^^^^^^^^^^^^^^^^^^^^ -In some cases, it is desirable to load not just a module, but also all -the modules it depends on. This is not required for most modules +In some cases, it is desirable to use a Spack-generated module, rather +than relying on Spack's built-in user-environment modification +capabilities. To translate a spec into a module name, use ``spack +module tcl loads`` or ``spack module lmod loads`` depending on the +module system desired. + + +To load not just a module, but also all the modules it depends on, use +the ``--dependencies`` option. This is not required for most modules because Spack builds binaries with RPATH support. However, not all packages use RPATH to find their dependencies: this can be true in particular for Python extensions, which are currently *not* built with diff --git a/lib/spack/docs/package_list.rst b/lib/spack/docs/package_list.rst index 6c1e053e9e..8b5a4d332f 100644 --- a/lib/spack/docs/package_list.rst +++ b/lib/spack/docs/package_list.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 7fc9d09e2d..6e1271b12c 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -553,6 +553,34 @@ version. This is useful for packages that have an easy to extrapolate URL, but keep changing their URL format every few releases. With this method, you only need to specify the ``url`` when the URL changes. +""""""""""""""""""""""" +Mirrors of the main URL +""""""""""""""""""""""" + +Spack supports listing mirrors of the main URL in a package by defining +the ``urls`` attribute: + +.. code-block:: python + + class Foo(Package): + + urls = [ + 'http://example.com/foo-1.0.tar.gz', + 'http://mirror.com/foo-1.0.tar.gz' + ] + +instead of just a single ``url``. This attribute is a list of possible URLs that +will be tried in order when fetching packages. Notice that either one of ``url`` +or ``urls`` can be present in a package, but not both at the same time. + +A well-known case of packages that can be fetched from multiple mirrors is that +of GNU. For that, Spack goes a step further and defines a mixin class that +takes care of all of the plumbing and requires packagers to just define a proper +``gnu_mirror_path`` attribute: + +.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/autoconf/package.py + :lines: 9-18 + ^^^^^^^^^^^^^^^^^^^^^^^^ Skipping the expand step ^^^^^^^^^^^^^^^^^^^^^^^^ @@ -901,6 +929,9 @@ Git fetching supports the following parameters to ``version``: * ``tag``: Name of a tag to fetch. * ``commit``: SHA hash (or prefix) of a commit to fetch. * ``submodules``: Also fetch submodules recursively when checking out this repository. +* ``submodules_delete``: A list of submodules to forcibly delete from the repository + after fetching. Useful if a version in the repository has submodules that + have disappeared/are no longer accessible. * ``get_full_repo``: Ensure the full git history is checked out with all remote branch information. Normally (``get_full_repo=False``, the default), the git option ``--depth 1`` will be used if the version of git and the specified @@ -1479,8 +1510,8 @@ that the same package with different patches applied will have different hash identifiers. To ensure that the hashing scheme is consistent, you must use a ``sha256`` checksum for the patch. Patches will be fetched from their URLs, checked, and applied to your source code. You can use -the ``spack sha256`` command to generate a checksum for a patch file or -URL. +the GNU utils ``sha256sum`` or the macOS ``shasum -a 256`` commands to +generate a checksum for a patch file. Spack can also handle compressed patches. If you use these, Spack needs a little more help. Specifically, it needs *two* checksums: the @@ -1922,6 +1953,8 @@ issues with 1.64.0, 1.65.0, and 1.66.0, you can say: depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:') +.. _dependency-types: + ^^^^^^^^^^^^^^^^ Dependency types ^^^^^^^^^^^^^^^^ @@ -1959,6 +1992,28 @@ inject the dependency's ``prefix/lib`` directory, but the package needs to be in ``PATH`` and ``PYTHONPATH`` during the build process and later when a user wants to run the package. +^^^^^^^^^^^^^^^^^^^^^^^^ +Conditional dependencies +^^^^^^^^^^^^^^^^^^^^^^^^ + +You may have a package that only requires a dependency under certain +conditions. For example, you may have a package that has optional MPI support, +- MPI is only a dependency when you want to enable MPI support for the +package. In that case, you could say something like: + +.. code-block:: python + + variant('mpi', default=False) + depends_on('mpi', when='+mpi') + +``when`` can include constraints on the variant, version, compiler, etc. and +the :mod:`syntax<spack.spec>` is the same as for Specs written on the command +line. + +If a dependency/feature of a package isn't typically used, you can save time +by making it conditional (since Spack will not build the dependency unless it +is required for the Spec). + .. _dependency_dependency_patching: ^^^^^^^^^^^^^^^^^^^ diff --git a/lib/spack/docs/pipelines.rst b/lib/spack/docs/pipelines.rst new file mode 100644 index 0000000000..f70b39a16d --- /dev/null +++ b/lib/spack/docs/pipelines.rst @@ -0,0 +1,439 @@ +.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other + Spack Project Developers. See the top-level COPYRIGHT file for details. + + SPDX-License-Identifier: (Apache-2.0 OR MIT) + +.. _pipelines: + +========= +Pipelines +========= + +Spack provides commands that support generating and running automated build +pipelines designed for Gitlab CI. At the highest level it works like this: +provide a spack environment describing the set of packages you care about, +and include within that environment file a description of how those packages +should be mapped to Gitlab runners. Spack can then generate a ``.gitlab-ci.yml`` +file containing job descriptions for all your packages that can be run by a +properly configured Gitlab CI instance. When run, the generated pipeline will +build and deploy binaries, and it can optionally report to a CDash instance +regarding the health of the builds as they evolve over time. + +------------------------------ +Getting started with pipelines +------------------------------ + +It is fairly straightforward to get started with automated build pipelines. At +a minimum, you'll need to set up a Gitlab instance (more about Gitlab CI +`here <https://about.gitlab.com/product/continuous-integration/>`_) and configure +at least one `runner <https://docs.gitlab.com/runner/>`_. Then the basic steps +for setting up a build pipeline are as follows: + +#. Create a repository on your gitlab instance +#. Add a ``spack.yaml`` at the root containing your pipeline environment (see + below for details) +#. Add a ``.gitlab-ci.yml`` at the root containing a single job, similar to + this one: + + .. code-block:: yaml + + pipeline-job: + tags: + - <custom-tag> + ... + script: + - spack ci start + +#. Add any secrets required by the CI process to environment variables using the + CI web ui +#. Push a commit containing the ``spack.yaml`` and ``.gitlab-ci.yml`` mentioned above + to the gitlab repository + +The ``<custom-tag>``, above, is used to pick one of your configured runners, +while the use of the ``spack ci start`` command implies that runner has an +appropriate version of spack installed and configured for use. Of course, there +are myriad ways to customize the process. You can configure CDash reporting +on the progress of your builds, set up S3 buckets to mirror binaries built by +the pipeline, clone a custom spack repository/ref for use by the pipeline, and +more. + +While it is possible to set up pipelines on gitlab.com, the builds there are +limited to 60 minutes and generic hardware. It is also possible to +`hook up <https://about.gitlab.com/blog/2018/04/24/getting-started-gitlab-ci-gcp>`_ +Gitlab to Google Kubernetes Engine (`GKE <https://cloud.google.com/kubernetes-engine/>`_) +or Amazon Elastic Kubernetes Service (`EKS <https://aws.amazon.com/eks>`_), though those +topics are outside the scope of this document. + +----------------------------------- +Spack commands supporting pipelines +----------------------------------- + +Spack provides a command `ci` with sub-commands for doing various things related +to automated build pipelines. All of the ``spack ci ...`` commands must be run +from within a environment, as each one makes use of the environment for different +purposes. Additionally, some options to the commands (or conditions present in +the spack environment file) may require particular environment variables to be +set in order to function properly. Examples of these are typically secrets +needed for pipeline operation that should not be visible in a spack environment +file. These environment variables are described in more detail +:ref:`ci_environment_variables`. + +.. _cmd_spack_ci: + +^^^^^^^^^^^^^^^^^^ +``spack ci`` +^^^^^^^^^^^^^^^^^^ + +Super-command for functionality related to generating pipelines and executing +pipeline jobs. + +.. _cmd_spack_ci_start: + +^^^^^^^^^^^^^^^^^^ +``spack ci start`` +^^^^^^^^^^^^^^^^^^ + +Currently this command is a short-cut to first run ``spack ci generate``, followed +by ``spack ci pushyaml``. + +.. _cmd_spack_ci_generate: + +^^^^^^^^^^^^^^^^^^^^^ +``spack ci generate`` +^^^^^^^^^^^^^^^^^^^^^ + +Concretizes the specs in the active environment, stages them (as described in +:ref:`staging_algorithm`), and writes the resulting ``.gitlab-ci.yml`` to disk. + +.. _cmd_spack_ci_pushyaml: + +^^^^^^^^^^^^^^^^^^^^^ +``spack ci pushyaml`` +^^^^^^^^^^^^^^^^^^^^^ + +Generates a commit containing the generated ``.gitlab-ci.yml`` and pushes it to a +``DOWNSTREAM_CI_REPO``, which is frequently the same repository. The branch +created has the same name as the current branch being tested, but has ``multi-ci-`` +prepended to the branch name. Once Gitlab CI has full support for dynamically +defined workloads, this command will be deprecated. + +.. _cmd_spack_ci_rebuild: + +^^^^^^^^^^^^^^^^^^^^ +``spack ci rebuild`` +^^^^^^^^^^^^^^^^^^^^ + +This sub-command is responsible for ensuring a single spec from the release +environment is up to date on the remote mirror configured in the environment, +and as such, corresponds to a single job in the ``.gitlab-ci.yml`` file. + +------------------------------------ +A pipeline-enabled spack environment +------------------------------------ + +Here's an example of a spack environment file that has been enhanced with +sections desribing a build pipeline: + +.. code-block:: yaml + + spack: + definitions: + - pkgs: + - readline@7.0 + - compilers: + - '%gcc@5.5.0' + - oses: + - os=ubuntu18.04 + - os=centos7 + specs: + - matrix: + - [$pkgs] + - [$compilers] + - [$oses] + mirrors: + cloud_gitlab: https://mirror.spack.io + gitlab-ci: + mappings: + - match: + - os=ubuntu18.04 + runner-attributes: + tags: + - spack-k8s + image: spack/spack_builder_ubuntu_18.04 + - match: + - os=centos7 + runner-attributes: + tags: + - spack-k8s + image: spack/spack_builder_centos_7 + cdash: + build-group: Release Testing + url: https://cdash.spack.io + project: Spack + site: Spack AWS Gitlab Instance + +Hopefully, the ``definitions``, ``specs``, ``mirrors``, etc. sections are already +familiar, as they are part of spack :ref:`environments`. So let's take a more +in-depth look some of the pipeline-related sections in that environment file +that might not be as familiar. + +The ``gitlab-ci`` section is used to configure how the pipeline workload should be +generated, mainly how the jobs for building specs should be assigned to the +configured runners on your instance. Each entry within the list of ``mappings`` +corresponds to a known gitlab runner, where the ``match`` section is used +in assigning a release spec to one of the runners, and the ``runner-attributes`` +section is used to configure the spec/job for that particular runner. + +There are other pipeline options you can configure within the ``gitlab-ci`` section +as well. The ``bootstrap`` section allows you to specify lists of specs from +your ``definitions`` that should be staged ahead of the environment's ``specs`` (this +section is described in more detail below). The ``enable-artifacts-buildcache`` key +takes a boolean and determines whether the pipeline uses artifacts to store and +pass along the buildcaches from one stage to the next (the default if you don't +provide this option is ``False``). The ``enable-debug-messages`` key takes a boolean +and allows you to choose whether the pipeline build jobs are run as ``spack -d ci rebuild`` +or just ``spack ci rebuild`` (the default is not to enable debug messages). The +``final-stage-rebuild-index`` section controls whether an extra job is added to the +end of your pipeline (in a stage by itself) which will regenerate the mirror's +buildcache index. Under normal operation, each pipeline job that rebuilds a package +will re-generate the mirror's buildcache index after the buildcache entry for that +job has been created and pushed to the mirror. Since jobs in the same stage can run in +parallel, there is the possibility that at the end of some stage, the index may not +reflect all the binaries in the buildcache. Adding the ``final-stage-rebuild-index`` +section ensures that at the end of the pipeline, the index will be in sync with the +binaries on the mirror. If the mirror lives in an S3 bucket, this job will need to +run on a machine with the Python ``boto3`` module installed, and consequently the +``final-stage-rebuild-index`` needs to specify a list of ``tags`` to pick a runner +satisfying that condition. It can also take an ``image`` key so Docker executor type +runners can pick the right image for the index regeneration job. + +The optional ``cdash`` section provides information that will be used by the +``spack ci generate`` command (invoked by ``spack ci start``) for reporting +to CDash. All the jobs generated from this environment will belong to a +"build group" within CDash that can be tracked over time. As the release +progresses, this build group may have jobs added or removed. The url, project, +and site are used to specify the CDash instance to which build results should +be reported. + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Assignment of specs to runners +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The ``mappings`` section corresponds to a list of runners, and during assignment +of specs to runners, the list is traversed in order looking for matches, the +first runner that matches a release spec is assigned to build that spec. The +``match`` section within each runner mapping section is a list of specs, and +if any of those specs match the release spec (the ``spec.satisfies()`` method +is used), then that runner is considered a match. + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Configuration of specs/jobs for a runner +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Once a runner has been chosen to build a release spec, the ``runner-attributes`` +section provides information determining details of the job in the context of +the runner. The ``runner-attributes`` section must have a ``tags`` key, which +is a list containing at least one tag used to select the runner from among the +runners known to the gitlab instance. For Docker executor type runners, the +``image`` key is used to specify the Docker image used to build the release spec +(and could also appear as a dictionary with a ``name`` specifying the image name, +as well as an ``entrypoint`` to override whatever the default for that image is). +For other types of runners the ``variables`` key will be useful to pass any +information on to the runner that it needs to do its work (e.g. scheduler +parameters, etc.). + +.. _staging_algorithm: + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Summary of ``.gitlab-ci.yml`` generation algorithm +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +All specs yielded by the matrix (or all the specs in the environment) have their +dependencies computed, and the entire resulting set of specs are staged together +before being run through the ``gitlab-ci/mappings`` entries, where each staged +spec is assigned a runner. "Staging" is the name we have given to the process +of figuring out in what order the specs should be built, taking into consideration +Gitlab CI rules about jobs/stages. In the staging process the goal is to maximize +the number of jobs in any stage of the pipeline, while ensuring that the jobs in +any stage only depend on jobs in previous stages (since those jobs are guaranteed +to have completed already). As a runner is determined for a job, the information +in the ``runner-attributes`` is used to populate various parts of the job +description that will be used by Gitlab CI. Once all the jobs have been assigned +a runner, the ``.gitlab-ci.yml`` is written to disk. + +The short example provided above would result in the ``readline``, ``ncurses``, +and ``pkgconf`` packages getting staged and built on the runner chosen by the +``spack-k8s`` tag. In this example, we assume the runner is a Docker executor +type runner, and thus certain jobs will be run in the ``centos7`` container, +and others in the ``ubuntu-18.04`` container. The resulting ``.gitlab-ci.yml`` +will contain 6 jobs in three stages. Once the jobs have been generated, the +presence of a ``SPACK_CDASH_AUTH_TOKEN`` environment variable during the +``spack ci generate`` command would result in all of the jobs being put in a +build group on CDash called "Release Testing" (that group will be created if +it didn't already exist). + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Optional compiler bootstrapping +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Spack pipelines also have support for bootstrapping compilers on systems that +may not already have the desired compilers installed. The idea here is that +you can specify a list of things to bootstrap in your ``definitions``, and +spack will guarantee those will be installed in a phase of the pipeline before +your release specs, so that you can rely on those packages being available in +the binary mirror when you need them later on in the pipeline. At the moment +the only viable use-case for bootstrapping is to install compilers. + +Here's an example of what bootstrapping some compilers might look like: + +.. code-block:: yaml + + spack: + definitions: + - compiler-pkgs: + - 'llvm+clang@6.0.1 os=centos7' + - 'gcc@6.5.0 os=centos7' + - 'llvm+clang@6.0.1 os=ubuntu18.04' + - 'gcc@6.5.0 os=ubuntu18.04' + - pkgs: + - readline@7.0 + - compilers: + - '%gcc@5.5.0' + - '%gcc@6.5.0' + - '%gcc@7.3.0' + - '%clang@6.0.0' + - '%clang@6.0.1' + - oses: + - os=ubuntu18.04 + - os=centos7 + specs: + - matrix: + - [$pkgs] + - [$compilers] + - [$oses] + exclude: + - '%gcc@7.3.0 os=centos7' + - '%gcc@5.5.0 os=ubuntu18.04' + gitlab-ci: + bootstrap: + - name: compiler-pkgs + compiler-agnostic: true + mappings: + # mappings similar to the example higher up in this description + ... + +In the example above, we have added a list to the ``definitions`` called +``compiler-pkgs`` (you can add any number of these), which lists compiler packages +we want to be staged ahead of the full matrix of release specs (which consists +only of readline in our example). Then within the ``gitlab-ci`` section, we +have added a ``bootstrap`` section, which can contain a list of items, each +referring to a list in the ``definitions`` section. These items can either +be a dictionary or a string. If you supply a dictionary, it must have a name +key whose value must match one of the lists in definitions and it can have a +``compiler-agnostic`` key whose value is a boolean. If you supply a string, +then it needs to match one of the lists provided in ``definitions``. You can +think of the bootstrap list as an ordered list of pipeline "phases" that will +be staged before your actual release specs. While this introduces another +layer of bottleneck in the pipeline (all jobs in all stages of one phase must +complete before any jobs in the next phase can begin), it also means you are +guaranteed your bootstrapped compilers will be available when you need them. + +The ``compiler-agnostic`` key can be provided with each item in the +bootstrap list. It tells the ``spack ci generate`` command that any jobs staged +from that particular list should have the compiler removed from the spec, so +that any compiler available on the runner where the job is run can be used to +build the package. + +When including a bootstrapping phase as in the example above, the result is that +the bootstrapped compiler packages will be pushed to the binary mirror (and the +local artifacts mirror) before the actual release specs are built. In this case, +the jobs corresponding to subsequent release specs are configured to +``install_missing_compilers``, so that if spack is asked to install a package +with a compiler it doesn't know about, it can be quickly installed from the +binary mirror first. + +Since bootstrapping compilers is optional, those items can be left out of the +environment/stack file, and in that case no bootstrapping will be done (only the +specs will be staged for building) and the runners will be expected to already +have all needed compilers installed and configured for spack to use. + +------------------------------------- +Using a custom spack in your pipeline +------------------------------------- + +If your runners will not have a version of spack ready to invoke, or if for some +other reason you want to use a custom version of spack to run your pipelines, +this can be accomplished fairly simply. First, create CI environment variables +containing the url and branch/tag you want to clone (calling them, for example, +``SPACK_REPO`` and ``SPACK_REF``), use them to clone spack in your pre-ci +``before_script``, and finally pass those same values along to the workload +generation process via the ``spack-repo`` and ``spack-ref`` cli args. Here's +an example: + +.. code-block:: yaml + + pipeline-job: + tags: + - <some-other-tag> + before_script: + - git clone ${SPACK_REPO} --branch ${SPACK_REF} + - . ./spack/share/spack/setup-env.sh + script: + - spack ci start --spack-repo ${SPACK_REPO} --spack-ref ${SPACK_REF} <...args> + after_script: + - rm -rf ./spack + +If the ``spack ci start`` command receives those extra command line arguments, +then it adds similar ``before_script`` and ``after_script`` sections for each of +the ``spack ci rebuild`` jobs it generates (cloning and sourcing a custom +spack in the ``before_script`` and removing it again in the ``after_script``). +This gives you control over the version of spack used when the rebuild jobs +are actually run on the gitlab runner. + +.. _ci_environment_variables: + +-------------------------------------------------- +Environment variables affecting pipeline operation +-------------------------------------------------- + +Certain secrets and some other information should be provided to the pipeline +infrastructure via environment variables, usually for reasons of security, but +in some cases to support other pipeline use cases such as PR testing. The +environment variables used by the pipeline infrastructure are described here. + +^^^^^^^^^^^^^^^^^ +AWS_ACCESS_KEY_ID +^^^^^^^^^^^^^^^^^ + +Needed when binary mirror is an S3 bucket. + +^^^^^^^^^^^^^^^^^^^^^ +AWS_SECRET_ACCESS_KEY +^^^^^^^^^^^^^^^^^^^^^ + +Needed when binary mirror is an S3 bucket. + +^^^^^^^^^^^^^^^ +S3_ENDPOINT_URL +^^^^^^^^^^^^^^^ + +Needed when binary mirror is an S3 bucket that is *not* on AWS. + +^^^^^^^^^^^^^^^^^ +CDASH_AUTH_TOKEN +^^^^^^^^^^^^^^^^^ + +Needed in order to report build groups to CDash. + +^^^^^^^^^^^^^^^^^ +SPACK_SIGNING_KEY +^^^^^^^^^^^^^^^^^ + +Needed to sign/verify binary packages from the remote binary mirror. + +^^^^^^^^^^^^^^^^^^ +DOWNSTREAM_CI_REPO +^^^^^^^^^^^^^^^^^^ + +Needed until Gitlab CI supports dynamic job generation. Can contain connection +credentials, and could be the same repository or a different one. diff --git a/lib/spack/docs/repositories.rst b/lib/spack/docs/repositories.rst index 45693fd2c5..6c2050a4be 100644 --- a/lib/spack/docs/repositories.rst +++ b/lib/spack/docs/repositories.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/requirements.txt b/lib/spack/docs/requirements.txt index 190b018a0b..f5c50b0199 100644 --- a/lib/spack/docs/requirements.txt +++ b/lib/spack/docs/requirements.txt @@ -1,7 +1,7 @@ # These dependencies should be installed using pip in order # to build the documentation. -sphinx==2.0.1 -sphinxcontrib-programoutput==0.14 -sphinx-rtd-theme==0.4.3 +sphinx +sphinxcontrib-programoutput +sphinx-rtd-theme python-levenshtein diff --git a/lib/spack/docs/spack.yaml b/lib/spack/docs/spack.yaml index bade961fce..3c8cd14d10 100644 --- a/lib/spack/docs/spack.yaml +++ b/lib/spack/docs/spack.yaml @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/docs/workflows.rst b/lib/spack/docs/workflows.rst index 454cb15ecc..b329a0205c 100644 --- a/lib/spack/docs/workflows.rst +++ b/lib/spack/docs/workflows.rst @@ -1,4 +1,4 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +.. Copyright 2013-2020 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -253,14 +253,14 @@ However, other more powerful methods are generally preferred for user environments. -^^^^^^^^^^^^^^^^^^^^^^^ -Spack-Generated Modules -^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Using ``spack load`` to Manage the User Environment +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Suppose that Spack has been used to install a set of command-line programs, which users now wish to use. One can in principle put a number of ``spack load`` commands into ``.bashrc``, for example, to -load a set of Spack-generated modules: +load a set of Spack packages: .. code-block:: sh @@ -273,7 +273,7 @@ load a set of Spack-generated modules: Although simple load scripts like this are useful in many cases, they have some drawbacks: -1. The set of modules loaded by them will in general not be +1. The set of packages loaded by them will in general not be consistent. They are a decent way to load commands to be called from command shells. See below for better ways to assemble a consistent set of packages for building application programs. @@ -285,19 +285,24 @@ have some drawbacks: other hand, are not very smart: if the user-supplied spec matches more than one installed package, then ``spack module tcl loads`` will fail. This may change in the future. For now, the workaround is to - be more specific on any ``spack module tcl loads`` lines that fail. + be more specific on any ``spack load`` commands that fail. """""""""""""""""""""" Generated Load Scripts """""""""""""""""""""" -Another problem with using `spack load` is, it is slow; a typical user -environment could take several seconds to load, and would not be -appropriate to put into ``.bashrc`` directly. It is preferable to use -a series of ``spack module tcl loads`` commands to pre-compute which -modules to load. These can be put in a script that is run whenever -installed Spack packages change. For example: +Another problem with using `spack load` is, it can be slow; a typical +user environment could take several seconds to load, and would not be +appropriate to put into ``.bashrc`` directly. This is because it +requires the full start-up overhead of python/Spack for each command. +In some circumstances it is preferable to use a series of ``spack +module tcl loads`` (or ``spack module lmod loads``) commands to +pre-compute which modules to load. This will generate the modulenames +to load the packages using environment modules, rather than Spack's +built-in support for environment modifications. These can be put in a +script that is run whenever installed Spack packages change. For +example: .. code-block:: sh @@ -634,7 +639,7 @@ Global Activations Python (and similar systems) packages directly or creating a view. If extensions are globally activated, then ``spack load python`` will also load all the extensions activated for the given ``python``. -This reduces the need for users to load a large number of modules. +This reduces the need for users to load a large number of packages. However, Spack global activations have two potential drawbacks: @@ -1090,6 +1095,248 @@ or filesystem views. However, it has some drawbacks: integrate Spack explicitly in their workflow. Not all users are willing to do this. +------------------------------------- +Using Spack to Replace Homebrew/Conda +------------------------------------- + +Spack is an incredibly powerful package manager, designed for supercomputers +where users have diverse installation needs. But Spack can also be used to +handle simple single-user installations on your laptop. Most macOS users are +already familiar with package managers like Homebrew and Conda, where all +installed packages are symlinked to a single central location like ``/usr/local``. +In this section, we will show you how to emulate the behavior of Homebrew/Conda +using :ref:`environments`! + +^^^^^ +Setup +^^^^^ + +First, let's create a new environment. We'll assume that Spack is already set up +correctly, and that you've already sourced the setup script for your shell. +To create a new environment, simply run: + +.. code-block:: console + + $ spack env create myenv + ==> Updating view at /Users/me/spack/var/spack/environments/myenv/.spack-env/view + ==> Created environment 'myenv' in /Users/me/spack/var/spack/environments/myenv + $ spack env activate myenv + +Here, *myenv* can be anything you want to name your environment. Next, we can add +a list of packages we would like to install into our environment. Let's say we +want a newer version of Bash than the one that comes with macOS, and we want a +few Python libraries. We can run: + +.. code-block:: console + + $ spack add bash + ==> Adding bash to environment myenv + ==> Updating view at /Users/me/spack/var/spack/environments/myenv/.spack-env/view + $ spack add python@3: + ==> Adding python@3: to environment myenv + ==> Updating view at /Users/me/spack/var/spack/environments/myenv/.spack-env/view + $ spack add py-numpy py-scipy py-matplotlib + ==> Adding py-numpy to environment myenv + ==> Adding py-scipy to environment myenv + ==> Adding py-matplotlib to environment myenv + ==> Updating view at /Users/me/spack/var/spack/environments/myenv/.spack-env/view + +Each package can be listed on a separate line, or combined into a single line. +Notice that we're explicitly asking for Python 3 here. You can use any spec +you would normally use on the command line with other Spack commands. + +Next, we want to manually configure a couple of things. In the ``myenv`` +directory, we can find the ``spack.yaml`` that actually defines our environment. + +.. code-block:: console + + $ vim ~/spack/var/spack/environments/myenv/spack.yaml + +.. code-block:: yaml + + # This is a Spack Environment file. + # + # It describes a set of packages to be installed, along with + # configuration settings. + spack: + # add package specs to the `specs` list + specs: [bash, 'python@3:', py-numpy, py-scipy, py-matplotlib] + view: + default: + root: /Users/me/spack/var/spack/environments/myenv/.spack-env/view + projections: {} + config: {} + mirrors: {} + modules: + enable: [] + packages: {} + repos: [] + upstreams: {} + definitions: [] + concretization: separately + +You can see the packages we added earlier in the ``specs:`` section. If you +ever want to add more packages, you can either use ``spack add`` or manually +edit this file. + +We also need to change the ``concretization:`` option. By default, Spack +concretizes each spec *separately*, allowing multiple versions of the same +package to coexist. Since we want a single consistent environment, we want to +concretize all of the specs *together*. + +Here is what your ``spack.yaml`` looks like with these new settings, and with +some of the sections we don't plan on using removed: + +.. code-block:: diff + + spack: + - specs: [bash, 'python@3:', py-numpy, py-scipy, py-matplotlib] + + specs: + + - bash + + - 'python@3:' + + - py-numpy + + - py-scipy + + - py-matplotlib + - view: + - default: + - root: /Users/me/spack/var/spack/environments/myenv/.spack-env/view + - projections: {} + + view: /Users/me/spack/var/spack/environments/myenv/.spack-env/view + - config: {} + - mirrors: {} + - modules: + - enable: [] + - packages: {} + - repos: [] + - upstreams: {} + - definitions: [] + + concretization: together + - concretization: separately + +"""""""""""""""" +Symlink location +"""""""""""""""" + +In the ``spack.yaml`` file above, you'll notice that by default, Spack symlinks +all installations to ``/Users/me/spack/var/spack/environments/myenv/.spack-env/view``. +You can actually change this to any directory you want. For example, Homebrew +uses ``/usr/local``, while Conda uses ``/Users/me/anaconda``. In order to access +files in these locations, you need to update ``PATH`` and other environment variables +to point to them. Activating the Spack environment does this automatically, but +you can also manually set them in your ``.bashrc``. + +.. warning:: + + There are several reasons why you shouldn't use ``/usr/local``: + + 1. If you are on macOS 10.11+ (El Capitan and newer), Apple makes it hard + for you. You may notice permissions issues on ``/usr/local`` due to their + `System Integrity Protection <https://support.apple.com/en-us/HT204899>`_. + By default, users don't have permissions to install anything in ``/usr/local``, + and you can't even change this using ``sudo chown`` or ``sudo chmod``. + 2. Other package managers like Homebrew will try to install things to the + same directory. If you plan on using Homebrew in conjunction with Spack, + don't symlink things to ``/usr/local``. + 3. If you are on a shared workstation, or don't have sudo priveleges, you + can't do this. + + If you still want to do this anyway, there are several ways around SIP. + You could disable SIP by booting into recovery mode and running + ``csrutil disable``, but this is not recommended, as it can open up your OS + to security vulnerabilities. Another technique is to run ``spack concretize`` + and ``spack install`` using ``sudo``. This is also not recommended. + + The safest way I've found is to create your installation directories using + sudo, then change ownership back to the user like so: + + .. code-block:: bash + + for directory in .spack bin contrib include lib man share + do + sudo mkdir -p /usr/local/$directory + sudo chown $(id -un):$(id -gn) /usr/local/$directory + done + + Depending on the packages you install in your environment, the exact list of + directories you need to create may vary. You may also find some packages + like Java libraries that install a single file to the installation prefix + instead of in a subdirectory. In this case, the action is the same, just replace + ``mkdir -p`` with ``touch`` in the for-loop above. + + But again, it's safer just to use the default symlink location. + + +^^^^^^^^^^^^ +Installation +^^^^^^^^^^^^ + +To actually concretize the environment, run: + +.. code-block:: console + + $ spack concretize + +This will tell you which if any packages are already installed, and alert you +to any conflicting specs. + +To actually install these packages and symlink them to your ``view:`` +directory, simply run: + +.. code-block:: console + + $ spack install + +Now, when you type ``which python3``, it should find the one you just installed. + +In order to change the default shell to our newer Bash installation, we first +need to add it to this list of acceptable shells. Run: + +.. code-block:: console + + $ sudo vim /etc/shells + +and add the absolute path to your bash executable. Then run: + +.. code-block:: console + + $ chsh -s /path/to/bash + +Now, when you log out and log back in, ``echo $SHELL`` should point to the +newer version of Bash. + +^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Updating Installed Packages +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Let's say you upgraded to a new version of macOS, or a new version of Python +was released, and you want to rebuild your entire software stack. To do this, +simply run the following commands: + +.. code-block:: console + + $ spack env activate myenv + $ spack concretize --force + $ spack install + +The ``--force`` flag tells Spack to overwrite its previous concretization +decisions, allowing you to choose a new version of Python. If any of the new +packages like Bash are already installed, ``spack install`` won't re-install +them, it will keep the symlinks in place. + +^^^^^^^^^^^^^^ +Uninstallation +^^^^^^^^^^^^^^ + +If you decide that Spack isn't right for you, uninstallation is simple. +Just run: + +.. code-block:: console + + $ spack env activate myenv + $ spack uninstall --all + +This will uninstall all packages in your environment and remove the symlinks. + ------------------------ Using Spack on Travis-CI ------------------------ @@ -1254,7 +1501,7 @@ In order to build and run the image, execute: RUN spack install tar \ && spack clean -a - # need the modules already during image build? + # need the executables from a package already during image build? #RUN /bin/bash -l -c ' \ # spack load tar \ # && which tar' diff --git a/lib/spack/env/cc b/lib/spack/env/cc index 2d6fe9998a..73c5759dfe 100755 --- a/lib/spack/env/cc +++ b/lib/spack/env/cc @@ -1,6 +1,6 @@ #!/bin/bash # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/external/__init__.py b/lib/spack/external/__init__.py index 1001ff5fff..27f00efb09 100644 --- a/lib/spack/external/__init__.py +++ b/lib/spack/external/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -82,14 +82,6 @@ py ini-parsing, io, code, and log facilities. * Version: 1.4.34 (last version supporting Python 2.6) -pyqver ------- - -* Homepage: https://github.com/ghewgill/pyqver -* Usage: External script to query required python version of - python source code. Used for ensuring 2.6 compatibility. -* Version: Unversioned - pytest ------ diff --git a/lib/spack/external/_pytest/pytester.py b/lib/spack/external/_pytest/pytester.py index 2db85dff22..82aa00e0d2 100644 --- a/lib/spack/external/_pytest/pytester.py +++ b/lib/spack/external/_pytest/pytester.py @@ -569,7 +569,7 @@ class Testdir: def _possibly_invalidate_import_caches(self): # invalidate caches if we can (py33 and above) try: - import importlib # nopyqver + import importlib except ImportError: pass else: diff --git a/lib/spack/external/ordereddict_backport.py b/lib/spack/external/ordereddict_backport.py index ecb7c29966..5ec8493cc9 100644 --- a/lib/spack/external/ordereddict_backport.py +++ b/lib/spack/external/ordereddict_backport.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/external/pyqver2.py b/lib/spack/external/pyqver2.py deleted file mode 100755 index 07b191425b..0000000000 --- a/lib/spack/external/pyqver2.py +++ /dev/null @@ -1,344 +0,0 @@ -#!/usr/bin/env python -# -# pyqver2.py -# by Greg Hewgill -# https://github.com/ghewgill/pyqver -# -# This software is provided 'as-is', without any express or implied -# warranty. In no event will the author be held liable for any damages -# arising from the use of this software. -# -# Permission is granted to anyone to use this software for any purpose, -# including commercial applications, and to alter it and redistribute it -# freely, subject to the following restrictions: -# -# 1. The origin of this software must not be misrepresented; you must not -# claim that you wrote the original software. If you use this software -# in a product, an acknowledgment in the product documentation would be -# appreciated but is not required. -# 2. Altered source versions must be plainly marked as such, and must not be -# misrepresented as being the original software. -# 3. This notice may not be removed or altered from any source distribution. -# -# Copyright (c) 2009-2013 Greg Hewgill http://hewgill.com -# - -import compiler -import platform -import sys - -StandardModules = { - "__future__": (2, 1), - "abc": (2, 6), -# skip argparse now that it's in lib/spack/external -# "argparse": (2, 7), - "ast": (2, 6), - "atexit": (2, 0), - "bz2": (2, 3), - "cgitb": (2, 2), - "collections": (2, 4), - "contextlib": (2, 5), - "cookielib": (2, 4), - "cProfile": (2, 5), - "csv": (2, 3), - "ctypes": (2, 5), - "datetime": (2, 3), - "decimal": (2, 4), - "difflib": (2, 1), - "DocXMLRPCServer": (2, 3), - "dummy_thread": (2, 3), - "dummy_threading": (2, 3), - "email": (2, 2), - "fractions": (2, 6), - "functools": (2, 5), - "future_builtins": (2, 6), - "hashlib": (2, 5), - "heapq": (2, 3), - "hmac": (2, 2), - "hotshot": (2, 2), - "HTMLParser": (2, 2), - "importlib": (2, 7), - "inspect": (2, 1), - "io": (2, 6), - "itertools": (2, 3), - "json": (2, 6), - "logging": (2, 3), - "modulefinder": (2, 3), - "msilib": (2, 5), - "multiprocessing": (2, 6), - "netrc": (1, 5, 2), - "numbers": (2, 6), - "optparse": (2, 3), - "ossaudiodev": (2, 3), - "pickletools": (2, 3), - "pkgutil": (2, 3), - "platform": (2, 3), - "pydoc": (2, 1), - "runpy": (2, 5), - "sets": (2, 3), - "shlex": (1, 5, 2), - "SimpleXMLRPCServer": (2, 2), - "spwd": (2, 5), - "sqlite3": (2, 5), - "ssl": (2, 6), - "stringprep": (2, 3), - "subprocess": (2, 4), - "sysconfig": (2, 7), - "tarfile": (2, 3), - "textwrap": (2, 3), - "timeit": (2, 3), - "unittest": (2, 1), - "uuid": (2, 5), - "warnings": (2, 1), - "weakref": (2, 1), - "winsound": (1, 5, 2), - "wsgiref": (2, 5), - "xml.dom": (2, 0), - "xml.dom.minidom": (2, 0), - "xml.dom.pulldom": (2, 0), - "xml.etree.ElementTree": (2, 5), - "xml.parsers.expat":(2, 0), - "xml.sax": (2, 0), - "xml.sax.handler": (2, 0), - "xml.sax.saxutils": (2, 0), - "xml.sax.xmlreader":(2, 0), - "xmlrpclib": (2, 2), - "zipfile": (1, 6), - "zipimport": (2, 3), - "_ast": (2, 5), - "_winreg": (2, 0), -} - -Functions = { - "all": (2, 5), - "any": (2, 5), - "collections.Counter": (2, 7), - "collections.defaultdict": (2, 5), - "collections.OrderedDict": (2, 7), - "functools.total_ordering": (2, 7), - "enumerate": (2, 3), - "frozenset": (2, 4), - "itertools.compress": (2, 7), - "math.erf": (2, 7), - "math.erfc": (2, 7), - "math.expm1": (2, 7), - "math.gamma": (2, 7), - "math.lgamma": (2, 7), - "memoryview": (2, 7), - "next": (2, 6), - "os.getresgid": (2, 7), - "os.getresuid": (2, 7), - "os.initgroups": (2, 7), - "os.setresgid": (2, 7), - "os.setresuid": (2, 7), - "reversed": (2, 4), - "set": (2, 4), - "subprocess.check_call": (2, 5), - "subprocess.check_output": (2, 7), - "sum": (2, 3), - "symtable.is_declared_global": (2, 7), - "weakref.WeakSet": (2, 7), -} - -Identifiers = { - "False": (2, 2), - "True": (2, 2), -} - -def uniq(a): - if len(a) == 0: - return [] - else: - return [a[0]] + uniq([x for x in a if x != a[0]]) - -class NodeChecker(object): - def __init__(self): - self.vers = dict() - self.vers[(2,0)] = [] - def add(self, node, ver, msg): - if ver not in self.vers: - self.vers[ver] = [] - self.vers[ver].append((node.lineno, msg)) - def default(self, node): - for child in node.getChildNodes(): - self.visit(child) - def visitCallFunc(self, node): - def rollup(n): - if isinstance(n, compiler.ast.Name): - return n.name - elif isinstance(n, compiler.ast.Const): - return type(n.value).__name__ - elif isinstance(n, compiler.ast.Getattr): - r = rollup(n.expr) - if r: - return r + "." + n.attrname - name = rollup(node.node) - if name: - # Special handling for empty format strings, which aren't - # allowed in Python 2.6 - if name in ('unicode.format', 'str.format'): - n = node.node - if isinstance(n, compiler.ast.Getattr): - n = n.expr - if isinstance(n, compiler.ast.Const): - if '{}' in n.value: - self.add(node, (2,7), name + ' with {} format string') - - v = Functions.get(name) - if v is not None: - self.add(node, v, name) - self.default(node) - def visitClass(self, node): - if node.bases: - self.add(node, (2,2), "new-style class") - if node.decorators: - self.add(node, (2,6), "class decorator") - self.default(node) - def visitDictComp(self, node): - self.add(node, (2,7), "dictionary comprehension") - self.default(node) - def visitFloorDiv(self, node): - self.add(node, (2,2), "// operator") - self.default(node) - def visitFrom(self, node): - v = StandardModules.get(node.modname) - if v is not None: - self.add(node, v, node.modname) - for n in node.names: - name = node.modname + "." + n[0] - v = Functions.get(name) - if v is not None: - self.add(node, v, name) - def visitFunction(self, node): - if node.decorators: - self.add(node, (2,4), "function decorator") - self.default(node) - def visitGenExpr(self, node): - self.add(node, (2,4), "generator expression") - self.default(node) - def visitGetattr(self, node): - if (isinstance(node.expr, compiler.ast.Const) - and isinstance(node.expr.value, str) - and node.attrname == "format"): - self.add(node, (2,6), "string literal .format()") - self.default(node) - def visitIfExp(self, node): - self.add(node, (2,5), "inline if expression") - self.default(node) - def visitImport(self, node): - for n in node.names: - v = StandardModules.get(n[0]) - if v is not None: - self.add(node, v, n[0]) - self.default(node) - def visitName(self, node): - v = Identifiers.get(node.name) - if v is not None: - self.add(node, v, node.name) - self.default(node) - def visitSet(self, node): - self.add(node, (2,7), "set literal") - self.default(node) - def visitSetComp(self, node): - self.add(node, (2,7), "set comprehension") - self.default(node) - def visitTryFinally(self, node): - # try/finally with a suite generates a Stmt node as the body, - # but try/except/finally generates a TryExcept as the body - if isinstance(node.body, compiler.ast.TryExcept): - self.add(node, (2,5), "try/except/finally") - self.default(node) - def visitWith(self, node): - if isinstance(node.body, compiler.ast.With): - self.add(node, (2,7), "with statement with multiple contexts") - else: - self.add(node, (2,5), "with statement") - self.default(node) - def visitYield(self, node): - self.add(node, (2,2), "yield expression") - self.default(node) - -def get_versions(source, filename=None): - """Return information about the Python versions required for specific features. - - The return value is a dictionary with keys as a version number as a tuple - (for example Python 2.6 is (2,6)) and the value are a list of features that - require the indicated Python version. - """ - tree = compiler.parse(source) - checker = compiler.walk(tree, NodeChecker()) - return checker.vers - -def v27(source): - if sys.version_info >= (2, 7): - return qver(source) - else: - print >>sys.stderr, "Not all features tested, run --test with Python 2.7" - return (2, 7) - -def qver(source): - """Return the minimum Python version required to run a particular bit of code. - - >>> qver('print "hello world"') - (2, 0) - >>> qver('class test(object): pass') - (2, 2) - >>> qver('yield 1') - (2, 2) - >>> qver('a // b') - (2, 2) - >>> qver('True') - (2, 2) - >>> qver('enumerate(a)') - (2, 3) - >>> qver('total = sum') - (2, 0) - >>> qver('sum(a)') - (2, 3) - >>> qver('(x*x for x in range(5))') - (2, 4) - >>> qver('class C:\\n @classmethod\\n def m(): pass') - (2, 4) - >>> qver('y if x else z') - (2, 5) - >>> qver('import hashlib') - (2, 5) - >>> qver('from hashlib import md5') - (2, 5) - >>> qver('import xml.etree.ElementTree') - (2, 5) - >>> qver('try:\\n try: pass;\\n except: pass;\\nfinally: pass') - (2, 0) - >>> qver('try: pass;\\nexcept: pass;\\nfinally: pass') - (2, 5) - >>> qver('from __future__ import with_statement\\nwith x: pass') - (2, 5) - >>> qver('collections.defaultdict(list)') - (2, 5) - >>> qver('from collections import defaultdict') - (2, 5) - >>> qver('"{0}".format(0)') - (2, 6) - >>> qver('memoryview(x)') - (2, 7) - >>> v27('{1, 2, 3}') - (2, 7) - >>> v27('{x for x in s}') - (2, 7) - >>> v27('{x: y for x in s}') - (2, 7) - >>> qver('from __future__ import with_statement\\nwith x:\\n with y: pass') - (2, 5) - >>> v27('from __future__ import with_statement\\nwith x, y: pass') - (2, 7) - >>> qver('@decorator\\ndef f(): pass') - (2, 4) - >>> qver('@decorator\\nclass test:\\n pass') - (2, 6) - - #>>> qver('0o0') - #(2, 6) - #>>> qver('@foo\\nclass C: pass') - #(2, 6) - """ - return max(get_versions(source).keys()) diff --git a/lib/spack/external/pyqver3.py b/lib/spack/external/pyqver3.py deleted file mode 100755 index b63576a064..0000000000 --- a/lib/spack/external/pyqver3.py +++ /dev/null @@ -1,248 +0,0 @@ -#!/usr/bin/env python3 -# -# pyqver3.py -# by Greg Hewgill -# https://github.com/ghewgill/pyqver -# -# This software is provided 'as-is', without any express or implied -# warranty. In no event will the author be held liable for any damages -# arising from the use of this software. -# -# Permission is granted to anyone to use this software for any purpose, -# including commercial applications, and to alter it and redistribute it -# freely, subject to the following restrictions: -# -# 1. The origin of this software must not be misrepresented; you must not -# claim that you wrote the original software. If you use this software -# in a product, an acknowledgment in the product documentation would be -# appreciated but is not required. -# 2. Altered source versions must be plainly marked as such, and must not be -# misrepresented as being the original software. -# 3. This notice may not be removed or altered from any source distribution. -# -# Copyright (c) 2009-2013 Greg Hewgill http://hewgill.com -# -import ast -import platform -import sys - -StandardModules = { -# skip argparse now that it's in lib/spack/external -# "argparse": (3, 2), - "faulthandler": (3, 3), - "importlib": (3, 1), - "ipaddress": (3, 3), - "lzma": (3, 3), - "tkinter.ttk": (3, 1), - "unittest.mock": (3, 3), - "venv": (3, 3), -} - -Functions = { - "bytearray.maketrans": (3, 1), - "bytes.maketrans": (3, 1), - "bz2.open": (3, 3), - "collections.Counter": (3, 1), - "collections.OrderedDict": (3, 1), - "crypt.mksalt": (3, 3), - "email.generator.BytesGenerator": (3, 2), - "email.message_from_binary_file": (3, 2), - "email.message_from_bytes": (3, 2), - "functools.lru_cache": (3, 2), - "gzip.compress": (3, 2), - "gzip.decompress": (3, 2), - "inspect.getclosurevars": (3, 3), - "inspect.getgeneratorlocals": (3, 3), - "inspect.getgeneratorstate": (3, 2), - "itertools.combinations_with_replacement": (3, 1), - "itertools.compress": (3, 1), - "logging.config.dictConfig": (3, 2), - "logging.NullHandler": (3, 1), - "math.erf": (3, 2), - "math.erfc": (3, 2), - "math.expm1": (3, 2), - "math.gamma": (3, 2), - "math.isfinite": (3, 2), - "math.lgamma": (3, 2), - "math.log2": (3, 3), - "os.environb": (3, 2), - "os.fsdecode": (3, 2), - "os.fsencode": (3, 2), - "os.fwalk": (3, 3), - "os.getenvb": (3, 2), - "os.get_exec_path": (3, 2), - "os.getgrouplist": (3, 3), - "os.getpriority": (3, 3), - "os.getresgid": (3, 2), - "os.getresuid": (3, 2), - "os.get_terminal_size": (3, 3), - "os.getxattr": (3, 3), - "os.initgroups": (3, 2), - "os.listxattr": (3, 3), - "os.lockf": (3, 3), - "os.pipe2": (3, 3), - "os.posix_fadvise": (3, 3), - "os.posix_fallocate": (3, 3), - "os.pread": (3, 3), - "os.pwrite": (3, 3), - "os.readv": (3, 3), - "os.removexattr": (3, 3), - "os.replace": (3, 3), - "os.sched_get_priority_max": (3, 3), - "os.sched_get_priority_min": (3, 3), - "os.sched_getaffinity": (3, 3), - "os.sched_getparam": (3, 3), - "os.sched_getscheduler": (3, 3), - "os.sched_rr_get_interval": (3, 3), - "os.sched_setaffinity": (3, 3), - "os.sched_setparam": (3, 3), - "os.sched_setscheduler": (3, 3), - "os.sched_yield": (3, 3), - "os.sendfile": (3, 3), - "os.setpriority": (3, 3), - "os.setresgid": (3, 2), - "os.setresuid": (3, 2), - "os.setxattr": (3, 3), - "os.sync": (3, 3), - "os.truncate": (3, 3), - "os.waitid": (3, 3), - "os.writev": (3, 3), - "shutil.chown": (3, 3), - "shutil.disk_usage": (3, 3), - "shutil.get_archive_formats": (3, 3), - "shutil.get_terminal_size": (3, 3), - "shutil.get_unpack_formats": (3, 3), - "shutil.make_archive": (3, 3), - "shutil.register_archive_format": (3, 3), - "shutil.register_unpack_format": (3, 3), - "shutil.unpack_archive": (3, 3), - "shutil.unregister_archive_format": (3, 3), - "shutil.unregister_unpack_format": (3, 3), - "shutil.which": (3, 3), - "signal.pthread_kill": (3, 3), - "signal.pthread_sigmask": (3, 3), - "signal.sigpending": (3, 3), - "signal.sigtimedwait": (3, 3), - "signal.sigwait": (3, 3), - "signal.sigwaitinfo": (3, 3), - "socket.CMSG_LEN": (3, 3), - "socket.CMSG_SPACE": (3, 3), - "socket.fromshare": (3, 3), - "socket.if_indextoname": (3, 3), - "socket.if_nameindex": (3, 3), - "socket.if_nametoindex": (3, 3), - "socket.sethostname": (3, 3), - "ssl.match_hostname": (3, 2), - "ssl.RAND_bytes": (3, 3), - "ssl.RAND_pseudo_bytes": (3, 3), - "ssl.SSLContext": (3, 2), - "ssl.SSLEOFError": (3, 3), - "ssl.SSLSyscallError": (3, 3), - "ssl.SSLWantReadError": (3, 3), - "ssl.SSLWantWriteError": (3, 3), - "ssl.SSLZeroReturnError": (3, 3), - "stat.filemode": (3, 3), - "textwrap.indent": (3, 3), - "threading.get_ident": (3, 3), - "time.clock_getres": (3, 3), - "time.clock_gettime": (3, 3), - "time.clock_settime": (3, 3), - "time.get_clock_info": (3, 3), - "time.monotonic": (3, 3), - "time.perf_counter": (3, 3), - "time.process_time": (3, 3), - "types.new_class": (3, 3), - "types.prepare_class": (3, 3), -} - -def uniq(a): - if len(a) == 0: - return [] - else: - return [a[0]] + uniq([x for x in a if x != a[0]]) - -class NodeChecker(ast.NodeVisitor): - def __init__(self): - self.vers = dict() - self.vers[(3,0)] = [] - def add(self, node, ver, msg): - if ver not in self.vers: - self.vers[ver] = [] - self.vers[ver].append((node.lineno, msg)) - def visit_Call(self, node): - def rollup(n): - if isinstance(n, ast.Name): - return n.id - elif isinstance(n, ast.Attribute): - r = rollup(n.value) - if r: - return r + "." + n.attr - name = rollup(node.func) - if name: - v = Functions.get(name) - if v is not None: - self.add(node, v, name) - self.generic_visit(node) - def visit_Import(self, node): - for n in node.names: - v = StandardModules.get(n.name) - if v is not None: - self.add(node, v, n.name) - self.generic_visit(node) - def visit_ImportFrom(self, node): - v = StandardModules.get(node.module) - if v is not None: - self.add(node, v, node.module) - for n in node.names: - name = node.module + "." + n.name - v = Functions.get(name) - if v is not None: - self.add(node, v, name) - def visit_Raise(self, node): - if isinstance(node.cause, ast.Name) and node.cause.id == "None": - self.add(node, (3,3), "raise ... from None") - def visit_YieldFrom(self, node): - self.add(node, (3,3), "yield from") - -def get_versions(source, filename=None): - """Return information about the Python versions required for specific features. - - The return value is a dictionary with keys as a version number as a tuple - (for example Python 3.1 is (3,1)) and the value are a list of features that - require the indicated Python version. - """ - tree = ast.parse(source, filename=filename) - checker = NodeChecker() - checker.visit(tree) - return checker.vers - -def v33(source): - if sys.version_info >= (3, 3): - return qver(source) - else: - print("Not all features tested, run --test with Python 3.3", file=sys.stderr) - return (3, 3) - -def qver(source): - """Return the minimum Python version required to run a particular bit of code. - - >>> qver('print("hello world")') - (3, 0) - >>> qver("import importlib") - (3, 1) - >>> qver("from importlib import x") - (3, 1) - >>> qver("import tkinter.ttk") - (3, 1) - >>> qver("from collections import Counter") - (3, 1) - >>> qver("collections.OrderedDict()") - (3, 1) - >>> qver("import functools\\n@functools.lru_cache()\\ndef f(x): x*x") - (3, 2) - >>> v33("yield from x") - (3, 3) - >>> v33("raise x from None") - (3, 3) - """ - return max(get_versions(source).keys()) diff --git a/lib/spack/external/ruamel/yaml/compat.py b/lib/spack/external/ruamel/yaml/compat.py index 6eee151c51..a1778bef28 100644 --- a/lib/spack/external/ruamel/yaml/compat.py +++ b/lib/spack/external/ruamel/yaml/compat.py @@ -12,7 +12,7 @@ try: from ruamel.ordereddict import ordereddict except: try: - from collections import OrderedDict # nopyqver + from collections import OrderedDict except ImportError: from ordereddict import OrderedDict # to get the right name import ... as ordereddict doesn't do that diff --git a/lib/spack/llnl/__init__.py b/lib/spack/llnl/__init__.py index 94f8ac4d9e..9f87532b85 100644 --- a/lib/spack/llnl/__init__.py +++ b/lib/spack/llnl/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/llnl/util/__init__.py b/lib/spack/llnl/util/__init__.py index 94f8ac4d9e..9f87532b85 100644 --- a/lib/spack/llnl/util/__init__.py +++ b/lib/spack/llnl/util/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/llnl/util/argparsewriter.py b/lib/spack/llnl/util/argparsewriter.py index 16bb570a77..f43595145e 100644 --- a/lib/spack/llnl/util/argparsewriter.py +++ b/lib/spack/llnl/util/argparsewriter.py @@ -1,203 +1,379 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from __future__ import print_function + import re import argparse import errno import sys - -class ArgparseWriter(object): +from six import StringIO + + +class Command(object): + """Parsed representation of a command from argparse. + + This is a single command from an argparse parser. ``ArgparseWriter`` + creates these and returns them from ``parse()``, and it passes one of + these to each call to ``format()`` so that we can take an action for + a single command. + + Parts of a Command: + - prog: command name (str) + - description: command description (str) + - usage: command usage (str) + - positionals: list of positional arguments (list) + - optionals: list of optional arguments (list) + - subcommands: list of subcommand parsers (list) + """ + def __init__(self, prog, description, usage, + positionals, optionals, subcommands): + self.prog = prog + self.description = description + self.usage = usage + self.positionals = positionals + self.optionals = optionals + self.subcommands = subcommands + + +# NOTE: The only reason we subclass argparse.HelpFormatter is to get access +# to self._expand_help(), ArgparseWriter is not intended to be used as a +# formatter_class. +class ArgparseWriter(argparse.HelpFormatter): """Analyzes an argparse ArgumentParser for easy generation of help.""" - def __init__(self, out=sys.stdout): + + def __init__(self, prog, out=sys.stdout, aliases=False): + """Initializes a new ArgparseWriter instance. + + Parameters: + prog (str): the program name + out (file object): the file to write to + aliases (bool): whether or not to include subparsers for aliases + """ + super(ArgparseWriter, self).__init__(prog) self.level = 0 + self.prog = prog self.out = out + self.aliases = aliases + + def parse(self, parser, prog): + """Parses the parser object and returns the relavent components. - def _write(self, parser, root=True, level=0): + Parameters: + parser (argparse.ArgumentParser): the parser + prog (str): the command name + + Returns: + (Command) information about the command from the parser + """ self.parser = parser - self.level = level - actions = parser._actions - # allow root level to be flattened with rest of commands - if type(root) == int: - self.level = root - root = True + split_prog = parser.prog.split(' ') + split_prog[-1] = prog + prog = ' '.join(split_prog) + description = parser.description - # go through actions and split them into optionals, positionals, + fmt = parser._get_formatter() + actions = parser._actions + groups = parser._mutually_exclusive_groups + usage = fmt._format_usage(None, actions, groups, '').strip() + + # Go through actions and split them into optionals, positionals, # and subcommands optionals = [] positionals = [] subcommands = [] for action in actions: if action.option_strings: - optionals.append(action) + flags = action.option_strings + dest_flags = fmt._format_action_invocation(action) + help = self._expand_help(action) if action.help else '' + help = help.replace('\n', ' ') + optionals.append((flags, dest_flags, help)) elif isinstance(action, argparse._SubParsersAction): for subaction in action._choices_actions: subparser = action._name_parser_map[subaction.dest] - subcommands.append(subparser) + subcommands.append((subparser, subaction.dest)) + + # Look for aliases of the form 'name (alias, ...)' + if self.aliases: + match = re.match(r'(.*) \((.*)\)', subaction.metavar) + if match: + aliases = match.group(2).split(', ') + for alias in aliases: + subparser = action._name_parser_map[alias] + subcommands.append((subparser, alias)) else: - positionals.append(action) + args = fmt._format_action_invocation(action) + help = self._expand_help(action) if action.help else '' + help = help.replace('\n', ' ') + positionals.append((args, help)) - groups = parser._mutually_exclusive_groups - fmt = parser._get_formatter() - description = parser.description + return Command( + prog, description, usage, positionals, optionals, subcommands) - def action_group(function, actions): - for action in actions: - arg = fmt._format_action_invocation(action) - help = action.help if action.help else '' - function(arg, re.sub('\n', ' ', help)) + def format(self, cmd): + """Returns the string representation of a single node in the + parser tree. - if root: - self.begin_command(parser.prog) + Override this in subclasses to define how each subcommand + should be displayed. - if description: - self.description(parser.description) + Parameters: + (Command): parsed information about a command or subcommand - usage = fmt._format_usage(None, actions, groups, '').strip() - self.usage(usage) + Returns: + str: the string representation of this subcommand + """ + raise NotImplementedError - if positionals: - self.begin_positionals() - action_group(self.positional, positionals) - self.end_positionals() + def _write(self, parser, prog, level=0): + """Recursively writes a parser. - if optionals: - self.begin_optionals() - action_group(self.optional, optionals) - self.end_optionals() + Parameters: + parser (argparse.ArgumentParser): the parser + prog (str): the command name + level (int): the current level + """ + self.level = level - if subcommands: - self.begin_subcommands(subcommands) - for subparser in subcommands: - self._write(subparser, root=True, level=level + 1) - self.end_subcommands(subcommands) + cmd = self.parse(parser, prog) + self.out.write(self.format(cmd)) - if root: - self.end_command(parser.prog) + for subparser, prog in cmd.subcommands: + self._write(subparser, prog, level=level + 1) - def write(self, parser, root=True): + def write(self, parser): """Write out details about an ArgumentParser. Args: - parser (ArgumentParser): an ``argparse`` parser - root (bool or int): if bool, whether to include the root parser; - or ``1`` to flatten the root parser with first-level - subcommands + parser (argparse.ArgumentParser): the parser """ try: - self._write(parser, root, level=0) + self._write(parser, self.prog) except IOError as e: - # swallow pipe errors + # Swallow pipe errors + # Raises IOError in Python 2 and BrokenPipeError in Python 3 if e.errno != errno.EPIPE: raise + +_rst_levels = ['=', '-', '^', '~', ':', '`'] + + +class ArgparseRstWriter(ArgparseWriter): + """Write argparse output as rst sections.""" + + def __init__(self, prog, out=sys.stdout, aliases=False, + rst_levels=_rst_levels): + """Create a new ArgparseRstWriter. + + Parameters: + prog (str): program name + out (file object): file to write to + aliases (bool): whether or not to include subparsers for aliases + rst_levels (list of str): list of characters + for rst section headings + """ + super(ArgparseRstWriter, self).__init__(prog, out, aliases) + self.rst_levels = rst_levels + + def format(self, cmd): + string = StringIO() + string.write(self.begin_command(cmd.prog)) + + if cmd.description: + string.write(self.description(cmd.description)) + + string.write(self.usage(cmd.usage)) + + if cmd.positionals: + string.write(self.begin_positionals()) + for args, help in cmd.positionals: + string.write(self.positional(args, help)) + string.write(self.end_positionals()) + + if cmd.optionals: + string.write(self.begin_optionals()) + for flags, dest_flags, help in cmd.optionals: + string.write(self.optional(dest_flags, help)) + string.write(self.end_optionals()) + + if cmd.subcommands: + string.write(self.begin_subcommands(cmd.subcommands)) + + return string.getvalue() + def begin_command(self, prog): - pass + return """ +---- + +.. _{0}: - def end_command(self, prog): - pass +{1} +{2} + +""".format(prog.replace(' ', '-'), prog, + self.rst_levels[self.level] * len(prog)) def description(self, description): - pass + return description + '\n\n' def usage(self, usage): - pass + return """\ +.. code-block:: console + + {0} + +""".format(usage) def begin_positionals(self): - pass + return '\n**Positional arguments**\n\n' def positional(self, name, help): - pass + return """\ +{0} + {1} + +""".format(name, help) def end_positionals(self): - pass + return '' def begin_optionals(self): - pass + return '\n**Optional arguments**\n\n' + + def optional(self, opts, help): + return """\ +``{0}`` + {1} - def optional(self, option, help): - pass +""".format(opts, help) def end_optionals(self): - pass + return '' def begin_subcommands(self, subcommands): - pass + string = """ +**Subcommands** - def end_subcommands(self, subcommands): - pass +.. hlist:: + :columns: 4 +""" -_rst_levels = ['=', '-', '^', '~', ':', '`'] + for cmd, _ in subcommands: + prog = re.sub(r'^[^ ]* ', '', cmd.prog) + string += ' * :ref:`{0} <{1}>`\n'.format( + prog, cmd.prog.replace(' ', '-')) + return string + '\n' -class ArgparseRstWriter(ArgparseWriter): - """Write argparse output as rst sections.""" - def __init__(self, out=sys.stdout, rst_levels=_rst_levels, - strip_root_prog=True): - """Create a new ArgparseRstWriter. +class ArgparseCompletionWriter(ArgparseWriter): + """Write argparse output as shell programmable tab completion functions.""" - Args: - out (file object): file to write to - rst_levels (list of str): list of characters - for rst section headings - strip_root_prog (bool): if ``True``, strip the base command name - from subcommands in output + def format(self, cmd): + """Returns the string representation of a single node in the + parser tree. + + Override this in subclasses to define how each subcommand + should be displayed. + + Parameters: + (Command): parsed information about a command or subcommand + + Returns: + str: the string representation of this subcommand """ - super(ArgparseRstWriter, self).__init__(out) - self.rst_levels = rst_levels - self.strip_root_prog = strip_root_prog - def line(self, string=''): - self.out.write('%s\n' % string) + assert cmd.optionals # we should always at least have -h, --help + assert not (cmd.positionals and cmd.subcommands) # one or the other - def begin_command(self, prog): - self.line() - self.line('----') - self.line() - self.line('.. _%s:\n' % prog.replace(' ', '-')) - self.line('%s' % prog) - self.line(self.rst_levels[self.level] * len(prog) + '\n') + # We only care about the arguments/flags, not the help messages + positionals = [] + if cmd.positionals: + positionals, _ = zip(*cmd.positionals) + optionals, _, _ = zip(*cmd.optionals) + subcommands = [] + if cmd.subcommands: + _, subcommands = zip(*cmd.subcommands) - def description(self, description): - self.line('%s\n' % description) + # Flatten lists of lists + optionals = [x for xx in optionals for x in xx] - def usage(self, usage): - self.line('.. code-block:: console\n') - self.line(' %s\n' % usage) + return (self.start_function(cmd.prog) + + self.body(positionals, optionals, subcommands) + + self.end_function(cmd.prog)) - def begin_positionals(self): - self.line() - self.line('**Positional arguments**\n') + def start_function(self, prog): + """Returns the syntax needed to begin a function definition. - def positional(self, name, help): - self.line(name) - self.line(' %s\n' % help) + Parameters: + prog (str): the command name - def begin_optionals(self): - self.line() - self.line('**Optional arguments**\n') + Returns: + str: the function definition beginning + """ + name = prog.replace('-', '_').replace(' ', '_') + return '\n_{0}() {{'.format(name) - def optional(self, opts, help): - self.line('``%s``' % opts) - self.line(' %s\n' % help) + def end_function(self, prog=None): + """Returns the syntax needed to end a function definition. - def begin_subcommands(self, subcommands): - self.line() - self.line('**Subcommands**\n') - self.line('.. hlist::') - self.line(' :columns: 4\n') - - for cmd in subcommands: - prog = cmd.prog - if self.strip_root_prog: - prog = re.sub(r'^[^ ]* ', '', prog) - - self.line(' * :ref:`%s <%s>`' - % (prog, cmd.prog.replace(' ', '-'))) - self.line() + Parameters: + prog (str, optional): the command name + + Returns: + str: the function definition ending + """ + return '}\n' + + def body(self, positionals, optionals, subcommands): + """Returns the body of the function. + + Parameters: + positionals (list): list of positional arguments + optionals (list): list of optional arguments + subcommands (list): list of subcommand parsers + + Returns: + str: the function body + """ + return '' + + def positionals(self, positionals): + """Returns the syntax for reporting positional arguments. + + Parameters: + positionals (list): list of positional arguments + + Returns: + str: the syntax for positional arguments + """ + return '' + + def optionals(self, optionals): + """Returns the syntax for reporting optional flags. + + Parameters: + optionals (list): list of optional arguments + + Returns: + str: the syntax for optional flags + """ + return '' + + def subcommands(self, subcommands): + """Returns the syntax for reporting subcommands. + + Parameters: + subcommands (list): list of subcommand parsers + + Returns: + str: the syntax for subcommand parsers + """ + return '' diff --git a/lib/spack/llnl/util/cpu/__init__.py b/lib/spack/llnl/util/cpu/__init__.py index cf3c3ef50c..5a4943c965 100644 --- a/lib/spack/llnl/util/cpu/__init__.py +++ b/lib/spack/llnl/util/cpu/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/llnl/util/cpu/alias.py b/lib/spack/llnl/util/cpu/alias.py index f52ecf7354..abb4ea22f5 100644 --- a/lib/spack/llnl/util/cpu/alias.py +++ b/lib/spack/llnl/util/cpu/alias.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/llnl/util/cpu/detect.py b/lib/spack/llnl/util/cpu/detect.py index c89f67c852..66b09f5e9e 100644 --- a/lib/spack/llnl/util/cpu/detect.py +++ b/lib/spack/llnl/util/cpu/detect.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ import warnings import six from .microarchitecture import generic_microarchitecture, targets +from .schema import targets_json #: Mapping from operating systems to chain of commands #: to obtain a dictionary of raw info on the current cpu @@ -108,21 +109,37 @@ def sysctl_info_dict(): 'model': sysctl('-n', 'machdep.cpu.model'), 'model name': sysctl('-n', 'machdep.cpu.brand_string') } + return info - # Super hacky way to deal with slight representation differences - # Would be better to somehow consider these "identical" - if 'sse4.1' in info['flags']: - info['flags'] += ' sse4_1' - if 'sse4.2' in info['flags']: - info['flags'] += ' sse4_2' - if 'avx1.0' in info['flags']: - info['flags'] += ' avx' - if 'clfsopt' in info['flags']: - info['flags'] += ' clflushopt' - if 'xsave' in info['flags']: - info['flags'] += ' xsavec xsaveopt' - return info +def adjust_raw_flags(info): + """Adjust the flags detected on the system to homogenize + slightly different representations. + """ + # Flags detected on Darwin turned to their linux counterpart + flags = info.get('flags', []) + d2l = targets_json['conversions']['darwin_flags'] + for darwin_flag, linux_flag in d2l.items(): + if darwin_flag in flags: + info['flags'] += ' ' + linux_flag + + +def adjust_raw_vendor(info): + """Adjust the vendor field to make it human readable""" + if 'CPU implementer' not in info: + return + + # Mapping numeric codes to vendor (ARM). This list is a merge from + # different sources: + # + # https://github.com/karelzak/util-linux/blob/master/sys-utils/lscpu-arm.c + # https://developer.arm.com/docs/ddi0487/latest/arm-architecture-reference-manual-armv8-for-armv8-a-architecture-profile + # https://github.com/gcc-mirror/gcc/blob/master/gcc/config/aarch64/aarch64-cores.def + # https://patchwork.kernel.org/patch/10524949/ + arm_vendors = targets_json['conversions']['arm_vendors'] + arm_code = info['CPU implementer'] + if arm_code in arm_vendors: + info['CPU implementer'] = arm_vendors[arm_code] def raw_info_dictionary(): @@ -139,6 +156,8 @@ def raw_info_dictionary(): warnings.warn(str(e)) if info: + adjust_raw_flags(info) + adjust_raw_vendor(info) break return info @@ -223,3 +242,15 @@ def compatibility_check_for_x86_64(info, target): return (target == arch_root or arch_root in target.ancestors) \ and (target.vendor == vendor or target.vendor == 'generic') \ and target.features.issubset(features) + + +@compatibility_check(architecture_family='aarch64') +def compatibility_check_for_aarch64(info, target): + basename = 'aarch64' + features = set(info.get('Features', '').split()) + vendor = info.get('CPU implementer', 'generic') + + arch_root = targets[basename] + return (target == arch_root or arch_root in target.ancestors) \ + and (target.vendor == vendor or target.vendor == 'generic') \ + and target.features.issubset(features) diff --git a/lib/spack/llnl/util/cpu/microarchitecture.py b/lib/spack/llnl/util/cpu/microarchitecture.py index 3d1590376a..f507837f89 100644 --- a/lib/spack/llnl/util/cpu/microarchitecture.py +++ b/lib/spack/llnl/util/cpu/microarchitecture.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,7 +8,7 @@ import re import warnings try: - from collections.abc import Sequence + from collections.abc import Sequence # novm except ImportError: from collections import Sequence diff --git a/lib/spack/llnl/util/cpu/microarchitectures.json b/lib/spack/llnl/util/cpu/microarchitectures.json index bb3b4db21a..51411d4a24 100644 --- a/lib/spack/llnl/util/cpu/microarchitectures.json +++ b/lib/spack/llnl/util/cpu/microarchitectures.json @@ -64,13 +64,13 @@ "clang": [ { "versions": "0.0.0-apple:", - "family": "x86-64", - "flags": "-march={family}" + "name": "x86-64", + "flags": "-march={name}" }, { "versions": ":", - "family": "x86-64", - "flags": "-march={family} -mcpu=generic" + "name": "x86-64", + "flags": "-march={name} -mtune=generic" } ], "intel": { @@ -96,8 +96,7 @@ }, "clang": { "versions": "3.9:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -122,8 +121,7 @@ }, "clang": { "versions": "3.9:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -157,8 +155,7 @@ ], "clang": { "versions": "3.9:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -188,8 +185,7 @@ }, "clang": { "versions": "3.9:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -227,8 +223,7 @@ ], "clang": { "versions": "3.9:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": [ { @@ -274,8 +269,7 @@ ], "clang": { "versions": "3.9:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": [ { @@ -326,8 +320,7 @@ ], "clang": { "versions": "3.9:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": [ { @@ -373,8 +366,7 @@ }, "clang": { "versions": "3.9:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "18.0:", @@ -416,8 +408,7 @@ }, "clang": { "versions": "3.9:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "18.0:", @@ -463,8 +454,7 @@ "clang": { "versions": "3.9:", "name": "knl", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "18.0:", @@ -515,8 +505,7 @@ "clang": { "versions": "3.9:", "name": "skylake-avx512", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "18.0:", @@ -568,8 +557,7 @@ }, "clang": { "versions": "3.9:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "18.0:", @@ -609,7 +597,7 @@ "avx512bw", "avx512dq", "avx512cd", - "avx512vnni" + "avx512_vnni" ], "compilers": { "gcc": { @@ -618,8 +606,7 @@ }, "clang": { "versions": "8.0:", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "19.0:", @@ -685,13 +672,11 @@ { "versions": "7.0:", "name": "icelake-client", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, { "versions": "6.0:6.9", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" } ], "intel": { @@ -723,8 +708,7 @@ "clang": { "versions": "3.9:", "name": "amdfam10", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -761,8 +745,7 @@ "clang": { "versions": "3.9:", "name": "bdver1", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -803,8 +786,7 @@ "clang": { "versions": "3.9:", "name": "bdver2", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -846,8 +828,7 @@ "clang": { "versions": "3.9:", "name": "bdver3", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -892,8 +873,7 @@ "clang": { "versions": "3.9:", "name": "bdver4", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -942,8 +922,7 @@ "clang": { "versions": "4.0:", "name": "znver1", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -993,8 +972,7 @@ "clang": { "versions": "9.0:", "name": "znver2", - "family": "x86-64", - "flags": "-march={family} -mcpu={name}" + "flags": "-march={name} -mtune={name}" }, "intel": { "versions": "16.0:", @@ -1016,8 +994,7 @@ }, "clang": { "versions": ":", - "family": "ppc64", - "flags": "-march={family} -mcpu=generic" + "flags": "-mcpu={name} -mtune={name}" } } }, @@ -1033,9 +1010,7 @@ }, "clang": { "versions": "3.9:", - "family": "ppc64", - "name": "pwr7", - "flags": "-march={family} -mcpu={name}" + "flags": "-mcpu={name} -mtune={name}" } } }, @@ -1058,9 +1033,7 @@ ], "clang": { "versions": "3.9:", - "family": "ppc64", - "name": "pwr8", - "flags": "-march={family} -mcpu={name}" + "flags": "-mcpu={name} -mtune={name}" } } }, @@ -1076,9 +1049,7 @@ }, "clang": { "versions": "3.9:", - "family": "ppc64", - "name": "pwr9", - "flags": "-march={family} -mcpu={name}" + "flags": "-mcpu={name} -mtune={name}" } } }, @@ -1094,8 +1065,7 @@ }, "clang": { "versions": ":", - "family": "ppc64le", - "flags": "-march={family} -mcpu=generic" + "flags": "-mcpu={name} -mtune={name}" } } }, @@ -1121,8 +1091,8 @@ "clang": { "versions": "3.9:", "family": "ppc64le", - "name": "pwr8", - "flags": "-march={family} -mcpu={name}" + "name": "power8", + "flags": "-mcpu={name} -mtune={name}" } } }, @@ -1140,8 +1110,8 @@ "clang": { "versions": "3.9:", "family": "ppc64le", - "name": "pwr9", - "flags": "-march={family} -mcpu={name}" + "name": "power9", + "flags": "-mcpu={name} -mtune={name}" } } }, @@ -1156,11 +1126,113 @@ }, "clang": { "versions": ":", - "family": "aarch64", - "flags": "-march={family} -mcpu=generic" + "flags": "-march=armv8-a -mtune=generic" } } }, + "thunderx2": { + "from": "aarch64", + "vendor": "Cavium", + "features": [ + "fp", + "asimd", + "evtstrm", + "aes", + "pmull", + "sha1", + "sha2", + "crc32", + "atomics", + "cpuid", + "asimdrdm" + ], + "compilers": { + "gcc": [ + { + "versions": "4.8:4.8.9", + "flags": "-march=armv8-a" + }, + { + "versions": "4.9:5.9", + "flags": "-march=armv8-a+crc+crypto" + }, + { + "versions": "6:6.9", + "flags": "-march=armv8.1-a+crc+crypto" + }, + { + "versions": "7:", + "flags": "-mcpu=thunderx2t99" + } + ], + "clang": [ + { + "versions": "3.9:4.9", + "flags": "-march=armv8.1-a+crc+crypto" + }, + { + "versions": "5:", + "flags": "-mcpu=thunderx2t99" + } + ] + } + }, + "a64fx": { + "from": "aarch64", + "vendor": "Fujitsu", + "features": [ + "fp", + "asimd", + "evtstrm", + "aes", + "pmull", + "sha1", + "sha2", + "crc32", + "atomics", + "cpuid", + "asimdrdm", + "fphp", + "asimdhp", + "fcma", + "dcpop", + "sve" + ], + "compilers": { + "gcc": [ + { + "versions": "4.8:4.8.9", + "flags": "-march=armv8-a" + }, + { + "versions": "4.9:5.9", + "flags": "-march=armv8-a+crc+crypto" + }, + { + "versions": "6:6.9", + "flags": "-march=armv8.1-a+crc+crypto" + }, + { + "versions": "7:7.9", + "flags": "-march=armv8.2-a+crc+crypto+fp16" + }, + { + "versions": "8:", + "flags": "-march=armv8.2-a+crc+aes+sha2+fp16+sve -msve-vector-bits=512" + } + ], + "clang": [ + { + "versions": "3.9:4.9", + "flags": "-march=armv8.2-a+crc+crypto+fp16" + }, + { + "versions": "5:", + "flags": "-march=armv8.2-a+crc+crypto+fp16+sve" + } + ] + } + }, "arm": { "from": null, "vendor": "generic", @@ -1226,6 +1298,20 @@ "ppc64" ] }, + "vsx": { + "reason": "VSX alitvec extensions are supported by PowerISA from v2.06 (Power7+), but might not be listed in features", + "families": [ + "ppc64le", + "ppc64" + ] + }, + "fma": { + "reason": "FMA has been supported by PowerISA since Power1, but might not be listed in features", + "families": [ + "ppc64le", + "ppc64" + ] + }, "sse4.1": { "reason": "permits to refer to sse4_1 also as sse4.1", "any_of": [ @@ -1244,5 +1330,34 @@ "aarch64" ] } + }, + "conversions": { + "description": "Conversions that map some platform specific values to canonical values", + "arm_vendors": { + "0x41": "ARM", + "0x42": "Broadcom", + "0x43": "Cavium", + "0x44": "DEC", + "0x46": "Fujitsu", + "0x48": "HiSilicon", + "0x49": "Infineon Technologies AG", + "0x4d": "Motorola", + "0x4e": "Nvidia", + "0x50": "APM", + "0x51": "Qualcomm", + "0x53": "Samsung", + "0x56": "Marvell", + "0x61": "Apple", + "0x66": "Faraday", + "0x68": "HXT", + "0x69": "Intel" + }, + "darwin_flags": { + "sse4.1": "sse4_1", + "sse4.2": "sse4_2", + "avx1.0": "avx", + "clfsopt": "clflushopt", + "xsave": "xsavec xsaveopt" + } } } diff --git a/lib/spack/llnl/util/cpu/schema.py b/lib/spack/llnl/util/cpu/schema.py index d13d014c01..2cb456730e 100644 --- a/lib/spack/llnl/util/cpu/schema.py +++ b/lib/spack/llnl/util/cpu/schema.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ import json import os.path try: - from collections.abc import MutableMapping + from collections.abc import MutableMapping # novm except ImportError: from collections import MutableMapping @@ -72,7 +72,21 @@ properties = { 'additionalProperties': False } }, - + }, + 'conversions': { + 'type': 'object', + 'properties': { + 'description': { + 'type': 'string' + }, + 'arm_vendors': { + 'type': 'object', + }, + 'darwin_flags': { + 'type': 'object' + } + }, + 'additionalProperties': False } } diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index f6c8d161d7..273840a424 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -201,7 +201,6 @@ def filter_file(regex, repl, *filenames, **kwargs): output_file.writelines(input_file.readlines()) except BaseException: - os.remove(tmp_filename) # clean up the original file on failure. shutil.move(backup_filename, filename) raise @@ -1154,7 +1153,9 @@ class HeaderList(FileList): # Make sure to only match complete words, otherwise path components such # as "xinclude" will cause false matches. - include_regex = re.compile(r'(.*)(\binclude\b)(.*)') + # Avoid matching paths such as <prefix>/include/something/detail/include, + # e.g. in the CUDA Toolkit which ships internal libc++ headers. + include_regex = re.compile(r'(.*?)(\binclude\b)(.*)') def __init__(self, files): super(HeaderList, self).__init__(files) diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py index 11820a7f58..55407992a1 100644 --- a/lib/spack/llnl/util/lang.py +++ b/lib/spack/llnl/util/lang.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,12 +19,6 @@ import sys ignore_modules = [r'^\.#', '~$'] -class classproperty(property): - """classproperty decorator: like property but for classmethods.""" - def __get__(self, cls, owner): - return self.fget.__get__(None, owner)() - - def index_by(objects, *funcs): """Create a hierarchy of dictionaries by splitting the supplied set of objects on unique values of the supplied functions. @@ -612,12 +606,14 @@ def load_module_from_file(module_name, module_path): """ if sys.version_info[0] == 3 and sys.version_info[1] >= 5: import importlib.util - spec = importlib.util.spec_from_file_location(module_name, module_path) - module = importlib.util.module_from_spec(spec) + spec = importlib.util.spec_from_file_location( # novm + module_name, module_path) + module = importlib.util.module_from_spec(spec) # novm spec.loader.exec_module(module) elif sys.version_info[0] == 3 and sys.version_info[1] < 5: import importlib.machinery - loader = importlib.machinery.SourceFileLoader(module_name, module_path) + loader = importlib.machinery.SourceFileLoader( # novm + module_name, module_path) module = loader.load_module() elif sys.version_info[0] == 2: import imp diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py index e9d8e72161..d29b1289e3 100644 --- a/lib/spack/llnl/util/link_tree.py +++ b/lib/spack/llnl/util/link_tree.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/llnl/util/lock.py b/lib/spack/llnl/util/lock.py index 3a58093491..63f970c98b 100644 --- a/lib/spack/llnl/util/lock.py +++ b/lib/spack/llnl/util/lock.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/llnl/util/multiproc.py b/lib/spack/llnl/util/multiproc.py index ff21d0f758..f87b32c307 100644 --- a/lib/spack/llnl/util/multiproc.py +++ b/lib/spack/llnl/util/multiproc.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/llnl/util/tty/__init__.py b/lib/spack/llnl/util/tty/__init__.py index 8581c16045..668e881b2a 100644 --- a/lib/spack/llnl/util/tty/__init__.py +++ b/lib/spack/llnl/util/tty/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/llnl/util/tty/colify.py b/lib/spack/llnl/util/tty/colify.py index d5e0aa8def..e0b4a5fa05 100644 --- a/lib/spack/llnl/util/tty/colify.py +++ b/lib/spack/llnl/util/tty/colify.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -199,10 +199,16 @@ def colify(elts, **options): def colify_table(table, **options): """Version of ``colify()`` for data expressed in rows, (list of lists). - Same as regular colify but takes a list of lists, where each - sub-list must be the same length, and each is interpreted as a - row in a table. Regular colify displays a sequential list of - values in columns. + Same as regular colify but: + + 1. This takes a list of lists, where each sub-list must be the + same length, and each is interpreted as a row in a table. + Regular colify displays a sequential list of values in columns. + + 2. Regular colify will always print with 1 column when the output + is not a tty. This will always print with same dimensions of + the table argument. + """ if table is None: raise TypeError("Can't call colify_table on NoneType") @@ -220,6 +226,9 @@ def colify_table(table, **options): raise ValueError("Cannot override columsn in colify_table.") options['cols'] = columns + # don't reduce to 1 column for non-tty + options['tty'] = True + colify(transpose(), **options) diff --git a/lib/spack/llnl/util/tty/color.py b/lib/spack/llnl/util/tty/color.py index 6789ecbdb3..79f62c0040 100644 --- a/lib/spack/llnl/util/tty/color.py +++ b/lib/spack/llnl/util/tty/color.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/llnl/util/tty/log.py b/lib/spack/llnl/util/tty/log.py index b061e13b0e..10516e59d2 100644 --- a/lib/spack/llnl/util/tty/log.py +++ b/lib/spack/llnl/util/tty/log.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index 953ec89f9f..fa061756f0 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/abi.py b/lib/spack/spack/abi.py index aaccc50461..9e1ef14551 100644 --- a/lib/spack/spack/abi.py +++ b/lib/spack/spack/abi.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py index 378fb5d5d9..38ed5baa7b 100644 --- a/lib/spack/spack/architecture.py +++ b/lib/spack/spack/architecture.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -69,6 +69,7 @@ from llnl.util.lang import memoized, list_modules, key_ordering import spack.compiler import spack.paths import spack.error as serr +import spack.util.executable import spack.version from spack.util.naming import mod_to_class from spack.util.spack_yaml import syaml_dict @@ -214,7 +215,11 @@ class Target(object): import spack.spec if isinstance(compiler, spack.spec.CompilerSpec): compiler = spack.compilers.compilers_for_spec(compiler).pop() - compiler_version = compiler.cc_version(compiler.cc) + try: + compiler_version = compiler.cc_version(compiler.cc) + except spack.util.executable.ProcessError as e: + # log this and just return compiler.version instead + tty.debug(str(e)) return self.microarchitecture.optimization_flags( compiler.name, str(compiler_version) diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index 3b10cca180..515a6166d2 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,7 +23,7 @@ from llnl.util.filesystem import mkdirp, install_tree import spack.cmd import spack.config as config import spack.fetch_strategy as fs -import spack.util.gpg as gpg_util +import spack.util.gpg import spack.relocate as relocate import spack.util.spack_yaml as syaml import spack.mirror @@ -33,7 +33,7 @@ import spack.util.web as web_util from spack.spec import Spec from spack.stage import Stage from spack.util.gpg import Gpg -from spack.util.executable import ProcessError +import spack.architecture as architecture _build_cache_relative_path = 'build_cache' @@ -110,14 +110,6 @@ class NewLayoutException(spack.error.SpackError): pass -def has_gnupg2(): - try: - gpg_util.Gpg.gpg()('--version', output=os.devnull) - return True - except ProcessError: - return False - - def build_cache_relative_path(): return _build_cache_relative_path @@ -243,27 +235,31 @@ def checksum_tarball(file): def sign_tarball(key, force, specfile_path): # Sign the packages if keys available - if not has_gnupg2(): + if spack.util.gpg.Gpg.gpg() is None: raise NoGpgException( "gpg2 is not available in $PATH .\n" "Use spack install gnupg and spack load gnupg.") - else: - if key is None: - keys = Gpg.signing_keys() - if len(keys) == 1: - key = keys[0] - if len(keys) > 1: - raise PickKeyException(str(keys)) - if len(keys) == 0: - msg = "No default key available for signing.\n" - msg += "Use spack gpg init and spack gpg create" - msg += " to create a default key." - raise NoKeyException(msg) + + if key is None: + keys = Gpg.signing_keys() + if len(keys) == 1: + key = keys[0] + + if len(keys) > 1: + raise PickKeyException(str(keys)) + + if len(keys) == 0: + msg = "No default key available for signing.\n" + msg += "Use spack gpg init and spack gpg create" + msg += " to create a default key." + raise NoKeyException(msg) + if os.path.exists('%s.asc' % specfile_path): if force: os.remove('%s.asc' % specfile_path) else: raise NoOverwriteException('%s.asc' % specfile_path) + Gpg.sign(key, specfile_path, '%s.asc' % specfile_path) @@ -272,7 +268,7 @@ def generate_package_index(cache_prefix): Creates (or replaces) the "index.html" page at the location given in cache_prefix. This page contains a link for each binary package (*.yaml) - and signing key (*.key) under cache_prefix. + and public key (*.key) under cache_prefix. """ tmpdir = tempfile.mkdtemp() try: @@ -664,22 +660,88 @@ def extract_tarball(spec, filename, allow_root=False, unsigned=False, shutil.rmtree(tmpdir) -#: Internal cache for get_specs -_cached_specs = None +# Internal cache for downloaded specs +_cached_specs = set() -def get_specs(force=False): +def try_download_specs(urls=None, force=False): + ''' + Try to download the urls and cache them + ''' + global _cached_specs + if urls is None: + return {} + for link in urls: + with Stage(link, name="build_cache", keep=True) as stage: + if force and os.path.exists(stage.save_filename): + os.remove(stage.save_filename) + if not os.path.exists(stage.save_filename): + try: + stage.fetch() + except fs.FetchError: + continue + with open(stage.save_filename, 'r') as f: + # read the spec from the build cache file. All specs + # in build caches are concrete (as they are built) so + # we need to mark this spec concrete on read-in. + spec = Spec.from_yaml(f) + spec._mark_concrete() + _cached_specs.add(spec) + + return _cached_specs + + +def get_spec(spec=None, force=False): """ - Get spec.yaml's for build caches available on mirror + Check if spec.yaml exists on mirrors and return it if it does """ global _cached_specs + urls = set() + if spec is None: + return {} + specfile_name = tarball_name(spec, '.spec.yaml') - if _cached_specs: - tty.debug("Using previously-retrieved specs") + if not spack.mirror.MirrorCollection(): + tty.debug("No Spack mirrors are currently configured") + return {} + + if spec in _cached_specs: return _cached_specs + for mirror in spack.mirror.MirrorCollection().values(): + fetch_url_build_cache = url_util.join( + mirror.fetch_url, _build_cache_relative_path) + + mirror_dir = url_util.local_file_path(fetch_url_build_cache) + if mirror_dir: + tty.msg("Finding buildcaches in %s" % mirror_dir) + link = url_util.join(fetch_url_build_cache, specfile_name) + urls.add(link) + + else: + tty.msg("Finding buildcaches at %s" % + url_util.format(fetch_url_build_cache)) + link = url_util.join(fetch_url_build_cache, specfile_name) + urls.add(link) + + return try_download_specs(urls=urls, force=force) + + +def get_specs(force=False, allarch=False): + """ + Get spec.yaml's for build caches available on mirror + """ + arch = architecture.Arch(architecture.platform(), + 'default_os', 'default_target') + arch_pattern = ('([^-]*-[^-]*-[^-]*)') + if not allarch: + arch_pattern = '(%s-%s-[^-]*)' % (arch.platform, arch.os) + + regex_pattern = '%s(.*)(spec.yaml$)' % (arch_pattern) + arch_re = re.compile(regex_pattern) + if not spack.mirror.MirrorCollection(): - tty.warn("No Spack mirrors are currently configured") + tty.debug("No Spack mirrors are currently configured") return {} urls = set() @@ -693,7 +755,8 @@ def get_specs(force=False): if os.path.exists(mirror_dir): files = os.listdir(mirror_dir) for file in files: - if re.search('spec.yaml', file): + m = arch_re.search(file) + if m: link = url_util.join(fetch_url_build_cache, file) urls.add(link) else: @@ -702,28 +765,11 @@ def get_specs(force=False): p, links = web_util.spider( url_util.join(fetch_url_build_cache, 'index.html')) for link in links: - if re.search("spec.yaml", link): + m = arch_re.search(link) + if m: urls.add(link) - _cached_specs = [] - for link in urls: - with Stage(link, name="build_cache", keep=True) as stage: - if force and os.path.exists(stage.save_filename): - os.remove(stage.save_filename) - if not os.path.exists(stage.save_filename): - try: - stage.fetch() - except fs.FetchError: - continue - with open(stage.save_filename, 'r') as f: - # read the spec from the build cache file. All specs - # in build caches are concrete (as they are built) so - # we need to mark this spec concrete on read-in. - spec = Spec.from_yaml(f) - spec._mark_concrete() - _cached_specs.append(spec) - - return _cached_specs + return try_download_specs(urls=urls, force=force) def get_keys(install=False, trust=False, force=False): @@ -803,10 +849,10 @@ def needs_rebuild(spec, mirror_url, rebuild_on_errors=False): try: _, _, yaml_file = web_util.read_from_url(file_path) yaml_contents = codecs.getreader('utf-8')(yaml_file).read() - except URLError as url_err: + except (URLError, web_util.SpackWebError) as url_err: err_msg = [ 'Unable to determine whether {0} needs rebuilding,', - ' caught URLError attempting to read from {1}.', + ' caught exception attempting to read from {1}.', ] tty.error(''.join(err_msg).format(spec.short_spec, file_path)) tty.debug(url_err) @@ -908,11 +954,16 @@ def _download_buildcache_entry(mirror_root, descriptions): return True -def download_buildcache_entry(file_descriptions): - if not spack.mirror.MirrorCollection(): - tty.die("Please add a spack mirror to allow " + +def download_buildcache_entry(file_descriptions, mirror_url=None): + if not mirror_url and not spack.mirror.MirrorCollection(): + tty.die("Please provide or add a spack mirror to allow " + "download of buildcache entries.") + if mirror_url: + mirror_root = os.path.join( + mirror_url, _build_cache_relative_path) + return _download_buildcache_entry(mirror_root, file_descriptions) + for mirror in spack.mirror.MirrorCollection().values(): mirror_root = os.path.join( mirror.fetch_url, diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 13ee99d177..4809a1010e 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -39,7 +39,6 @@ import shutil import sys import traceback import types -from six import iteritems from six import StringIO import llnl.util.tty as tty @@ -52,6 +51,7 @@ import spack.build_systems.meson import spack.config import spack.main import spack.paths +import spack.schema.environment import spack.store from spack.util.string import plural from spack.util.environment import ( @@ -342,21 +342,7 @@ def set_build_environment_variables(pkg, env, dirty): # Set environment variables if specified for # the given compiler compiler = pkg.compiler - environment = compiler.environment - - for command, variable in iteritems(environment): - if command == 'set': - for name, value in iteritems(variable): - env.set(name, value) - elif command == 'unset': - for name, _ in iteritems(variable): - env.unset(name) - elif command == 'prepend-path': - for name, value in iteritems(variable): - env.prepend_path(name, value) - elif command == 'append-path': - for name, value in iteritems(variable): - env.append_path(name, value) + env.extend(spack.schema.environment.parse(compiler.environment)) if compiler.extra_rpaths: extra_rpaths = ':'.join(compiler.extra_rpaths) diff --git a/lib/spack/spack/build_systems/__init__.py b/lib/spack/spack/build_systems/__init__.py index 94f8ac4d9e..9f87532b85 100644 --- a/lib/spack/spack/build_systems/__init__.py +++ b/lib/spack/spack/build_systems/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/aspell_dict.py b/lib/spack/spack/build_systems/aspell_dict.py index e9019a1948..7da4d2f10c 100644 --- a/lib/spack/spack/build_systems/aspell_dict.py +++ b/lib/spack/spack/build_systems/aspell_dict.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/autotools.py b/lib/spack/spack/build_systems/autotools.py index ce0e40b34c..c21b8dad71 100644 --- a/lib/spack/spack/build_systems/autotools.py +++ b/lib/spack/spack/build_systems/autotools.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/cmake.py b/lib/spack/spack/build_systems/cmake.py index 0c6a166409..14f33e94e6 100644 --- a/lib/spack/spack/build_systems/cmake.py +++ b/lib/spack/spack/build_systems/cmake.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/cuda.py b/lib/spack/spack/build_systems/cuda.py index b75807fd06..fc96cffe60 100644 --- a/lib/spack/spack/build_systems/cuda.py +++ b/lib/spack/spack/build_systems/cuda.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -61,12 +61,13 @@ class CudaPackage(PackageBase): conflicts('%gcc@6:', when='+cuda ^cuda@:8' + arch_platform) conflicts('%gcc@7:', when='+cuda ^cuda@:9.1' + arch_platform) conflicts('%gcc@8:', when='+cuda ^cuda@:10.0.130' + arch_platform) - conflicts('%gcc@9:', when='+cuda ^cuda@:10.1.243' + arch_platform) + conflicts('%gcc@9:', when='+cuda ^cuda@:10.2.89' + arch_platform) conflicts('%pgi@:14.8', when='+cuda ^cuda@:7.0.27' + arch_platform) conflicts('%pgi@:15.3,15.5:', when='+cuda ^cuda@7.5' + arch_platform) conflicts('%pgi@:16.2,16.0:16.3', when='+cuda ^cuda@8' + arch_platform) conflicts('%pgi@:15,18:', when='+cuda ^cuda@9.0:9.1' + arch_platform) conflicts('%pgi@:16', when='+cuda ^cuda@9.2.88:10' + arch_platform) + conflicts('%pgi@:17', when='+cuda ^cuda@10.2.89' + arch_platform) conflicts('%clang@:3.4', when='+cuda ^cuda@:7.5' + arch_platform) conflicts('%clang@:3.7,4:', when='+cuda ^cuda@8.0:9.0' + arch_platform) @@ -74,6 +75,10 @@ class CudaPackage(PackageBase): when='+cuda ^cuda@9.1' + arch_platform) conflicts('%clang@:3.7,5.1:', when='+cuda ^cuda@9.2' + arch_platform) conflicts('%clang@:3.7,6.1:', when='+cuda ^cuda@10.0.130' + arch_platform) + conflicts('%clang@:3.7,7.1:', when='+cuda ^cuda@10.1.105' + arch_platform) + conflicts('%clang@:3.7,8.1:', + when='+cuda ^cuda@10.1.105:10.1.243' + arch_platform) + conflicts('%clang@:3.2,9.0:', when='+cuda ^cuda@10.2.89' + arch_platform) # x86_64 vs. ppc64le differ according to NVidia docs # Linux ppc64le compiler conflicts from Table from the docs below: @@ -95,6 +100,8 @@ class CudaPackage(PackageBase): conflicts('%clang@5:', when='+cuda ^cuda@:9.1' + arch_platform) conflicts('%clang@6:', when='+cuda ^cuda@:9.2' + arch_platform) conflicts('%clang@7:', when='+cuda ^cuda@10.0.130' + arch_platform) + conflicts('%clang@7.1:', when='+cuda ^cuda@:10.1.105' + arch_platform) + conflicts('%clang@8.1:', when='+cuda ^cuda@:10.2.89' + arch_platform) # Intel is mostly relevant for x86_64 Linux, even though it also # exists for Mac OS X. No information prior to CUDA 3.2 or Intel 11.1 @@ -107,12 +114,12 @@ class CudaPackage(PackageBase): conflicts('%intel@16.0:', when='+cuda ^cuda@:8.0.43') conflicts('%intel@17.0:', when='+cuda ^cuda@:8.0.60') conflicts('%intel@18.0:', when='+cuda ^cuda@:9.9') - conflicts('%intel@19.0:', when='+cuda ^cuda@:10.0') + conflicts('%intel@19.0:', when='+cuda ^cuda@:10.2.89') # XL is mostly relevant for ppc64le Linux conflicts('%xl@:12,14:', when='+cuda ^cuda@:9.1') conflicts('%xl@:12,14:15,17:', when='+cuda ^cuda@9.2') - conflicts('%xl@17:', when='+cuda ^cuda@10.0.130') + conflicts('%xl@17:', when='+cuda ^cuda@10.0.130:10.2.89') # Mac OS X # platform = ' platform=darwin' diff --git a/lib/spack/spack/build_systems/gnu.py b/lib/spack/spack/build_systems/gnu.py new file mode 100644 index 0000000000..c5b5e74bb9 --- /dev/null +++ b/lib/spack/spack/build_systems/gnu.py @@ -0,0 +1,37 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import spack.util.url +import spack.package + + +class GNUMirrorPackage(spack.package.PackageBase): + """Mixin that takes care of setting url and mirrors for GNU packages.""" + #: Path of the package in a GNU mirror + gnu_mirror_path = None + + #: List of GNU mirrors used by Spack + base_mirrors = [ + 'https://ftpmirror.gnu.org/', + 'https://ftp.gnu.org/gnu/', + # Fall back to http if https didn't work (for instance because + # Spack is bootstrapping curl) + 'http://ftpmirror.gnu.org/' + ] + + @property + def urls(self): + self._ensure_gnu_mirror_path_is_set_or_raise() + return [ + spack.util.url.join(m, self.gnu_mirror_path, resolve_href=True) + for m in self.base_mirrors + ] + + def _ensure_gnu_mirror_path_is_set_or_raise(self): + if self.gnu_mirror_path is None: + cls_name = type(self).__name__ + msg = ('{0} must define a `gnu_mirror_path` attribute' + ' [none defined]') + raise AttributeError(msg.format(cls_name)) diff --git a/lib/spack/spack/build_systems/intel.py b/lib/spack/spack/build_systems/intel.py index 858b4e37fb..4017f2e526 100644 --- a/lib/spack/spack/build_systems/intel.py +++ b/lib/spack/spack/build_systems/intel.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -89,7 +89,7 @@ class IntelPackage(PackageBase): 2. :py:meth:`~.IntelPackage.install` They both have sensible defaults and for many packages the - only thing necessary will be to override setup_environment + only thing necessary will be to override setup_run_environment to set the appropriate environment variables. """ #: Phases of an Intel package @@ -455,9 +455,7 @@ class IntelPackage(PackageBase): break if not matching_dirs: - # No match -- this *will* happen during pre-build call to - # setup_environment() when the destination dir is still empty. - # Return a sensible value anyway. + # No match -- return a sensible value anyway. d = unversioned_dirname debug_print(d) @@ -786,7 +784,8 @@ class IntelPackage(PackageBase): debug_print(mkl_libs) if len(mkl_libs) < 3: - raise_lib_error('Cannot locate core MKL libraries:', mkl_libnames) + raise_lib_error('Cannot locate core MKL libraries:', mkl_libnames, + 'in:', self.component_lib_dir('mkl')) # The Intel MKL link line advisor recommends these system libraries system_libs = find_system_libraries( @@ -888,15 +887,15 @@ class IntelPackage(PackageBase): # debug_print("wrapper_vars =", wrapper_vars) return wrapper_vars - def mpi_setup_dependent_environment( - self, spack_env, run_env, dependent_spec, compilers_of_client={}): - '''Unified back-end for setup_dependent_environment() of Intel packages - that provide 'mpi'. + def mpi_setup_dependent_build_environment( + self, env, dependent_spec, compilers_of_client={}): + '''Unified back-end for setup_dependent_build_environment() of + Intel packages that provide 'mpi'. Parameters: - spack_env, run_env, dependent_spec: same as in - setup_dependent_environment(). + env, dependent_spec: same as in + setup_dependent_build_environment(). compilers_of_client (dict): Conveys spack_cc, spack_cxx, etc., from the scope of dependent packages; constructed in caller. @@ -938,12 +937,12 @@ class IntelPackage(PackageBase): # Ensure that the directory containing the compiler wrappers is in the # PATH. Spack packages add `prefix.bin` to their dependents' paths, # but because of the intel directory hierarchy that is insufficient. - spack_env.prepend_path('PATH', os.path.dirname(wrapper_vars['MPICC'])) + env.prepend_path('PATH', os.path.dirname(wrapper_vars['MPICC'])) for key, value in wrapper_vars.items(): - spack_env.set(key, value) + env.set(key, value) - debug_print("adding to spack_env:", wrapper_vars) + debug_print("adding to build env:", wrapper_vars) # --------------------------------------------------------------------- # General support for child packages @@ -994,7 +993,7 @@ class IntelPackage(PackageBase): debug_print(result) return result - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Adds environment variables to the generated module file. These environment variables come from running: @@ -1004,24 +1003,7 @@ class IntelPackage(PackageBase): $ source parallel_studio_xe_2017/bin/psxevars.sh intel64 [and likewise for MKL, MPI, and other components] """ - # https://spack.readthedocs.io/en/latest/spack.html#spack.package.PackageBase.setup_environment - # - # spack_env -> Applied when dependent is built within Spack. - # Not used here. - # run_env -> Applied to the modulefile of dependent. - # - # NOTE: Spack runs setup_environment twice, once pre-build to set up - # the build environment, and once post-installation to determine - # the environment variables needed at run-time to add to the module - # file. The script we need to source is only present post-installation, - # so check for its existence before sourcing. - # TODO: At some point we should split setup_environment into - # setup_build_environment and setup_run_environment to get around - # this problem. f = self.file_to_source - if not f or not os.path.isfile(f): - return - tty.debug("sourcing " + f) # All Intel packages expect at least the architecture as argument. @@ -1033,15 +1015,9 @@ class IntelPackage(PackageBase): # if sys.platform == 'darwin': # args = () - run_env.extend(EnvironmentModifications.from_sourcing_file(f, *args)) + env.extend(EnvironmentModifications.from_sourcing_file(f, *args)) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - # https://spack.readthedocs.io/en/latest/spack.html#spack.package.PackageBase.setup_dependent_environment - # - # spack_env -> Applied when dependent is built within Spack. - # run_env -> Applied to the modulefile of dependent. - # Not used here. - # + def setup_dependent_build_environment(self, env, dependent_spec): # NB: This function is overwritten by 'mpi' provider packages: # # var/spack/repos/builtin/packages/intel-mpi/package.py @@ -1051,18 +1027,20 @@ class IntelPackage(PackageBase): # dictionary kwarg compilers_of_client{} present and populated. # Handle everything in a callback version. - self._setup_dependent_env_callback(spack_env, run_env, dependent_spec) + self._setup_dependent_env_callback(env, dependent_spec) def _setup_dependent_env_callback( - self, spack_env, run_env, dependent_spec, compilers_of_client={}): - # Expected to be called from a client's setup_dependent_environment(), + self, env, dependent_spec, compilers_of_client={}): + # Expected to be called from a client's + # setup_dependent_build_environment(), # with args extended to convey the client's compilers as needed. if '+mkl' in self.spec or self.provides('mkl'): # Spack's env philosophy demands that we replicate some of the # settings normally handled by file_to_source ... # - # TODO: Why is setup_environment() [which uses file_to_source()] + # TODO: Why is setup_run_environment() + # [which uses file_to_source()] # not called as a matter of course upon entering the current # function? (guarding against multiple calls notwithstanding) # @@ -1070,18 +1048,26 @@ class IntelPackage(PackageBase): env_mods = { 'MKLROOT': self.normalize_path('mkl'), 'SPACK_COMPILER_EXTRA_RPATHS': self.component_lib_dir('mkl'), + 'CMAKE_PREFIX_PATH': self.normalize_path('mkl'), + 'CMAKE_LIBRARY_PATH': self.component_lib_dir('mkl'), + 'CMAKE_INCLUDE_PATH': self.component_include_dir('mkl'), } - spack_env.set('MKLROOT', env_mods['MKLROOT']) - spack_env.append_path('SPACK_COMPILER_EXTRA_RPATHS', - env_mods['SPACK_COMPILER_EXTRA_RPATHS']) + env.set('MKLROOT', env_mods['MKLROOT']) + env.append_path('SPACK_COMPILER_EXTRA_RPATHS', + env_mods['SPACK_COMPILER_EXTRA_RPATHS']) + env.append_path('CMAKE_PREFIX_PATH', env_mods['CMAKE_PREFIX_PATH']) + env.append_path('CMAKE_LIBRARY_PATH', + env_mods['CMAKE_LIBRARY_PATH']) + env.append_path('CMAKE_INCLUDE_PATH', + env_mods['CMAKE_INCLUDE_PATH']) - debug_print("adding/modifying spack_env:", env_mods) + debug_print("adding/modifying build env:", env_mods) if '+mpi' in self.spec or self.provides('mpi'): if compilers_of_client: - self.mpi_setup_dependent_environment( - spack_env, run_env, dependent_spec, compilers_of_client) + self.mpi_setup_dependent_build_environment( + env, dependent_spec, compilers_of_client) # We could forego this nonce function and inline its code here, # but (a) it sisters mpi_compiler_wrappers() [needed twice] # which performs dizzyingly similar but necessarily different diff --git a/lib/spack/spack/build_systems/makefile.py b/lib/spack/spack/build_systems/makefile.py index 3f8d5bf1be..6cd05c7ad9 100644 --- a/lib/spack/spack/build_systems/makefile.py +++ b/lib/spack/spack/build_systems/makefile.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/meson.py b/lib/spack/spack/build_systems/meson.py index 646c3a18f1..825b4c98c3 100644 --- a/lib/spack/spack/build_systems/meson.py +++ b/lib/spack/spack/build_systems/meson.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/octave.py b/lib/spack/spack/build_systems/octave.py index 677e623bd6..16d6a0a1b8 100644 --- a/lib/spack/spack/build_systems/octave.py +++ b/lib/spack/spack/build_systems/octave.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -29,12 +29,11 @@ class OctavePackage(PackageBase): extends('octave') depends_on('octave', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): - """Set up the compile and runtime environments for a package.""" + def setup_build_environment(self, env): # octave does not like those environment variables to be set: - spack_env.unset('CC') - spack_env.unset('CXX') - spack_env.unset('FC') + env.unset('CC') + env.unset('CXX') + env.unset('FC') def install(self, spec, prefix): """Install the package from the archive file""" diff --git a/lib/spack/spack/build_systems/perl.py b/lib/spack/spack/build_systems/perl.py index 28f1fc5608..d134dc06f2 100644 --- a/lib/spack/spack/build_systems/perl.py +++ b/lib/spack/spack/build_systems/perl.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/python.py b/lib/spack/spack/build_systems/python.py index 6dee28e4ed..5a054a77b4 100644 --- a/lib/spack/spack/build_systems/python.py +++ b/lib/spack/spack/build_systems/python.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/qmake.py b/lib/spack/spack/build_systems/qmake.py index 06a5f2c431..22914d4d3a 100644 --- a/lib/spack/spack/build_systems/qmake.py +++ b/lib/spack/spack/build_systems/qmake.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/r.py b/lib/spack/spack/build_systems/r.py index d97bde4374..6ee2668833 100644 --- a/lib/spack/spack/build_systems/r.py +++ b/lib/spack/spack/build_systems/r.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/scons.py b/lib/spack/spack/build_systems/scons.py index be0f06cd28..ffa4390249 100644 --- a/lib/spack/spack/build_systems/scons.py +++ b/lib/spack/spack/build_systems/scons.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/sip.py b/lib/spack/spack/build_systems/sip.py index da2c770ba7..314f91d5d2 100644 --- a/lib/spack/spack/build_systems/sip.py +++ b/lib/spack/spack/build_systems/sip.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/build_systems/waf.py b/lib/spack/spack/build_systems/waf.py index b46b37aba9..6bf9a432e0 100644 --- a/lib/spack/spack/build_systems/waf.py +++ b/lib/spack/spack/build_systems/waf.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/caches.py b/lib/spack/spack/caches.py index ce2f8a6371..98fa8d5795 100644 --- a/lib/spack/spack/caches.py +++ b/lib/spack/spack/caches.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/release_jobs.py b/lib/spack/spack/ci.py index 44fcc8511a..ed06524073 100644 --- a/lib/spack/spack/cmd/release_jobs.py +++ b/lib/spack/spack/ci.py @@ -1,10 +1,14 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) import base64 +import datetime import json +import os +import shutil +import tempfile import zlib from six import iteritems @@ -14,31 +18,36 @@ from six.moves.urllib.request import build_opener, HTTPHandler, Request import llnl.util.tty as tty -import spack.environment as ev +import spack +import spack.binary_distribution as bindist +import spack.cmd.buildcache as buildcache import spack.compilers as compilers +import spack.config as cfg +import spack.environment as ev from spack.dependency import all_deptypes from spack.error import SpackError import spack.hash_types as ht +from spack.main import SpackCommand +import spack.repo from spack.spec import Spec import spack.util.spack_yaml as syaml +import spack.util.web as web_util -description = "generate release build set as .gitlab-ci.yml" -section = "build" -level = "long" +spack_gpg = SpackCommand('gpg') +spack_compiler = SpackCommand('compiler') -def setup_parser(subparser): - subparser.add_argument( - '-o', '--output-file', default=".gitlab-ci.yml", - help="path to output file to write") - subparser.add_argument( - '-p', '--print-summary', action='store_true', default=False, - help="Print summary of staged jobs to standard output") +class TemporaryDirectory(object): + def __init__(self): + self.temporary_directory = tempfile.mkdtemp() - subparser.add_argument( - '--cdash-credentials', default=None, - help="Path to file containing CDash authentication token") + def __enter__(self): + return self.temporary_directory + + def __exit__(self, exc_type, exc_value, exc_traceback): + shutil.rmtree(self.temporary_directory) + return False def _create_buildgroup(opener, headers, url, project, group_name, group_type): @@ -131,6 +140,10 @@ def get_job_name(phase, strip_compiler, spec, osarch, build_group): format_args.append(spec.name) item_idx += 1 + format_str += '/{{{0}}}'.format(item_idx) + format_args.append(spec.dag_hash(7)) + item_idx += 1 + format_str += ' {{{0}}}'.format(item_idx) format_args.append(spec.version) item_idx += 1 @@ -368,6 +381,10 @@ def compute_spec_deps(spec_list): rkey, rlabel = spec_deps_key_label(spec) for s in spec.traverse(deptype=deptype): + if s.external: + tty.msg('Will not stage external pkg: {0}'.format(s)) + continue + skey, slabel = spec_deps_key_label(s) spec_labels[slabel] = { 'spec': get_spec_string(s), @@ -377,6 +394,10 @@ def compute_spec_deps(spec_list): for d in s.dependencies(deptype=deptype): dkey, dlabel = spec_deps_key_label(d) + if d.external: + tty.msg('Will not stage external dep: {0}'.format(d)) + continue + append_dep(slabel, dlabel) for l, d in spec_labels.items(): @@ -406,15 +427,28 @@ def find_matching_config(spec, ci_mappings): return None -def release_jobs(parser, args): - env = ev.get_env(args, 'release-jobs', required=True) +def pkg_name_from_spec_label(spec_label): + return spec_label[:spec_label.index('/')] + + +def generate_gitlab_ci_yaml(env, print_summary, output_file, + custom_spack_repo=None, custom_spack_ref=None): + # FIXME: What's the difference between one that opens with 'spack' + # and one that opens with 'env'? This will only handle the former. + with spack.concretize.disable_compiler_existence_check(): + env.concretize() yaml_root = ev.config_dict(env.yaml) if 'gitlab-ci' not in yaml_root: tty.die('Environment yaml does not have "gitlab-ci" section') - ci_mappings = yaml_root['gitlab-ci']['mappings'] + gitlab_ci = yaml_root['gitlab-ci'] + ci_mappings = gitlab_ci['mappings'] + + final_job_config = None + if 'final-stage-rebuild-index' in gitlab_ci: + final_job_config = gitlab_ci['final-stage-rebuild-index'] build_group = None enable_cdash_reporting = False @@ -426,23 +460,40 @@ def release_jobs(parser, args): build_group = ci_cdash['build-group'] cdash_url = ci_cdash['url'] cdash_project = ci_cdash['project'] - proj_enc = urlencode({'project': cdash_project}) - eq_idx = proj_enc.find('=') + 1 - cdash_project_enc = proj_enc[eq_idx:] cdash_site = ci_cdash['site'] - if args.cdash_credentials: - with open(args.cdash_credentials) as fd: - cdash_auth_token = fd.read() - cdash_auth_token = cdash_auth_token.strip() + if 'SPACK_CDASH_AUTH_TOKEN' in os.environ: + tty.verbose("Using CDash auth token from environment") + cdash_auth_token = os.environ.get('SPACK_CDASH_AUTH_TOKEN') + + # Make sure we use a custom spack if necessary + before_script = None + after_script = None + if custom_spack_repo: + if not custom_spack_ref: + custom_spack_ref = 'master' + before_script = [ + ('git clone "{0}" --branch "{1}" --depth 1 ' + '--single-branch'.format(custom_spack_repo, custom_spack_ref)), + # Next line just shows spack version in pipeline output + 'pushd ./spack && git rev-parse HEAD && popd', + '. "./spack/share/spack/setup-env.sh"', + ] + after_script = [ + 'rm -rf "./spack"' + ] ci_mirrors = yaml_root['mirrors'] mirror_urls = [url for url in ci_mirrors.values()] + enable_artifacts_buildcache = False + if 'enable-artifacts-buildcache' in gitlab_ci: + enable_artifacts_buildcache = gitlab_ci['enable-artifacts-buildcache'] + bootstrap_specs = [] phases = [] - if 'bootstrap' in yaml_root['gitlab-ci']: - for phase in yaml_root['gitlab-ci']['bootstrap']: + if 'bootstrap' in gitlab_ci: + for phase in gitlab_ci['bootstrap']: try: phase_name = phase.get('name') strip_compilers = phase.get('compiler-agnostic') @@ -469,9 +520,11 @@ def release_jobs(parser, args): staged_phases = {} for phase in phases: phase_name = phase['name'] - staged_phases[phase_name] = stage_spec_jobs(env.spec_lists[phase_name]) + with spack.concretize.disable_compiler_existence_check(): + staged_phases[phase_name] = stage_spec_jobs( + env.spec_lists[phase_name]) - if args.print_summary: + if print_summary: for phase in phases: phase_name = phase['name'] tty.msg('Stages for phase "{0}"'.format(phase_name)) @@ -498,10 +551,12 @@ def release_jobs(parser, args): stage_id += 1 for spec_label in stage_jobs: - release_spec = spec_labels[spec_label]['spec'] root_spec = spec_labels[spec_label]['rootSpec'] + pkg_name = pkg_name_from_spec_label(spec_label) + release_spec = root_spec[pkg_name] - runner_attribs = find_matching_config(root_spec, ci_mappings) + runner_attribs = find_matching_config( + release_spec, ci_mappings) if not runner_attribs: tty.warn('No match found for {0}, skipping it'.format( @@ -529,7 +584,11 @@ def release_jobs(parser, args): job_name = get_job_name(phase_name, strip_compilers, release_spec, osname, build_group) - job_scripts = ['./bin/rebuild-package.sh'] + debug_flag = '' + if 'enable-debug-messages' in gitlab_ci: + debug_flag = '-d ' + + job_scripts = ['spack {0}ci rebuild'.format(debug_flag)] compiler_action = 'NONE' if len(phases) > 1: @@ -538,7 +597,6 @@ def release_jobs(parser, args): compiler_action = 'INSTALL_MISSING' job_vars = { - 'SPACK_MIRROR_URL': mirror_urls[0], 'SPACK_ROOT_SPEC': format_root_spec( root_spec, main_phase, strip_compilers), 'SPACK_JOB_SPEC_PKG_NAME': release_spec.name, @@ -547,11 +605,13 @@ def release_jobs(parser, args): job_dependencies = [] if spec_label in dependencies: - job_dependencies = ( - [get_job_name(phase_name, strip_compilers, - spec_labels[dep_label]['spec'], - osname, build_group) - for dep_label in dependencies[spec_label]]) + for dep_label in dependencies[spec_label]: + dep_pkg = pkg_name_from_spec_label(dep_label) + dep_spec = spec_labels[dep_label]['rootSpec'][dep_pkg] + dep_job_name = get_job_name( + phase_name, strip_compilers, dep_spec, osname, + build_group) + job_dependencies.append(dep_job_name) # This next section helps gitlab make sure the right # bootstrapped compiler exists in the artifacts buildcache by @@ -585,34 +645,38 @@ def release_jobs(parser, args): [spec_labels[d]['spec'].name for d in dependencies[spec_label]]) - job_vars['SPACK_CDASH_BASE_URL'] = cdash_url - job_vars['SPACK_CDASH_PROJECT'] = cdash_project - job_vars['SPACK_CDASH_PROJECT_ENC'] = cdash_project_enc job_vars['SPACK_CDASH_BUILD_NAME'] = cdash_build_name - job_vars['SPACK_CDASH_SITE'] = cdash_site - job_vars['SPACK_RELATED_BUILDS'] = ';'.join(related_builds) - job_vars['SPACK_JOB_SPEC_BUILDGROUP'] = build_group - - job_vars['SPACK_ENABLE_CDASH'] = str(enable_cdash_reporting) + job_vars['SPACK_RELATED_BUILDS_CDASH'] = ';'.join( + related_builds) variables.update(job_vars) + artifact_paths = [ + 'jobs_scratch_dir', + 'cdash_report', + ] + + if enable_artifacts_buildcache: + artifact_paths.append('local_mirror/build_cache') + job_object = { 'stage': stage_name, 'variables': variables, 'script': job_scripts, 'tags': tags, 'artifacts': { - 'paths': [ - 'jobs_scratch_dir', - 'cdash_report', - 'local_mirror/build_cache', - ], + 'paths': artifact_paths, 'when': 'always', }, 'dependencies': job_dependencies, } + if before_script: + job_object['before_script'] = before_script + + if after_script: + job_object['after_script'] = after_script + if image_name: job_object['image'] = image_name if image_entry is not None: @@ -624,7 +688,7 @@ def release_jobs(parser, args): output_object[job_name] = job_object job_id += 1 - tty.msg('{0} build jobs generated in {1} stages'.format( + tty.debug('{0} build jobs generated in {1} stages'.format( job_id, stage_id)) # Use "all_job_names" to populate the build group for this set @@ -637,20 +701,280 @@ def release_jobs(parser, args): else: tty.warn('Unable to populate buildgroup without CDash credentials') - # Add an extra, final job to regenerate the index - final_stage = 'stage-rebuild-index' - final_job = { - 'stage': final_stage, - 'variables': { - 'MIRROR_URL': mirror_urls[0], - }, - 'script': './bin/rebuild-index.sh', - 'tags': ['spack-post-ci'] # may want a runner to handle this - } - output_object['rebuild-index'] = final_job - stage_names.append(final_stage) + if final_job_config: + # Add an extra, final job to regenerate the index + final_stage = 'stage-rebuild-index' + final_job = { + 'stage': final_stage, + 'script': 'spack buildcache update-index -d {0}'.format( + mirror_urls[0]), + 'tags': final_job_config['tags'] + } + if 'image' in final_job_config: + final_job['image'] = final_job_config['image'] + if before_script: + final_job['before_script'] = before_script + if after_script: + final_job['after_script'] = after_script + output_object['rebuild-index'] = final_job + stage_names.append(final_stage) output_object['stages'] = stage_names - with open(args.output_file, 'w') as outf: + with open(output_file, 'w') as outf: outf.write(syaml.dump_config(output_object, default_flow_style=True)) + + +def url_encode_string(input_string): + encoded_keyval = urlencode({'donotcare': input_string}) + eq_idx = encoded_keyval.find('=') + 1 + encoded_value = encoded_keyval[eq_idx:] + return encoded_value + + +def import_signing_key(base64_signing_key): + if not base64_signing_key: + tty.warn('No key found for signing/verifying packages') + return + + tty.debug('ci.import_signing_key() will attempt to import a key') + + # This command has the side-effect of creating the directory referred + # to as GNUPGHOME in setup_environment() + list_output = spack_gpg('list', output=str) + + tty.debug('spack gpg list:') + tty.debug(list_output) + + decoded_key = base64.b64decode(base64_signing_key) + if isinstance(decoded_key, bytes): + decoded_key = decoded_key.decode('utf8') + + with TemporaryDirectory() as tmpdir: + sign_key_path = os.path.join(tmpdir, 'signing_key') + with open(sign_key_path, 'w') as fd: + fd.write(decoded_key) + + key_import_output = spack_gpg('trust', sign_key_path, output=str) + tty.debug('spack gpg trust {0}'.format(sign_key_path)) + tty.debug(key_import_output) + + # Now print the keys we have for verifying and signing + trusted_keys_output = spack_gpg('list', '--trusted', output=str) + signing_keys_output = spack_gpg('list', '--signing', output=str) + + tty.debug('spack gpg list --trusted') + tty.debug(trusted_keys_output) + tty.debug('spack gpg list --signing') + tty.debug(signing_keys_output) + + +def configure_compilers(compiler_action, scope=None): + if compiler_action == 'INSTALL_MISSING': + tty.debug('Make sure bootstrapped compiler will be installed') + config = cfg.get('config') + config['install_missing_compilers'] = True + cfg.set('config', config) + elif compiler_action == 'FIND_ANY': + tty.debug('Just find any available compiler') + find_args = ['find'] + if scope: + find_args.extend(['--scope', scope]) + output = spack_compiler(*find_args) + tty.debug('spack compiler find') + tty.debug(output) + output = spack_compiler('list') + tty.debug('spack compiler list') + tty.debug(output) + else: + tty.debug('No compiler action to be taken') + + return None + + +def get_concrete_specs(root_spec, job_name, related_builds, compiler_action): + spec_map = { + 'root': None, + 'deps': {}, + } + + if compiler_action == 'FIND_ANY': + # This corresponds to a bootstrapping phase where we need to + # rely on any available compiler to build the package (i.e. the + # compiler needed to be stripped from the spec when we generated + # the job), and thus we need to concretize the root spec again. + tty.debug('About to concretize {0}'.format(root_spec)) + concrete_root = Spec(root_spec).concretized() + tty.debug('Resulting concrete root: {0}'.format(concrete_root)) + else: + # in this case, either we're relying on Spack to install missing + # compiler bootstrapped in a previous phase, or else we only had one + # phase (like a site which already knows what compilers are available + # on it's runners), so we don't want to concretize that root spec + # again. The reason we take this path in the first case (bootstrapped + # compiler), is that we can't concretize a spec at this point if we're + # going to ask spack to "install_missing_compilers". + concrete_root = Spec.from_yaml( + str(zlib.decompress(base64.b64decode(root_spec)).decode('utf-8'))) + + spec_map['root'] = concrete_root + spec_map[job_name] = concrete_root[job_name] + + if related_builds: + for dep_job_name in related_builds.split(';'): + spec_map['deps'][dep_job_name] = concrete_root[dep_job_name] + + return spec_map + + +def register_cdash_build(build_name, base_url, project, site, track): + url = base_url + '/api/v1/addBuild.php' + time_stamp = datetime.datetime.now().strftime('%Y%m%d-%H%M') + build_stamp = '{0}-{1}'.format(time_stamp, track) + payload = { + "project": project, + "site": site, + "name": build_name, + "stamp": build_stamp, + } + + tty.debug('Registering cdash build to {0}, payload:'.format(url)) + tty.debug(payload) + + enc_data = json.dumps(payload).encode('utf-8') + + headers = { + 'Content-Type': 'application/json', + } + + opener = build_opener(HTTPHandler) + + request = Request(url, data=enc_data, headers=headers) + + response = opener.open(request) + response_code = response.getcode() + + if response_code != 200 and response_code != 201: + msg = 'Adding build failed (response code = {0}'.format(response_code) + raise SpackError(msg) + + response_text = response.read() + response_json = json.loads(response_text) + build_id = response_json['buildid'] + + return (build_id, build_stamp) + + +def relate_cdash_builds(spec_map, cdash_base_url, job_build_id, cdash_project, + cdashids_mirror_url): + if not job_build_id: + return + + dep_map = spec_map['deps'] + + headers = { + 'Content-Type': 'application/json', + 'Accept': 'application/json', + } + + cdash_api_url = '{0}/api/v1/relateBuilds.php'.format(cdash_base_url) + + for dep_pkg_name in dep_map: + tty.debug('Fetching cdashid file for {0}'.format(dep_pkg_name)) + dep_spec = dep_map[dep_pkg_name] + dep_build_id = read_cdashid_from_mirror(dep_spec, cdashids_mirror_url) + + payload = { + "project": cdash_project, + "buildid": job_build_id, + "relatedid": dep_build_id, + "relationship": "depends on" + } + + enc_data = json.dumps(payload).encode('utf-8') + + opener = build_opener(HTTPHandler) + + request = Request(cdash_api_url, data=enc_data, headers=headers) + + response = opener.open(request) + response_code = response.getcode() + + if response_code != 200 and response_code != 201: + msg = 'Relate builds ({0} -> {1}) failed (resp code = {2})'.format( + job_build_id, dep_build_id, response_code) + raise SpackError(msg) + + response_text = response.read() + tty.debug('Relate builds response: {0}'.format(response_text)) + + +def write_cdashid_to_mirror(cdashid, spec, mirror_url): + if not spec.concrete: + tty.die('Can only write cdashid for concrete spec to mirror') + + with TemporaryDirectory() as tmpdir: + local_cdash_path = os.path.join(tmpdir, 'job.cdashid') + with open(local_cdash_path, 'w') as fd: + fd.write(cdashid) + + buildcache_name = bindist.tarball_name(spec, '') + cdashid_file_name = '{0}.cdashid'.format(buildcache_name) + remote_url = os.path.join( + mirror_url, bindist.build_cache_relative_path(), cdashid_file_name) + + tty.debug('pushing cdashid to url') + tty.debug(' local file path: {0}'.format(local_cdash_path)) + tty.debug(' remote url: {0}'.format(remote_url)) + web_util.push_to_url(local_cdash_path, remote_url) + + +def read_cdashid_from_mirror(spec, mirror_url): + if not spec.concrete: + tty.die('Can only read cdashid for concrete spec from mirror') + + buildcache_name = bindist.tarball_name(spec, '') + cdashid_file_name = '{0}.cdashid'.format(buildcache_name) + url = os.path.join( + mirror_url, bindist.build_cache_relative_path(), cdashid_file_name) + + resp_url, resp_headers, response = web_util.read_from_url(url) + contents = response.fp.read() + + return int(contents) + + +def push_mirror_contents(env, spec, yaml_path, mirror_url, build_id): + if mirror_url: + tty.debug('Creating buildcache') + buildcache._createtarball(env, yaml_path, None, mirror_url, None, + True, True, False, False, True, False) + if build_id: + tty.debug('Writing cdashid ({0}) to remote mirror: {1}'.format( + build_id, mirror_url)) + write_cdashid_to_mirror(build_id, spec, mirror_url) + + +def copy_stage_logs_to_artifacts(job_spec, job_log_dir): + try: + job_pkg = spack.repo.get(job_spec) + tty.debug('job package: {0}'.format(job_pkg)) + stage_dir = job_pkg.stage.path + tty.debug('stage dir: {0}'.format(stage_dir)) + build_env_src = os.path.join(stage_dir, 'spack-build-env.txt') + build_out_src = os.path.join(stage_dir, 'spack-build-out.txt') + build_env_dst = os.path.join( + job_log_dir, 'spack-build-env.txt') + build_out_dst = os.path.join( + job_log_dir, 'spack-build-out.txt') + tty.debug('Copying logs to artifacts:') + tty.debug(' 1: {0} -> {1}'.format( + build_env_src, build_env_dst)) + shutil.copyfile(build_env_src, build_env_dst) + tty.debug(' 2: {0} -> {1}'.format( + build_out_src, build_out_dst)) + shutil.copyfile(build_out_src, build_out_dst) + except Exception as inst: + msg = ('Unable to copy build logs from stage to artifacts ' + 'due to exception: {0}').format(inst) + tty.error(msg) diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py index 0d2e92940b..2a75a87b54 100644 --- a/lib/spack/spack/cmd/__init__.py +++ b/lib/spack/spack/cmd/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,13 +19,13 @@ from llnl.util.tty.color import colorize from llnl.util.filesystem import working_dir import spack.config +import spack.error import spack.extensions import spack.paths import spack.spec import spack.store import spack.util.spack_json as sjson import spack.util.string -from spack.error import SpackError # cmd has a submodule called "list" so preserve the python list module @@ -150,15 +150,15 @@ def parse_specs(args, **kwargs): except spack.spec.SpecParseError as e: msg = e.message + "\n" + str(e.string) + "\n" msg += (e.pos + 2) * " " + "^" - raise SpackError(msg) + raise spack.error.SpackError(msg) - except spack.spec.SpecError as e: + except spack.error.SpecError as e: msg = e.message if e.long_message: msg += e.long_message - raise SpackError(msg) + raise spack.error.SpackError(msg) def elide_list(line_list, max_num=10): @@ -190,6 +190,20 @@ def disambiguate_spec(spec, env, local=False, installed=True): database query. See ``spack.database.Database._query`` for details. """ hashes = env.all_hashes() if env else None + return disambiguate_spec_from_hashes(spec, hashes, local, installed) + + +def disambiguate_spec_from_hashes(spec, hashes, local=False, installed=True): + """Given a spec and a list of hashes, get concrete spec the spec refers to. + + Arguments: + spec (spack.spec.Spec): a spec to disambiguate + hashes (iterable): a set of hashes of specs among which to disambiguate + local (boolean, default False): do not search chained spack instances + installed (boolean or any, or spack.database.InstallStatus or iterable + of spack.database.InstallStatus): install status argument passed to + database query. See ``spack.database.Database._query`` for details. + """ if local: matching_specs = spack.store.db.query_local(spec, hashes=hashes, installed=installed) @@ -212,6 +226,9 @@ def disambiguate_spec(spec, env, local=False, installed=True): def gray_hash(spec, length): + if not length: + # default to maximum hash length + length = 32 h = spec.dag_hash(length) if spec.concrete else '-' * length return colorize('@K{%s}' % h) diff --git a/lib/spack/spack/cmd/activate.py b/lib/spack/spack/cmd/activate.py index 6a7297432d..bfca9f5604 100644 --- a/lib/spack/spack/cmd/activate.py +++ b/lib/spack/spack/cmd/activate.py @@ -1,13 +1,12 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse - import llnl.util.tty as tty import spack.cmd +import spack.cmd.common.arguments as arguments import spack.environment as ev from spack.filesystem_view import YamlFilesystemView @@ -23,9 +22,7 @@ def setup_parser(subparser): subparser.add_argument( '-v', '--view', metavar='VIEW', type=str, help="the view to operate on") - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, - help="spec of package extension to activate") + arguments.add_common_arguments(subparser, ['installed_spec']) def activate(parser, args): diff --git a/lib/spack/spack/cmd/add.py b/lib/spack/spack/cmd/add.py index 894161fe00..94c8620dbb 100644 --- a/lib/spack/spack/cmd/add.py +++ b/lib/spack/spack/cmd/add.py @@ -1,13 +1,12 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse - import llnl.util.tty as tty import spack.cmd +import spack.cmd.common.arguments as arguments import spack.environment as ev @@ -20,17 +19,17 @@ def setup_parser(subparser): subparser.add_argument('-l', '--list-name', dest='list_name', default='specs', help="name of the list to add specs to") - subparser.add_argument( - 'specs', nargs=argparse.REMAINDER, help="specs of packages to add") + arguments.add_common_arguments(subparser, ['specs']) def add(parser, args): env = ev.get_env(args, 'add', required=True) - for spec in spack.cmd.parse_specs(args.specs): - if not env.add(spec, args.list_name): - tty.msg("Package {0} was already added to {1}" - .format(spec.name, env.name)) - else: - tty.msg('Adding %s to environment %s' % (spec, env.name)) - env.write() + with env.write_transaction(): + for spec in spack.cmd.parse_specs(args.specs): + if not env.add(spec, args.list_name): + tty.msg("Package {0} was already added to {1}" + .format(spec.name, env.name)) + else: + tty.msg('Adding %s to environment %s' % (spec, env.name)) + env.write() diff --git a/lib/spack/spack/cmd/arch.py b/lib/spack/spack/cmd/arch.py index 081722c05b..6f5dad758f 100644 --- a/lib/spack/spack/cmd/arch.py +++ b/lib/spack/spack/cmd/arch.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/blame.py b/lib/spack/spack/cmd/blame.py index 5e3f4095a4..b806058aec 100644 --- a/lib/spack/spack/cmd/blame.py +++ b/lib/spack/spack/cmd/blame.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -35,7 +35,7 @@ def setup_parser(subparser): help='show git blame output instead of summary') subparser.add_argument( - 'package_name', help='name of package to show contributions for, ' + 'package_or_file', help='name of package to show contributions for, ' 'or path to a file in the spack repo') @@ -47,13 +47,13 @@ def blame(parser, args): # Get name of file to blame blame_file = None - if os.path.isfile(args.package_name): - path = os.path.realpath(args.package_name) + if os.path.isfile(args.package_or_file): + path = os.path.realpath(args.package_or_file) if path.startswith(spack.paths.prefix): blame_file = path if not blame_file: - pkg = spack.repo.get(args.package_name) + pkg = spack.repo.get(args.package_or_file) blame_file = pkg.module.__file__.rstrip('c') # .pyc -> .py # get git blame for the package diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py index 96cb8ccaa9..53c284ab6d 100644 --- a/lib/spack/spack/cmd/bootstrap.py +++ b/lib/spack/spack/cmd/bootstrap.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/build.py b/lib/spack/spack/cmd/build.py index 8687e9a741..a56c37fdd4 100644 --- a/lib/spack/spack/cmd/build.py +++ b/lib/spack/spack/cmd/build.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/build_env.py b/lib/spack/spack/cmd/build_env.py index 87961fcb9c..128d167a29 100644 --- a/lib/spack/spack/cmd/build_env.py +++ b/lib/spack/spack/cmd/build_env.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -33,7 +33,7 @@ def setup_parser(subparser): subparser.add_argument( 'spec', nargs=argparse.REMAINDER, metavar='spec [--] [cmd]...', - help="specs of package environment to emulate") + help="spec of package environment to emulate") subparser.epilog\ = 'If a command is not specified, the environment will be printed ' \ 'to standard output (cf /usr/bin/env) unless --dump and/or --pickle ' \ diff --git a/lib/spack/spack/cmd/buildcache.py b/lib/spack/spack/cmd/buildcache.py index ee09a33f39..392984f852 100644 --- a/lib/spack/spack/cmd/buildcache.py +++ b/lib/spack/spack/cmd/buildcache.py @@ -1,9 +1,8 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse import os import shutil import sys @@ -61,11 +60,9 @@ def setup_parser(subparser): "building package(s)") create.add_argument('-y', '--spec-yaml', default=None, help='Create buildcache entry for spec from yaml file') - create.add_argument( - 'packages', nargs=argparse.REMAINDER, - help="specs of packages to create buildcache for") create.add_argument('--no-deps', action='store_true', default='false', help='Create buildcache entry wo/ dependencies') + arguments.add_common_arguments(create, ['specs']) create.set_defaults(func=createtarball) install = subparsers.add_parser('install', help=installtarball.__doc__) @@ -79,9 +76,7 @@ def setup_parser(subparser): install.add_argument('-u', '--unsigned', action='store_true', help="install unsigned buildcache" + " tarballs for testing") - install.add_argument( - 'packages', nargs=argparse.REMAINDER, - help="specs of packages to install buildcache for") + arguments.add_common_arguments(install, ['specs']) install.set_defaults(func=installtarball) listcache = subparsers.add_parser('list', help=listspecs.__doc__) @@ -92,9 +87,10 @@ def setup_parser(subparser): help='show variants in output (can be long)') listcache.add_argument('-f', '--force', action='store_true', help="force new download of specs") - listcache.add_argument( - 'packages', nargs=argparse.REMAINDER, - help="specs of packages to search for") + listcache.add_argument('-a', '--allarch', action='store_true', + help="list specs for all available architectures" + + " instead of default platform and OS") + arguments.add_common_arguments(listcache, ['specs']) listcache.set_defaults(func=listspecs) dlkeys = subparsers.add_parser('keys', help=getkeys.__doc__) @@ -113,10 +109,9 @@ def setup_parser(subparser): help='analyzes an installed spec and reports whether ' 'executables and libraries are relocatable' ) - preview_parser.add_argument( - 'packages', nargs='+', help='list of installed packages' - ) + arguments.add_common_arguments(preview_parser, ['installed_specs']) preview_parser.set_defaults(func=preview) + # Check if binaries need to be rebuilt on remote mirror check = subparsers.add_parser('check', help=check_binaries.__doc__) check.add_argument( @@ -271,7 +266,8 @@ def match_downloaded_specs(pkgs, allow_multiple_matches=False, force=False): # List of specs that match expressions given via command line specs_from_cli = [] has_errors = False - specs = bindist.get_specs(force) + allarch = False + specs = bindist.get_specs(force, allarch) for pkg in pkgs: matches = [] tty.msg("buildcache spec(s) matching %s \n" % pkg) @@ -303,19 +299,20 @@ def match_downloaded_specs(pkgs, allow_multiple_matches=False, force=False): return specs_from_cli -def createtarball(args): - """create a binary package from an existing install""" - if args.spec_yaml: +def _createtarball(env, spec_yaml, packages, directory, key, no_deps, force, + rel, unsigned, allow_root, no_rebuild_index): + if spec_yaml: packages = set() - tty.msg('createtarball, reading spec from {0}'.format(args.spec_yaml)) - with open(args.spec_yaml, 'r') as fd: + with open(spec_yaml, 'r') as fd: yaml_text = fd.read() tty.debug('createtarball read spec yaml:') tty.debug(yaml_text) s = Spec.from_yaml(yaml_text) packages.add('/{0}'.format(s.dag_hash())) - elif args.packages: - packages = args.packages + + elif packages: + packages = packages + else: tty.die("build cache file creation requires at least one" + " installed package argument or else path to a" + @@ -324,18 +321,15 @@ def createtarball(args): specs = set() outdir = '.' - if args.directory: - outdir = args.directory + if directory: + outdir = directory mirror = spack.mirror.MirrorCollection().lookup(outdir) outdir = url_util.format(mirror.push_url) signkey = None - if args.key: - signkey = args.key - - # restrict matching to current environment if one is active - env = ev.get_env(args, 'buildcache create') + if key: + signkey = key matches = find_matching_specs(pkgs, env=env) @@ -350,7 +344,7 @@ def createtarball(args): else: tty.debug('adding matching spec %s' % match.format()) specs.add(match) - if args.no_deps is True: + if no_deps is True: continue tty.debug('recursing dependencies') for d, node in match.traverse(order='post', @@ -368,20 +362,31 @@ def createtarball(args): for spec in specs: tty.msg('creating binary cache file for package %s ' % spec.format()) try: - bindist.build_tarball(spec, outdir, args.force, args.rel, - args.unsigned, args.allow_root, signkey, - not args.no_rebuild_index) + bindist.build_tarball(spec, outdir, force, rel, + unsigned, allow_root, signkey, + not no_rebuild_index) except Exception as e: tty.warn('%s' % e) pass +def createtarball(args): + """create a binary package from an existing install""" + + # restrict matching to current environment if one is active + env = ev.get_env(args, 'buildcache create') + + _createtarball(env, args.spec_yaml, args.specs, args.directory, + args.key, args.no_deps, args.force, args.rel, args.unsigned, + args.allow_root, args.no_rebuild_index) + + def installtarball(args): """install from a binary package""" - if not args.packages: + if not args.specs: tty.die("build cache file installation requires" + " at least one package spec argument") - pkgs = set(args.packages) + pkgs = set(args.specs) matches = match_downloaded_specs(pkgs, args.multiple, args.force) for match in matches: @@ -414,13 +419,11 @@ def install_tarball(spec, args): def listspecs(args): """list binary packages available from mirrors""" - specs = bindist.get_specs(args.force) - if args.packages: - pkgs = set(args.packages) - specs = [s for s in specs for p in pkgs if s.satisfies(p)] - display_specs(specs, args, all_headers=True) - else: - display_specs(specs, args, all_headers=True) + specs = bindist.get_specs(args.force, args.allarch) + if args.specs: + constraints = set(args.specs) + specs = [s for s in specs if any(s.satisfies(c) for c in constraints)] + display_specs(specs, args, all_headers=True) def getkeys(args): @@ -435,7 +438,7 @@ def preview(args): Args: args: command line arguments """ - specs = find_matching_specs(args.packages, allow_multiple_matches=True) + specs = find_matching_specs(args.specs, allow_multiple_matches=True) # Cycle over the specs that match for spec in specs: @@ -479,6 +482,32 @@ def check_binaries(args): configured_mirrors, specs, args.output_file, args.rebuild_on_error)) +def download_buildcache_files(concrete_spec, local_dest, require_cdashid, + mirror_url=None): + tarfile_name = bindist.tarball_name(concrete_spec, '.spack') + tarball_dir_name = bindist.tarball_directory_name(concrete_spec) + tarball_path_name = os.path.join(tarball_dir_name, tarfile_name) + local_tarball_path = os.path.join(local_dest, tarball_dir_name) + + files_to_fetch = [ + { + 'url': tarball_path_name, + 'path': local_tarball_path, + 'required': True, + }, { + 'url': bindist.tarball_name(concrete_spec, '.spec.yaml'), + 'path': local_dest, + 'required': True, + }, { + 'url': bindist.tarball_name(concrete_spec, '.cdashid'), + 'path': local_dest, + 'required': require_cdashid, + }, + ] + + return bindist.download_buildcache_entry(files_to_fetch, mirror_url) + + def get_tarball(args): """Download buildcache entry from a remote mirror to local folder. This command uses the process exit code to indicate its result, specifically, @@ -495,34 +524,10 @@ def get_tarball(args): sys.exit(0) spec = get_concrete_spec(args) + result = download_buildcache_files(spec, args.path, args.require_cdashid) - tarfile_name = bindist.tarball_name(spec, '.spack') - tarball_dir_name = bindist.tarball_directory_name(spec) - tarball_path_name = os.path.join(tarball_dir_name, tarfile_name) - local_tarball_path = os.path.join(args.path, tarball_dir_name) - - files_to_fetch = [ - { - 'url': tarball_path_name, - 'path': local_tarball_path, - 'required': True, - }, { - 'url': bindist.tarball_name(spec, '.spec.yaml'), - 'path': args.path, - 'required': True, - }, { - 'url': bindist.tarball_name(spec, '.cdashid'), - 'path': args.path, - 'required': args.require_cdashid, - }, - ] - - result = bindist.download_buildcache_entry(files_to_fetch) - - if result: - sys.exit(0) - - sys.exit(1) + if not result: + sys.exit(1) def get_concrete_spec(args): diff --git a/lib/spack/spack/cmd/cd.py b/lib/spack/spack/cmd/cd.py index e293b9f220..a810e36ef3 100644 --- a/lib/spack/spack/cmd/cd.py +++ b/lib/spack/spack/cmd/cd.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py index 2518dfef9f..343915868c 100644 --- a/lib/spack/spack/cmd/checksum.py +++ b/lib/spack/spack/cmd/checksum.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,6 +10,7 @@ import argparse import llnl.util.tty as tty import spack.cmd +import spack.cmd.common.arguments as arguments import spack.repo import spack.stage import spack.util.crypto @@ -23,11 +24,9 @@ level = "long" def setup_parser(subparser): subparser.add_argument( - 'package', - help='package to checksum versions for') - subparser.add_argument( '--keep-stage', action='store_true', help="don't clean up staging area when command completes") + arguments.add_common_arguments(subparser, ['package']) subparser.add_argument( 'versions', nargs=argparse.REMAINDER, help='versions to generate checksums for') @@ -61,3 +60,4 @@ def checksum(parser, args): print() print(version_lines) + print() diff --git a/lib/spack/spack/cmd/ci.py b/lib/spack/spack/cmd/ci.py new file mode 100644 index 0000000000..22c555d85a --- /dev/null +++ b/lib/spack/spack/cmd/ci.py @@ -0,0 +1,482 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import os +import shutil +import sys + +from six.moves.urllib.parse import urlencode + +import llnl.util.tty as tty + +import spack.binary_distribution as bindist +import spack.ci as spack_ci +import spack.cmd.buildcache as buildcache +import spack.environment as ev +import spack.hash_types as ht +import spack.util.executable as exe + + +description = "manage continuous integration pipelines" +section = "build" +level = "long" + + +def get_env_var(variable_name): + if variable_name in os.environ: + return os.environ.get(variable_name) + return None + + +def setup_parser(subparser): + setup_parser.parser = subparser + subparsers = subparser.add_subparsers(help='CI sub-commands') + + start = subparsers.add_parser('start', help=ci_start.__doc__) + start.add_argument( + '--output-file', default=None, + help="Absolute path to file where generated jobs file should be " + + "written. The default is .gitlab-ci.yml in the root of the " + + "repository.") + start.add_argument( + '--copy-to', default=None, + help="Absolute path of additional location where generated jobs " + + "yaml file should be copied. Default is not to copy.") + start.add_argument( + '--spack-repo', default=None, + help="Provide a url for this argument if a custom spack repo " + + "should be cloned as a step in each generated job.") + start.add_argument( + '--spack-ref', default=None, + help="Provide a git branch or tag if a custom spack branch " + + "should be checked out as a step in each generated job. " + + "This argument is ignored if no --spack-repo is provided.") + start.add_argument( + '--downstream-repo', default=None, + help="Url to repository where commit containing jobs yaml file " + + "should be pushed.") + start.add_argument( + '--branch-name', default='default-branch', + help="Name of current branch, used in generation of pushed commit.") + start.add_argument( + '--commit-sha', default='none', + help="SHA of current commit, used in generation of pushed commit.") + start.set_defaults(func=ci_start) + + # Dynamic generation of the jobs yaml from a spack environment + generate = subparsers.add_parser('generate', help=ci_generate.__doc__) + generate.add_argument( + '--output-file', default=None, + help="Absolute path to file where generated jobs file should be " + + "written. The default is .gitlab-ci.yml in the root of the " + + "repository.") + generate.add_argument( + '--copy-to', default=None, + help="Absolute path of additional location where generated jobs " + + "yaml file should be copied. Default is not to copy.") + generate.add_argument( + '--spack-repo', default=None, + help="Provide a url for this argument if a custom spack repo " + + "should be cloned as a step in each generated job.") + generate.add_argument( + '--spack-ref', default=None, + help="Provide a git branch or tag if a custom spack branch " + + "should be checked out as a step in each generated job. " + + "This argument is ignored if no --spack-repo is provided.") + generate.set_defaults(func=ci_generate) + + # Commit and push jobs yaml to a downstream CI repo + pushyaml = subparsers.add_parser('pushyaml', help=ci_pushyaml.__doc__) + pushyaml.add_argument( + '--downstream-repo', default=None, + help="Url to repository where commit containing jobs yaml file " + + "should be pushed.") + pushyaml.add_argument( + '--branch-name', default='default-branch', + help="Name of current branch, used in generation of pushed commit.") + pushyaml.add_argument( + '--commit-sha', default='none', + help="SHA of current commit, used in generation of pushed commit.") + pushyaml.set_defaults(func=ci_pushyaml) + + # Check a spec against mirror. Rebuild, create buildcache and push to + # mirror (if necessary). + rebuild = subparsers.add_parser('rebuild', help=ci_rebuild.__doc__) + rebuild.set_defaults(func=ci_rebuild) + + +def ci_generate(args): + """Generate jobs file from a spack environment file containing CI info. + Before invoking this command, you can set the environment variable + SPACK_CDASH_AUTH_TOKEN to contain the CDash authorization token + for creating a build group for the generated workload and registering + all generated jobs under that build group. If this environment + variable is not set, no build group will be created on CDash.""" + env = ev.get_env(args, 'ci generate', required=True) + + output_file = args.output_file + copy_yaml_to = args.copy_to + spack_repo = args.spack_repo + spack_ref = args.spack_ref + + if not output_file: + gen_ci_dir = os.getcwd() + output_file = os.path.join(gen_ci_dir, '.gitlab-ci.yml') + else: + gen_ci_dir = os.path.dirname(output_file) + if not os.path.exists(gen_ci_dir): + os.makedirs(gen_ci_dir) + + # Generate the jobs + spack_ci.generate_gitlab_ci_yaml( + env, True, output_file, spack_repo, spack_ref) + + if copy_yaml_to: + copy_to_dir = os.path.dirname(copy_yaml_to) + if not os.path.exists(copy_to_dir): + os.makedirs(copy_to_dir) + shutil.copyfile(output_file, copy_yaml_to) + + +def ci_pushyaml(args): + """Push the generated jobs yaml file to a remote repository. The file + (.gitlab-ci.yaml) is expected to be in the current directory, which + should be the root of the repository.""" + downstream_repo = args.downstream_repo + branch_name = args.branch_name + commit_sha = args.commit_sha + + if not downstream_repo: + tty.die('No downstream repo to push to, exiting') + + working_dir = os.getcwd() + jobs_yaml = os.path.join(working_dir, '.gitlab-ci.yml') + git_dir = os.path.join(working_dir, '.git') + + if not os.path.exists(jobs_yaml): + tty.die('.gitlab-ci.yml must exist in current directory') + + if not os.path.exists(git_dir): + tty.die('.git directory must exist in current directory') + + # Create a temporary working directory + with spack_ci.TemporaryDirectory() as temp_dir: + git = exe.which('git', required=True) + + # Push a commit with the generated file to the downstream ci repo + saved_git_dir = os.path.join(temp_dir, 'original-git-dir') + + shutil.move('.git', saved_git_dir) + + git('init', '.') + + git('config', 'user.email', 'robot@spack.io') + git('config', 'user.name', 'Spack Build Bot') + + git('add', '.') + + # If the environment contains a spack directory, do not commit + # or push it with any other generated products + if os.path.exists('./spack') and os.path.isdir('./spack'): + git('rm', '-rf', '--cached', 'spack') + + tty.msg('git commit') + commit_message = '{0} {1} ({2})'.format( + 'Auto-generated commit testing', branch_name, commit_sha) + + git('commit', '-m', '{0}'.format(commit_message)) + + tty.msg('git push') + git('remote', 'add', 'downstream', downstream_repo) + push_to_branch = 'master:multi-ci-{0}'.format(branch_name) + git('push', '--force', 'downstream', push_to_branch) + + shutil.rmtree('.git') + shutil.move(saved_git_dir, '.git') + git('reset', '--hard', 'HEAD') + + +def ci_rebuild(args): + """This command represents a gitlab-ci job, corresponding to a single + release spec. As such it must first decide whether or not the spec it + has been assigned to build is up to date on the remote binary mirror. + If it is not (i.e. the full_hash of the spec as computed locally does + not match the one stored in the metadata on the mirror), this script + will build the package, create a binary cache for it, and then push all + related files to the remote binary mirror. This script also + communicates with a remote CDash instance to share status on the package + build process. + + The spec to be built by this job is represented by essentially two + pieces of information: 1) a root spec (possibly already concrete, but + maybe still needing to be concretized) and 2) a package name used to + index that root spec (once the root is, for certain, concrete).""" + env = ev.get_env(args, 'ci rebuild', required=True) + yaml_root = ev.config_dict(env.yaml) + + # The following environment variables should defined in the CI + # infrastructre (or some other external source) in the case that the + # remote mirror is an S3 bucket. The AWS keys are used to upload + # buildcache entries to S3 using the boto3 api. + # + # AWS_ACCESS_KEY_ID + # AWS_SECRET_ACCESS_KEY + # S3_ENDPOINT_URL (only needed for non-AWS S3 implementations) + # + # If present, we will import the SPACK_SIGNING_KEY using the + # "spack gpg trust" command, so it can be used both for verifying + # dependency buildcache entries and signing the buildcache entry we create + # for our target pkg. + # + # SPACK_SIGNING_KEY + + ci_artifact_dir = get_env_var('CI_PROJECT_DIR') + signing_key = get_env_var('SPACK_SIGNING_KEY') + root_spec = get_env_var('SPACK_ROOT_SPEC') + job_spec_pkg_name = get_env_var('SPACK_JOB_SPEC_PKG_NAME') + compiler_action = get_env_var('SPACK_COMPILER_ACTION') + cdash_build_name = get_env_var('SPACK_CDASH_BUILD_NAME') + related_builds = get_env_var('SPACK_RELATED_BUILDS_CDASH') + + gitlab_ci = None + if 'gitlab-ci' in yaml_root: + gitlab_ci = yaml_root['gitlab-ci'] + + if not gitlab_ci: + tty.die('spack ci rebuild requires an env containing gitlab-ci cfg') + + enable_cdash = False + if 'cdash' in yaml_root: + enable_cdash = True + ci_cdash = yaml_root['cdash'] + job_spec_buildgroup = ci_cdash['build-group'] + cdash_base_url = ci_cdash['url'] + cdash_project = ci_cdash['project'] + proj_enc = urlencode({'project': cdash_project}) + eq_idx = proj_enc.find('=') + 1 + cdash_project_enc = proj_enc[eq_idx:] + cdash_site = ci_cdash['site'] + tty.debug('cdash_base_url = {0}'.format(cdash_base_url)) + tty.debug('cdash_project = {0}'.format(cdash_project)) + tty.debug('cdash_project_enc = {0}'.format(cdash_project_enc)) + tty.debug('cdash_build_name = {0}'.format(cdash_build_name)) + tty.debug('cdash_site = {0}'.format(cdash_site)) + tty.debug('related_builds = {0}'.format(related_builds)) + tty.debug('job_spec_buildgroup = {0}'.format(job_spec_buildgroup)) + + remote_mirror_url = None + if 'mirrors' in yaml_root: + ci_mirrors = yaml_root['mirrors'] + mirror_urls = [url for url in ci_mirrors.values()] + remote_mirror_url = mirror_urls[0] + + if not remote_mirror_url: + tty.die('spack ci rebuild requires an env containing a mirror') + + tty.debug('ci_artifact_dir = {0}'.format(ci_artifact_dir)) + tty.debug('root_spec = {0}'.format(root_spec)) + tty.debug('remote_mirror_url = {0}'.format(remote_mirror_url)) + tty.debug('job_spec_pkg_name = {0}'.format(job_spec_pkg_name)) + tty.debug('compiler_action = {0}'.format(compiler_action)) + + spack_cmd = exe.which('spack') + + os.environ['FORCE_UNSAFE_CONFIGURE'] = '1' + + cdash_report_dir = os.path.join(ci_artifact_dir, 'cdash_report') + temp_dir = os.path.join(ci_artifact_dir, 'jobs_scratch_dir') + job_log_dir = os.path.join(temp_dir, 'logs') + spec_dir = os.path.join(temp_dir, 'specs') + + local_mirror_dir = os.path.join(ci_artifact_dir, 'local_mirror') + build_cache_dir = os.path.join(local_mirror_dir, 'build_cache') + + enable_artifacts_mirror = False + artifact_mirror_url = None + if 'enable-artifacts-buildcache' in gitlab_ci: + enable_artifacts_mirror = gitlab_ci['enable-artifacts-buildcache'] + if enable_artifacts_mirror: + artifact_mirror_url = 'file://' + local_mirror_dir + mirror_msg = 'artifact buildcache enabled, mirror url: {0}'.format( + artifact_mirror_url) + tty.debug(mirror_msg) + + # Clean out scratch directory from last stage + if os.path.exists(temp_dir): + shutil.rmtree(temp_dir) + + if os.path.exists(cdash_report_dir): + shutil.rmtree(cdash_report_dir) + + os.makedirs(job_log_dir) + os.makedirs(spec_dir) + + job_spec_yaml_path = os.path.join( + spec_dir, '{0}.yaml'.format(job_spec_pkg_name)) + job_log_file = os.path.join(job_log_dir, 'pipeline_log.txt') + + cdash_build_id = None + cdash_build_stamp = None + + with open(job_log_file, 'w') as log_fd: + os.dup2(log_fd.fileno(), sys.stdout.fileno()) + os.dup2(log_fd.fileno(), sys.stderr.fileno()) + + current_directory = os.getcwd() + tty.debug('Current working directory: {0}, Contents:'.format( + current_directory)) + directory_list = os.listdir(current_directory) + for next_entry in directory_list: + tty.debug(' {0}'.format(next_entry)) + + # Make a copy of the environment file, so we can overwrite the changed + # version in between the two invocations of "spack install" + env_src_path = os.path.join(current_directory, 'spack.yaml') + env_dst_path = os.path.join(current_directory, 'spack.yaml_BACKUP') + shutil.copyfile(env_src_path, env_dst_path) + + tty.debug('job concrete spec path: {0}'.format(job_spec_yaml_path)) + + if signing_key: + spack_ci.import_signing_key(signing_key) + + spack_ci.configure_compilers(compiler_action) + + spec_map = spack_ci.get_concrete_specs( + root_spec, job_spec_pkg_name, related_builds, compiler_action) + + job_spec = spec_map[job_spec_pkg_name] + + tty.debug('Here is the concrete spec: {0}'.format(job_spec)) + + with open(job_spec_yaml_path, 'w') as fd: + fd.write(job_spec.to_yaml(hash=ht.build_hash)) + + tty.debug('Done writing concrete spec') + + # DEBUG + with open(job_spec_yaml_path) as fd: + tty.debug('Wrote spec file, read it back. Contents:') + tty.debug(fd.read()) + + # DEBUG the root spec + root_spec_yaml_path = os.path.join(spec_dir, 'root.yaml') + with open(root_spec_yaml_path, 'w') as fd: + fd.write(spec_map['root'].to_yaml(hash=ht.build_hash)) + + if bindist.needs_rebuild(job_spec, remote_mirror_url, True): + # Binary on remote mirror is not up to date, we need to rebuild + # it. + # + # FIXME: ensure mirror precedence causes this local mirror to + # be chosen ahead of the remote one when installing deps + if enable_artifacts_mirror: + mirror_add_output = spack_cmd( + 'mirror', 'add', 'local_mirror', artifact_mirror_url) + tty.debug('spack mirror add:') + tty.debug(mirror_add_output) + + mirror_list_output = spack_cmd('mirror', 'list') + tty.debug('listing spack mirrors:') + tty.debug(mirror_list_output) + + # 2) build up install arguments + install_args = ['-d', '-v', '-k', 'install', '--keep-stage'] + + # 3) create/register a new build on CDash (if enabled) + cdash_args = [] + if enable_cdash: + tty.debug('Registering build with CDash') + (cdash_build_id, + cdash_build_stamp) = spack_ci.register_cdash_build( + cdash_build_name, cdash_base_url, cdash_project, + cdash_site, job_spec_buildgroup) + + cdash_upload_url = '{0}/submit.php?project={1}'.format( + cdash_base_url, cdash_project_enc) + + cdash_args = [ + '--cdash-upload-url', cdash_upload_url, + '--cdash-build', cdash_build_name, + '--cdash-site', cdash_site, + '--cdash-buildstamp', cdash_build_stamp, + ] + + spec_cli_arg = [job_spec_yaml_path] + + tty.debug('Installing package') + + try: + # Two-pass install is intended to avoid spack trying to + # install from buildcache even though the locally computed + # full hash is different than the one stored in the spec.yaml + # file on the remote mirror. + first_pass_args = install_args + [ + '--cache-only', + '--only', + 'dependencies', + ] + first_pass_args.extend(spec_cli_arg) + tty.debug('First pass install arguments: {0}'.format( + first_pass_args)) + spack_cmd(*first_pass_args) + + # Overwrite the changed environment file so it doesn't + # the next install invocation. + shutil.copyfile(env_dst_path, env_src_path) + + second_pass_args = install_args + [ + '--no-cache', + '--only', + 'package', + ] + second_pass_args.extend(cdash_args) + second_pass_args.extend(spec_cli_arg) + tty.debug('Second pass install arguments: {0}'.format( + second_pass_args)) + spack_cmd(*second_pass_args) + except Exception as inst: + tty.error('Caught exception during install:') + tty.error(inst) + + spack_ci.copy_stage_logs_to_artifacts(job_spec, job_log_dir) + + # 4) create buildcache on remote mirror + spack_ci.push_mirror_contents(env, job_spec, job_spec_yaml_path, + remote_mirror_url, cdash_build_id) + + # 5) create another copy of that buildcache on "local artifact + # mirror" (only done if cash reporting is enabled) + spack_ci.push_mirror_contents(env, job_spec, job_spec_yaml_path, + artifact_mirror_url, cdash_build_id) + + # 6) relate this build to its dependencies on CDash (if enabled) + if enable_cdash: + spack_ci.relate_cdash_builds( + spec_map, cdash_base_url, cdash_build_id, cdash_project, + artifact_mirror_url or remote_mirror_url) + else: + # There is nothing to do here unless "local artifact mirror" is + # enabled, in which case, we need to download the buildcache to + # the local artifacts directory to be used by dependent jobs in + # subsequent stages + tty.debug('No need to rebuild {0}'.format(job_spec_pkg_name)) + if enable_artifacts_mirror: + tty.debug('Getting {0} buildcache'.format(job_spec_pkg_name)) + tty.debug('Downloading to {0}'.format(build_cache_dir)) + buildcache.download_buildcache_files( + job_spec, build_cache_dir, True, remote_mirror_url) + + +def ci_start(args): + """Kicks of the CI process (currently just calls ci_generate() then + ci_push())""" + ci_generate(args) + ci_pushyaml(args) + + +def ci(parser, args): + if args.func: + args.func(args) diff --git a/lib/spack/spack/cmd/clean.py b/lib/spack/spack/cmd/clean.py index 5dc7396ed4..791a1b7dc3 100644 --- a/lib/spack/spack/cmd/clean.py +++ b/lib/spack/spack/cmd/clean.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,6 +11,7 @@ import llnl.util.tty as tty import spack.caches import spack.cmd +import spack.cmd.common.arguments as arguments import spack.repo import spack.stage from spack.paths import lib_path, var_path @@ -43,11 +44,7 @@ def setup_parser(subparser): subparser.add_argument( '-a', '--all', action=AllClean, help="equivalent to -sdmp", nargs=0 ) - subparser.add_argument( - 'specs', - nargs=argparse.REMAINDER, - help="removes the build stages and tarballs for specs" - ) + arguments.add_common_arguments(subparser, ['specs']) def clean(parser, args): diff --git a/lib/spack/spack/cmd/clone.py b/lib/spack/spack/cmd/clone.py index 0385adf100..ecf5855dab 100644 --- a/lib/spack/spack/cmd/clone.py +++ b/lib/spack/spack/cmd/clone.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/commands.py b/lib/spack/spack/cmd/commands.py index 8c1a6b1e77..3664fce477 100644 --- a/lib/spack/spack/cmd/commands.py +++ b/lib/spack/spack/cmd/commands.py @@ -1,21 +1,26 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from __future__ import print_function -import sys +import argparse +import copy import os import re -import argparse +import sys +import llnl.util.filesystem as fs import llnl.util.tty as tty -from llnl.util.argparsewriter import ArgparseWriter, ArgparseRstWriter +from llnl.util.argparsewriter import ( + ArgparseWriter, ArgparseRstWriter, ArgparseCompletionWriter +) from llnl.util.tty.colify import colify import spack.cmd import spack.main +import spack.paths from spack.main import section_descriptions @@ -28,6 +33,20 @@ level = "long" formatters = {} +#: standard arguments for updating completion scripts +#: we iterate through these when called with --update-completion +update_completion_args = { + "bash": { + "aliases": True, + "format": "bash", + "header": os.path.join( + spack.paths.share_path, "bash", "spack-completion.in"), + "update": os.path.join( + spack.paths.share_path, "spack-completion.bash"), + }, +} + + def formatter(func): """Decorator used to register formatters""" formatters[func.__name__] = func @@ -36,6 +55,13 @@ def formatter(func): def setup_parser(subparser): subparser.add_argument( + "--update-completion", action='store_true', default=False, + help="regenerate spack's tab completion scripts") + + subparser.add_argument( + '-a', '--aliases', action='store_true', default=False, + help='include command aliases') + subparser.add_argument( '--format', default='names', choices=formatters, help='format to be used to print the output (default: names)') subparser.add_argument( @@ -52,29 +78,97 @@ def setup_parser(subparser): class SpackArgparseRstWriter(ArgparseRstWriter): """RST writer tailored for spack documentation.""" - def __init__(self, documented_commands, out=sys.stdout): - super(SpackArgparseRstWriter, self).__init__(out) - self.documented = documented_commands if documented_commands else [] + def __init__(self, prog, out=sys.stdout, aliases=False, + documented_commands=[], + rst_levels=['-', '-', '^', '~', ':', '`']): + super(SpackArgparseRstWriter, self).__init__( + prog, out, aliases, rst_levels) + self.documented = documented_commands def usage(self, *args): - super(SpackArgparseRstWriter, self).usage(*args) - cmd = re.sub(' ', '-', self.parser.prog) + string = super(SpackArgparseRstWriter, self).usage(*args) + + cmd = self.parser.prog.replace(' ', '-') if cmd in self.documented: - self.line() - self.line(':ref:`More documentation <cmd-%s>`' % cmd) + string += '\n:ref:`More documentation <cmd-{0}>`\n'.format(cmd) + + return string class SubcommandWriter(ArgparseWriter): - def begin_command(self, prog): - self.out.write(' ' * self.level + prog) - self.out.write('\n') + def format(self, cmd): + return ' ' * self.level + cmd.prog + '\n' + + +_positional_to_subroutine = { + 'package': '_all_packages', + 'spec': '_all_packages', + 'filter': '_all_packages', + 'installed': '_installed_packages', + 'compiler': '_installed_compilers', + 'section': '_config_sections', + 'env': '_environments', + 'extendable': '_extensions', + 'keys': '_keys', + 'help_command': '_subcommands', + 'mirror': '_mirrors', + 'virtual': '_providers', + 'namespace': '_repos', + 'hash': '_all_resource_hashes', + 'pytest': '_tests', +} + + +class BashCompletionWriter(ArgparseCompletionWriter): + """Write argparse output as bash programmable tab completion.""" + + def body(self, positionals, optionals, subcommands): + if positionals: + return """ + if $list_options + then + {0} + else + {1} + fi +""".format(self.optionals(optionals), self.positionals(positionals)) + elif subcommands: + return """ + if $list_options + then + {0} + else + {1} + fi +""".format(self.optionals(optionals), self.subcommands(subcommands)) + else: + return """ + {0} +""".format(self.optionals(optionals)) + + def positionals(self, positionals): + # If match found, return function name + for positional in positionals: + for key, value in _positional_to_subroutine.items(): + if positional.startswith(key): + return value + + # If no matches found, return empty list + return 'SPACK_COMPREPLY=""' + + def optionals(self, optionals): + return 'SPACK_COMPREPLY="{0}"'.format(' '.join(optionals)) + + def subcommands(self, subcommands): + return 'SPACK_COMPREPLY="{0}"'.format(' '.join(subcommands)) @formatter def subcommands(args, out): parser = spack.main.make_argument_parser() spack.main.add_all_commands(parser) - SubcommandWriter(out).write(parser) + writer = SubcommandWriter(parser.prog, out, args.aliases) + writer.write(parser) def rst_index(out): @@ -124,12 +218,28 @@ def rst(args, out): out.write('\n') # print sections for each command and subcommand - SpackArgparseRstWriter(documented_commands, out).write(parser, root=1) + writer = SpackArgparseRstWriter( + parser.prog, out, args.aliases, documented_commands) + writer.write(parser) @formatter def names(args, out): - colify(spack.cmd.all_commands(), output=out) + commands = copy.copy(spack.cmd.all_commands()) + + if args.aliases: + commands.extend(spack.main.aliases.keys()) + + colify(commands, output=out) + + +@formatter +def bash(args, out): + parser = spack.main.make_argument_parser() + spack.main.add_all_commands(parser) + + writer = BashCompletionWriter(parser.prog, out, args.aliases) + writer.write(parser) def prepend_header(args, out): @@ -140,7 +250,11 @@ def prepend_header(args, out): out.write(header.read()) -def commands(parser, args): +def _commands(parser, args): + """This is the 'regular' command, which can be called multiple times. + + See ``commands()`` below for ``--update-completion`` handling. + """ formatter = formatters[args.format] # check header first so we don't open out files unnecessarily @@ -148,12 +262,14 @@ def commands(parser, args): tty.die("No such file: '%s'" % args.header) # if we're updating an existing file, only write output if a command - # is newer than the file. + # or the header is newer than the file. if args.update: if os.path.exists(args.update): files = [ spack.cmd.get_module(command).__file__.rstrip('c') # pyc -> py for command in spack.cmd.all_commands()] + if args.header: + files.append(args.header) last_update = os.path.getmtime(args.update) if not any(os.path.getmtime(f) > last_update for f in files): tty.msg('File is up to date: %s' % args.update) @@ -164,6 +280,37 @@ def commands(parser, args): prepend_header(args, f) formatter(args, f) + if args.update_completion: + fs.set_executable(args.update) + else: prepend_header(args, sys.stdout) formatter(args, sys.stdout) + + +def update_completion(parser, args): + """Iterate through the shells and update the standard completion files. + + This is a convenience method to avoid calling this command many + times, and to simplify completion update for developers. + + """ + for shell, shell_args in update_completion_args.items(): + for attr, value in shell_args.items(): + setattr(args, attr, value) + _commands(parser, args) + + +def commands(parser, args): + if args.update_completion: + if args.format != 'names' or any([ + args.aliases, args.update, args.header + ]): + tty.die("--update-completion can only be specified alone.") + + # this runs the command multiple times with different arguments + return update_completion(parser, args) + + else: + # run commands normally + return _commands(parser, args) diff --git a/lib/spack/spack/cmd/common/__init__.py b/lib/spack/spack/cmd/common/__init__.py index ea7eced004..00804493cd 100644 --- a/lib/spack/spack/cmd/common/__init__.py +++ b/lib/spack/spack/cmd/common/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/common/arguments.py b/lib/spack/spack/cmd/common/arguments.py index 8a38d09f03..b93f265c7a 100644 --- a/lib/spack/spack/cmd/common/arguments.py +++ b/lib/spack/spack/cmd/common/arguments.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,9 +18,22 @@ from spack.util.pattern import Args __all__ = ['add_common_arguments'] +#: dictionary of argument-generating functions, keyed by name _arguments = {} +def arg(fn): + """Decorator for a function that generates a common argument. + + This ensures that argument bunches are created lazily. Decorate + argument-generating functions below with @arg so that + ``add_common_arguments()`` can find them. + + """ + _arguments[fn.__name__] = fn + return fn + + def add_common_arguments(parser, list_of_arguments): """Extend a parser with extra arguments @@ -32,7 +45,8 @@ def add_common_arguments(parser, list_of_arguments): if argument not in _arguments: message = 'Trying to add non existing argument "{0}" to a command' raise KeyError(message.format(argument)) - x = _arguments[argument] + + x = _arguments[argument]() parser.add_argument(*x.flags, **x.kwargs) @@ -106,7 +120,7 @@ class SetParallelJobs(argparse.Action): class DeptypeAction(argparse.Action): - """Creates a tuple of valid dependency tpyes from a deptype argument.""" + """Creates a tuple of valid dependency types from a deptype argument.""" def __call__(self, parser, namespace, values, option_string=None): deptype = dep.all_deptypes if values: @@ -118,64 +132,146 @@ class DeptypeAction(argparse.Action): setattr(namespace, self.dest, deptype) -_arguments['constraint'] = Args( - 'constraint', nargs=argparse.REMAINDER, action=ConstraintAction, - help='constraint to select a subset of installed packages') - -_arguments['yes_to_all'] = Args( - '-y', '--yes-to-all', action='store_true', dest='yes_to_all', - help='assume "yes" is the answer to every confirmation request') - -_arguments['recurse_dependencies'] = Args( - '-r', '--dependencies', action='store_true', dest='recurse_dependencies', - help='recursively traverse spec dependencies') - -_arguments['recurse_dependents'] = Args( - '-R', '--dependents', action='store_true', dest='dependents', - help='also uninstall any packages that depend on the ones given ' - 'via command line') - -_arguments['clean'] = Args( - '--clean', - action='store_false', - default=spack.config.get('config:dirty'), - dest='dirty', - help='unset harmful variables in the build environment (default)') - -_arguments['deptype'] = Args( - '--deptype', action=DeptypeAction, default=dep.all_deptypes, - help="comma-separated list of deptypes to traverse\ndefault=%s" - % ','.join(dep.all_deptypes)) - -_arguments['dirty'] = Args( - '--dirty', - action='store_true', - default=spack.config.get('config:dirty'), - dest='dirty', - help='preserve user environment in the spack build environment (danger!)') - -_arguments['long'] = Args( - '-l', '--long', action='store_true', - help='show dependency hashes as well as versions') - -_arguments['very_long'] = Args( - '-L', '--very-long', action='store_true', - help='show full dependency hashes as well as versions') - -_arguments['tags'] = Args( - '-t', '--tags', action='append', - help='filter a package query by tags') - -_arguments['jobs'] = Args( - '-j', '--jobs', action=SetParallelJobs, type=int, dest='jobs', - help='explicitly set number of parallel jobs') - -_arguments['install_status'] = Args( - '-I', '--install-status', action='store_true', default=False, - help='show install status of packages. packages can be: ' - 'installed [+], missing and needed by an installed package [-], ' - 'or not installed (no annotation)') - -_arguments['no_checksum'] = Args( - '-n', '--no-checksum', action='store_true', default=False, - help="do not use checksums to verify downloaded files (unsafe)") +# TODO: merge constraint and installed_specs +@arg +def constraint(): + return Args( + 'constraint', nargs=argparse.REMAINDER, action=ConstraintAction, + help='constraint to select a subset of installed packages', + metavar='installed_specs') + + +@arg +def package(): + return Args('package', help='package name') + + +@arg +def packages(): + return Args( + 'packages', nargs='+', help='one or more package names', + metavar='package') + + +# Specs must use `nargs=argparse.REMAINDER` because a single spec can +# contain spaces, and contain variants like '-mpi' that argparse thinks +# are a collection of optional flags. +@arg +def spec(): + return Args('spec', nargs=argparse.REMAINDER, help='package spec') + + +@arg +def specs(): + return Args( + 'specs', nargs=argparse.REMAINDER, help='one or more package specs') + + +@arg +def installed_spec(): + return Args( + 'spec', nargs=argparse.REMAINDER, help='installed package spec', + metavar='installed_spec') + + +@arg +def installed_specs(): + return Args( + 'specs', nargs=argparse.REMAINDER, + help='one or more installed package specs', metavar='installed_specs') + + +@arg +def yes_to_all(): + return Args( + '-y', '--yes-to-all', action='store_true', dest='yes_to_all', + help='assume "yes" is the answer to every confirmation request') + + +@arg +def recurse_dependencies(): + return Args( + '-r', '--dependencies', action='store_true', + dest='recurse_dependencies', + help='recursively traverse spec dependencies') + + +@arg +def recurse_dependents(): + return Args( + '-R', '--dependents', action='store_true', dest='dependents', + help='also uninstall any packages that depend on the ones given ' + 'via command line') + + +@arg +def clean(): + return Args( + '--clean', + action='store_false', + default=spack.config.get('config:dirty'), + dest='dirty', + help='unset harmful variables in the build environment (default)') + + +@arg +def deptype(): + return Args( + '--deptype', action=DeptypeAction, default=dep.all_deptypes, + help="comma-separated list of deptypes to traverse\ndefault=%s" + % ','.join(dep.all_deptypes)) + + +@arg +def dirty(): + return Args( + '--dirty', + action='store_true', + default=spack.config.get('config:dirty'), + dest='dirty', + help="preserve user environment in spack's build environment (danger!)" + ) + + +@arg +def long(): + return Args( + '-l', '--long', action='store_true', + help='show dependency hashes as well as versions') + + +@arg +def very_long(): + return Args( + '-L', '--very-long', action='store_true', + help='show full dependency hashes as well as versions') + + +@arg +def tags(): + return Args( + '-t', '--tags', action='append', + help='filter a package query by tags') + + +@arg +def jobs(): + return Args( + '-j', '--jobs', action=SetParallelJobs, type=int, dest='jobs', + help='explicitly set number of parallel jobs') + + +@arg +def install_status(): + return Args( + '-I', '--install-status', action='store_true', default=False, + help='show install status of packages. packages can be: ' + 'installed [+], missing and needed by an installed package [-], ' + 'or not installed (no annotation)') + + +@arg +def no_checksum(): + return Args( + '-n', '--no-checksum', action='store_true', default=False, + help="do not use checksums to verify downloaded files (unsafe)") diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py index c52a3c7081..c9647898ef 100644 --- a/lib/spack/spack/cmd/compiler.py +++ b/lib/spack/spack/cmd/compiler.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/compilers.py b/lib/spack/spack/cmd/compilers.py index a67735fd8d..c29e2257b7 100644 --- a/lib/spack/spack/cmd/compilers.py +++ b/lib/spack/spack/cmd/compilers.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/concretize.py b/lib/spack/spack/cmd/concretize.py index dd88fe8534..d28f7b4a5d 100644 --- a/lib/spack/spack/cmd/concretize.py +++ b/lib/spack/spack/cmd/concretize.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,6 +18,7 @@ def setup_parser(subparser): def concretize(parser, args): env = ev.get_env(args, 'concretize', required=True) - concretized_specs = env.concretize(force=args.force) - ev.display_specs(concretized_specs) - env.write() + with env.write_transaction(): + concretized_specs = env.concretize(force=args.force) + ev.display_specs(concretized_specs) + env.write() diff --git a/lib/spack/spack/cmd/config.py b/lib/spack/spack/cmd/config.py index 2a11af9f51..b1a6454555 100644 --- a/lib/spack/spack/cmd/config.py +++ b/lib/spack/spack/cmd/config.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -34,7 +34,7 @@ def setup_parser(subparser): help="configuration section to print. " "options: %(choices)s", nargs='?', - metavar='SECTION', + metavar='section', choices=spack.config.section_schemas) blame_parser = sp.add_parser( @@ -42,20 +42,22 @@ def setup_parser(subparser): blame_parser.add_argument('section', help="configuration section to print. " "options: %(choices)s", - metavar='SECTION', + metavar='section', choices=spack.config.section_schemas) edit_parser = sp.add_parser('edit', help='edit configuration file') edit_parser.add_argument('section', help="configuration section to edit. " "options: %(choices)s", - metavar='SECTION', + metavar='section', nargs='?', choices=spack.config.section_schemas) edit_parser.add_argument( '--print-file', action='store_true', help="print the file name that would be edited") + sp.add_parser('list', help='list configuration sections') + def _get_scope_and_section(args): """Extract config scope and section from arguments.""" @@ -83,7 +85,6 @@ def config_get(args): With no arguments and an active environment, print the contents of the environment's manifest file (spack.yaml). - """ scope, section = _get_scope_and_section(args) @@ -113,7 +114,6 @@ def config_edit(args): With no arguments and an active environment, edit the spack.yaml for the active environment. - """ scope, section = _get_scope_and_section(args) if not scope and not section: @@ -127,8 +127,19 @@ def config_edit(args): editor(config_file) +def config_list(args): + """List the possible configuration sections. + + Used primarily for shell tab completion scripts. + """ + print(' '.join(list(spack.config.section_schemas))) + + def config(parser, args): - action = {'get': config_get, - 'blame': config_blame, - 'edit': config_edit} + action = { + 'get': config_get, + 'blame': config_blame, + 'edit': config_edit, + 'list': config_list, + } action[args.config_command](args) diff --git a/lib/spack/spack/cmd/configure.py b/lib/spack/spack/cmd/configure.py index 10a1294a41..3df3c87413 100644 --- a/lib/spack/spack/cmd/configure.py +++ b/lib/spack/spack/cmd/configure.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,6 +7,7 @@ import argparse import llnl.util.tty as tty import spack.cmd +import spack.cmd.common.arguments as arguments import spack.cmd.install as inst from spack.build_systems.autotools import AutotoolsPackage @@ -37,15 +38,11 @@ build_system_to_phase = { def setup_parser(subparser): subparser.add_argument( - 'package', - nargs=argparse.REMAINDER, - help="spec of the package to install" - ) - subparser.add_argument( '-v', '--verbose', action='store_true', help="print additional output during builds" ) + arguments.add_common_arguments(subparser, ['spec']) def _stop_at_phase_during_install(args, calling_fn, phase_mapping): @@ -64,15 +61,15 @@ def _stop_at_phase_during_install(args, calling_fn, phase_mapping): # Install package dependencies if needed parser = argparse.ArgumentParser() inst.setup_parser(parser) - tty.msg('Checking dependencies for {0}'.format(args.package[0])) + tty.msg('Checking dependencies for {0}'.format(args.spec[0])) cli_args = ['-v'] if args.verbose else [] install_args = parser.parse_args(cli_args + ['--only=dependencies']) - install_args.package = args.package + install_args.spec = args.spec inst.install(parser, install_args) # Install package and stop at the given phase cli_args = ['-v'] if args.verbose else [] install_args = parser.parse_args(cli_args + ['--only=package']) - install_args.package = args.package + install_args.spec = args.spec inst.install(parser, install_args, stop_at=phase) except IndexError: tty.error( diff --git a/lib/spack/spack/cmd/containerize.py b/lib/spack/spack/cmd/containerize.py new file mode 100644 index 0000000000..cc2c001560 --- /dev/null +++ b/lib/spack/spack/cmd/containerize.py @@ -0,0 +1,25 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os +import os.path +import spack.container + +description = ("creates recipes to build images for different" + " container runtimes") +section = "container" +level = "long" + + +def containerize(parser, args): + config_dir = args.env_dir or os.getcwd() + config_file = os.path.abspath(os.path.join(config_dir, 'spack.yaml')) + if not os.path.exists(config_file): + msg = 'file not found: {0}' + raise ValueError(msg.format(config_file)) + + config = spack.container.validate(config_file) + + recipe = spack.container.recipe(config) + print(recipe) diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index ee0fb3a347..f9b7a382ea 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,7 +28,7 @@ level = "short" package_template = '''\ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -246,6 +246,7 @@ class PythonPackageTemplate(PackageTemplate): dependencies = """\ # FIXME: Add dependencies if required. + # depends_on('python@2.X:2.Y,3.Z:', type=('build', 'run')) # depends_on('py-setuptools', type='build') # depends_on('py-foo', type=('build', 'run'))""" @@ -426,7 +427,8 @@ def setup_parser(subparser): '-n', '--name', help="name of the package to create") subparser.add_argument( - '-t', '--template', metavar='TEMPLATE', choices=templates.keys(), + '-t', '--template', metavar='TEMPLATE', + choices=sorted(templates.keys()), help="build system template to use. options: %(choices)s") subparser.add_argument( '-r', '--repo', @@ -458,7 +460,7 @@ class BuildSystemGuesser: the contents of its archive or the URL it was downloaded from.""" # Most octave extensions are hosted on Octave-Forge: - # http://octave.sourceforge.net/index.html + # https://octave.sourceforge.net/index.html # They all have the same base URL. if url is not None and 'downloads.sourceforge.net/octave/' in url: self.build_system = 'octave' @@ -471,13 +473,13 @@ class BuildSystemGuesser: # build systems, we choose the first match in this list. clues = [ (r'/CMakeLists\.txt$', 'cmake'), + (r'/NAMESPACE$', 'r'), (r'/configure$', 'autotools'), (r'/configure\.(in|ac)$', 'autoreconf'), (r'/Makefile\.am$', 'autoreconf'), (r'/SConstruct$', 'scons'), (r'/waf$', 'waf'), (r'/setup\.py$', 'python'), - (r'/NAMESPACE$', 'r'), (r'/WORKSPACE$', 'bazel'), (r'/Build\.PL$', 'perlbuild'), (r'/Makefile\.PL$', 'perlmake'), @@ -571,7 +573,7 @@ def get_url(args): """ # Default URL - url = 'http://www.example.com/example-1.2.3.tar.gz' + url = 'https://www.example.com/example-1.2.3.tar.gz' if args.url: # Use a user-supplied URL if one is present diff --git a/lib/spack/spack/cmd/deactivate.py b/lib/spack/spack/cmd/deactivate.py index 722112ead2..3c72531a9c 100644 --- a/lib/spack/spack/cmd/deactivate.py +++ b/lib/spack/spack/cmd/deactivate.py @@ -1,12 +1,12 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse import llnl.util.tty as tty import spack.cmd +import spack.cmd.common.arguments as arguments import spack.environment as ev import spack.store from spack.filesystem_view import YamlFilesystemView @@ -28,9 +28,7 @@ def setup_parser(subparser): '-a', '--all', action='store_true', help="deactivate all extensions of an extendable package, or " "deactivate an extension AND its dependencies") - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, - help="spec of package extension to deactivate") + arguments.add_common_arguments(subparser, ['installed_spec']) def deactivate(parser, args): diff --git a/lib/spack/spack/cmd/debug.py b/lib/spack/spack/cmd/debug.py index e729373194..4fc39251af 100644 --- a/lib/spack/spack/cmd/debug.py +++ b/lib/spack/spack/cmd/debug.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/dependencies.py b/lib/spack/spack/cmd/dependencies.py index 671224edb4..e65e050bfa 100644 --- a/lib/spack/spack/cmd/dependencies.py +++ b/lib/spack/spack/cmd/dependencies.py @@ -1,10 +1,8 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse - import llnl.util.tty as tty from llnl.util.tty.colify import colify @@ -31,8 +29,7 @@ def setup_parser(subparser): subparser.add_argument( '-V', '--no-expand-virtuals', action='store_false', default=True, dest="expand_virtuals", help="do not expand virtual dependencies") - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help="spec or package name") + arguments.add_common_arguments(subparser, ['spec']) def dependencies(parser, args): diff --git a/lib/spack/spack/cmd/dependents.py b/lib/spack/spack/cmd/dependents.py index 368dae8f55..e60733f589 100644 --- a/lib/spack/spack/cmd/dependents.py +++ b/lib/spack/spack/cmd/dependents.py @@ -1,17 +1,16 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse - import llnl.util.tty as tty from llnl.util.tty.colify import colify +import spack.cmd +import spack.cmd.common.arguments as arguments import spack.environment as ev import spack.repo import spack.store -import spack.cmd description = "show packages that depend on another" section = "basic" @@ -26,8 +25,7 @@ def setup_parser(subparser): subparser.add_argument( '-t', '--transitive', action='store_true', default=False, help="Show all transitive dependents.") - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help="spec or package name") + arguments.add_common_arguments(subparser, ['spec']) def inverted_dependencies(): diff --git a/lib/spack/spack/cmd/deprecate.py b/lib/spack/spack/cmd/deprecate.py index 286d2e995a..6172033fa7 100644 --- a/lib/spack/spack/cmd/deprecate.py +++ b/lib/spack/spack/cmd/deprecate.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/dev_build.py b/lib/spack/spack/cmd/dev_build.py index 7c92b004ca..c1004f24b3 100644 --- a/lib/spack/spack/cmd/dev_build.py +++ b/lib/spack/spack/cmd/dev_build.py @@ -1,18 +1,17 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) import sys import os -import argparse import llnl.util.tty as tty import spack.config import spack.cmd -import spack.repo import spack.cmd.common.arguments as arguments +import spack.repo from spack.stage import DIYStage description = "developer build: build from code in current working directory" @@ -41,9 +40,7 @@ def setup_parser(subparser): subparser.add_argument( '-u', '--until', type=str, dest='until', default=None, help="phase to stop after when installing (default None)") - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, - help="specs to use for install. must contain package AND version") + arguments.add_common_arguments(subparser, ['spec']) cd_group = subparser.add_mutually_exclusive_group() arguments.add_common_arguments(cd_group, ['clean', 'dirty']) diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py index 127a6bbed1..186745d80c 100644 --- a/lib/spack/spack/cmd/diy.py +++ b/lib/spack/spack/cmd/diy.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/docs.py b/lib/spack/spack/cmd/docs.py index 696bfb3a13..a7f2a641ee 100644 --- a/lib/spack/spack/cmd/docs.py +++ b/lib/spack/spack/cmd/docs.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/edit.py b/lib/spack/spack/cmd/edit.py index cca52618e8..6cdc3b788d 100644 --- a/lib/spack/spack/cmd/edit.py +++ b/lib/spack/spack/cmd/edit.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -84,12 +84,11 @@ def setup_parser(subparser): help="namespace of package to edit") subparser.add_argument( - 'name', nargs='?', default=None, - help="name of package to edit") + 'package', nargs='?', default=None, help="package name") def edit(parser, args): - name = args.name + name = args.package # By default, edit package files path = spack.paths.packages_path diff --git a/lib/spack/spack/cmd/env.py b/lib/spack/spack/cmd/env.py index 64ba9d53a4..a8bc1e5bbe 100644 --- a/lib/spack/spack/cmd/env.py +++ b/lib/spack/spack/cmd/env.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -157,7 +157,7 @@ def env_deactivate(args): def env_create_setup_parser(subparser): """create a new environment""" subparser.add_argument( - 'create_env', metavar='ENV', help='name of environment to create') + 'create_env', metavar='env', help='name of environment to create') subparser.add_argument( '-d', '--dir', action='store_true', help='create an environment in a specific directory') @@ -221,7 +221,7 @@ def _env_create(name_or_path, init_file=None, dir=False, with_view=None): def env_remove_setup_parser(subparser): """remove an existing environment""" subparser.add_argument( - 'rm_env', metavar='ENV', nargs='+', + 'rm_env', metavar='env', nargs='+', help='environment(s) to remove') arguments.add_common_arguments(subparser, ['yes_to_all']) diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py index c9dcf6c4eb..e834d7fd18 100644 --- a/lib/spack/spack/cmd/extensions.py +++ b/lib/spack/spack/cmd/extensions.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -37,7 +37,7 @@ def setup_parser(subparser): subparser.add_argument( 'spec', nargs=argparse.REMAINDER, - help='spec of package to list extensions for') + help='spec of package to list extensions for', metavar='extendable') def extensions(parser, args): diff --git a/lib/spack/spack/cmd/fetch.py b/lib/spack/spack/cmd/fetch.py index 68ec635d26..b91eb52ab8 100644 --- a/lib/spack/spack/cmd/fetch.py +++ b/lib/spack/spack/cmd/fetch.py @@ -1,16 +1,14 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse - import llnl.util.tty as tty import spack.cmd +import spack.cmd.common.arguments as arguments import spack.config import spack.repo -import spack.cmd.common.arguments as arguments description = "fetch archives for packages" section = "build" @@ -25,19 +23,17 @@ def setup_parser(subparser): subparser.add_argument( '-D', '--dependencies', action='store_true', help="also fetch all dependencies") - subparser.add_argument( - 'packages', nargs=argparse.REMAINDER, - help="specs of packages to fetch") + arguments.add_common_arguments(subparser, ['specs']) def fetch(parser, args): - if not args.packages: + if not args.specs: tty.die("fetch requires at least one package argument") if args.no_checksum: spack.config.set('config:checksum', False, scope='command_line') - specs = spack.cmd.parse_specs(args.packages, concretize=True) + specs = spack.cmd.parse_specs(args.specs, concretize=True) for spec in specs: if args.missing or args.dependencies: for s in spec.traverse(): diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py index 37cfcd30d5..fa36e1cd26 100644 --- a/lib/spack/spack/cmd/find.py +++ b/lib/spack/spack/cmd/find.py @@ -1,10 +1,13 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from __future__ import print_function +import copy +import os + import llnl.util.tty as tty import llnl.util.tty.color as color import llnl.util.lang @@ -13,6 +16,7 @@ import spack.environment as ev import spack.repo import spack.cmd as cmd import spack.cmd.common.arguments as arguments +import spack.user_environment as uenv from spack.util.string import plural from spack.database import InstallStatuses @@ -80,6 +84,9 @@ def setup_parser(subparser): action='store_true', dest='variants', help='show variants in output (can be long)') + subparser.add_argument( + '--loaded', action='store_true', + help='show only packages loaded in the user environment') subparser.add_argument('-M', '--only-missing', action='store_true', dest='only_missing', @@ -166,11 +173,16 @@ def display_env(env, args, decorator): else: tty.msg('Root specs') + # Root specs cannot be displayed with prefixes, since those are not + # set for abstract specs. Same for hashes + root_args = copy.copy(args) + root_args.paths = False + # Roots are displayed with variants, etc. so that we can see # specifically what the user asked for. cmd.display_specs( env.user_specs, - args, + root_args, decorator=lambda s, f: color.colorize('@*{%s}' % f), namespace=True, show_flags=True, @@ -214,6 +226,10 @@ def find(parser, args): packages_with_tags = spack.repo.path.packages_with_tags(*args.tags) results = [x for x in results if x.name in packages_with_tags] + if args.loaded: + hashes = os.environ.get(uenv.spack_loaded_hashes_var, '').split(':') + results = [x for x in results if x.dag_hash() in hashes] + # Display the result if args.json: cmd.display_specs_as_json(results, deps=args.deps) diff --git a/lib/spack/spack/cmd/flake8.py b/lib/spack/spack/cmd/flake8.py index cc5b168c4b..cdfce2cab2 100644 --- a/lib/spack/spack/cmd/flake8.py +++ b/lib/spack/spack/cmd/flake8.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/gc.py b/lib/spack/spack/cmd/gc.py new file mode 100644 index 0000000000..ca9d88169a --- /dev/null +++ b/lib/spack/spack/cmd/gc.py @@ -0,0 +1,47 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import llnl.util.tty as tty + +import spack.cmd.common.arguments +import spack.cmd.uninstall +import spack.environment +import spack.store + +description = "remove specs that are now no longer needed" +section = "build" +level = "short" + + +def setup_parser(subparser): + spack.cmd.common.arguments.add_common_arguments(subparser, ['yes_to_all']) + + +def gc(parser, args): + specs = spack.store.db.unused_specs + + # Restrict garbage collection to the active environment + # speculating over roots that are yet to be installed + env = spack.environment.get_env(args=None, cmd_name='gc') + if env: + msg = 'Restricting the garbage collection to the "{0}" environment' + tty.msg(msg.format(env.name)) + env.concretize() + roots = [s for s in env.roots()] + all_hashes = set([s.dag_hash() for r in roots for s in r.traverse()]) + lr_hashes = set([s.dag_hash() for r in roots + for s in r.traverse(deptype=('link', 'run'))]) + maybe_to_be_removed = all_hashes - lr_hashes + specs = [s for s in specs if s.dag_hash() in maybe_to_be_removed] + + if not specs: + msg = "There are no unused specs. Spack's store is clean." + tty.msg(msg) + return + + if not args.yes_to_all: + spack.cmd.uninstall.confirm_removal(specs) + + spack.cmd.uninstall.do_uninstall(None, specs, force=False) diff --git a/lib/spack/spack/cmd/gpg.py b/lib/spack/spack/cmd/gpg.py index dcd4f798a2..0a77812c12 100644 --- a/lib/spack/spack/cmd/gpg.py +++ b/lib/spack/spack/cmd/gpg.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,6 +6,7 @@ import os import argparse +import spack.cmd.common.arguments as arguments import spack.paths from spack.util.gpg import Gpg @@ -19,8 +20,7 @@ def setup_parser(subparser): subparsers = subparser.add_subparsers(help='GPG sub-commands') verify = subparsers.add_parser('verify', help=gpg_verify.__doc__) - verify.add_argument('package', type=str, - help='the package to verify') + arguments.add_common_arguments(verify, ['installed_spec']) verify.add_argument('signature', type=str, nargs='?', help='the signature file') verify.set_defaults(func=gpg_verify) @@ -44,8 +44,7 @@ def setup_parser(subparser): help='the key to use for signing') sign.add_argument('--clearsign', action='store_true', help='if specified, create a clearsign signature') - sign.add_argument('package', type=str, - help='the package to sign') + arguments.add_common_arguments(sign, ['installed_spec']) sign.set_defaults(func=gpg_sign) create = subparsers.add_parser('create', help=gpg_create.__doc__) @@ -122,9 +121,9 @@ def gpg_sign(args): 'please choose one') output = args.output if not output: - output = args.package + '.asc' + output = args.spec[0] + '.asc' # TODO: Support the package format Spack creates. - Gpg.sign(key, args.package, output, args.clearsign) + Gpg.sign(key, ' '.join(args.spec), output, args.clearsign) def gpg_trust(args): @@ -155,8 +154,8 @@ def gpg_verify(args): # TODO: Support the package format Spack creates. signature = args.signature if signature is None: - signature = args.package + '.asc' - Gpg.verify(signature, args.package) + signature = args.spec[0] + '.asc' + Gpg.verify(signature, ' '.join(args.spec)) def gpg(parser, args): diff --git a/lib/spack/spack/cmd/graph.py b/lib/spack/spack/cmd/graph.py index c07b009286..d0fbf8e6c6 100644 --- a/lib/spack/spack/cmd/graph.py +++ b/lib/spack/spack/cmd/graph.py @@ -1,11 +1,10 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from __future__ import print_function -import argparse import llnl.util.tty as tty import spack.cmd @@ -38,11 +37,7 @@ def setup_parser(subparser): '-i', '--installed', action='store_true', help="graph all installed specs in dot format (implies --dot)") - arguments.add_common_arguments(subparser, ['deptype']) - - subparser.add_argument( - 'specs', nargs=argparse.REMAINDER, - help="specs of packages to graph") + arguments.add_common_arguments(subparser, ['deptype', 'specs']) def graph(parser, args): diff --git a/lib/spack/spack/cmd/help.py b/lib/spack/spack/cmd/help.py index 8178ef79ed..3af82312df 100644 --- a/lib/spack/spack/cmd/help.py +++ b/lib/spack/spack/cmd/help.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py index 37a1aeb0a4..81a68dae96 100644 --- a/lib/spack/spack/cmd/info.py +++ b/lib/spack/spack/cmd/info.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,6 +11,7 @@ from six.moves import zip_longest import llnl.util.tty.color as color from llnl.util.tty.colify import colify +import spack.cmd.common.arguments as arguments import spack.repo import spack.spec import spack.fetch_strategy as fs @@ -36,8 +37,7 @@ def padder(str_list, extra=0): def setup_parser(subparser): - subparser.add_argument( - 'name', metavar='PACKAGE', help='name of package to get info for') + arguments.add_common_arguments(subparser, ['package']) def section_title(s): @@ -106,7 +106,9 @@ class VariantFormatter(object): yield ' None' else: yield ' ' + self.fmt % self.headers - yield '\n' + underline = tuple([l * "=" for l in self.column_widths]) + yield ' ' + self.fmt % underline + yield '' for k, v in sorted(self.variants.items()): name = textwrap.wrap( '{0} [{1}]'.format(k, self.default(v)), @@ -235,5 +237,5 @@ def print_text_info(pkg): def info(parser, args): - pkg = spack.repo.get(args.name) + pkg = spack.repo.get(args.package) print_text_info(pkg) diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py index ab012eaead..9e13643920 100644 --- a/lib/spack/spack/cmd/install.py +++ b/lib/spack/spack/cmd/install.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,6 +7,7 @@ import argparse import os import shutil import sys +import textwrap import llnl.util.filesystem as fs import llnl.util.tty as tty @@ -41,7 +42,8 @@ def update_kwargs_from_args(args, kwargs): 'use_cache': args.use_cache, 'cache_only': args.cache_only, 'explicit': True, # Always true for install command - 'stop_at': args.until + 'stop_at': args.until, + 'unsigned': args.unsigned, }) kwargs.update({ @@ -72,7 +74,7 @@ the dependencies""" subparser.add_argument( '-u', '--until', type=str, dest='until', default=None, help="phase to stop after when installing (default None)") - arguments.add_common_arguments(subparser, ['jobs', 'install_status']) + arguments.add_common_arguments(subparser, ['jobs']) subparser.add_argument( '--overwrite', action='store_true', help="reinstall an existing spec, even if it has dependents") @@ -98,6 +100,10 @@ the dependencies""" help="only install package from binary mirrors") subparser.add_argument( + '--no-check-signature', action='store_true', + dest='unsigned', default=False, + help="do not check signatures of binary packages") + subparser.add_argument( '--show-log-on-error', action='store_true', help="print full build log to stderr if build fails") subparser.add_argument( @@ -121,11 +127,6 @@ the dependencies""" cd_group = subparser.add_mutually_exclusive_group() arguments.add_common_arguments(cd_group, ['clean', 'dirty']) - subparser.add_argument( - 'package', - nargs=argparse.REMAINDER, - help="spec of the package to install" - ) testing = subparser.add_mutually_exclusive_group() testing.add_argument( '--test', default=None, @@ -151,38 +152,62 @@ packages. If neither are chosen, don't run tests for any packages.""" help="filename for the log file. if not passed a default will be used" ) subparser.add_argument( + '--help-cdash', + action='store_true', + help="Show usage instructions for CDash reporting" + ) + add_cdash_args(subparser, False) + arguments.add_common_arguments(subparser, ['yes_to_all', 'spec']) + + +def add_cdash_args(subparser, add_help): + cdash_help = {} + if add_help: + cdash_help['upload-url'] = "CDash URL where reports will be uploaded" + cdash_help['build'] = """The name of the build that will be reported to CDash. +Defaults to spec of the package to install.""" + cdash_help['site'] = """The site name that will be reported to CDash. +Defaults to current system hostname.""" + cdash_help['track'] = """Results will be reported to this group on CDash. +Defaults to Experimental.""" + cdash_help['buildstamp'] = """Instead of letting the CDash reporter prepare the +buildstamp which, when combined with build name, site and project, +uniquely identifies the build, provide this argument to identify +the build yourself. Format: %%Y%%m%%d-%%H%%M-[cdash-track]""" + else: + cdash_help['upload-url'] = argparse.SUPPRESS + cdash_help['build'] = argparse.SUPPRESS + cdash_help['site'] = argparse.SUPPRESS + cdash_help['track'] = argparse.SUPPRESS + cdash_help['buildstamp'] = argparse.SUPPRESS + + subparser.add_argument( '--cdash-upload-url', default=None, - help="CDash URL where reports will be uploaded" + help=cdash_help['upload-url'] ) subparser.add_argument( '--cdash-build', default=None, - help="""The name of the build that will be reported to CDash. -Defaults to spec of the package to install.""" + help=cdash_help['build'] ) subparser.add_argument( '--cdash-site', default=None, - help="""The site name that will be reported to CDash. -Defaults to current system hostname.""" + help=cdash_help['site'] ) + cdash_subgroup = subparser.add_mutually_exclusive_group() cdash_subgroup.add_argument( '--cdash-track', default='Experimental', - help="""Results will be reported to this group on CDash. -Defaults to Experimental.""" + help=cdash_help['track'] ) cdash_subgroup.add_argument( '--cdash-buildstamp', default=None, - help="""Instead of letting the CDash reporter prepare the -buildstamp which, when combined with build name, site and project, -uniquely identifies the build, provide this argument to identify -the build yourself. Format: %%Y%%m%%d-%%H%%M-[cdash-track]""" + help=cdash_help['buildstamp'] ) - arguments.add_common_arguments(subparser, ['yes_to_all']) def default_log_file(spec): @@ -203,8 +228,13 @@ def install_spec(cli_args, kwargs, abstract_spec, spec): # handle active environment, if any env = ev.get_env(cli_args, 'install') if env: - env.install(abstract_spec, spec, **kwargs) - env.write() + with env.write_transaction(): + concrete = env.concretize_and_add( + abstract_spec, spec) + env.write(regenerate_views=False) + env._install(concrete, **kwargs) + with env.write_transaction(): + env.regenerate_views() else: spec.package.do_install(**kwargs) @@ -221,22 +251,38 @@ def install_spec(cli_args, kwargs, abstract_spec, spec): def install(parser, args, **kwargs): - if not args.package and not args.specfiles: + if args.help_cdash: + parser = argparse.ArgumentParser( + formatter_class=argparse.RawDescriptionHelpFormatter, + epilog=textwrap.dedent('''\ +environment variables: + SPACK_CDASH_AUTH_TOKEN + authentication token to present to CDash + ''')) + add_cdash_args(parser, True) + parser.print_help() + return + + if not args.spec and not args.specfiles: # if there are no args but an active environment or spack.yaml file # then install the packages from it. env = ev.get_env(args, 'install') if env: if not args.only_concrete: - concretized_specs = env.concretize() - ev.display_specs(concretized_specs) + with env.write_transaction(): + concretized_specs = env.concretize() + ev.display_specs(concretized_specs) - # save view regeneration for later, so that we only do it - # once, as it can be slow. - env.write(regenerate_views=False) + # save view regeneration for later, so that we only do it + # once, as it can be slow. + env.write(regenerate_views=False) tty.msg("Installing environment %s" % env.name) env.install_all(args) - env.regenerate_views() + with env.write_transaction(): + # It is not strictly required to synchronize view regeneration + # but doing so can prevent redundant work in the filesystem. + env.regenerate_views() return else: tty.die("install requires a package argument or a spack.yaml file") @@ -256,7 +302,7 @@ def install(parser, args, **kwargs): if args.log_file: reporter.filename = args.log_file - abstract_specs = spack.cmd.parse_specs(args.package) + abstract_specs = spack.cmd.parse_specs(args.spec) tests = False if args.test == 'all' or args.run_tests: tests = True @@ -266,7 +312,7 @@ def install(parser, args, **kwargs): try: specs = spack.cmd.parse_specs( - args.package, concretize=True, tests=tests) + args.spec, concretize=True, tests=tests) except SpackError as e: tty.debug(e) reporter.concretization_report(e.message) diff --git a/lib/spack/spack/cmd/license.py b/lib/spack/spack/cmd/license.py index 4c69dba0e7..5fd57c39c9 100644 --- a/lib/spack/spack/cmd/license.py +++ b/lib/spack/spack/cmd/license.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -124,7 +124,7 @@ def _check_license(lines, path): r'SPDX-License-Identifier: \(Apache-2\.0 OR MIT\)' ] - strict_date = r'Copyright 2013-2019' + strict_date = r'Copyright 2013-2020' found = [] diff --git a/lib/spack/spack/cmd/list.py b/lib/spack/spack/cmd/list.py index fe6983ce74..656282599d 100644 --- a/lib/spack/spack/cmd/list.py +++ b/lib/spack/spack/cmd/list.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,7 +23,7 @@ import spack.cmd.common.arguments as arguments from spack.version import VersionList if sys.version_info > (3, 1): - from html import escape + from html import escape # novm else: from cgi import escape diff --git a/lib/spack/spack/cmd/load.py b/lib/spack/spack/cmd/load.py index ef8e29816a..09f3fd31ee 100644 --- a/lib/spack/spack/cmd/load.py +++ b/lib/spack/spack/cmd/load.py @@ -1,25 +1,80 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse -from spack.cmd.common import print_module_placeholder_help, arguments +import sys -description = "add package to environment using `module load`" -section = "modules" +import llnl.util.tty as tty + +import spack.cmd +import spack.cmd.common.arguments as arguments +import spack.environment as ev +import spack.util.environment +import spack.user_environment as uenv +import spack.store + +description = "add package to the user environment" +section = "user environment" level = "short" def setup_parser(subparser): """Parser is only constructed so that this prints a nice help message with -h. """ + arguments.add_common_arguments( + subparser, ['recurse_dependencies', 'installed_specs']) + + shells = subparser.add_mutually_exclusive_group() + shells.add_argument( + '--sh', action='store_const', dest='shell', const='sh', + help="print sh commands to load the package") + shells.add_argument( + '--csh', action='store_const', dest='shell', const='csh', + help="print csh commands to load the package") + subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, - help="spec of package to load with modules " + '--only', + default='package,dependencies', + dest='things_to_load', + choices=['package', 'dependencies'], + help="""select whether to load the package and its dependencies +the default is to load the package and all dependencies +alternatively one can decide to load only the package or only +the dependencies""" ) - arguments.add_common_arguments(subparser, ['recurse_dependencies']) def load(parser, args): - print_module_placeholder_help() + env = ev.get_env(args, 'load') + specs = [spack.cmd.disambiguate_spec(spec, env) + for spec in spack.cmd.parse_specs(args.specs)] + + if not args.shell: + msg = [ + "This command works best with Spack's shell support", + "" + ] + spack.cmd.common.shell_init_instructions + [ + 'Or, if you want to use `spack load` without initializing', + 'shell support, you can run one of these:', + '', + ' eval `spack load --sh %s` # for bash/sh' % args.specs, + ' eval `spack load --csh %s` # for csh/tcsh' % args.specs, + ] + tty.msg(*msg) + return 1 + + with spack.store.db.read_transaction(): + if 'dependencies' in args.things_to_load: + include_roots = 'package' in args.things_to_load + specs = [dep for spec in specs + for dep in + spec.traverse(root=include_roots, order='post')] + + env_mod = spack.util.environment.EnvironmentModifications() + for spec in specs: + env_mod.extend(uenv.environment_modifications_for_spec(spec)) + env_mod.prepend_path(uenv.spack_loaded_hashes_var, spec.dag_hash()) + cmds = env_mod.shell_modifications(args.shell) + + sys.stdout.write(cmds) diff --git a/lib/spack/spack/cmd/location.py b/lib/spack/spack/cmd/location.py index d6716233f9..60978fe404 100644 --- a/lib/spack/spack/cmd/location.py +++ b/lib/spack/spack/cmd/location.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,11 @@ from __future__ import print_function import os -import argparse import llnl.util.tty as tty import spack.environment as ev import spack.cmd +import spack.cmd.common.arguments as arguments import spack.environment import spack.paths import spack.repo @@ -55,9 +55,7 @@ def setup_parser(subparser): '-e', '--env', action='store', help="location of an environment managed by spack") - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, - help="spec of package to fetch directory for") + arguments.add_common_arguments(subparser, ['spec']) def location(parser, args): diff --git a/lib/spack/spack/cmd/log_parse.py b/lib/spack/spack/cmd/log_parse.py index 6932047511..faa44a4ef0 100644 --- a/lib/spack/spack/cmd/log_parse.py +++ b/lib/spack/spack/cmd/log_parse.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/maintainers.py b/lib/spack/spack/cmd/maintainers.py index 361437ece5..a1cf477146 100644 --- a/lib/spack/spack/cmd/maintainers.py +++ b/lib/spack/spack/cmd/maintainers.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -40,7 +40,7 @@ def setup_parser(subparser): # options for commands that take package arguments subparser.add_argument( - 'pkg_or_user', nargs=argparse.REMAINDER, + 'package_or_user', nargs=argparse.REMAINDER, help='names of packages or users to get info for') @@ -104,31 +104,31 @@ def maintainers(parser, args): if args.all: if args.by_user: - maintainers = maintainers_to_packages(args.pkg_or_user) + maintainers = maintainers_to_packages(args.package_or_user) for user, packages in sorted(maintainers.items()): color.cprint('@c{%s}: %s' % (user, ', '.join(sorted(packages)))) return 0 if maintainers else 1 else: - packages = packages_to_maintainers(args.pkg_or_user) + packages = packages_to_maintainers(args.package_or_user) for pkg, maintainers in sorted(packages.items()): color.cprint('@c{%s}: %s' % (pkg, ', '.join(sorted(maintainers)))) return 0 if packages else 1 if args.by_user: - if not args.pkg_or_user: + if not args.package_or_user: tty.die('spack maintainers --by-user requires a user or --all') - packages = union_values(maintainers_to_packages(args.pkg_or_user)) + packages = union_values(maintainers_to_packages(args.package_or_user)) colify(packages) return 0 if packages else 1 else: - if not args.pkg_or_user: + if not args.package_or_user: tty.die('spack maintainers requires a package or --all') - users = union_values(packages_to_maintainers(args.pkg_or_user)) + users = union_values(packages_to_maintainers(args.package_or_user)) colify(users) return 0 if users else 1 diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py index 21723e4965..5206927895 100644 --- a/lib/spack/spack/cmd/mirror.py +++ b/lib/spack/spack/cmd/mirror.py @@ -1,11 +1,10 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) import sys -import argparse import llnl.util.tty as tty from llnl.util.tty.colify import colify @@ -40,9 +39,6 @@ def setup_parser(subparser): help="directory in which to create mirror") create_parser.add_argument( - 'specs', nargs=argparse.REMAINDER, - help="specs of packages to put in mirror") - create_parser.add_argument( '-a', '--all', action='store_true', help="mirror all versions of all packages in Spack, or all packages" " in the current environment if there is an active environment" @@ -57,6 +53,7 @@ def setup_parser(subparser): '-n', '--versions-per-spec', help="the number of versions to fetch for each spec, choose 'all' to" " retrieve all versions of each package") + arguments.add_common_arguments(create_parser, ['specs']) # used to construct scope arguments below scopes = spack.config.scopes() @@ -64,7 +61,8 @@ def setup_parser(subparser): # Add add_parser = sp.add_parser('add', help=mirror_add.__doc__) - add_parser.add_argument('name', help="mnemonic name for mirror") + add_parser.add_argument( + 'name', help="mnemonic name for mirror", metavar="mirror") add_parser.add_argument( 'url', help="url of mirror directory from 'spack mirror create'") add_parser.add_argument( @@ -75,7 +73,8 @@ def setup_parser(subparser): # Remove remove_parser = sp.add_parser('remove', aliases=['rm'], help=mirror_remove.__doc__) - remove_parser.add_argument('name') + remove_parser.add_argument( + 'name', help="mnemonic name for mirror", metavar="mirror") remove_parser.add_argument( '--scope', choices=scopes, metavar=scopes_metavar, default=spack.config.default_modify_scope(), @@ -83,7 +82,8 @@ def setup_parser(subparser): # Set-Url set_url_parser = sp.add_parser('set-url', help=mirror_set_url.__doc__) - set_url_parser.add_argument('name', help="mnemonic name for mirror") + set_url_parser.add_argument( + 'name', help="mnemonic name for mirror", metavar="mirror") set_url_parser.add_argument( 'url', help="url of mirror directory from 'spack mirror create'") set_url_parser.add_argument( diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 86a27786da..f86f3e5f25 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ import spack.cmd.modules.lmod import spack.cmd.modules.tcl description = "manipulate module files" -section = "modules" +section = "user environment" level = "short" diff --git a/lib/spack/spack/cmd/modules/__init__.py b/lib/spack/spack/cmd/modules/__init__.py index fbf93e9b2b..6555b8c8a7 100644 --- a/lib/spack/spack/cmd/modules/__init__.py +++ b/lib/spack/spack/cmd/modules/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/modules/lmod.py b/lib/spack/spack/cmd/modules/lmod.py index 2725ec4892..d3610bf333 100644 --- a/lib/spack/spack/cmd/modules/lmod.py +++ b/lib/spack/spack/cmd/modules/lmod.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/modules/tcl.py b/lib/spack/spack/cmd/modules/tcl.py index 441ea326e0..cdde21e821 100644 --- a/lib/spack/spack/cmd/modules/tcl.py +++ b/lib/spack/spack/cmd/modules/tcl.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/patch.py b/lib/spack/spack/cmd/patch.py index 258c9035df..8f91edb8f1 100644 --- a/lib/spack/spack/cmd/patch.py +++ b/lib/spack/spack/cmd/patch.py @@ -1,10 +1,8 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse - import llnl.util.tty as tty import spack.repo @@ -18,20 +16,17 @@ level = "long" def setup_parser(subparser): - arguments.add_common_arguments(subparser, ['no_checksum']) - subparser.add_argument( - 'packages', nargs=argparse.REMAINDER, - help="specs of packages to stage") + arguments.add_common_arguments(subparser, ['no_checksum', 'specs']) def patch(parser, args): - if not args.packages: - tty.die("patch requires at least one package argument") + if not args.specs: + tty.die("patch requires at least one spec argument") if args.no_checksum: spack.config.set('config:checksum', False, scope='command_line') - specs = spack.cmd.parse_specs(args.packages, concretize=True) + specs = spack.cmd.parse_specs(args.specs, concretize=True) for spec in specs: package = spack.repo.get(spec) package.do_patch() diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py index 534e7b9c69..b988d6a848 100644 --- a/lib/spack/spack/cmd/pkg.py +++ b/lib/spack/spack/cmd/pkg.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,6 @@ from __future__ import print_function import os -import argparse import re import llnl.util.tty as tty @@ -14,6 +13,7 @@ from llnl.util.tty.colify import colify from llnl.util.filesystem import working_dir import spack.cmd +import spack.cmd.common.arguments as arguments import spack.paths import spack.repo from spack.util.executable import which @@ -28,8 +28,7 @@ def setup_parser(subparser): metavar='SUBCOMMAND', dest='pkg_command') add_parser = sp.add_parser('add', help=pkg_add.__doc__) - add_parser.add_argument('packages', nargs=argparse.REMAINDER, - help="names of packages to add to git repo") + arguments.add_common_arguments(add_parser, ['packages']) list_parser = sp.add_parser('list', help=pkg_list.__doc__) list_parser.add_argument('rev', default='HEAD', nargs='?', diff --git a/lib/spack/spack/cmd/providers.py b/lib/spack/spack/cmd/providers.py index 74dc8f4c60..8ca34542eb 100644 --- a/lib/spack/spack/cmd/providers.py +++ b/lib/spack/spack/cmd/providers.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/pydoc.py b/lib/spack/spack/cmd/pydoc.py index 422129ab35..1f81718e38 100644 --- a/lib/spack/spack/cmd/pydoc.py +++ b/lib/spack/spack/cmd/pydoc.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/python.py b/lib/spack/spack/cmd/python.py index 9c0e683fe2..492c8f98e0 100644 --- a/lib/spack/spack/cmd/python.py +++ b/lib/spack/spack/cmd/python.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/reindex.py b/lib/spack/spack/cmd/reindex.py index a309798f7e..b9f3a2ac3b 100644 --- a/lib/spack/spack/cmd/reindex.py +++ b/lib/spack/spack/cmd/reindex.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/remove.py b/lib/spack/spack/cmd/remove.py index 1d07830f03..ef01052c29 100644 --- a/lib/spack/spack/cmd/remove.py +++ b/lib/spack/spack/cmd/remove.py @@ -1,13 +1,12 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse - import llnl.util.tty as tty import spack.cmd +import spack.cmd.common.arguments as arguments import spack.environment as ev @@ -26,17 +25,17 @@ def setup_parser(subparser): subparser.add_argument( '-f', '--force', action='store_true', help="remove concretized spec (if any) immediately") - subparser.add_argument( - 'specs', nargs=argparse.REMAINDER, help="specs to be removed") + arguments.add_common_arguments(subparser, ['specs']) def remove(parser, args): env = ev.get_env(args, 'remove', required=True) - if args.all: - env.clear() - else: - for spec in spack.cmd.parse_specs(args.specs): - tty.msg('Removing %s from environment %s' % (spec, env.name)) - env.remove(spec, args.list_name, force=args.force) - env.write() + with env.write_transaction(): + if args.all: + env.clear() + else: + for spec in spack.cmd.parse_specs(args.specs): + tty.msg('Removing %s from environment %s' % (spec, env.name)) + env.remove(spec, args.list_name, force=args.force) + env.write() diff --git a/lib/spack/spack/cmd/repo.py b/lib/spack/spack/cmd/repo.py index ea5a34fc0d..83acf796a2 100644 --- a/lib/spack/spack/cmd/repo.py +++ b/lib/spack/spack/cmd/repo.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -51,8 +51,8 @@ def setup_parser(subparser): remove_parser = sp.add_parser( 'remove', help=repo_remove.__doc__, aliases=['rm']) remove_parser.add_argument( - 'path_or_namespace', - help="path or namespace of a Spack package repository") + 'namespace_or_path', + help="namespace or path of a Spack package repository") remove_parser.add_argument( '--scope', choices=scopes, metavar=scopes_metavar, default=spack.config.default_modify_scope(), @@ -101,10 +101,10 @@ def repo_add(args): def repo_remove(args): """Remove a repository from Spack's configuration.""" repos = spack.config.get('repos', scope=args.scope) - path_or_namespace = args.path_or_namespace + namespace_or_path = args.namespace_or_path # If the argument is a path, remove that repository from config. - canon_path = canonicalize_path(path_or_namespace) + canon_path = canonicalize_path(namespace_or_path) for repo_path in repos: repo_canon_path = canonicalize_path(repo_path) if canon_path == repo_canon_path: @@ -117,7 +117,7 @@ def repo_remove(args): for path in repos: try: repo = Repo(path) - if repo.namespace == path_or_namespace: + if repo.namespace == namespace_or_path: repos.remove(path) spack.config.set('repos', repos, args.scope) tty.msg("Removed repository %s with namespace '%s'." @@ -127,7 +127,7 @@ def repo_remove(args): continue tty.die("No repository with path or namespace: %s" - % path_or_namespace) + % namespace_or_path) def repo_list(args): diff --git a/lib/spack/spack/cmd/resource.py b/lib/spack/spack/cmd/resource.py index 3e5080cd7a..0d26c39ab8 100644 --- a/lib/spack/spack/cmd/resource.py +++ b/lib/spack/spack/cmd/resource.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/restage.py b/lib/spack/spack/cmd/restage.py index 5d04890794..0f55884bfe 100644 --- a/lib/spack/spack/cmd/restage.py +++ b/lib/spack/spack/cmd/restage.py @@ -1,13 +1,12 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse - import llnl.util.tty as tty import spack.cmd +import spack.cmd.common.arguments as arguments import spack.repo description = "revert checked out package source code" @@ -16,15 +15,14 @@ level = "long" def setup_parser(subparser): - subparser.add_argument('packages', nargs=argparse.REMAINDER, - help="specs of packages to restage") + arguments.add_common_arguments(subparser, ['specs']) def restage(parser, args): - if not args.packages: + if not args.specs: tty.die("spack restage requires at least one package spec.") - specs = spack.cmd.parse_specs(args.packages, concretize=True) + specs = spack.cmd.parse_specs(args.specs, concretize=True) for spec in specs: package = spack.repo.get(spec) package.do_restage() diff --git a/lib/spack/spack/cmd/setup.py b/lib/spack/spack/cmd/setup.py index aa391b2b35..246e3b4275 100644 --- a/lib/spack/spack/cmd/setup.py +++ b/lib/spack/spack/cmd/setup.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,13 +30,10 @@ def setup_parser(subparser): subparser.add_argument( '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps', help="do not try to install dependencies of requested packages") - arguments.add_common_arguments(subparser, ['no_checksum']) + arguments.add_common_arguments(subparser, ['no_checksum', 'spec']) subparser.add_argument( '-v', '--verbose', action='store_true', dest='verbose', help="display verbose build output while installing") - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, - help="specs to use for install. must contain package AND version") cd_group = subparser.add_mutually_exclusive_group() arguments.add_common_arguments(cd_group, ['clean', 'dirty']) diff --git a/lib/spack/spack/cmd/spec.py b/lib/spack/spack/cmd/spec.py index f10eef9c73..fd03f09e57 100644 --- a/lib/spack/spack/cmd/spec.py +++ b/lib/spack/spack/cmd/spec.py @@ -1,11 +1,10 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from __future__ import print_function -import argparse import contextlib import sys @@ -24,6 +23,10 @@ level = "short" def setup_parser(subparser): + subparser.epilog = """\ +for further documentation regarding the spec syntax, see: + spack help --spec +""" arguments.add_common_arguments( subparser, ['long', 'very_long', 'install_status']) subparser.add_argument( @@ -43,8 +46,7 @@ def setup_parser(subparser): subparser.add_argument( '-t', '--types', action='store_true', default=False, help='show dependency types') - subparser.add_argument( - 'specs', nargs=argparse.REMAINDER, help="specs of packages") + arguments.add_common_arguments(subparser, ['specs']) @contextlib.contextmanager diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py index e4daf1778b..1acefb723c 100644 --- a/lib/spack/spack/cmd/stage.py +++ b/lib/spack/spack/cmd/stage.py @@ -1,10 +1,8 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse - import llnl.util.tty as tty import spack.environment as ev @@ -18,14 +16,11 @@ level = "long" def setup_parser(subparser): - arguments.add_common_arguments(subparser, ['no_checksum']) + arguments.add_common_arguments(subparser, ['no_checksum', 'specs']) subparser.add_argument( '-p', '--path', dest='path', help="path to stage package, does not add to spack tree") - subparser.add_argument( - 'specs', nargs=argparse.REMAINDER, help="specs of packages to stage") - def stage(parser, args): if not args.specs: diff --git a/lib/spack/spack/cmd/test.py b/lib/spack/spack/cmd/test.py index 63e3778a6b..f2ca8fc93b 100644 --- a/lib/spack/spack/cmd/test.py +++ b/lib/spack/spack/cmd/test.py @@ -1,23 +1,25 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from __future__ import print_function +from __future__ import division +import collections import sys -import os import re import argparse import pytest from six import StringIO +import llnl.util.tty.color as color from llnl.util.filesystem import working_dir from llnl.util.tty.colify import colify import spack.paths -description = "run spack's unit tests" +description = "run spack's unit tests (wrapper around pytest)" section = "developer" level = "long" @@ -25,61 +27,130 @@ level = "long" def setup_parser(subparser): subparser.add_argument( '-H', '--pytest-help', action='store_true', default=False, - help="print full pytest help message, showing advanced options") - - list_group = subparser.add_mutually_exclusive_group() - list_group.add_argument( - '-l', '--list', action='store_true', default=False, - help="list basic test names") - list_group.add_argument( - '-L', '--long-list', action='store_true', default=False, - help="list the entire hierarchy of tests") + help="show full pytest help, with advanced options") + + # extra spack arguments to list tests + list_group = subparser.add_argument_group("listing tests") + list_mutex = list_group.add_mutually_exclusive_group() + list_mutex.add_argument( + '-l', '--list', action='store_const', default=None, + dest='list', const='list', help="list test filenames") + list_mutex.add_argument( + '-L', '--list-long', action='store_const', default=None, + dest='list', const='long', help="list all test functions") + list_mutex.add_argument( + '-N', '--list-names', action='store_const', default=None, + dest='list', const='names', help="list full names of all tests") + + # use tests for extension subparser.add_argument( '--extension', default=None, - help="run test for a given Spack extension" - ) + help="run test for a given spack extension") + + # spell out some common pytest arguments, so they'll show up in help + pytest_group = subparser.add_argument_group( + "common pytest arguments (spack test --pytest-help for more details)") + pytest_group.add_argument( + "-s", action='append_const', dest='parsed_args', const='-s', + help="print output while tests run (disable capture)") + pytest_group.add_argument( + "-k", action='store', metavar="EXPRESSION", dest='expression', + help="filter tests by keyword (can also use w/list options)") + pytest_group.add_argument( + "--showlocals", action='append_const', dest='parsed_args', + const='--showlocals', help="show local variable values in tracebacks") + + # remainder is just passed to pytest subparser.add_argument( - 'tests', nargs=argparse.REMAINDER, - help="list of tests to run (will be passed to pytest -k)") + 'pytest_args', nargs=argparse.REMAINDER, help="arguments for pytest") -def do_list(args, unknown_args): +def do_list(args, extra_args): """Print a lists of tests than what pytest offers.""" # Run test collection and get the tree out. old_output = sys.stdout try: sys.stdout = output = StringIO() - pytest.main(['--collect-only']) + pytest.main(['--collect-only'] + extra_args) finally: sys.stdout = old_output - # put the output in a more readable tree format. lines = output.getvalue().split('\n') - output_lines = [] + tests = collections.defaultdict(lambda: set()) + prefix = [] + + # collect tests into sections for line in lines: match = re.match(r"(\s*)<([^ ]*) '([^']*)'", line) if not match: continue indent, nodetype, name = match.groups() - # only print top-level for short list - if args.list: - if not indent: - output_lines.append( - os.path.basename(name).replace('.py', '')) - else: - print(indent + name) + # strip parametrized tests + if "[" in name: + name = name[:name.index("[")] + + depth = len(indent) // 2 - if args.list: - colify(output_lines) + if nodetype.endswith("Function"): + key = tuple(prefix) + tests[key].add(name) + else: + prefix = prefix[:depth] + prefix.append(name) + + def colorize(c, prefix): + if isinstance(prefix, tuple): + return "::".join( + color.colorize("@%s{%s}" % (c, p)) + for p in prefix if p != "()" + ) + return color.colorize("@%s{%s}" % (c, prefix)) + + if args.list == "list": + files = set(prefix[0] for prefix in tests) + color_files = [colorize("B", file) for file in sorted(files)] + colify(color_files) + + elif args.list == "long": + for prefix, functions in sorted(tests.items()): + path = colorize("*B", prefix) + "::" + functions = [colorize("c", f) for f in sorted(functions)] + color.cprint(path) + colify(functions, indent=4) + print() + + else: # args.list == "names" + all_functions = [ + colorize("*B", prefix) + "::" + colorize("c", f) + for prefix, functions in sorted(tests.items()) + for f in sorted(functions) + ] + colify(all_functions) + + +def add_back_pytest_args(args, unknown_args): + """Add parsed pytest args, unknown args, and remainder together. + + We add some basic pytest arguments to the Spack parser to ensure that + they show up in the short help, so we have to reassemble things here. + """ + result = args.parsed_args or [] + result += unknown_args or [] + result += args.pytest_args or [] + if args.expression: + result += ["-k", args.expression] + return result def test(parser, args, unknown_args): if args.pytest_help: # make the pytest.main help output more accurate sys.argv[0] = 'spack test' - pytest.main(['-h']) - return + return pytest.main(['-h']) + + # add back any parsed pytest args we need to pass to pytest + pytest_args = add_back_pytest_args(args, unknown_args) # The default is to test the core of Spack. If the option `--extension` # has been used, then test that extension. @@ -91,15 +162,8 @@ def test(parser, args, unknown_args): # pytest.ini lives in the root of the spack repository. with working_dir(pytest_root): - # --list and --long-list print the test output better. - if args.list or args.long_list: - do_list(args, unknown_args) + if args.list: + do_list(args, pytest_args) return - # Allow keyword search without -k if no options are specified - if (args.tests and not unknown_args and - not any(arg.startswith('-') for arg in args.tests)): - return pytest.main(['-k'] + args.tests) - - # Just run the pytest command - return pytest.main(unknown_args + args.tests) + return pytest.main(pytest_args) diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py index 2d903fdd47..2757d5d232 100644 --- a/lib/spack/spack/cmd/uninstall.py +++ b/lib/spack/spack/cmd/uninstall.py @@ -1,11 +1,12 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from __future__ import print_function -import argparse +import sys +import itertools import spack.cmd import spack.environment as ev @@ -31,23 +32,19 @@ error_message = """You can either: # Arguments for display_specs when we find ambiguity display_args = { 'long': True, - 'show_flags': True, - 'variants': True, + 'show_flags': False, + 'variants': False, 'indent': 4, } -def add_common_arguments(subparser): +def setup_parser(subparser): subparser.add_argument( '-f', '--force', action='store_true', dest='force', help="remove regardless of whether other packages or environments " "depend on this one") arguments.add_common_arguments( - subparser, ['recurse_dependents', 'yes_to_all']) - - -def setup_parser(subparser): - add_common_arguments(subparser) + subparser, ['recurse_dependents', 'yes_to_all', 'installed_specs']) subparser.add_argument( '-a', '--all', action='store_true', dest='all', help="USE CAREFULLY. Remove ALL installed packages that match each " @@ -57,11 +54,6 @@ def setup_parser(subparser): "If used in an environment, all packages in the environment " "will be uninstalled.") - subparser.add_argument( - 'packages', - nargs=argparse.REMAINDER, - help="specs of packages to uninstall") - def find_matching_specs(env, specs, allow_multiple_matches=False, force=False): """Returns a list of specs matching the not necessarily @@ -214,9 +206,6 @@ def do_uninstall(env, specs, force): # want to uninstall. spack.package.Package.uninstall_by_spec(item, force=True) - if env: - _remove_from_env(item, env) - # A package is ready to be uninstalled when nothing else references it, # unless we are requested to force uninstall it. is_ready = lambda x: not spack.store.db.query_by_spec_hash(x)[1].ref_count @@ -235,10 +224,6 @@ def do_uninstall(env, specs, force): for item in ready: item.do_uninstall(force=force) - # write any changes made to the active environment - if env: - env.write() - def get_uninstall_list(args, specs, env): # Gets the list of installed specs that match the ones give via cli @@ -324,25 +309,40 @@ def uninstall_specs(args, specs): return if not args.yes_to_all: - tty.msg('The following packages will be uninstalled:\n') - spack.cmd.display_specs(anything_to_do, **display_args) - answer = tty.get_yes_or_no('Do you want to proceed?', default=False) - if not answer: - tty.die('Will not uninstall any packages.') + confirm_removal(anything_to_do) - # just force-remove things in the remove list - for spec in remove_list: - _remove_from_env(spec, env) + if env: + # Remove all the specs that are supposed to be uninstalled or just + # removed. + with env.write_transaction(): + for spec in itertools.chain(remove_list, uninstall_list): + _remove_from_env(spec, env) + env.write() # Uninstall everything on the list do_uninstall(env, uninstall_list, args.force) +def confirm_removal(specs): + """Display the list of specs to be removed and ask for confirmation. + + Args: + specs (list): specs to be removed + """ + tty.msg('The following packages will be uninstalled:\n') + spack.cmd.display_specs(specs, **display_args) + print('') + answer = tty.get_yes_or_no('Do you want to proceed?', default=False) + if not answer: + tty.msg('Aborting uninstallation') + sys.exit(0) + + def uninstall(parser, args): - if not args.packages and not args.all: + if not args.specs and not args.all: tty.die('uninstall requires at least one package argument.', ' Use `spack uninstall --all` to uninstall ALL packages.') # [any] here handles the --all case by forcing all specs to be returned - specs = spack.cmd.parse_specs(args.packages) if args.packages else [any] + specs = spack.cmd.parse_specs(args.specs) if args.specs else [any] uninstall_specs(args, specs) diff --git a/lib/spack/spack/cmd/unload.py b/lib/spack/spack/cmd/unload.py index b12fbfa454..d19a33102f 100644 --- a/lib/spack/spack/cmd/unload.py +++ b/lib/spack/spack/cmd/unload.py @@ -1,23 +1,73 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import argparse -from spack.cmd.common import print_module_placeholder_help +import sys +import os -description = "remove package from environment using `module unload`" -section = "modules" +import llnl.util.tty as tty + +import spack.cmd +import spack.cmd.common.arguments as arguments +import spack.util.environment +import spack.user_environment as uenv +import spack.error + +description = "remove package from the user environment" +section = "user environment" level = "short" def setup_parser(subparser): """Parser is only constructed so that this prints a nice help message with -h. """ - subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, - help='spec of package to unload with modules') + arguments.add_common_arguments(subparser, ['installed_specs']) + + shells = subparser.add_mutually_exclusive_group() + shells.add_argument( + '--sh', action='store_const', dest='shell', const='sh', + help="print sh commands to activate the environment") + shells.add_argument( + '--csh', action='store_const', dest='shell', const='csh', + help="print csh commands to activate the environment") + + subparser.add_argument('-a', '--all', action='store_true', + help='unload all loaded Spack packages.') def unload(parser, args): - print_module_placeholder_help() + """Unload spack packages from the user environment.""" + if args.specs and args.all: + raise spack.error.SpackError("Cannot specify specs on command line" + " when unloading all specs with '--all'") + + hashes = os.environ.get(uenv.spack_loaded_hashes_var, '').split(':') + if args.specs: + specs = [spack.cmd.disambiguate_spec_from_hashes(spec, hashes) + for spec in spack.cmd.parse_specs(args.specs)] + else: + specs = spack.store.db.query(hashes=hashes) + + if not args.shell: + msg = [ + "This command works best with Spack's shell support", + "" + ] + spack.cmd.common.shell_init_instructions + [ + 'Or, if you want to use `spack unload` without initializing', + 'shell support, you can run one of these:', + '', + ' eval `spack unload --sh %s` # for bash/sh' % args.specs, + ' eval `spack unload --csh %s` # for csh/tcsh' % args.specs, + ] + tty.msg(*msg) + return 1 + + env_mod = spack.util.environment.EnvironmentModifications() + for spec in specs: + env_mod.extend( + uenv.environment_modifications_for_spec(spec).reversed()) + env_mod.remove_path(uenv.spack_loaded_hashes_var, spec.dag_hash()) + cmds = env_mod.shell_modifications(args.shell) + + sys.stdout.write(cmds) diff --git a/lib/spack/spack/cmd/upload_s3.py b/lib/spack/spack/cmd/upload_s3.py index f3be69c10d..56d03758cf 100644 --- a/lib/spack/spack/cmd/upload_s3.py +++ b/lib/spack/spack/cmd/upload_s3.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/cmd/url.py b/lib/spack/spack/cmd/url.py index a24fcc575c..db8f358887 100644 --- a/lib/spack/spack/cmd/url.py +++ b/lib/spack/spack/cmd/url.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -135,7 +135,7 @@ def url_list(args): # Gather set of URLs from all packages for pkg in spack.repo.path.all_packages(): - url = getattr(pkg.__class__, 'url', None) + url = getattr(pkg, 'url', None) urls = url_list_parsing(args, urls, url, pkg) for params in pkg.versions.values(): @@ -174,7 +174,7 @@ def url_summary(args): for pkg in spack.repo.path.all_packages(): urls = set() - url = getattr(pkg.__class__, 'url', None) + url = getattr(pkg, 'url', None) if url: urls.add(url) @@ -434,23 +434,10 @@ def name_parsed_correctly(pkg, name): Returns: bool: True if the name was correctly parsed, else False """ - pkg_name = pkg.name + pkg_name = remove_prefix(pkg.name) name = simplify_name(name) - # After determining a name, `spack create` determines a build system. - # Some build systems prepend a special string to the front of the name. - # Since this can't be guessed from the URL, it would be unfair to say - # that these names are incorrectly parsed, so we remove them. - if pkg_name.startswith('r-'): - pkg_name = pkg_name[2:] - elif pkg_name.startswith('py-'): - pkg_name = pkg_name[3:] - elif pkg_name.startswith('perl-'): - pkg_name = pkg_name[5:] - elif pkg_name.startswith('octave-'): - pkg_name = pkg_name[7:] - return name == pkg_name @@ -475,8 +462,32 @@ def version_parsed_correctly(pkg, version): return False +def remove_prefix(pkg_name): + """Remove build system prefix ('py-', 'perl-', etc.) from a package name. + + After determining a name, `spack create` determines a build system. + Some build systems prepend a special string to the front of the name. + Since this can't be guessed from the URL, it would be unfair to say + that these names are incorrectly parsed, so we remove them. + + Args: + pkg_name (str): the name of the package + + Returns: + str: the name of the package with any build system prefix removed + """ + prefixes = [ + 'r-', 'py-', 'tcl-', 'lua-', 'perl-', 'ruby-', 'llvm-', + 'intel-', 'votca-', 'octave-', 'gtkorvo-' + ] + + prefix = next((p for p in prefixes if pkg_name.startswith(p)), '') + + return pkg_name[len(prefix):] + + def remove_separators(version): - """Removes separator characters ('.', '_', and '-') from a version. + """Remove separator characters ('.', '_', and '-') from a version. A version like 1.2.3 may be displayed as 1_2_3 in the URL. Make sure 1.2.3, 1-2-3, 1_2_3, and 123 are considered equal. diff --git a/lib/spack/spack/cmd/verify.py b/lib/spack/spack/cmd/verify.py index 4bd7b39fea..b20d795ce5 100644 --- a/lib/spack/spack/cmd/verify.py +++ b/lib/spack/spack/cmd/verify.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,8 +25,8 @@ def setup_parser(subparser): help="Ouptut json-formatted errors") subparser.add_argument('-a', '--all', action='store_true', help="Verify all packages") - subparser.add_argument('files_or_specs', nargs=argparse.REMAINDER, - help="Files or specs to verify") + subparser.add_argument('specs_or_files', nargs=argparse.REMAINDER, + help="Specs or files to verify") type = subparser.add_mutually_exclusive_group() type.add_argument( @@ -47,7 +47,7 @@ def verify(parser, args): setup_parser.parser.print_help() return 1 - for file in args.files_or_specs: + for file in args.specs_or_files: results = spack.verify.check_file_manifest(file) if results.has_errors(): if args.json: @@ -57,21 +57,21 @@ def verify(parser, args): return 0 else: - spec_args = spack.cmd.parse_specs(args.files_or_specs) + spec_args = spack.cmd.parse_specs(args.specs_or_files) if args.all: query = spack.store.db.query_local if local else spack.store.db.query # construct spec list if spec_args: - spec_list = spack.cmd.parse_specs(args.files_or_specs) + spec_list = spack.cmd.parse_specs(args.specs_or_files) specs = [] for spec in spec_list: specs += query(spec, installed=True) else: specs = query(installed=True) - elif args.files_or_specs: + elif args.specs_or_files: # construct disambiguated spec list env = ev.get_env(args, 'verify') specs = list(map(lambda x: spack.cmd.disambiguate_spec(x, env, diff --git a/lib/spack/spack/cmd/versions.py b/lib/spack/spack/cmd/versions.py index b264c1aaf0..723f89ce08 100644 --- a/lib/spack/spack/cmd/versions.py +++ b/lib/spack/spack/cmd/versions.py @@ -1,15 +1,17 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from __future__ import print_function +import sys + from llnl.util.tty.colify import colify import llnl.util.tty as tty +import spack.cmd.common.arguments as arguments import spack.repo -import sys description = "list available versions of a package" section = "packaging" @@ -17,10 +19,9 @@ level = "long" def setup_parser(subparser): - subparser.add_argument('package', metavar='PACKAGE', - help='package to list versions for') subparser.add_argument('-s', '--safe-only', action='store_true', help='only list safe versions of the package') + arguments.add_common_arguments(subparser, ['package']) def versions(parser, args): diff --git a/lib/spack/spack/cmd/view.py b/lib/spack/spack/cmd/view.py index 5480c28c6d..18c836736e 100644 --- a/lib/spack/spack/cmd/view.py +++ b/lib/spack/spack/cmd/view.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py index f2b62dc3f9..36a2704eac 100644 --- a/lib/spack/spack/compiler.py +++ b/lib/spack/spack/compiler.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -32,7 +32,7 @@ def _verify_executables(*paths): @llnl.util.lang.memoized -def get_compiler_version_output(compiler_path, version_arg): +def get_compiler_version_output(compiler_path, version_arg, ignore_errors=()): """Invokes the compiler at a given path passing a single version argument and returns the output. @@ -41,7 +41,8 @@ def get_compiler_version_output(compiler_path, version_arg): version_arg (str): the argument used to extract version information """ compiler = spack.util.executable.Executable(compiler_path) - output = compiler(version_arg, output=str, error=str) + output = compiler( + version_arg, output=str, error=str, ignore_errors=ignore_errors) return output @@ -199,6 +200,9 @@ class Compiler(object): #: Compiler argument that produces version information version_argument = '-dumpversion' + #: Return values to ignore when invoking the compiler to get its version + ignore_version_errors = () + #: Regex used to extract version from compiler's output version_regex = '(.*)' @@ -412,7 +416,8 @@ class Compiler(object): @classmethod def default_version(cls, cc): """Override just this to override all compiler version functions.""" - output = get_compiler_version_output(cc, cls.version_argument) + output = get_compiler_version_output( + cc, cls.version_argument, tuple(cls.ignore_version_errors)) return cls.extract_version_from_output(output) @classmethod diff --git a/lib/spack/spack/compilers/__init__.py b/lib/spack/spack/compilers/__init__.py index bc2e4df391..a092c930d7 100644 --- a/lib/spack/spack/compilers/__init__.py +++ b/lib/spack/spack/compilers/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/compilers/arm.py b/lib/spack/spack/compilers/arm.py index ff4c208531..ffce1e2b01 100644 --- a/lib/spack/spack/compilers/arm.py +++ b/lib/spack/spack/compilers/arm.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/compilers/cce.py b/lib/spack/spack/compilers/cce.py index 50b9694188..23a1771e9c 100644 --- a/lib/spack/spack/compilers/cce.py +++ b/lib/spack/spack/compilers/cce.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py index ea4ddaf401..c8df63e533 100644 --- a/lib/spack/spack/compilers/clang.py +++ b/lib/spack/spack/compilers/clang.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -208,7 +208,9 @@ class Clang(Compiler): r'^Apple (?:LLVM|clang) version ([^ )]+)|' # Normal clang compiler versions are left as-is r'clang version ([^ )]+)-svn[~.\w\d-]*|' - r'clang version ([^ )]+)-[~.\w\d-]*|' + # Don't include hyphenated patch numbers in the version + # (see https://github.com/spack/spack/pull/14365 for details) + r'clang version ([^ )]+?)-[~.\w\d-]*|' r'clang version ([^ )]+)', output ) diff --git a/lib/spack/spack/compilers/fj.py b/lib/spack/spack/compilers/fj.py index 1868972e96..083fe35b0d 100644 --- a/lib/spack/spack/compilers/fj.py +++ b/lib/spack/spack/compilers/fj.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -61,3 +61,7 @@ class Fj(spack.compiler.Compiler): @property def pic_flag(self): return "-KPIC" + + def setup_custom_environment(self, pkg, env): + env.append_flags('fcc_ENV', '-Nclang') + env.append_flags('FCC_ENV', '-Nclang') diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py index 3ac78ccccf..da559d554c 100644 --- a/lib/spack/spack/compilers/gcc.py +++ b/lib/spack/spack/compilers/gcc.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/compilers/intel.py b/lib/spack/spack/compilers/intel.py index f06f5b07cb..bc0e44b274 100644 --- a/lib/spack/spack/compilers/intel.py +++ b/lib/spack/spack/compilers/intel.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/compilers/nag.py b/lib/spack/spack/compilers/nag.py index bd0040c9a9..b7ef2297b8 100644 --- a/lib/spack/spack/compilers/nag.py +++ b/lib/spack/spack/compilers/nag.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/compilers/pgi.py b/lib/spack/spack/compilers/pgi.py index 90560f7c63..7da991754f 100644 --- a/lib/spack/spack/compilers/pgi.py +++ b/lib/spack/spack/compilers/pgi.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,6 +30,7 @@ class Pgi(Compiler): PrgEnv_compiler = 'pgi' version_argument = '-V' + ignore_version_errors = [2] # `pgcc -V` on PowerPC annoyingly returns 2 version_regex = r'pg[^ ]* ([0-9.]+)-[0-9]+ (LLVM )?[^ ]+ target on ' @classmethod diff --git a/lib/spack/spack/compilers/xl.py b/lib/spack/spack/compilers/xl.py index fcfaa29d12..36aa4dae7d 100644 --- a/lib/spack/spack/compilers/xl.py +++ b/lib/spack/spack/compilers/xl.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/compilers/xl_r.py b/lib/spack/spack/compilers/xl_r.py index 18c4e32564..c9a785d5d8 100644 --- a/lib/spack/spack/compilers/xl_r.py +++ b/lib/spack/spack/compilers/xl_r.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py index 417afed35b..8814d03d06 100644 --- a/lib/spack/spack/concretize.py +++ b/lib/spack/spack/concretize.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -74,7 +74,7 @@ class Concretizer(object): if spec.virtual: candidates = spack.repo.path.providers_for(spec) if not candidates: - raise spack.spec.UnsatisfiableProviderSpecError( + raise spack.error.UnsatisfiableProviderSpecError( candidates[0], spec) # Find nearest spec in the DAG (up then down) that has prefs. diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py index 3f536f3793..b1c0ad73c7 100644 --- a/lib/spack/spack/config.py +++ b/lib/spack/spack/config.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/container/__init__.py b/lib/spack/spack/container/__init__.py new file mode 100644 index 0000000000..fc3750355a --- /dev/null +++ b/lib/spack/spack/container/__init__.py @@ -0,0 +1,81 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +"""Package that provides functions and classes to +generate container recipes from a Spack environment +""" +import warnings + +import spack.environment +import spack.schema.env as env +import spack.util.spack_yaml as syaml +from .writers import recipe + +__all__ = ['validate', 'recipe'] + + +def validate(configuration_file): + """Validate a Spack environment YAML file that is being used to generate a + recipe for a container. + + Since a few attributes of the configuration must have specific values for + the container recipe, this function returns a sanitized copy of the + configuration in the input file. If any modification is needed, a warning + will be issued. + + Args: + configuration_file (str): path to the Spack environment YAML file + + Returns: + A sanitized copy of the configuration stored in the input file + """ + import jsonschema + with open(configuration_file) as f: + config = syaml.load(f) + + # Ensure we have a "container" attribute with sensible defaults set + env_dict = spack.environment.config_dict(config) + env_dict.setdefault('container', { + 'format': 'docker', + 'base': {'image': 'ubuntu:18.04', 'spack': 'develop'} + }) + env_dict['container'].setdefault('format', 'docker') + env_dict['container'].setdefault( + 'base', {'image': 'ubuntu:18.04', 'spack': 'develop'} + ) + + # Remove attributes that are not needed / allowed in the + # container recipe + for subsection in ('cdash', 'gitlab_ci', 'modules'): + if subsection in env_dict: + msg = ('the subsection "{0}" in "{1}" is not used when generating' + ' container recipes and will be discarded') + warnings.warn(msg.format(subsection, configuration_file)) + env_dict.pop(subsection) + + # Set the default value of the concretization strategy to "together" and + # warn if the user explicitly set another value + env_dict.setdefault('concretization', 'together') + if env_dict['concretization'] != 'together': + msg = ('the "concretization" attribute of the environment is set ' + 'to "{0}" [the advised value is instead "together"]') + warnings.warn(msg.format(env_dict['concretization'])) + + # Check if the install tree was explicitly set to a custom value and warn + # that it will be overridden + environment_config = env_dict.get('config', {}) + if environment_config.get('install_tree', None): + msg = ('the "config:install_tree" attribute has been set explicitly ' + 'and will be overridden in the container image') + warnings.warn(msg) + + # Likewise for the view + environment_view = env_dict.get('view', None) + if environment_view: + msg = ('the "view" attribute has been set explicitly ' + 'and will be overridden in the container image') + warnings.warn(msg) + + jsonschema.validate(config, schema=env.schema) + return config diff --git a/lib/spack/spack/container/images.json b/lib/spack/spack/container/images.json new file mode 100644 index 0000000000..ecd911815d --- /dev/null +++ b/lib/spack/spack/container/images.json @@ -0,0 +1,50 @@ +{ + "ubuntu:18.04": { + "update": "apt-get -yqq update && apt-get -yqq upgrade", + "install": "apt-get -yqq install", + "clean": "rm -rf /var/lib/apt/lists/*", + "environment": [], + "build": "spack/ubuntu-bionic", + "build_tags": { + "develop": "latest", + "0.14": "0.14", + "0.14.0": "0.14.0" + } + }, + "ubuntu:16.04": { + "update": "apt-get -yqq update && apt-get -yqq upgrade", + "install": "apt-get -yqq install", + "clean": "rm -rf /var/lib/apt/lists/*", + "environment": [], + "build": "spack/ubuntu-xenial", + "build_tags": { + "develop": "latest", + "0.14": "0.14", + "0.14.0": "0.14.0" + } + }, + "centos:7": { + "update": "yum update -y && yum install -y epel-release && yum update -y", + "install": "yum install -y", + "clean": "rm -rf /var/cache/yum && yum clean all", + "environment": [], + "build": "spack/centos7", + "build_tags": { + "develop": "latest", + "0.14": "0.14", + "0.14.0": "0.14.0" + } + }, + "centos:6": { + "update": "yum update -y && yum install -y epel-release && yum update -y", + "install": "yum install -y", + "clean": "rm -rf /var/cache/yum && yum clean all", + "environment": [], + "build": "spack/centos6", + "build_tags": { + "develop": "latest", + "0.14": "0.14", + "0.14.0": "0.14.0" + } + } +}
\ No newline at end of file diff --git a/lib/spack/spack/container/images.py b/lib/spack/spack/container/images.py new file mode 100644 index 0000000000..421fc24425 --- /dev/null +++ b/lib/spack/spack/container/images.py @@ -0,0 +1,72 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +"""Manages the details on the images used in the build and the run stage.""" +import json +import os.path + +#: Global variable used to cache in memory the content of images.json +_data = None + + +def data(): + """Returns a dictionary with the static data on the images. + + The dictionary is read from a JSON file lazily the first time + this function is called. + """ + global _data + if not _data: + json_dir = os.path.abspath(os.path.dirname(__file__)) + json_file = os.path.join(json_dir, 'images.json') + with open(json_file) as f: + _data = json.load(f) + return _data + + +def build_info(image, spack_version): + """Returns the name of the build image and its tag. + + Args: + image (str): image to be used at run-time. Should be of the form + <image_name>:<image_tag> e.g. "ubuntu:18.04" + spack_version (str): version of Spack that we want to use to build + + Returns: + A tuple with (image_name, image_tag) for the build image + """ + # Don't handle error here, as a wrong image should have been + # caught by the JSON schema + image_data = data()[image] + build_image = image_data['build'] + + # Try to check if we have a tag for this Spack version + try: + build_tag = image_data['build_tags'][spack_version] + except KeyError: + msg = ('the image "{0}" has no tag for Spack version "{1}" ' + '[valid versions are {2}]') + msg = msg.format(build_image, spack_version, + ', '.join(image_data['build_tags'].keys())) + raise ValueError(msg) + + return build_image, build_tag + + +def package_info(image): + """Returns the commands used to update system repositories, install + system packages and clean afterwards. + + Args: + image (str): image to be used at run-time. Should be of the form + <image_name>:<image_tag> e.g. "ubuntu:18.04" + + Returns: + A tuple of (update, install, clean) commands. + """ + image_data = data()[image] + update = image_data['update'] + install = image_data['install'] + clean = image_data['clean'] + return update, install, clean diff --git a/lib/spack/spack/container/writers/__init__.py b/lib/spack/spack/container/writers/__init__.py new file mode 100644 index 0000000000..a1d2fa3102 --- /dev/null +++ b/lib/spack/spack/container/writers/__init__.py @@ -0,0 +1,154 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +"""Writers for different kind of recipes and related +convenience functions. +""" +import collections +import copy + +import spack.environment +import spack.schema.env +import spack.tengine as tengine +import spack.util.spack_yaml as syaml + +from spack.container.images import build_info, package_info + +#: Caches all the writers that are currently supported +_writer_factory = {} + + +def writer(name): + """Decorator to register a factory for a recipe writer. + + Each factory should take a configuration dictionary and return a + properly configured writer that, when called, prints the + corresponding recipe. + """ + def _decorator(factory): + _writer_factory[name] = factory + return factory + return _decorator + + +def create(configuration): + """Returns a writer that conforms to the configuration passed as input. + + Args: + configuration: how to generate the current recipe + """ + name = spack.environment.config_dict(configuration)['container']['format'] + return _writer_factory[name](configuration) + + +def recipe(configuration): + """Returns a recipe that conforms to the configuration passed as input. + + Args: + configuration: how to generate the current recipe + """ + return create(configuration)() + + +class PathContext(tengine.Context): + """Generic context used to instantiate templates of recipes that + install software in a common location and make it available + directly via PATH. + """ + def __init__(self, config): + self.config = spack.environment.config_dict(config) + self.container_config = self.config['container'] + + @tengine.context_property + def run(self): + """Information related to the run image.""" + image = self.container_config['base']['image'] + Run = collections.namedtuple('Run', ['image']) + return Run(image=image) + + @tengine.context_property + def build(self): + """Information related to the build image.""" + + # Map the final image to the correct build image + run_image = self.container_config['base']['image'] + spack_version = self.container_config['base']['spack'] + image, tag = build_info(run_image, spack_version) + + Build = collections.namedtuple('Build', ['image', 'tag']) + return Build(image=image, tag=tag) + + @tengine.context_property + def strip(self): + """Whether or not to strip binaries in the image""" + return self.container_config.get('strip', True) + + @tengine.context_property + def paths(self): + """Important paths in the image""" + Paths = collections.namedtuple('Paths', [ + 'environment', 'store', 'view' + ]) + return Paths( + environment='/opt/spack-environment', + store='/opt/software', + view='/opt/view' + ) + + @tengine.context_property + def manifest(self): + """The spack.yaml file that should be used in the image""" + import jsonschema + # Copy in the part of spack.yaml prescribed in the configuration file + manifest = copy.deepcopy(self.config) + manifest.pop('container') + + # Ensure that a few paths are where they need to be + manifest.setdefault('config', syaml.syaml_dict()) + manifest['config']['install_tree'] = self.paths.store + manifest['view'] = self.paths.view + manifest = {'spack': manifest} + + # Validate the manifest file + jsonschema.validate(manifest, schema=spack.schema.env.schema) + + return syaml.dump(manifest, default_flow_style=False).strip() + + @tengine.context_property + def os_packages(self): + """Additional system packages that are needed at run-time.""" + package_list = self.container_config.get('os_packages', None) + if not package_list: + return package_list + + image = self.container_config['base']['image'] + update, install, clean = package_info(image) + Packages = collections.namedtuple( + 'Packages', ['update', 'install', 'list', 'clean'] + ) + return Packages(update=update, install=install, + list=package_list, clean=clean) + + @tengine.context_property + def extra_instructions(self): + Extras = collections.namedtuple('Extra', ['build', 'final']) + extras = self.container_config.get('extra_instructions', {}) + build, final = extras.get('build', None), extras.get('final', None) + return Extras(build=build, final=final) + + @tengine.context_property + def labels(self): + return self.container_config.get('labels', {}) + + def __call__(self): + """Returns the recipe as a string""" + env = tengine.make_environment() + t = env.get_template(self.template_name) + return t.render(**self.to_dict()) + + +# Import after function definition all the modules in this package, +# so that registration of writers will happen automatically +import spack.container.writers.singularity # noqa +import spack.container.writers.docker # noqa diff --git a/lib/spack/spack/container/writers/docker.py b/lib/spack/spack/container/writers/docker.py new file mode 100644 index 0000000000..557d22c803 --- /dev/null +++ b/lib/spack/spack/container/writers/docker.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import spack.tengine as tengine + +from . import writer, PathContext + + +@writer('docker') +class DockerContext(PathContext): + """Context used to instantiate a Dockerfile""" + #: Name of the template used for Dockerfiles + template_name = 'container/Dockerfile' + + @tengine.context_property + def manifest(self): + manifest_str = super(DockerContext, self).manifest + # Docker doesn't support HEREDOC so we need to resort to + # a horrible echo trick to have the manifest in the Dockerfile + echoed_lines = [] + for idx, line in enumerate(manifest_str.split('\n')): + if idx == 0: + echoed_lines.append('&& (echo "' + line + '" \\') + continue + echoed_lines.append('&& echo "' + line + '" \\') + + echoed_lines[-1] = echoed_lines[-1].replace(' \\', ')') + + return '\n'.join(echoed_lines) diff --git a/lib/spack/spack/container/writers/singularity.py b/lib/spack/spack/container/writers/singularity.py new file mode 100644 index 0000000000..32f29eb83d --- /dev/null +++ b/lib/spack/spack/container/writers/singularity.py @@ -0,0 +1,33 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import spack.tengine as tengine +from . import writer, PathContext + + +@writer('singularity') +class SingularityContext(PathContext): + """Context used to instantiate a Singularity definition file""" + #: Name of the template used for Singularity definition files + template_name = 'container/singularity.def' + + @property + def singularity_config(self): + return self.container_config.get('singularity', {}) + + @tengine.context_property + def runscript(self): + return self.singularity_config.get('runscript', '') + + @tengine.context_property + def startscript(self): + return self.singularity_config.get('startscript', '') + + @tengine.context_property + def test(self): + return self.singularity_config.get('test', '') + + @tengine.context_property + def help(self): + return self.singularity_config.get('help', '') diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index 243f1a20d5..c06d1ae546 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -1118,7 +1118,27 @@ class Database(object): continue # TODO: conditional way to do this instead of catching exceptions - def get_by_hash_local(self, dag_hash, default=None, installed=any): + def _get_by_hash_local(self, dag_hash, default=None, installed=any): + # hash is a full hash and is in the data somewhere + if dag_hash in self._data: + rec = self._data[dag_hash] + if rec.install_type_matches(installed): + return [rec.spec] + else: + return default + + # check if hash is a prefix of some installed (or previously + # installed) spec. + matches = [record.spec for h, record in self._data.items() + if h.startswith(dag_hash) and + record.install_type_matches(installed)] + if matches: + return matches + + # nothing found + return default + + def get_by_hash_local(self, *args, **kwargs): """Look up a spec in *this DB* by DAG hash, or by a DAG hash prefix. Arguments: @@ -1142,24 +1162,7 @@ class Database(object): """ with self.read_transaction(): - # hash is a full hash and is in the data somewhere - if dag_hash in self._data: - rec = self._data[dag_hash] - if rec.install_type_matches(installed): - return [rec.spec] - else: - return default - - # check if hash is a prefix of some installed (or previously - # installed) spec. - matches = [record.spec for h, record in self._data.items() - if h.startswith(dag_hash) and - record.install_type_matches(installed)] - if matches: - return matches - - # nothing found - return default + return self._get_by_hash_local(*args, **kwargs) def get_by_hash(self, dag_hash, default=None, installed=any): """Look up a spec by DAG hash, or by a DAG hash prefix. @@ -1184,9 +1187,14 @@ class Database(object): (list): a list of specs matching the hash or hash prefix """ - search_path = [self] + self.upstream_dbs - for db in search_path: - spec = db.get_by_hash_local( + + spec = self.get_by_hash_local( + dag_hash, default=default, installed=installed) + if spec is not None: + return spec + + for upstream_db in self.upstream_dbs: + spec = upstream_db._get_by_hash_local( dag_hash, default=default, installed=installed) if spec is not None: return spec @@ -1295,6 +1303,30 @@ class Database(object): upstream, record = self.query_by_spec_hash(key) return record and not record.installed + @property + def unused_specs(self): + """Return all the specs that are currently installed but not needed + at runtime to satisfy user's requests. + + Specs in the return list are those which are not either: + 1. Installed on an explicit user request + 2. Installed as a "run" or "link" dependency (even transitive) of + a spec at point 1. + """ + needed, visited = set(), set() + with self.read_transaction(): + for key, rec in self._data.items(): + if rec.explicit: + # recycle `visited` across calls to avoid + # redundantly traversing + for spec in rec.spec.traverse(visited=visited): + needed.add(spec.dag_hash()) + + unused = [rec.spec for key, rec in self._data.items() + if key not in needed and rec.installed] + + return unused + class UpstreamDatabaseLockingError(SpackError): """Raised when an operation would need to lock an upstream database""" diff --git a/lib/spack/spack/dependency.py b/lib/spack/spack/dependency.py index 3e427196b5..e6b6c9cedc 100644 --- a/lib/spack/spack/dependency.py +++ b/lib/spack/spack/dependency.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/directives.py b/lib/spack/spack/directives.py index d877d4a193..f6496bb62a 100644 --- a/lib/spack/spack/directives.py +++ b/lib/spack/spack/directives.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index f8a42bf42b..a2e871ee1a 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index bf9af075ce..fff1485e3c 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -29,15 +29,14 @@ import spack.store import spack.util.spack_json as sjson import spack.util.spack_yaml as syaml import spack.config -import spack.build_environment as build_env - -from spack.util.prefix import Prefix +import spack.user_environment as uenv from spack.filesystem_view import YamlFilesystemView import spack.util.environment import spack.architecture as architecture from spack.spec import Spec from spack.spec_list import SpecList, InvalidSpecConstraintError from spack.variant import UnknownVariantError +import spack.util.lock as lk #: environment variable used to indicate the active environment spack_env_var = 'SPACK_ENV' @@ -559,12 +558,18 @@ class Environment(object): path to the view. """ self.path = os.path.abspath(path) + + self.txlock = lk.Lock(self._transaction_lock_path) + # This attribute will be set properly from configuration # during concretization self.concretization = None self.clear() if init_file: + # If we are creating the environment from an init file, we don't + # need to lock, because there are no Spack operations that alter + # the init file. with fs.open_if_filename(init_file) as f: if hasattr(f, 'name') and f.name.endswith('.lock'): self._read_manifest(default_manifest_yaml) @@ -573,26 +578,8 @@ class Environment(object): else: self._read_manifest(f, raw_yaml=default_manifest_yaml) else: - default_manifest = not os.path.exists(self.manifest_path) - if default_manifest: - # No manifest, use default yaml - self._read_manifest(default_manifest_yaml) - else: - with open(self.manifest_path) as f: - self._read_manifest(f) - - if os.path.exists(self.lock_path): - with open(self.lock_path) as f: - read_lock_version = self._read_lockfile(f) - if default_manifest: - # No manifest, set user specs from lockfile - self._set_user_specs_from_lockfile() - - if read_lock_version == 1: - tty.debug( - "Storing backup of old lockfile {0} at {1}".format( - self.lock_path, self._lock_backup_v1_path)) - shutil.copy(self.lock_path, self._lock_backup_v1_path) + with lk.ReadTransaction(self.txlock): + self._read() if with_view is False: self.views = {} @@ -604,6 +591,42 @@ class Environment(object): # If with_view is None, then defer to the view settings determined by # the manifest file + def _re_read(self): + """Reinitialize the environment object if it has been written (this + may not be true if the environment was just created in this running + instance of Spack).""" + if not os.path.exists(self.manifest_path): + return + + self.clear() + self._read() + + def _read(self): + default_manifest = not os.path.exists(self.manifest_path) + if default_manifest: + # No manifest, use default yaml + self._read_manifest(default_manifest_yaml) + else: + with open(self.manifest_path) as f: + self._read_manifest(f) + + if os.path.exists(self.lock_path): + with open(self.lock_path) as f: + read_lock_version = self._read_lockfile(f) + if default_manifest: + # No manifest, set user specs from lockfile + self._set_user_specs_from_lockfile() + + if read_lock_version == 1: + tty.debug( + "Storing backup of old lockfile {0} at {1}".format( + self.lock_path, self._lock_backup_v1_path)) + shutil.copy(self.lock_path, self._lock_backup_v1_path) + + def write_transaction(self): + """Get a write lock context manager for use in a `with` block.""" + return lk.WriteTransaction(self.txlock, acquire=self._re_read) + def _read_manifest(self, f, raw_yaml=None): """Read manifest file and set up user specs.""" if raw_yaml: @@ -697,6 +720,13 @@ class Environment(object): return os.path.join(self.path, manifest_name) @property + def _transaction_lock_path(self): + """The location of the lock file used to synchronize multiple + processes updating the same environment. + """ + return os.path.join(self.env_subdir_path, 'transaction_lock') + + @property def lock_path(self): """Path to spack.lock file in this environment.""" return os.path.join(self.path, lockfile_name) @@ -825,7 +855,10 @@ class Environment(object): raise SpackEnvironmentError( 'cannot add anonymous specs to an environment!') elif not spack.repo.path.exists(spec.name): - raise SpackEnvironmentError('no such package: %s' % spec.name) + virtuals = spack.repo.path.provider_index.providers.keys() + if spec.name not in virtuals: + msg = 'no such package: %s' % spec.name + raise SpackEnvironmentError(msg) list_to_change = self.spec_lists[list_name] existing = str(spec) in list_to_change.yaml_list @@ -985,11 +1018,18 @@ class Environment(object): concretized_specs.append((uspec, concrete)) return concretized_specs - def install(self, user_spec, concrete_spec=None, **install_args): - """Install a single spec into an environment. + def concretize_and_add(self, user_spec, concrete_spec=None): + """Concretize and add a single spec to the environment. - This will automatically concretize the single spec, but it won't - affect other as-yet unconcretized specs. + Concretize the provided ``user_spec`` and add it along with the + concretized result to the environment. If the given ``user_spec`` was + already present in the environment, this does not add a duplicate. + The concretized spec will be added unless the ``user_spec`` was + already present and an associated concrete spec was already present. + + Args: + concrete_spec: if provided, then it is assumed that it is the + result of concretizing the provided ``user_spec`` """ if self.concretization == 'together': msg = 'cannot install a single spec in an environment that is ' \ @@ -1000,37 +1040,21 @@ class Environment(object): spec = Spec(user_spec) - with spack.store.db.read_transaction(): - if self.add(spec): - concrete = concrete_spec or spec.concretized() + if self.add(spec): + concrete = concrete_spec or spec.concretized() + self._add_concrete_spec(spec, concrete) + else: + # spec might be in the user_specs, but not installed. + # TODO: Redo name-based comparison for old style envs + spec = next( + s for s in self.user_specs if s.satisfies(user_spec) + ) + concrete = self.specs_by_hash.get(spec.build_hash()) + if not concrete: + concrete = spec.concretized() self._add_concrete_spec(spec, concrete) - else: - # spec might be in the user_specs, but not installed. - # TODO: Redo name-based comparison for old style envs - spec = next( - s for s in self.user_specs if s.satisfies(user_spec) - ) - concrete = self.specs_by_hash.get(spec.build_hash()) - if not concrete: - concrete = spec.concretized() - self._add_concrete_spec(spec, concrete) - - self._install(concrete, **install_args) - def _install(self, spec, **install_args): - spec.package.do_install(**install_args) - - # Make sure log directory exists - log_path = self.log_path - fs.mkdirp(log_path) - - with fs.working_dir(self.path): - # Link the resulting log file into logs dir - build_log_link = os.path.join( - log_path, '%s-%s.log' % (spec.name, spec.dag_hash(7))) - if os.path.lexists(build_log_link): - os.remove(build_log_link) - os.symlink(spec.package.build_log_path, build_log_link) + return concrete @property def default_view(self): @@ -1067,62 +1091,6 @@ class Environment(object): for view in self.views.values(): view.regenerate(specs, self.roots()) - prefix_inspections = { - 'bin': ['PATH'], - 'lib': ['LD_LIBRARY_PATH', 'LIBRARY_PATH', 'DYLD_LIBRARY_PATH'], - 'lib64': ['LD_LIBRARY_PATH', 'LIBRARY_PATH', 'DYLD_LIBRARY_PATH'], - 'man': ['MANPATH'], - 'share/man': ['MANPATH'], - 'share/aclocal': ['ACLOCAL_PATH'], - 'include': ['CPATH'], - 'lib/pkgconfig': ['PKG_CONFIG_PATH'], - 'lib64/pkgconfig': ['PKG_CONFIG_PATH'], - '': ['CMAKE_PREFIX_PATH'] - } - - def unconditional_environment_modifications(self, view): - """List of environment (shell) modifications to be processed for view. - - This list does not depend on the specs in this environment""" - env = spack.util.environment.EnvironmentModifications() - - for subdir, vars in self.prefix_inspections.items(): - full_subdir = os.path.join(view.root, subdir) - for var in vars: - env.prepend_path(var, full_subdir) - - return env - - def environment_modifications_for_spec(self, spec, view=None): - """List of environment (shell) modifications to be processed for spec. - - This list is specific to the location of the spec or its projection in - the view.""" - spec = spec.copy() - if view: - spec.prefix = Prefix(view.view().get_projection_for_spec(spec)) - - # generic environment modifications determined by inspecting the spec - # prefix - env = spack.util.environment.inspect_path( - spec.prefix, - self.prefix_inspections, - exclude=spack.util.environment.is_system_path - ) - - # Let the extendee/dependency modify their extensions/dependents - # before asking for package-specific modifications - env.extend( - build_env.modifications_from_dependencies( - spec, context='run' - ) - ) - # Package specific modifications - build_env.set_module_variables_for_package(spec.package) - spec.package.setup_run_environment(env) - - return env - def add_default_view_to_shell(self, shell): env_mod = spack.util.environment.EnvironmentModifications() @@ -1130,12 +1098,12 @@ class Environment(object): # No default view to add to shell return env_mod.shell_modifications(shell) - env_mod.extend(self.unconditional_environment_modifications( + env_mod.extend(uenv.unconditional_environment_modifications( self.default_view)) for _, spec in self.concretized_specs(): if spec in self.default_view and spec.package.installed: - env_mod.extend(self.environment_modifications_for_spec( + env_mod.extend(uenv.environment_modifications_for_spec( spec, self.default_view)) # deduplicate paths from specs mapped to the same location @@ -1151,13 +1119,13 @@ class Environment(object): # No default view to add to shell return env_mod.shell_modifications(shell) - env_mod.extend(self.unconditional_environment_modifications( + env_mod.extend(uenv.unconditional_environment_modifications( self.default_view).reversed()) for _, spec in self.concretized_specs(): if spec in self.default_view and spec.package.installed: env_mod.extend( - self.environment_modifications_for_spec( + uenv.environment_modifications_for_spec( spec, self.default_view).reversed()) return env_mod.shell_modifications(shell) @@ -1186,6 +1154,33 @@ class Environment(object): self.concretized_order.append(h) self.specs_by_hash[h] = concrete + def install(self, user_spec, concrete_spec=None, **install_args): + """Install a single spec into an environment. + + This will automatically concretize the single spec, but it won't + affect other as-yet unconcretized specs. + """ + concrete = self.concretize_and_add(user_spec, concrete_spec) + + self._install(concrete, **install_args) + + def _install(self, spec, **install_args): + # "spec" must be concrete + spec.package.do_install(**install_args) + + if not spec.external: + # Make sure log directory exists + log_path = self.log_path + fs.mkdirp(log_path) + + with fs.working_dir(self.path): + # Link the resulting log file into logs dir + build_log_link = os.path.join( + log_path, '%s-%s.log' % (spec.name, spec.dag_hash(7))) + if os.path.lexists(build_log_link): + os.remove(build_log_link) + os.symlink(spec.package.build_log_path, build_log_link) + def install_all(self, args=None): """Install all concretized specs in an environment. @@ -1193,25 +1188,27 @@ class Environment(object): that needs to be done separately with a call to write(). """ + + # If "spack install" is invoked repeatedly for a large environment + # where all specs are already installed, the operation can take + # a large amount of time due to repeatedly acquiring and releasing + # locks, this does an initial check across all specs within a single + # DB read transaction to reduce time spent in this case. + uninstalled_specs = [] with spack.store.db.read_transaction(): for concretized_hash in self.concretized_order: spec = self.specs_by_hash[concretized_hash] + if not spec.package.installed: + uninstalled_specs.append(spec) - # Parse cli arguments and construct a dictionary - # that will be passed to Package.do_install API - kwargs = dict() - if args: - spack.cmd.install.update_kwargs_from_args(args, kwargs) - - self._install(spec, **kwargs) + for spec in uninstalled_specs: + # Parse cli arguments and construct a dictionary + # that will be passed to Package.do_install API + kwargs = dict() + if args: + spack.cmd.install.update_kwargs_from_args(args, kwargs) - if not spec.external: - # Link the resulting log file into logs dir - log_name = '%s-%s' % (spec.name, spec.dag_hash(7)) - build_log_link = os.path.join(self.log_path, log_name) - if os.path.lexists(build_log_link): - os.remove(build_log_link) - os.symlink(spec.package.build_log_path, build_log_link) + self._install(spec, **kwargs) def all_specs_by_hash(self): """Map of hashes to spec for all specs in this environment.""" @@ -1479,13 +1476,13 @@ class Environment(object): # Remove yaml sections that are shadowing defaults # construct garbage path to ensure we don't find a manifest by accident - bare_env = Environment(os.path.join(self.manifest_path, 'garbage'), - with_view=self.view_path_default) - keys_present = list(yaml_dict.keys()) - for key in keys_present: - if yaml_dict[key] == config_dict(bare_env.yaml).get(key, None): - if key not in raw_yaml_dict: - del yaml_dict[key] + with fs.temp_cwd() as env_dir: + bare_env = Environment(env_dir, with_view=self.view_path_default) + keys_present = list(yaml_dict.keys()) + for key in keys_present: + if yaml_dict[key] == config_dict(bare_env.yaml).get(key, None): + if key not in raw_yaml_dict: + del yaml_dict[key] # if all that worked, write out the manifest file at the top level # Only actually write if it has changed or was never written diff --git a/lib/spack/spack/error.py b/lib/spack/spack/error.py index 81968ac569..f79744f6a5 100644 --- a/lib/spack/spack/error.py +++ b/lib/spack/spack/error.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/extensions.py b/lib/spack/spack/extensions.py index 995464ea73..b8fde7d7fa 100644 --- a/lib/spack/spack/extensions.py +++ b/lib/spack/spack/extensions.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index 5a57703d27..5ae01286c4 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,33 +22,30 @@ in order to build it. They need to define the following methods: * archive() Archive a source directory, e.g. for creating a mirror. """ +import copy +import functools import os import os.path -import sys import re import shutil -import copy +import sys import xml.etree.ElementTree -from functools import wraps -from six import string_types, with_metaclass -import six.moves.urllib.parse as urllib_parse import llnl.util.tty as tty -from llnl.util.filesystem import ( - working_dir, mkdirp, temp_rename, temp_cwd, get_single_file) - +import six +import six.moves.urllib.parse as urllib_parse import spack.config import spack.error import spack.util.crypto as crypto import spack.util.pattern as pattern -import spack.util.web as web_util import spack.util.url as url_util - +import spack.util.web as web_util +from llnl.util.filesystem import ( + working_dir, mkdirp, temp_rename, temp_cwd, get_single_file) +from spack.util.compression import decompressor_for, extension from spack.util.executable import which from spack.util.string import comma_and, quote from spack.version import Version, ver -from spack.util.compression import decompressor_for, extension - #: List of all fetch strategies, created by FetchStrategy metaclass. all_strategies = [] @@ -69,7 +66,7 @@ def _needs_stage(fun): """Many methods on fetch strategies require a stage to be set using set_stage(). This decorator adds a check for self.stage.""" - @wraps(fun) + @functools.wraps(fun) def wrapper(self, *args, **kwargs): if not self.stage: raise NoStageError(fun) @@ -85,18 +82,14 @@ def _ensure_one_stage_entry(stage_path): return os.path.join(stage_path, stage_entries[0]) -class FSMeta(type): - """This metaclass registers all fetch strategies in a list.""" - def __init__(cls, name, bases, dict): - type.__init__(cls, name, bases, dict) - if cls.enabled: - all_strategies.append(cls) +def fetcher(cls): + """Decorator used to register fetch strategies.""" + all_strategies.append(cls) + return cls -class FetchStrategy(with_metaclass(FSMeta, object)): +class FetchStrategy(object): """Superclass of all fetch strategies.""" - enabled = False # Non-abstract subclasses should be enabled. - #: The URL attribute must be specified either at the package class #: level, or as a keyword argument to ``version()``. It is used to #: distinguish fetchers for different versions in the package DSL. @@ -113,16 +106,7 @@ class FetchStrategy(with_metaclass(FSMeta, object)): self.stage = None # Enable or disable caching for this strategy based on # 'no_cache' option from version directive. - self._cache_enabled = not kwargs.pop('no_cache', False) - - def set_stage(self, stage): - """This is called by Stage before any of the fetching - methods are called on the stage.""" - self.stage = stage - - @property - def cache_enabled(self): - return self._cache_enabled + self.cache_enabled = not kwargs.pop('no_cache', False) # Subclasses need to implement these methods def fetch(self): @@ -186,13 +170,18 @@ class FetchStrategy(with_metaclass(FSMeta, object)): def __str__(self): # Should be human readable URL. return "FetchStrategy.__str___" - # This method is used to match fetch strategies to version() - # arguments in packages. @classmethod def matches(cls, args): + """Predicate that matches fetch strategies to arguments of + the version directive. + + Args: + args: arguments of the version directive + """ return cls.url_attr in args +@fetcher class BundleFetchStrategy(FetchStrategy): """ Fetch strategy associated with bundle, or no-code, packages. @@ -204,9 +193,6 @@ class BundleFetchStrategy(FetchStrategy): TODO: Remove this class by refactoring resource handling and the link between composite stages and composite fetch strategies (see #11981). """ - #: This is a concrete fetch strategy for no-code packages. - enabled = True - #: There is no associated URL keyword in ``version()`` for no-code #: packages but this property is required for some strategy-related #: functions (e.g., check_pkg_attributes). @@ -225,6 +211,9 @@ class BundleFetchStrategy(FetchStrategy): """BundlePackages don't have a source id.""" return '' + def mirror_id(self): + """BundlePackages don't have a mirror id.""" + @pattern.composite(interface=FetchStrategy) class FetchStrategyComposite(object): @@ -233,7 +222,6 @@ class FetchStrategyComposite(object): Implements the GoF composite pattern. """ matches = FetchStrategy.matches - set_stage = FetchStrategy.set_stage def source_id(self): component_ids = tuple(i.source_id() for i in self) @@ -241,13 +229,13 @@ class FetchStrategyComposite(object): return component_ids +@fetcher class URLFetchStrategy(FetchStrategy): + """URLFetchStrategy pulls source code from a URL for an archive, check the + archive against a checksum, and decompresses the archive. + + The destination for the resulting file(s) is the standard stage path. """ - FetchStrategy that pulls source code from a URL for an archive, check the - archive against a checksum, and decompresses the archive. The destination - for the resulting file(s) is the standard stage source path. - """ - enabled = True url_attr = 'url' # these are checksum types. The generic 'checksum' is deprecated for @@ -259,6 +247,7 @@ class URLFetchStrategy(FetchStrategy): # Prefer values in kwargs to the positionals. self.url = kwargs.get('url', url) + self.mirrors = kwargs.get('mirrors', []) # digest can be set as the first argument, or from an explicit # kwarg by the hash name. @@ -294,20 +283,36 @@ class URLFetchStrategy(FetchStrategy): return os.path.sep.join( ['archive', self.digest[:2], self.digest]) + @property + def candidate_urls(self): + return [self.url] + (self.mirrors or []) + @_needs_stage def fetch(self): if self.archive_file: tty.msg("Already downloaded %s" % self.archive_file) return + for url in self.candidate_urls: + try: + partial_file, save_file = self._fetch_from_url(url) + if save_file: + os.rename(partial_file, save_file) + break + except FetchError as e: + tty.msg(str(e)) + pass + + if not self.archive_file: + raise FailedDownloadError(self.url) + + def _fetch_from_url(self, url): save_file = None partial_file = None if self.stage.save_filename: save_file = self.stage.save_filename partial_file = self.stage.save_filename + '.part' - - tty.msg("Fetching %s" % self.url) - + tty.msg("Fetching %s" % url) if partial_file: save_args = ['-C', '-', # continue partial downloads @@ -321,7 +326,9 @@ class URLFetchStrategy(FetchStrategy): '-D', '-', # print out HTML headers '-L', # resolve 3xx redirects - self.url, + # Timeout if can't establish a connection after 10 sec. + '--connect-timeout', '10', + url, ] if not spack.config.get('config:verify_ssl'): @@ -377,12 +384,7 @@ class URLFetchStrategy(FetchStrategy): flags=re.IGNORECASE) if content_types and 'text/html' in content_types[-1]: warn_content_type_mismatch(self.archive_file or "the archive") - - if save_file: - os.rename(partial_file, save_file) - - if not self.archive_file: - raise FailedDownloadError(self.url) + return partial_file, save_file @property @_needs_stage @@ -392,7 +394,7 @@ class URLFetchStrategy(FetchStrategy): @property def cachable(self): - return self._cache_enabled and bool(self.digest) + return self.cache_enabled and bool(self.digest) @_needs_stage def expand(self): @@ -519,6 +521,7 @@ class URLFetchStrategy(FetchStrategy): return "[no url]" +@fetcher class CacheURLFetchStrategy(URLFetchStrategy): """The resource associated with a cache URL may be out of date.""" @@ -594,7 +597,7 @@ class VCSFetchStrategy(FetchStrategy): patterns = kwargs.get('exclude', None) if patterns is not None: - if isinstance(patterns, string_types): + if isinstance(patterns, six.string_types): patterns = [patterns] for p in patterns: tar.add_default_arg('--exclude=%s' % p) @@ -618,6 +621,7 @@ class VCSFetchStrategy(FetchStrategy): return "%s<%s>" % (self.__class__, self.url) +@fetcher class GoFetchStrategy(VCSFetchStrategy): """Fetch strategy that employs the `go get` infrastructure. @@ -631,7 +635,6 @@ class GoFetchStrategy(VCSFetchStrategy): The fetched source will be moved to the standard stage sourcepath directory during the expand step. """ - enabled = True url_attr = 'go' def __init__(self, **kwargs): @@ -688,6 +691,7 @@ class GoFetchStrategy(VCSFetchStrategy): return "[go] %s" % self.url +@fetcher class GitFetchStrategy(VCSFetchStrategy): """ @@ -709,9 +713,9 @@ class GitFetchStrategy(VCSFetchStrategy): Repositories are cloned into the standard stage source path directory. """ - enabled = True url_attr = 'git' - optional_attrs = ['tag', 'branch', 'commit', 'submodules', 'get_full_repo'] + optional_attrs = ['tag', 'branch', 'commit', 'submodules', + 'get_full_repo', 'submodules_delete'] def __init__(self, **kwargs): # Discards the keywords in kwargs that may conflict with the next call @@ -722,6 +726,7 @@ class GitFetchStrategy(VCSFetchStrategy): self._git = None self.submodules = kwargs.get('submodules', False) + self.submodules_delete = kwargs.get('submodules_delete', False) self.get_full_repo = kwargs.get('get_full_repo', False) @property @@ -743,7 +748,7 @@ class GitFetchStrategy(VCSFetchStrategy): @property def cachable(self): - return self._cache_enabled and bool(self.commit or self.tag) + return self.cache_enabled and bool(self.commit or self.tag) def source_id(self): return self.commit or self.tag @@ -855,6 +860,14 @@ class GitFetchStrategy(VCSFetchStrategy): git(*pull_args, ignore_errors=1) git(*co_args) + if self.submodules_delete: + with working_dir(self.stage.source_path): + for submodule_to_delete in self.submodules_delete: + args = ['rm', submodule_to_delete] + if not spack.config.get('config:debug'): + args.insert(1, '--quiet') + git(*args) + # Init submodules if the user asked for them. if self.submodules: with working_dir(self.stage.source_path): @@ -889,6 +902,7 @@ class GitFetchStrategy(VCSFetchStrategy): return '[git] {0}'.format(self._repo_info()) +@fetcher class SvnFetchStrategy(VCSFetchStrategy): """Fetch strategy that gets source code from a subversion repository. @@ -903,7 +917,6 @@ class SvnFetchStrategy(VCSFetchStrategy): Repositories are checked out into the standard stage source path directory. """ - enabled = True url_attr = 'svn' optional_attrs = ['revision'] @@ -926,7 +939,7 @@ class SvnFetchStrategy(VCSFetchStrategy): @property def cachable(self): - return self._cache_enabled and bool(self.revision) + return self.cache_enabled and bool(self.revision) def source_id(self): return self.revision @@ -988,6 +1001,7 @@ class SvnFetchStrategy(VCSFetchStrategy): return "[svn] %s" % self.url +@fetcher class HgFetchStrategy(VCSFetchStrategy): """ @@ -1010,7 +1024,6 @@ class HgFetchStrategy(VCSFetchStrategy): Repositories are cloned into the standard stage source path directory. """ - enabled = True url_attr = 'hg' optional_attrs = ['revision'] @@ -1040,7 +1053,7 @@ class HgFetchStrategy(VCSFetchStrategy): @property def cachable(self): - return self._cache_enabled and bool(self.revision) + return self.cache_enabled and bool(self.revision) def source_id(self): return self.revision @@ -1105,9 +1118,9 @@ class HgFetchStrategy(VCSFetchStrategy): return "[hg] %s" % self.url +@fetcher class S3FetchStrategy(URLFetchStrategy): """FetchStrategy that pulls from an S3 bucket.""" - enabled = True url_attr = 's3' def __init__(self, *args, **kwargs): @@ -1139,7 +1152,7 @@ class S3FetchStrategy(URLFetchStrategy): with open(basename, 'wb') as f: shutil.copyfileobj(stream, f) - content_type = headers['Content-type'] + content_type = web_util.get_header(headers, 'Content-type') if content_type == 'text/html': warn_content_type_mismatch(self.archive_file or "the archive") @@ -1241,10 +1254,15 @@ def _from_merged_attrs(fetcher, pkg, version): """Create a fetcher from merged package and version attributes.""" if fetcher.url_attr == 'url': url = pkg.url_for_version(version) + # TODO: refactor this logic into its own method or function + # TODO: to avoid duplication + mirrors = [spack.url.substitute_version(u, version) + for u in getattr(pkg, 'urls', [])] + attrs = {fetcher.url_attr: url, 'mirrors': mirrors} else: url = getattr(pkg, fetcher.url_attr) + attrs = {fetcher.url_attr: url} - attrs = {fetcher.url_attr: url} attrs.update(pkg.versions[version]) return fetcher(**attrs) @@ -1308,7 +1326,9 @@ def from_url_scheme(url, *args, **kwargs): { 'file': 'url', 'http': 'url', - 'https': 'url' + 'https': 'url', + 'ftp': 'url', + 'ftps': 'url', }) scheme = parsed_url.scheme diff --git a/lib/spack/spack/filesystem_view.py b/lib/spack/spack/filesystem_view.py index 3d17d7e4ce..babe1b9c0e 100644 --- a/lib/spack/spack/filesystem_view.py +++ b/lib/spack/spack/filesystem_view.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py index 9a1571d75c..b41c923a16 100644 --- a/lib/spack/spack/graph.py +++ b/lib/spack/spack/graph.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/hash_types.py b/lib/spack/spack/hash_types.py index e4a238a93b..9404076e81 100644 --- a/lib/spack/spack/hash_types.py +++ b/lib/spack/spack/hash_types.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py index 860134112e..5a39f242fd 100644 --- a/lib/spack/spack/hooks/__init__.py +++ b/lib/spack/spack/hooks/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,7 +12,6 @@ Currently the following hooks are supported: - * pre_run() * pre_install(spec) * post_install(spec) * pre_uninstall(spec) @@ -60,11 +59,6 @@ class HookRunner(object): hook(*args, **kwargs) -# -# Define some functions that can be called to fire off hooks. -# -pre_run = HookRunner('pre_run') - pre_install = HookRunner('pre_install') post_install = HookRunner('post_install') diff --git a/lib/spack/spack/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py index bfda25918e..05fce302ac 100644 --- a/lib/spack/spack/hooks/extensions.py +++ b/lib/spack/spack/hooks/extensions.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/hooks/licensing.py b/lib/spack/spack/hooks/licensing.py index 8a56dc122f..d4e5376cda 100644 --- a/lib/spack/spack/hooks/licensing.py +++ b/lib/spack/spack/hooks/licensing.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/hooks/module_file_generation.py b/lib/spack/spack/hooks/module_file_generation.py index fb631694b9..ba30561d86 100644 --- a/lib/spack/spack/hooks/module_file_generation.py +++ b/lib/spack/spack/hooks/module_file_generation.py @@ -1,21 +1,21 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import spack.config import spack.modules import spack.modules.common import llnl.util.tty as tty -try: - enabled = spack.config.get('modules:enable') -except KeyError: - tty.debug('NO MODULE WRITTEN: list of enabled module files is empty') - enabled = [] - def _for_each_enabled(spec, method_name): """Calls a method for each enabled module""" + enabled = spack.config.get('modules:enable') + if not enabled: + tty.debug('NO MODULE WRITTEN: list of enabled module files is empty') + return + for name in enabled: generator = spack.modules.module_types[name](spec) try: @@ -26,5 +26,9 @@ def _for_each_enabled(spec, method_name): tty.warn(msg.format(method_name, str(e))) -post_install = lambda spec: _for_each_enabled(spec, 'write') -post_uninstall = lambda spec: _for_each_enabled(spec, 'remove') +def post_install(spec): + _for_each_enabled(spec, 'write') + + +def post_uninstall(spec): + _for_each_enabled(spec, 'remove') diff --git a/lib/spack/spack/hooks/permissions_setters.py b/lib/spack/spack/hooks/permissions_setters.py index 10d75906e2..0a3c2acf21 100644 --- a/lib/spack/spack/hooks/permissions_setters.py +++ b/lib/spack/spack/hooks/permissions_setters.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/hooks/sbang.py b/lib/spack/spack/hooks/sbang.py index 422f240ce8..b4ee0c1728 100644 --- a/lib/spack/spack/hooks/sbang.py +++ b/lib/spack/spack/hooks/sbang.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/hooks/write_install_manifest.py b/lib/spack/spack/hooks/write_install_manifest.py index 8118caae24..5b678fed88 100644 --- a/lib/spack/spack/hooks/write_install_manifest.py +++ b/lib/spack/spack/hooks/write_install_manifest.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/hooks/yaml_version_check.py b/lib/spack/spack/hooks/yaml_version_check.py deleted file mode 100644 index ff8be58481..0000000000 --- a/lib/spack/spack/hooks/yaml_version_check.py +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -"""Yaml Version Check is a module for ensuring that config file -formats are compatible with the current version of Spack.""" -import os.path -import os -import llnl.util.tty as tty -import spack.util.spack_yaml as syaml -import spack.config - - -def pre_run(): - check_compiler_yaml_version() - - -def check_compiler_yaml_version(): - config = spack.config.config - - for scope in config.file_scopes: - file_name = os.path.join(scope.path, 'compilers.yaml') - data = None - if os.path.isfile(file_name): - with open(file_name) as f: - data = syaml.load_config(f) - - if data: - compilers = data.get('compilers') - if compilers and len(compilers) > 0: - if (not isinstance(compilers, list) or - 'operating_system' not in compilers[0]['compiler']): - new_file = os.path.join(scope.path, '_old_compilers.yaml') - tty.warn('%s in out of date compilers format. ' - 'Moved to %s. Spack automatically generate ' - 'a compilers config file ' - % (file_name, new_file)) - os.rename(file_name, new_file) diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py index ff2ff74da3..4386f50435 100644 --- a/lib/spack/spack/main.py +++ b/lib/spack/spack/main.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ from __future__ import print_function import sys import re import os +import os.path import inspect import pstats import argparse @@ -30,12 +31,12 @@ import spack.architecture import spack.config import spack.cmd import spack.environment as ev -import spack.hooks import spack.paths import spack.repo import spack.store import spack.util.debug import spack.util.path +import spack.util.executable as exe from spack.error import SpackError @@ -108,6 +109,34 @@ def add_all_commands(parser): parser.add_command(cmd) +def get_version(): + """Get a descriptive version of this instance of Spack. + + If this is a git repository, and if it is not on a release tag, + return a string like: + + release_version-commits_since_release-commit + + If we *are* at a release tag, or if this is not a git repo, return + the real spack release number (e.g., 0.13.3). + + """ + git_path = os.path.join(spack.paths.prefix, ".git") + if os.path.exists(git_path): + git = exe.which("git") + if git: + desc = git("-C", spack.paths.prefix, "describe", "--tags", + output=str, fail_on_error=False) + + if git.returncode == 0: + match = re.match(r"v([^-]+)-([^-]+)-g([a-f\d]+)", desc) + if match: + v, n, commit = match.groups() + return "%s-%s-%s" % (v, n, commit) + + return spack.spack_version + + def index_commands(): """create an index of commands by section for this help level""" index = {} @@ -646,6 +675,17 @@ def main(argv=None): parser.add_argument('command', nargs=argparse.REMAINDER) args, unknown = parser.parse_known_args(argv) + # Recover stored LD_LIBRARY_PATH variables from spack shell function + # This is necessary because MacOS System Integrity Protection clears + # (DY?)LD_LIBRARY_PATH variables on process start. + # Spack clears these variables before building and installing packages, + # but needs to know the prior state for commands like `spack load` and + # `spack env activate that modify the user environment. + for var in ('LD_LIBRARY_PATH', 'DYLD_LIBRARY_PATH'): + stored_var_name = 'SPACK_%s' % var + if stored_var_name in os.environ: + os.environ[var] = os.environ[stored_var_name] + # activate an environment if one was specified on the command line if not args.no_env: env = ev.find_environment(args) @@ -669,7 +709,7 @@ def main(argv=None): # -h, -H, and -V are special as they do not require a command, but # all the other options do nothing without a command. if args.version: - print(spack.spack_version) + print(get_version()) return 0 elif args.help: sys.stdout.write(parser.format_help(level=args.help)) @@ -700,9 +740,6 @@ def main(argv=None): # many operations will fail without a working directory. set_working_dir() - # pre-run hooks happen after we know we have a valid working dir - spack.hooks.pre_run() - # now we can actually execute the command. if args.spack_profile or args.sorted_profile: _profile_wrapper(command, parser, args, unknown) diff --git a/lib/spack/spack/mirror.py b/lib/spack/spack/mirror.py index da9b20472a..3f6b2b6a0e 100644 --- a/lib/spack/spack/mirror.py +++ b/lib/spack/spack/mirror.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,8 +21,10 @@ import six import ruamel.yaml.error as yaml_error +from ordereddict_backport import OrderedDict + try: - from collections.abc import Mapping + from collections.abc import Mapping # novm except ImportError: from collections import Mapping @@ -166,7 +168,7 @@ class MirrorCollection(Mapping): """A mapping of mirror names to mirrors.""" def __init__(self, mirrors=None, scope=None): - self._mirrors = dict( + self._mirrors = OrderedDict( (name, Mirror.from_dict(mirror, name)) for name, mirror in ( mirrors.items() if mirrors is not None else @@ -178,6 +180,7 @@ class MirrorCollection(Mapping): def to_yaml(self, stream=None): return syaml.dump(self.to_dict(True), stream) + # TODO: this isn't called anywhere @staticmethod def from_yaml(stream, name=None): try: diff --git a/lib/spack/spack/mixins.py b/lib/spack/spack/mixins.py index 198bd03bcb..f7162a3a84 100644 --- a/lib/spack/spack/mixins.py +++ b/lib/spack/spack/mixins.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/modules/__init__.py b/lib/spack/spack/modules/__init__.py index 20864b5f27..2fb4d94b05 100644 --- a/lib/spack/spack/modules/__init__.py +++ b/lib/spack/spack/modules/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/modules/common.py b/lib/spack/spack/modules/common.py index 2e0090a449..d9407a1bf6 100644 --- a/lib/spack/spack/modules/common.py +++ b/lib/spack/spack/modules/common.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,35 +28,30 @@ and is divided among four classes: Each of the four classes needs to be sub-classed when implementing a new module type. """ +import collections import copy import datetime import inspect import os.path import re -import collections -import six import llnl.util.filesystem import llnl.util.tty as tty - -import spack.paths import spack.build_environment as build_environment -import spack.util.environment +import spack.error +import spack.paths +import spack.schema.environment import spack.tengine as tengine -import spack.util.path import spack.util.environment -import spack.error -import spack.util.spack_yaml as syaml import spack.util.file_permissions as fp +import spack.util.path +import spack.util.spack_yaml as syaml -#: config section for this file -configuration = spack.config.get('modules') -#: Root folders where the various module files should be written -roots = spack.config.get('config:module_roots', {}) +#: config section for this file +def configuration(): + return spack.config.get('modules', {}) -#: Inspections that needs to be done on spec prefixes -prefix_inspections = spack.config.get('modules:prefix_inspections', {}) #: Valid tokens for naming scheme and env variable names _valid_tokens = ( @@ -214,11 +209,13 @@ def root_path(name): """Returns the root folder for module file installation. Args: - name: name of the module system t be used (e.g. 'tcl') + name: name of the module system to be used (e.g. 'tcl') Returns: root folder for module file installation """ + # Root folders where the various module files should be written + roots = spack.config.get('config:module_roots', {}) path = roots.get(name, os.path.join(spack.paths.share_path, name)) return spack.util.path.canonicalize_path(path) @@ -387,12 +384,12 @@ class BaseConfiguration(object): self.spec = spec # Dictionary of configuration options that should be applied # to the spec - self.conf = merge_config_rules(self.module.configuration, self.spec) + self.conf = merge_config_rules(self.module.configuration(), self.spec) @property def naming_scheme(self): """Naming scheme suitable for non-hierarchical layouts""" - scheme = self.module.configuration.get( + scheme = self.module.configuration().get( 'naming_scheme', '{name}-{version}-{compiler.name}-{compiler.version}' ) @@ -416,22 +413,7 @@ class BaseConfiguration(object): """List of environment modifications that should be done in the module. """ - env_mods = spack.util.environment.EnvironmentModifications() - actions = self.conf.get('environment', {}) - - def process_arglist(arglist): - if method == 'unset': - for x in arglist: - yield (x,) - else: - for x in six.iteritems(arglist): - yield x - - for method, arglist in actions.items(): - for args in process_arglist(arglist): - getattr(env_mods, method)(*args) - - return env_mods + return spack.schema.environment.parse(self.conf.get('environment', {})) @property def suffixes(self): @@ -461,7 +443,7 @@ class BaseConfiguration(object): """ # A few variables for convenience of writing the method spec = self.spec - conf = self.module.configuration + conf = self.module.configuration() # Compute the list of whitelist rules that match wlrules = conf.get('whitelist', []) @@ -662,7 +644,7 @@ class BaseContext(tengine.Context): # Modifications guessed inspecting the spec prefix env = spack.util.environment.inspect_path( self.spec.prefix, - prefix_inspections, + spack.config.get('modules:prefix_inspections', {}), exclude=spack.util.environment.is_system_path ) @@ -804,10 +786,11 @@ class BaseModuleFileWriter(object): # Get the template for the module template_name = self._get_template() + import jinja2 try: env = tengine.make_environment() template = env.get_template(template_name) - except tengine.TemplateNotFound: + except jinja2.TemplateNotFound: # If the template was not found raise an exception with a little # more information msg = 'template \'{0}\' was not found for \'{1}\'' diff --git a/lib/spack/spack/modules/lmod.py b/lib/spack/spack/modules/lmod.py index e45b97773b..a9ebb0bba9 100644 --- a/lib/spack/spack/modules/lmod.py +++ b/lib/spack/spack/modules/lmod.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,8 +18,11 @@ import spack.tengine as tengine from .common import BaseConfiguration, BaseFileLayout from .common import BaseContext, BaseModuleFileWriter + #: lmod specific part of the configuration -configuration = spack.config.get('modules:lmod', {}) +def configuration(): + return spack.config.get('modules:lmod', {}) + #: Caches the configuration {spec_hash: configuration} configuration_registry = {} @@ -98,7 +101,7 @@ class LmodConfiguration(BaseConfiguration): specified in the configuration file or the sequence is empty """ - value = configuration.get( + value = configuration().get( 'core_compilers' ) or guess_core_compilers(store=True) @@ -112,7 +115,7 @@ class LmodConfiguration(BaseConfiguration): """Returns the list of tokens that are part of the modulefile hierarchy. 'compiler' is always present. """ - tokens = configuration.get('hierarchy', []) + tokens = configuration().get('hierarchy', []) # Check if all the tokens in the hierarchy are virtual specs. # If not warn the user and raise an error. diff --git a/lib/spack/spack/modules/tcl.py b/lib/spack/spack/modules/tcl.py index 1c9d741a2d..ec8032a0e1 100644 --- a/lib/spack/spack/modules/tcl.py +++ b/lib/spack/spack/modules/tcl.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,8 +16,11 @@ import spack.tengine as tengine from .common import BaseConfiguration, BaseFileLayout from .common import BaseContext, BaseModuleFileWriter + #: TCL specific part of the configuration -configuration = spack.config.get('modules:tcl', {}) +def configuration(): + return spack.config.get('modules:tcl', {}) + #: Caches the configuration {spec_hash: configuration} configuration_registry = {} diff --git a/lib/spack/spack/multimethod.py b/lib/spack/spack/multimethod.py index e0854a01c9..73cf342b5b 100644 --- a/lib/spack/spack/multimethod.py +++ b/lib/spack/spack/multimethod.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/operating_systems/__init__.py b/lib/spack/spack/operating_systems/__init__.py index 94f8ac4d9e..9f87532b85 100644 --- a/lib/spack/spack/operating_systems/__init__.py +++ b/lib/spack/spack/operating_systems/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/operating_systems/cnk.py b/lib/spack/spack/operating_systems/cnk.py index 99ea9455fa..53a12785da 100644 --- a/lib/spack/spack/operating_systems/cnk.py +++ b/lib/spack/spack/operating_systems/cnk.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/operating_systems/cnl.py b/lib/spack/spack/operating_systems/cnl.py index 24075de3fd..3d4036cb47 100644 --- a/lib/spack/spack/operating_systems/cnl.py +++ b/lib/spack/spack/operating_systems/cnl.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/operating_systems/cray_frontend.py b/lib/spack/spack/operating_systems/cray_frontend.py index 1e8d9f4111..15f5b23baf 100644 --- a/lib/spack/spack/operating_systems/cray_frontend.py +++ b/lib/spack/spack/operating_systems/cray_frontend.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/operating_systems/linux_distro.py b/lib/spack/spack/operating_systems/linux_distro.py index 8a18c27b41..a6608e6d3b 100644 --- a/lib/spack/spack/operating_systems/linux_distro.py +++ b/lib/spack/spack/operating_systems/linux_distro.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/operating_systems/mac_os.py b/lib/spack/spack/operating_systems/mac_os.py index 2f98c0cd79..fa7718f806 100644 --- a/lib/spack/spack/operating_systems/mac_os.py +++ b/lib/spack/spack/operating_systems/mac_os.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 26335ed2ff..d67c017a70 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -510,8 +510,8 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): maintainers = [] #: List of attributes to be excluded from a package's hash. - metadata_attrs = ['homepage', 'url', 'list_url', 'extendable', 'parallel', - 'make_jobs'] + metadata_attrs = ['homepage', 'url', 'urls', 'list_url', 'extendable', + 'parallel', 'make_jobs'] def __init__(self, spec): # this determines how the package should be built. @@ -524,6 +524,12 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): # a binary cache. self.installed_from_binary_cache = False + # Ensure that only one of these two attributes are present + if getattr(self, 'url', None) and getattr(self, 'urls', None): + msg = "a package can have either a 'url' or a 'urls' attribute" + msg += " [package '{0.name}' defines both]" + raise ValueError(msg.format(self)) + # Set a default list URL (place to find available versions) if not hasattr(self, 'list_url'): self.list_url = None @@ -556,16 +562,19 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): @classmethod def possible_dependencies( cls, transitive=True, expand_virtuals=True, deptype='all', - visited=None): + visited=None, missing=None): """Return dict of possible dependencies of this package. Args: - transitive (bool): return all transitive dependencies if True, - only direct dependencies if False. - expand_virtuals (bool): expand virtual dependencies into all - possible implementations. - deptype (str or tuple): dependency types to consider - visited (set): set of names of dependencies visited so far. + transitive (bool, optional): return all transitive dependencies if + True, only direct dependencies if False (default True).. + expand_virtuals (bool, optional): expand virtual dependencies into + all possible implementations (default True) + deptype (str or tuple, optional): dependency types to consider + visited (dicct, optional): dict of names of dependencies visited so + far, mapped to their immediate dependencies' names. + missing (dict, optional): dict to populate with packages and their + *missing* dependencies. Returns: (dict): dictionary mapping dependency names to *their* @@ -576,7 +585,12 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): *immediate* dependencies. If ``expand_virtuals`` is ``False``, virtual package names wil be inserted as keys mapped to empty sets of dependencies. Virtuals, if not expanded, are treated as - though they have no immediate dependencies + though they have no immediate dependencies. + + Missing dependencies by default are ignored, but if a + missing dict is provided, it will be populated with package names + mapped to any dependencies they have that are in no + repositories. This is only populated if transitive is True. Note: the returned dict *includes* the package itself. @@ -586,6 +600,9 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): if visited is None: visited = {cls.name: set()} + if missing is None: + missing = {cls.name: set()} + for name, conditions in cls.dependencies.items(): # check whether this dependency could be of the type asked for types = [dep.type for cond, dep in conditions.items()] @@ -609,12 +626,24 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): # recursively traverse dependencies for dep_name in dep_names: - if dep_name not in visited: - visited.setdefault(dep_name, set()) - if transitive: - dep_cls = spack.repo.path.get_pkg_class(dep_name) - dep_cls.possible_dependencies( - transitive, expand_virtuals, deptype, visited) + if dep_name in visited: + continue + + visited.setdefault(dep_name, set()) + + # skip the rest if not transitive + if not transitive: + continue + + try: + dep_cls = spack.repo.path.get_pkg_class(dep_name) + except spack.repo.UnknownPackageError: + # log unknown packages + missing.setdefault(cls.name, set()).add(dep_name) + continue + + dep_cls.possible_dependencies( + transitive, expand_virtuals, deptype, visited, missing) return visited @@ -727,7 +756,9 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): return version_urls[version] # If no specific URL, use the default, class-level URL - default_url = getattr(self, 'url', None) + url = getattr(self, 'url', None) + urls = getattr(self, 'urls', [None]) + default_url = url or urls.pop(0) # if no exact match AND no class-level default, use the nearest URL if not default_url: @@ -1231,7 +1262,10 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): raise spack.error.SpackError(err_msg) hash_content = list() - source_id = fs.for_package_version(self, self.version).source_id() + try: + source_id = fs.for_package_version(self, self.version).source_id() + except fs.ExtrapolationError: + source_id = None if not source_id: # TODO? in cases where a digest or source_id isn't available, # should this attempt to download the source and set one? This @@ -1474,9 +1508,10 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): message = '{s.name}@{s.version} : marking the package explicit' tty.msg(message.format(s=self)) - def try_install_from_binary_cache(self, explicit): + def try_install_from_binary_cache(self, explicit, unsigned=False): tty.msg('Searching for binary cache of %s' % self.name) - specs = binary_distribution.get_specs() + specs = binary_distribution.get_spec(spec=self.spec, + force=False) binary_spec = spack.spec.Spec.from_dict(self.spec.to_dict()) binary_spec._mark_concrete() if binary_spec not in specs: @@ -1490,7 +1525,7 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): tty.msg('Installing %s from binary cache' % self.name) binary_distribution.extract_tarball( binary_spec, tarball, allow_root=False, - unsigned=False, force=False) + unsigned=unsigned, force=False) self.installed_from_binary_cache = True spack.store.db.add( self.spec, spack.store.layout, explicit=explicit) @@ -1509,6 +1544,7 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): ) if not compilers: dep = spack.compilers.pkg_spec_for_compiler(self.spec.compiler) + dep.architecture = self.spec.architecture # concrete CompilerSpec has less info than concrete Spec # concretize as Spec to add that information dep.concretize() @@ -1630,14 +1666,16 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): tty.msg(colorize('@*{Installing} @*g{%s}' % self.name)) if kwargs.get('use_cache', True): - if self.try_install_from_binary_cache(explicit): + if self.try_install_from_binary_cache( + explicit, unsigned=kwargs.get('unsigned', False)): tty.msg('Successfully installed %s from binary cache' % self.name) print_pkg(self.prefix) spack.hooks.post_install(self.spec) return elif kwargs.get('cache_only', False): - tty.die('No binary for %s found and cache-only specified') + tty.die('No binary for %s found and cache-only specified' + % self.name) tty.msg('No binary for %s found: installing from source' % self.name) @@ -2662,6 +2700,35 @@ def dump_packages(spec, path): spack.repo.path.dump_provenance(node, dest_pkg_dir) +def possible_dependencies(*pkg_or_spec, **kwargs): + """Get the possible dependencies of a number of packages. + + See ``PackageBase.possible_dependencies`` for details. + """ + transitive = kwargs.get('transitive', True) + expand_virtuals = kwargs.get('expand_virtuals', True) + deptype = kwargs.get('deptype', 'all') + missing = kwargs.get('missing') + + packages = [] + for pos in pkg_or_spec: + if isinstance(pos, PackageMeta): + pkg = pos + elif isinstance(pos, spack.spec.Spec): + pkg = pos.package + else: + pkg = spack.spec.Spec(pos).package + + packages.append(pkg) + + visited = {} + for pkg in packages: + pkg.possible_dependencies( + transitive, expand_virtuals, deptype, visited, missing) + + return visited + + def print_pkg(message): """Outputs a message with a package icon.""" from llnl.util.tty.color import cwrite diff --git a/lib/spack/spack/package_prefs.py b/lib/spack/spack/package_prefs.py index e73ce7c947..2801a6d123 100644 --- a/lib/spack/spack/package_prefs.py +++ b/lib/spack/spack/package_prefs.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,8 +8,6 @@ import stat from six import string_types from six import iteritems -from llnl.util.lang import classproperty - import spack.repo import spack.error from spack.util.path import canonicalize_path @@ -75,14 +73,13 @@ class PackagePrefs(object): provider_spec_list.sort(key=kf) """ - _packages_config_cache = None - _spec_cache = {} - def __init__(self, pkgname, component, vpkg=None): self.pkgname = pkgname self.component = component self.vpkg = vpkg + self._spec_order = None + def __call__(self, spec): """Return a key object (an index) that can be used to sort spec. @@ -90,8 +87,10 @@ class PackagePrefs(object): this function as Python's sort functions already ensure that the key function is called at most once per sorted element. """ - spec_order = self._specs_for_pkg( - self.pkgname, self.component, self.vpkg) + if self._spec_order is None: + self._spec_order = self._specs_for_pkg( + self.pkgname, self.component, self.vpkg) + spec_order = self._spec_order # integer is the index of the first spec in order that satisfies # spec, or it's a number larger than any position in the order. @@ -107,13 +106,6 @@ class PackagePrefs(object): match_index -= 0.5 return match_index - @classproperty - @classmethod - def _packages_config(cls): - if cls._packages_config_cache is None: - cls._packages_config_cache = get_packages_config() - return cls._packages_config_cache - @classmethod def order_for_package(cls, pkgname, component, vpkg=None, all=True): """Given a package name, sort component (e.g, version, compiler, ...), @@ -124,7 +116,7 @@ class PackagePrefs(object): pkglist.append('all') for pkg in pkglist: - pkg_entry = cls._packages_config.get(pkg) + pkg_entry = get_packages_config().get(pkg) if not pkg_entry: continue @@ -150,21 +142,9 @@ class PackagePrefs(object): return a list of CompilerSpecs, VersionLists, or Specs for that sorting list. """ - key = (pkgname, component, vpkg) - - specs = cls._spec_cache.get(key) - if specs is None: - pkglist = cls.order_for_package(pkgname, component, vpkg) - spec_type = _spec_type(component) - specs = [spec_type(s) for s in pkglist] - cls._spec_cache[key] = specs - - return specs - - @classmethod - def clear_caches(cls): - cls._packages_config_cache = None - cls._spec_cache = {} + pkglist = cls.order_for_package(pkgname, component, vpkg) + spec_type = _spec_type(component) + return [spec_type(s) for s in pkglist] @classmethod def has_preferred_providers(cls, pkgname, vpkg): @@ -180,7 +160,7 @@ class PackagePrefs(object): def preferred_variants(cls, pkg_name): """Return a VariantMap of preferred variants/values for a spec.""" for pkg in (pkg_name, 'all'): - variants = cls._packages_config.get(pkg, {}).get('variants', '') + variants = get_packages_config().get(pkg, {}).get('variants', '') if variants: break diff --git a/lib/spack/spack/package_test.py b/lib/spack/spack/package_test.py index 559a8df3f5..6e9da9a985 100644 --- a/lib/spack/spack/package_test.py +++ b/lib/spack/spack/package_test.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/parse.py b/lib/spack/spack/parse.py index 6bfdec7b43..12bbcee588 100644 --- a/lib/spack/spack/parse.py +++ b/lib/spack/spack/parse.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/patch.py b/lib/spack/spack/patch.py index 73fdf4df25..bcb45387a8 100644 --- a/lib/spack/spack/patch.py +++ b/lib/spack/spack/patch.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/paths.py b/lib/spack/spack/paths.py index d91b01d87c..e5541eff10 100644 --- a/lib/spack/spack/paths.py +++ b/lib/spack/spack/paths.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/pkgkit.py b/lib/spack/spack/pkgkit.py index 7ad7279e73..a39ede3ab7 100644 --- a/lib/spack/spack/pkgkit.py +++ b/lib/spack/spack/pkgkit.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,6 +30,7 @@ from spack.build_systems.perl import PerlPackage from spack.build_systems.intel import IntelPackage from spack.build_systems.meson import MesonPackage from spack.build_systems.sip import SIPPackage +from spack.build_systems.gnu import GNUMirrorPackage from spack.mixins import filter_compiler_wrappers diff --git a/lib/spack/spack/platforms/__init__.py b/lib/spack/spack/platforms/__init__.py index 94f8ac4d9e..9f87532b85 100644 --- a/lib/spack/spack/platforms/__init__.py +++ b/lib/spack/spack/platforms/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/platforms/bgq.py b/lib/spack/spack/platforms/bgq.py index 3823864a64..64d71743c4 100644 --- a/lib/spack/spack/platforms/bgq.py +++ b/lib/spack/spack/platforms/bgq.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py index 3499f0b164..cbeba96461 100644 --- a/lib/spack/spack/platforms/cray.py +++ b/lib/spack/spack/platforms/cray.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/platforms/darwin.py b/lib/spack/spack/platforms/darwin.py index 7c36812d9d..9a3fffd881 100644 --- a/lib/spack/spack/platforms/darwin.py +++ b/lib/spack/spack/platforms/darwin.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/platforms/linux.py b/lib/spack/spack/platforms/linux.py index d2165c7d79..4ffd7ad8e9 100644 --- a/lib/spack/spack/platforms/linux.py +++ b/lib/spack/spack/platforms/linux.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/platforms/test.py b/lib/spack/spack/platforms/test.py index c9bbd02dfa..9be160731e 100644 --- a/lib/spack/spack/platforms/test.py +++ b/lib/spack/spack/platforms/test.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/provider_index.py b/lib/spack/spack/provider_index.py index 1d9b31add6..9bf4af8911 100644 --- a/lib/spack/spack/provider_index.py +++ b/lib/spack/spack/provider_index.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -135,7 +135,7 @@ class ProviderIndex(object): for lspec, rspec in iproduct(lmap, rmap): try: constrained = lspec.constrained(rspec) - except spack.spec.UnsatisfiableSpecError: + except spack.error.UnsatisfiableSpecError: continue # lp and rp are left and right provider specs. @@ -144,7 +144,7 @@ class ProviderIndex(object): try: const = lp_spec.constrained(rp_spec, deps=False) result.setdefault(constrained, set()).add(const) - except spack.spec.UnsatisfiableSpecError: + except spack.error.UnsatisfiableSpecError: continue return result diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index 434d681035..d722e587da 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,6 +6,7 @@ import os import re +import shutil import platform import spack.repo import spack.cmd @@ -86,7 +87,14 @@ def get_existing_elf_rpaths(path_name): Return the RPATHS returned by patchelf --print-rpath path_name as a list of strings. """ - patchelf = Executable(get_patchelf()) + + # if we're relocating patchelf itself, use it + + if path_name[-13:] == "/bin/patchelf": + patchelf = Executable(path_name) + else: + patchelf = Executable(get_patchelf()) + try: output = patchelf('--print-rpath', '%s' % path_name, output=str, error=str) @@ -326,8 +334,18 @@ def modify_elf_object(path_name, new_rpaths): """ Replace orig_rpath with new_rpath in RPATH of elf object path_name """ + new_joined = ':'.join(new_rpaths) - patchelf = Executable(get_patchelf()) + + # if we're relocating patchelf itself, use it + + if path_name[-13:] == "/bin/patchelf": + bak_path = path_name + ".bak" + shutil.copy(path_name, bak_path) + patchelf = Executable(bak_path) + else: + patchelf = Executable(get_patchelf()) + try: patchelf('--force-rpath', '--set-rpath', '%s' % new_joined, '%s' % path_name, output=str, error=str) @@ -665,7 +683,13 @@ def file_is_relocatable(file, paths_to_relocate=None): raise ValueError('{0} is not an absolute path'.format(file)) strings = Executable('strings') - patchelf = Executable(get_patchelf()) + + # if we're relocating patchelf itself, use it + + if file[-13:] == "/bin/patchelf": + patchelf = Executable(file) + else: + patchelf = Executable(get_patchelf()) # Remove the RPATHS from the strings in the executable set_of_strings = set(strings(file, output=str).split()) diff --git a/lib/spack/spack/repo.py b/lib/spack/spack/repo.py index 3ea196dd4d..8e3dae5d47 100644 --- a/lib/spack/spack/repo.py +++ b/lib/spack/spack/repo.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,7 +20,7 @@ import traceback from six import string_types, add_metaclass try: - from collections.abc import Mapping + from collections.abc import Mapping # novm except ImportError: from collections import Mapping @@ -932,7 +932,7 @@ class Repo(object): tty.warn("Patch file did not exist: %s" % patch.path) # Install the package.py file itself. - install(self.filename_for_package_name(spec), path) + install(self.filename_for_package_name(spec.name), path) def purge(self): """Clear entire package instance cache.""" @@ -974,20 +974,12 @@ class Repo(object): def extensions_for(self, extendee_spec): return [p for p in self.all_packages() if p.extends(extendee_spec)] - def _check_namespace(self, spec): - """Check that the spec's namespace is the same as this repository's.""" - if spec.namespace and spec.namespace != self.namespace: - raise UnknownNamespaceError(spec.namespace) - - @autospec - def dirname_for_package_name(self, spec): + def dirname_for_package_name(self, pkg_name): """Get the directory name for a particular package. This is the directory that contains its package.py file.""" - self._check_namespace(spec) - return os.path.join(self.packages_path, spec.name) + return os.path.join(self.packages_path, pkg_name) - @autospec - def filename_for_package_name(self, spec): + def filename_for_package_name(self, pkg_name): """Get the filename for the module we should load for a particular package. Packages for a Repo live in ``$root/<package_name>/package.py`` @@ -996,8 +988,7 @@ class Repo(object): package doesn't exist yet, so callers will need to ensure the package exists before importing. """ - self._check_namespace(spec) - pkg_dir = self.dirname_for_package_name(spec.name) + pkg_dir = self.dirname_for_package_name(pkg_name) return os.path.join(pkg_dir, package_file_name) @property diff --git a/lib/spack/spack/report.py b/lib/spack/spack/report.py index 292eeffd8c..04a20f36b8 100644 --- a/lib/spack/spack/report.py +++ b/lib/spack/spack/report.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -146,8 +146,9 @@ class InfoCollector(object): # An InstallError is considered a failure (the recipe # didn't work correctly) package['result'] = 'failure' - package['stdout'] = fetch_package_log(pkg) package['message'] = e.message or 'Installation failure' + package['stdout'] = fetch_package_log(pkg) + package['stdout'] += package['message'] package['exception'] = e.traceback except (Exception, BaseException) as e: diff --git a/lib/spack/spack/reporter.py b/lib/spack/spack/reporter.py index f99380f0c0..25d4042a5e 100644 --- a/lib/spack/spack/reporter.py +++ b/lib/spack/spack/reporter.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/reporters/__init__.py b/lib/spack/spack/reporters/__init__.py index 94f8ac4d9e..9f87532b85 100644 --- a/lib/spack/spack/reporters/__init__.py +++ b/lib/spack/spack/reporters/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/reporters/cdash.py b/lib/spack/spack/reporters/cdash.py index 58095b10ba..580df7866f 100644 --- a/lib/spack/spack/reporters/cdash.py +++ b/lib/spack/spack/reporters/cdash.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,7 @@ from six.moves.urllib.request import build_opener, HTTPHandler, Request from six.moves.urllib.parse import urlencode from llnl.util.filesystem import working_dir +import llnl.util.tty as tty from ordereddict_backport import OrderedDict import spack.build_environment import spack.fetch_strategy @@ -58,6 +59,7 @@ class CDash(Reporter): def __init__(self, args): Reporter.__init__(self, args) + tty.set_verbose(args.verbose) self.template_dir = os.path.join('reports', 'cdash') self.cdash_upload_url = args.cdash_upload_url @@ -65,8 +67,13 @@ class CDash(Reporter): self.buildid_regexp = re.compile("<buildId>([0-9]+)</buildId>") self.phase_regexp = re.compile(r"Executing phase: '(.*)'") - if args.package: - packages = args.package + self.authtoken = None + if 'SPACK_CDASH_AUTH_TOKEN' in os.environ: + tty.verbose("Using CDash auth token from environment") + self.authtoken = os.environ.get('SPACK_CDASH_AUTH_TOKEN') + + if args.spec: + packages = args.spec else: packages = [] for file in args.specfiles: @@ -225,7 +232,8 @@ class CDash(Reporter): # from the binary cache. spec['packages'] = [ x for x in spec['packages'] - if not x['installed_from_binary_cache'] + if 'installed_from_binary_cache' not in x or + not x['installed_from_binary_cache'] ] for package in spec['packages']: if 'stdout' in package: @@ -297,12 +305,18 @@ class CDash(Reporter): request = Request(url, data=f) request.add_header('Content-Type', 'text/xml') request.add_header('Content-Length', os.path.getsize(filename)) + if self.authtoken: + request.add_header('Authorization', + 'Bearer {0}'.format(self.authtoken)) # By default, urllib2 only support GET and POST. # CDash needs expects this file to be uploaded via PUT. request.get_method = lambda: 'PUT' response = opener.open(request) if self.current_package_name not in self.buildIds: - match = self.buildid_regexp.search(response.read()) + resp_value = response.read() + if isinstance(resp_value, bytes): + resp_value = resp_value.decode('utf-8') + match = self.buildid_regexp.search(resp_value) if match: buildid = match.group(1) self.buildIds[self.current_package_name] = buildid diff --git a/lib/spack/spack/reporters/junit.py b/lib/spack/spack/reporters/junit.py index d2c11dff4b..6c54c45b42 100644 --- a/lib/spack/spack/reporters/junit.py +++ b/lib/spack/spack/reporters/junit.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/resource.py b/lib/spack/spack/resource.py index 2786bcd1be..5cec54f6de 100644 --- a/lib/spack/spack/resource.py +++ b/lib/spack/spack/resource.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/s3_handler.py b/lib/spack/spack/s3_handler.py index 2a54b9ecb1..24f0a46221 100644 --- a/lib/spack/spack/s3_handler.py +++ b/lib/spack/spack/s3_handler.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,6 @@ import six.moves.urllib.error as urllib_error import spack.util.s3 as s3_util import spack.util.url as url_util -import spack.util.web as web_util # NOTE(opadron): Workaround issue in boto where its StreamingBody @@ -54,8 +53,7 @@ def _s3_open(url): # NOTE(opadron): Apply workaround here (see above) stream = WrapStream(obj['Body']) - headers = web_util.standardize_header_names( - obj['ResponseMetadata']['HTTPHeaders']) + headers = obj['ResponseMetadata']['HTTPHeaders'] return url, headers, stream diff --git a/lib/spack/spack/schema/__init__.py b/lib/spack/spack/schema/__init__.py index 894d1cd743..755e3d9086 100644 --- a/lib/spack/spack/schema/__init__.py +++ b/lib/spack/spack/schema/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/schema/cdash.py b/lib/spack/spack/schema/cdash.py index 14a24c5f41..2df2ea3f32 100644 --- a/lib/spack/spack/schema/cdash.py +++ b/lib/spack/spack/schema/cdash.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/schema/compilers.py b/lib/spack/spack/schema/compilers.py index c2f72c89d1..c994bef819 100644 --- a/lib/spack/spack/schema/compilers.py +++ b/lib/spack/spack/schema/compilers.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,7 +8,7 @@ .. literalinclude:: _spack_root/lib/spack/spack/schema/compilers.py :lines: 13- """ - +import spack.schema.environment #: Properties for inclusion in other schemas properties = { @@ -68,50 +68,7 @@ properties = { {'type': 'boolean'} ] }, - 'environment': { - 'type': 'object', - 'default': {}, - 'additionalProperties': False, - 'properties': { - 'set': { - 'type': 'object', - 'patternProperties': { - # Variable name - r'\w[\w-]*': { - 'anyOf': [{'type': 'string'}, - {'type': 'number'}] - } - } - }, - 'unset': { - 'type': 'object', - 'patternProperties': { - # Variable name - r'\w[\w-]*': {'type': 'null'} - } - }, - 'prepend-path': { - 'type': 'object', - 'patternProperties': { - # Variable name - r'\w[\w-]*': { - 'anyOf': [{'type': 'string'}, - {'type': 'number'}] - } - } - }, - 'append-path': { - 'type': 'object', - 'patternProperties': { - # Variable name - r'\w[\w-]*': { - 'anyOf': [{'type': 'string'}, - {'type': 'number'}] - } - } - } - } - }, + 'environment': spack.schema.environment.definition, 'extra_rpaths': { 'type': 'array', 'default': [], diff --git a/lib/spack/spack/schema/config.py b/lib/spack/spack/schema/config.py index 7d170bbc91..1378698825 100644 --- a/lib/spack/spack/schema/config.py +++ b/lib/spack/spack/schema/config.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/schema/container.py b/lib/spack/spack/schema/container.py new file mode 100644 index 0000000000..cb1ed8d63a --- /dev/null +++ b/lib/spack/spack/schema/container.py @@ -0,0 +1,82 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +"""Schema for the 'container' subsection of Spack environments.""" + +#: Schema for the container attribute included in Spack environments +container_schema = { + 'type': 'object', + 'additionalProperties': False, + 'properties': { + # The recipe formats that are currently supported by the command + 'format': { + 'type': 'string', + 'enum': ['docker', 'singularity'] + }, + # Describes the base image to start from and the version + # of Spack to be used + 'base': { + 'type': 'object', + 'additionalProperties': False, + 'properties': { + 'image': { + 'type': 'string', + 'enum': ['ubuntu:18.04', + 'ubuntu:16.04', + 'centos:7', + 'centos:6'] + }, + 'spack': { + 'type': 'string', + 'enum': ['develop', '0.14', '0.14.0'] + } + }, + 'required': ['image', 'spack'] + }, + # Whether or not to strip installed binaries + 'strip': { + 'type': 'boolean', + 'default': True + }, + # Additional system packages that are needed at runtime + 'os_packages': { + 'type': 'array', + 'items': { + 'type': 'string' + } + }, + # Add labels to the image + 'labels': { + 'type': 'object', + }, + # Add a custom extra section at the bottom of a stage + 'extra_instructions': { + 'type': 'object', + 'additionalProperties': False, + 'properties': { + 'build': {'type': 'string'}, + 'final': {'type': 'string'} + } + }, + # Reserved for properties that are specific to each format + 'singularity': { + 'type': 'object', + 'additionalProperties': False, + 'default': {}, + 'properties': { + 'runscript': {'type': 'string'}, + 'startscript': {'type': 'string'}, + 'test': {'type': 'string'}, + 'help': {'type': 'string'} + } + }, + 'docker': { + 'type': 'object', + 'additionalProperties': False, + 'default': {}, + } + } +} + +properties = {'container': container_schema} diff --git a/lib/spack/spack/schema/env.py b/lib/spack/spack/schema/env.py index dd3093d05d..907abc5c9a 100644 --- a/lib/spack/spack/schema/env.py +++ b/lib/spack/spack/schema/env.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/schema/environment.py b/lib/spack/spack/schema/environment.py new file mode 100644 index 0000000000..d251aeba96 --- /dev/null +++ b/lib/spack/spack/schema/environment.py @@ -0,0 +1,58 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +"""Schema for environment modifications. Meant for inclusion in other +schemas. +""" + +array_of_strings_or_num = { + 'type': 'array', 'default': [], 'items': + {'anyOf': [{'type': 'string'}, {'type': 'number'}]} +} + +dictionary_of_strings_or_num = { + 'type': 'object', 'patternProperties': + {r'\w[\w-]*': {'anyOf': [{'type': 'string'}, {'type': 'number'}]}} +} + +definition = { + 'type': 'object', + 'default': {}, + 'additionalProperties': False, + 'properties': { + 'set': dictionary_of_strings_or_num, + 'unset': array_of_strings_or_num, + 'prepend_path': dictionary_of_strings_or_num, + 'append_path': dictionary_of_strings_or_num, + 'remove_path': dictionary_of_strings_or_num + } +} + + +def parse(config_obj): + """Returns an EnvironmentModifications object containing the modifications + parsed from input. + + Args: + config_obj: a configuration dictionary conforming to the + schema definition for environment modifications + """ + import spack.util.environment as ev + try: + from collections import Sequence # novm + except ImportError: + from collections.abc import Sequence # novm + + env = ev.EnvironmentModifications() + for command, variable in config_obj.items(): + # Distinguish between commands that take only a name as argument + # (e.g. unset) and commands that take a name and a value. + if isinstance(variable, Sequence): + for name in variable: + getattr(env, command)(name) + else: + for name, value in variable.items(): + getattr(env, command)(name, value) + + return env diff --git a/lib/spack/spack/schema/gitlab_ci.py b/lib/spack/spack/schema/gitlab_ci.py index dc7b16fb21..9d0ba8a77b 100644 --- a/lib/spack/spack/schema/gitlab_ci.py +++ b/lib/spack/spack/schema/gitlab_ci.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,6 +9,24 @@ :lines: 13- """ +image_schema = { + 'oneOf': [ + { + 'type': 'string' + }, { + 'type': 'object', + 'properties': { + 'name': {'type': 'string'}, + 'entrypoint': { + 'type': 'array', + 'items': { + 'type': 'string', + }, + }, + }, + }, + ], +} #: Properties for inclusion in other schemas properties = { @@ -58,24 +76,7 @@ properties = { 'additionalProperties': True, 'required': ['tags'], 'properties': { - 'image': { - 'oneOf': [ - { - 'type': 'string' - }, { - 'type': 'object', - 'properties': { - 'name': {'type': 'string'}, - 'entrypoint': { - 'type': 'array', - 'items': { - 'type': 'string', - }, - }, - }, - }, - ], - }, + 'image': image_schema, 'tags': { 'type': 'array', 'default': [], @@ -95,6 +96,27 @@ properties = { }, }, }, + 'enable-artifacts-buildcache': { + 'type': 'boolean', + 'default': False, + }, + 'enable-debug-messages': { + 'type': 'boolean', + 'default': False, + }, + 'final-stage-rebuild-index': { + 'type': 'object', + 'additionalProperties': False, + 'required': ['tags'], + 'properties': { + 'image': image_schema, + 'tags': { + 'type': 'array', + 'default': [], + 'items': {'type': 'string'} + }, + }, + }, }, }, } diff --git a/lib/spack/spack/schema/merged.py b/lib/spack/spack/schema/merged.py index 76f8ffa2d5..e118acf286 100644 --- a/lib/spack/spack/schema/merged.py +++ b/lib/spack/spack/schema/merged.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ from llnl.util.lang import union_dicts import spack.schema.cdash import spack.schema.compilers import spack.schema.config +import spack.schema.container import spack.schema.gitlab_ci import spack.schema.mirrors import spack.schema.modules @@ -26,6 +27,7 @@ properties = union_dicts( spack.schema.cdash.properties, spack.schema.compilers.properties, spack.schema.config.properties, + spack.schema.container.properties, spack.schema.gitlab_ci.properties, spack.schema.mirrors.properties, spack.schema.modules.properties, diff --git a/lib/spack/spack/schema/mirrors.py b/lib/spack/spack/schema/mirrors.py index 92e6c9bca1..5bb641df05 100644 --- a/lib/spack/spack/schema/mirrors.py +++ b/lib/spack/spack/schema/mirrors.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/schema/modules.py b/lib/spack/spack/schema/modules.py index 14f185cfcc..1fbbf614c8 100644 --- a/lib/spack/spack/schema/modules.py +++ b/lib/spack/spack/schema/modules.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,6 +8,8 @@ .. literalinclude:: _spack_root/lib/spack/spack/schema/modules.py :lines: 13- """ +import spack.schema.environment + #: Matches a spec or a multi-valued variant but not another #: valid keyword. @@ -66,17 +68,7 @@ module_file_configuration = { } } }, - 'environment': { - 'type': 'object', - 'default': {}, - 'additionalProperties': False, - 'properties': { - 'set': dictionary_of_strings, - 'unset': array_of_strings, - 'prepend_path': dictionary_of_strings, - 'append_path': dictionary_of_strings - } - } + 'environment': spack.schema.environment.definition } } diff --git a/lib/spack/spack/schema/packages.py b/lib/spack/spack/schema/packages.py index f97d82d83a..4984471c73 100644 --- a/lib/spack/spack/schema/packages.py +++ b/lib/spack/spack/schema/packages.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/schema/projections.py b/lib/spack/spack/schema/projections.py index f076ed473b..d6f506f090 100644 --- a/lib/spack/spack/schema/projections.py +++ b/lib/spack/spack/schema/projections.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/schema/repos.py b/lib/spack/spack/schema/repos.py index fe74942872..6aa9bcf57e 100644 --- a/lib/spack/spack/schema/repos.py +++ b/lib/spack/spack/schema/repos.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/schema/upstreams.py b/lib/spack/spack/schema/upstreams.py index 5925782af2..f5192aa096 100644 --- a/lib/spack/spack/schema/upstreams.py +++ b/lib/spack/spack/schema/upstreams.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index f983e5c559..4b6bd67b6d 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -81,18 +81,16 @@ import sys import collections import hashlib import itertools +import operator import os import re import six - -from operator import attrgetter import ruamel.yaml as yaml -from llnl.util.filesystem import find_headers, find_libraries, is_exe -from llnl.util.lang import key_ordering, HashableMap, ObjectWrapper, dedupe -from llnl.util.lang import check_kwargs, memoized -from llnl.util.tty.color import cwrite, colorize, cescape, get_color_when +import llnl.util.filesystem as fs +import llnl.util.lang as lang +import llnl.util.tty.color as clr import llnl.util.tty as tty import spack.paths @@ -103,48 +101,34 @@ import spack.dependency as dp import spack.error import spack.hash_types as ht import spack.parse +import spack.provider_index import spack.repo import spack.store +import spack.util.crypto +import spack.util.executable +import spack.util.module_cmd as md +import spack.util.prefix import spack.util.spack_json as sjson import spack.util.spack_yaml as syaml - -from spack.util.module_cmd import get_path_from_module, load_module -from spack.error import NoLibrariesError, NoHeadersError -from spack.error import SpecError, UnsatisfiableSpecError -from spack.provider_index import ProviderIndex -from spack.util.crypto import prefix_bits -from spack.util.executable import Executable -from spack.util.prefix import Prefix -from spack.util.spack_yaml import syaml_dict -from spack.util.string import comma_or -from spack.variant import MultiValuedVariant, AbstractVariant -from spack.variant import BoolValuedVariant, substitute_abstract_variants -from spack.variant import VariantMap, UnknownVariantError -from spack.variant import DuplicateVariantError -from spack.variant import UnsatisfiableVariantSpecError -from spack.version import VersionList, VersionRange, Version, ver -from ruamel.yaml.error import MarkedYAMLError +import spack.util.string +import spack.variant as vt +import spack.version as vn __all__ = [ 'Spec', 'parse', - 'SpecError', 'SpecParseError', 'DuplicateDependencyError', - 'DuplicateVariantError', 'DuplicateCompilerSpecError', 'UnsupportedCompilerError', - 'UnknownVariantError', 'DuplicateArchitectureError', 'InconsistentSpecError', 'InvalidDependencyError', 'NoProviderError', 'MultipleProviderError', - 'UnsatisfiableSpecError', 'UnsatisfiableSpecNameError', 'UnsatisfiableVersionSpecError', 'UnsatisfiableCompilerSpecError', - 'UnsatisfiableVariantSpecError', 'UnsatisfiableCompilerFlagSpecError', 'UnsatisfiableArchitectureSpecError', 'UnsatisfiableProviderSpecError', @@ -183,7 +167,7 @@ _separators = '[\\%s]' % '\\'.join(color_formats.keys()) #: Versionlist constant so we don't have to build a list #: every time we call str() -_any_version = VersionList([':']) +_any_version = vn.VersionList([':']) default_format = '{name}{@version}' default_format += '{%compiler.name}{@compiler.version}{compiler_flags}' @@ -202,15 +186,15 @@ def colorize_spec(spec): # ignore compiler versions (color same as compiler) sep = match.group(0) if self.last == '%' and sep == '@': - return cescape(sep) + return clr.cescape(sep) self.last = sep - return '%s%s' % (color_formats[sep], cescape(sep)) + return '%s%s' % (color_formats[sep], clr.cescape(sep)) - return colorize(re.sub(_separators, insert_color(), str(spec)) + '@.') + return clr.colorize(re.sub(_separators, insert_color(), str(spec)) + '@.') -@key_ordering +@lang.key_ordering class ArchSpec(object): def __init__(self, spec_or_platform_tuple=(None, None, None)): """ Architecture specification a package should be built with. @@ -444,11 +428,11 @@ class ArchSpec(object): return self.platform and self.os and self.target def to_dict(self): - d = syaml_dict([ + d = syaml.syaml_dict([ ('platform', self.platform), ('platform_os', self.os), ('target', self.target.to_dict_or_value())]) - return syaml_dict([('arch', d)]) + return syaml.syaml_dict([('arch', d)]) @staticmethod def from_dict(d): @@ -487,7 +471,7 @@ class ArchSpec(object): return string in str(self) or string in self.target -@key_ordering +@lang.key_ordering class CompilerSpec(object): """The CompilerSpec field represents the compiler or range of compiler versions that a package should be built with. CompilerSpecs have a @@ -516,8 +500,8 @@ class CompilerSpec(object): elif nargs == 2: name, version = args self.name = name - self.versions = VersionList() - self.versions.add(ver(version)) + self.versions = vn.VersionList() + self.versions.add(vn.ver(version)) else: raise TypeError( @@ -558,7 +542,7 @@ class CompilerSpec(object): @property def version(self): if not self.concrete: - raise SpecError("Spec is not concrete: " + str(self)) + raise spack.error.SpecError("Spec is not concrete: " + str(self)) return self.versions[0] def copy(self): @@ -571,15 +555,15 @@ class CompilerSpec(object): return (self.name, self.versions) def to_dict(self): - d = syaml_dict([('name', self.name)]) + d = syaml.syaml_dict([('name', self.name)]) d.update(self.versions.to_dict()) - return syaml_dict([('compiler', d)]) + return syaml.syaml_dict([('compiler', d)]) @staticmethod def from_dict(d): d = d['compiler'] - return CompilerSpec(d['name'], VersionList.from_dict(d)) + return CompilerSpec(d['name'], vn.VersionList.from_dict(d)) def __str__(self): out = self.name @@ -592,7 +576,7 @@ class CompilerSpec(object): return str(self) -@key_ordering +@lang.key_ordering class DependencySpec(object): """DependencySpecs connect two nodes in the DAG, and contain deptypes. @@ -640,7 +624,7 @@ _valid_compiler_flags = [ 'cflags', 'cxxflags', 'fflags', 'ldflags', 'ldlibs', 'cppflags'] -class FlagMap(HashableMap): +class FlagMap(lang.HashableMap): def __init__(self, spec): super(FlagMap, self).__init__() @@ -698,7 +682,7 @@ class FlagMap(HashableMap): for key in sorted_keys) + cond_symbol -class DependencyMap(HashableMap): +class DependencyMap(lang.HashableMap): """Each spec has a DependencyMap containing specs for its dependencies. The DependencyMap is keyed by name. """ @@ -725,8 +709,8 @@ def _command_default_handler(descriptor, spec, cls): """ path = os.path.join(spec.prefix.bin, spec.name) - if is_exe(path): - return Executable(path) + if fs.is_exe(path): + return spack.util.executable.Executable(path) else: msg = 'Unable to locate {0} command in {1}' raise RuntimeError(msg.format(spec.name, spec.prefix.bin)) @@ -750,13 +734,14 @@ def _headers_default_handler(descriptor, spec, cls): Raises: NoHeadersError: If no headers are found """ - headers = find_headers('*', root=spec.prefix.include, recursive=True) + headers = fs.find_headers('*', root=spec.prefix.include, recursive=True) if headers: return headers else: msg = 'Unable to locate {0} headers in {1}' - raise NoHeadersError(msg.format(spec.name, spec.prefix.include)) + raise spack.error.NoHeadersError( + msg.format(spec.name, spec.prefix.include)) def _libs_default_handler(descriptor, spec, cls): @@ -801,12 +786,13 @@ def _libs_default_handler(descriptor, spec, cls): ([False] if ('~shared' in spec) else [True, False]) for shared in search_shared: - libs = find_libraries(name, spec.prefix, shared=shared, recursive=True) + libs = fs.find_libraries( + name, spec.prefix, shared=shared, recursive=True) if libs: return libs msg = 'Unable to recursively locate {0} libraries in {1}' - raise NoLibrariesError(msg.format(spec.name, spec.prefix)) + raise spack.error.NoLibrariesError(msg.format(spec.name, spec.prefix)) class ForwardQueryToPackage(object): @@ -920,7 +906,7 @@ class ForwardQueryToPackage(object): raise AttributeError(msg.format(cls_name, self.attribute_name)) -class SpecBuildInterface(ObjectWrapper): +class SpecBuildInterface(lang.ObjectWrapper): command = ForwardQueryToPackage( 'command', default_handler=_command_default_handler @@ -952,7 +938,7 @@ class SpecBuildInterface(ObjectWrapper): ) -@key_ordering +@lang.key_ordering class Spec(object): #: Cache for spec's prefix, computed lazily in the corresponding property @@ -985,8 +971,8 @@ class Spec(object): # init an empty spec that matches anything. self.name = None - self.versions = VersionList(':') - self.variants = VariantMap(self) + self.versions = vn.VersionList(':') + self.variants = vt.VariantMap(self) self.architecture = None self.compiler = None self.external_path = None @@ -1088,9 +1074,9 @@ class Spec(object): # map to '+foo' and '~foo' respectively. As such they need a # BoolValuedVariant instance. if str(value).upper() == 'TRUE' or str(value).upper() == 'FALSE': - self.variants[name] = BoolValuedVariant(name, value) + self.variants[name] = vt.BoolValuedVariant(name, value) else: - self.variants[name] = AbstractVariant(name, value) + self.variants[name] = vt.AbstractVariant(name, value) def _set_architecture(self, **kwargs): """Called by the parser to set the architecture.""" @@ -1131,6 +1117,18 @@ class Spec(object): self._dependencies[spec.name] = dspec spec._dependents[self.name] = dspec + def _add_default_platform(self): + """If a spec has an os or a target and no platform, give it + the default platform. + + This is private because it is used by the parser -- it's not + expected to be used outside of ``spec.py``. + + """ + arch = self.architecture + if arch and not arch.platform and (arch.os or arch.target): + self._set_architecture(platform=spack.architecture.platform().name) + # # Public interface # @@ -1256,7 +1254,7 @@ class Spec(object): depth = kwargs.get('depth', False) key_fun = kwargs.get('key', id) if isinstance(key_fun, six.string_types): - key_fun = attrgetter(key_fun) + key_fun = operator.attrgetter(key_fun) yield_root = kwargs.get('root', True) cover = kwargs.get('cover', 'nodes') direction = kwargs.get('direction', 'children') @@ -1340,7 +1338,7 @@ class Spec(object): @property def prefix(self): if not self._concrete: - raise SpecError("Spec is not concrete: " + str(self)) + raise spack.error.SpecError("Spec is not concrete: " + str(self)) if self._prefix is None: upstream, record = spack.store.db.query_by_spec_hash( @@ -1353,7 +1351,7 @@ class Spec(object): @prefix.setter def prefix(self, value): - self._prefix = Prefix(value) + self._prefix = spack.util.prefix.Prefix(value) def _spec_hash(self, hash): """Utility method for computing different types of Spec hashes. @@ -1481,7 +1479,7 @@ class Spec(object): Arguments: hash (SpecHashDescriptor) type of hash to generate. """ - d = syaml_dict() + d = syaml.syaml_dict() if self.versions: d.update(self.versions.to_dict()) @@ -1495,7 +1493,7 @@ class Spec(object): if self.namespace: d['namespace'] = self.namespace - params = syaml_dict( + params = syaml.syaml_dict( sorted( v.yaml_entry() for _, v in self.variants.items() ) @@ -1524,15 +1522,15 @@ class Spec(object): deps = self.dependencies_dict(deptype=hash.deptype) if deps: - d['dependencies'] = syaml_dict([ + d['dependencies'] = syaml.syaml_dict([ (name, - syaml_dict([ + syaml.syaml_dict([ ('hash', dspec.spec._cached_hash(hash)), ('type', sorted(str(s) for s in dspec.deptypes))]) ) for name, dspec in sorted(deps.items()) ]) - return syaml_dict([(self.name, d)]) + return syaml.syaml_dict([(self.name, d)]) def to_dict(self, hash=ht.dag_hash): """Create a dictionary suitable for writing this spec to YAML or JSON. @@ -1607,7 +1605,7 @@ class Spec(object): node[s.name]['build_hash'] = s.build_hash() node_list.append(node) - return syaml_dict([('spec', node_list)]) + return syaml.syaml_dict([('spec', node_list)]) def to_record_dict(self): """Return a "flat" dictionary with name and hash as top-level keys. @@ -1628,7 +1626,7 @@ class Spec(object): But is otherwise the same as ``to_node_dict()``. """ - dictionary = syaml_dict() + dictionary = syaml.syaml_dict() dictionary["name"] = self.name dictionary["hash"] = self.dag_hash() dictionary.update(self.to_node_dict()[self.name]) @@ -1652,7 +1650,7 @@ class Spec(object): spec._build_hash = node.get('build_hash', None) if 'version' in node or 'versions' in node: - spec.versions = VersionList.from_dict(node) + spec.versions = vn.VersionList.from_dict(node) if 'arch' in node: spec.architecture = ArchSpec.from_dict(node) @@ -1667,11 +1665,11 @@ class Spec(object): if name in _valid_compiler_flags: spec.compiler_flags[name] = value else: - spec.variants[name] = MultiValuedVariant.from_node_dict( + spec.variants[name] = vt.MultiValuedVariant.from_node_dict( name, value) elif 'variants' in node: for name, value in node['variants'].items(): - spec.variants[name] = MultiValuedVariant.from_node_dict( + spec.variants[name] = vt.MultiValuedVariant.from_node_dict( name, value ) for name in FlagMap.valid_compiler_flags(): @@ -1700,7 +1698,7 @@ class Spec(object): patches = node['patches'] if len(patches) > 0: mvar = spec.variants.setdefault( - 'patches', MultiValuedVariant('patches', ()) + 'patches', vt.MultiValuedVariant('patches', ()) ) mvar.value = patches # FIXME: Monkey patches mvar to store patches order @@ -1738,7 +1736,8 @@ class Spec(object): # new format: elements of dependency spec are keyed. dag_hash, deptypes = elt['hash'], elt['type'] else: - raise SpecError("Couldn't parse dependency types in spec.") + raise spack.error.SpecError( + "Couldn't parse dependency types in spec.") yield dep_name, dag_hash, list(deptypes) @@ -1907,7 +1906,7 @@ class Spec(object): # dependencies are the following elements. dep_list = [Spec.from_node_dict(node) for node in nodes] if not dep_list: - raise SpecError("YAML spec contains no nodes.") + raise spack.error.SpecError("YAML spec contains no nodes.") deps = dict((spec.name, spec) for spec in dep_list) spec = dep_list[0] @@ -1936,7 +1935,7 @@ class Spec(object): try: data = yaml.load(stream) return Spec.from_dict(data) - except MarkedYAMLError as e: + except yaml.error.MarkedYAMLError as e: raise syaml.SpackYAMLError("error parsing YAML spec:", str(e)) @staticmethod @@ -2032,7 +2031,8 @@ class Spec(object): a problem. """ # Make an index of stuff this spec already provides - self_index = ProviderIndex(self.traverse(), restrict=True) + self_index = spack.provider_index.ProviderIndex( + self.traverse(), restrict=True) changed = False done = False @@ -2072,7 +2072,7 @@ class Spec(object): # constraints. copy.normalize(force=True) break - except SpecError: + except spack.error.SpecError: # On error, we'll try the next replacement. continue @@ -2133,7 +2133,8 @@ class Spec(object): normalize() for more details on this. """ if not self.name: - raise SpecError("Attempting to concretize anonymous spec") + raise spack.error.SpecError( + "Attempting to concretize anonymous spec") if self._concrete: return @@ -2182,7 +2183,7 @@ class Spec(object): # Add any patches from the package to the spec. patches = [] for cond, patch_list in s.package_class.patches.items(): - if s.satisfies(cond): + if s.satisfies(cond, strict=True): for patch in patch_list: patches.append(patch) if patches: @@ -2201,7 +2202,7 @@ class Spec(object): patches = [] for cond, dependency in pkg_deps[dspec.spec.name].items(): - if dspec.parent.satisfies(cond): + if dspec.parent.satisfies(cond, strict=True): for pcond, patch_list in dependency.patches.items(): if dspec.spec.satisfies(pcond): for patch in patch_list: @@ -2214,9 +2215,9 @@ class Spec(object): if id(spec) not in spec_to_patches: continue - patches = list(dedupe(spec_to_patches[id(spec)])) + patches = list(lang.dedupe(spec_to_patches[id(spec)])) mvar = spec.variants.setdefault( - 'patches', MultiValuedVariant('patches', ()) + 'patches', vt.MultiValuedVariant('patches', ()) ) mvar.value = tuple(p.sha256 for p in patches) # FIXME: Monkey patches mvar to store patches order @@ -2234,9 +2235,9 @@ class Spec(object): compiler = spack.compilers.compiler_for_spec( s.compiler, s.architecture) for mod in compiler.modules: - load_module(mod) + md.load_module(mod) - s.external_path = get_path_from_module(s.external_module) + s.external_path = md.get_path_from_module(s.external_module) # Mark everything in the spec as concrete, as well. self._mark_concrete() @@ -2336,7 +2337,7 @@ class Spec(object): return flat_deps - except UnsatisfiableSpecError as e: + except spack.error.UnsatisfiableSpecError as e: # Here, the DAG contains two instances of the same package # with inconsistent constraints. Users cannot produce # inconsistent specs like this on the command line: the @@ -2369,7 +2370,7 @@ class Spec(object): """ conditions = self.package_class.dependencies[name] - substitute_abstract_variants(self) + vt.substitute_abstract_variants(self) # evaluate when specs to figure out constraints on the dependency. dep = None for when_spec, dependency in conditions.items(): @@ -2378,7 +2379,7 @@ class Spec(object): dep = dp.Dependency(self.name, Spec(name), type=()) try: dep.merge(dependency) - except UnsatisfiableSpecError as e: + except spack.error.UnsatisfiableSpecError as e: e.message = ( "Conflicting conditional dependencies for spec" "\n\n\t{0}\n\n" @@ -2468,7 +2469,7 @@ class Spec(object): if provider: dep = provider else: - index = ProviderIndex([dep], restrict=True) + index = spack.provider_index.ProviderIndex([dep], restrict=True) items = list(spec_deps.items()) for name, vspec in items: if not vspec.virtual: @@ -2498,7 +2499,7 @@ class Spec(object): # merge package/vdep information into spec try: changed |= spec_deps[dep.name].constrain(dep) - except UnsatisfiableSpecError as e: + except spack.error.UnsatisfiableSpecError as e: fmt = 'An unsatisfiable {0}'.format(e.constraint_type) fmt += ' constraint has been detected for spec:' fmt += '\n\n{0}\n\n'.format(spec_deps[dep.name].tree(indent=4)) @@ -2585,7 +2586,8 @@ class Spec(object): detection, to ensure that the spec is actually a DAG. """ if not self.name: - raise SpecError("Attempting to normalize anonymous spec") + raise spack.error.SpecError( + "Attempting to normalize anonymous spec") # Set _normal and _concrete to False when forced if force: @@ -2615,7 +2617,7 @@ class Spec(object): # Initialize index of virtual dependency providers if # concretize didn't pass us one already - provider_index = ProviderIndex( + provider_index = spack.provider_index.ProviderIndex( [s for s in all_spec_deps.values()], restrict=True) # traverse the package DAG and fill out dependencies according @@ -2663,9 +2665,9 @@ class Spec(object): not_existing = set(spec.variants) - ( set(pkg_variants) | set(spack.directives.reserved_names)) if not_existing: - raise UnknownVariantError(spec.name, not_existing) + raise vt.UnknownVariantError(spec, not_existing) - substitute_abstract_variants(spec) + vt.substitute_abstract_variants(spec) def constrain(self, other, deps=True): """Merge the constraints of other with self. @@ -2679,7 +2681,7 @@ class Spec(object): if self.satisfies(other): return False else: - raise UnsatisfiableSpecError( + raise spack.error.UnsatisfiableSpecError( self, other, 'constrain a concrete spec' ) @@ -2700,7 +2702,7 @@ class Spec(object): for v in [x for x in other.variants if x in self.variants]: if not self.variants[v].compatible(other.variants[v]): - raise UnsatisfiableVariantSpecError( + raise vt.UnsatisfiableVariantSpecError( self.variants[v], other.variants[v] ) @@ -2928,8 +2930,10 @@ class Spec(object): return False # For virtual dependencies, we need to dig a little deeper. - self_index = ProviderIndex(self.traverse(), restrict=True) - other_index = ProviderIndex(other.traverse(), restrict=True) + self_index = spack.provider_index.ProviderIndex( + self.traverse(), restrict=True) + other_index = spack.provider_index.ProviderIndex( + other.traverse(), restrict=True) # This handles cases where there are already providers for both vpkgs if not self_index.satisfies(other_index): @@ -2954,7 +2958,7 @@ class Spec(object): return [spec for spec in self.traverse() if spec.virtual] @property - @memoized + @lang.memoized def patches(self): """Return patch objects for any patch sha256 sums on this Spec. @@ -2965,7 +2969,7 @@ class Spec(object): patches from install directories, but it probably should. """ if not self.concrete: - raise SpecError("Spec is not concrete: " + str(self)) + raise spack.error.SpecError("Spec is not concrete: " + str(self)) if 'patches' not in self.variants: return [] @@ -3135,7 +3139,8 @@ class Spec(object): @property def version(self): if not self.versions.concrete: - raise SpecError("Spec version is not concrete: " + str(self)) + raise spack.error.SpecError( + "Spec version is not concrete: " + str(self)) return self.versions[0] def __getitem__(self, name): @@ -3375,10 +3380,10 @@ class Spec(object): out = six.StringIO() def write(s, c=None): - f = cescape(s) + f = clr.cescape(s) if c is not None: f = color_formats[c] + f + '@.' - cwrite(f, stream=out, color=color) + clr.cwrite(f, stream=out, color=color) def write_attribute(spec, attribute, color): current = spec @@ -3445,7 +3450,7 @@ class Spec(object): 'Attempted to format private attribute' ) else: - if isinstance(current, VariantMap): + if isinstance(current, vt.VariantMap): # subscript instead of getattr for variant names current = current[part] else: @@ -3463,7 +3468,7 @@ class Spec(object): m = 'Attempted to format attribute %s.' % attribute m += 'Spec.%s has no attribute %s' % (parent, part) raise SpecFormatStringError(m) - if isinstance(current, VersionList): + if isinstance(current, vn.VersionList): if current == _any_version: # We don't print empty version lists return @@ -3609,10 +3614,10 @@ class Spec(object): named_str = fmt = '' def write(s, c=None): - f = cescape(s) + f = clr.cescape(s) if c is not None: f = color_formats[c] + f + '@.' - cwrite(f, stream=out, color=color) + clr.cwrite(f, stream=out, color=color) iterator = enumerate(format_string) for i, c in iterator: @@ -3807,7 +3812,7 @@ class Spec(object): def tree(self, **kwargs): """Prints out this spec and its dependencies, tree-formatted with indentation.""" - color = kwargs.pop('color', get_color_when()) + color = kwargs.pop('color', clr.get_color_when()) depth = kwargs.pop('depth', False) hashes = kwargs.pop('hashes', False) hlen = kwargs.pop('hashlen', None) @@ -3819,7 +3824,7 @@ class Spec(object): show_types = kwargs.pop('show_types', False) deptypes = kwargs.pop('deptypes', 'all') recurse_dependencies = kwargs.pop('recurse_dependencies', True) - check_kwargs(kwargs, self.tree) + lang.check_kwargs(kwargs, self.tree) out = "" for d, dep_spec in self.traverse_edges( @@ -3836,16 +3841,17 @@ class Spec(object): if status_fn: status = status_fn(node) if node.package.installed_upstream: - out += colorize("@g{[^]} ", color=color) + out += clr.colorize("@g{[^]} ", color=color) elif status is None: - out += colorize("@K{ - } ", color=color) # not installed + out += clr.colorize("@K{ - } ", color=color) # !installed elif status: - out += colorize("@g{[+]} ", color=color) # installed + out += clr.colorize("@g{[+]} ", color=color) # installed else: - out += colorize("@r{[-]} ", color=color) # missing + out += clr.colorize("@r{[-]} ", color=color) # missing if hashes: - out += colorize('@K{%s} ', color=color) % node.dag_hash(hlen) + out += clr.colorize( + '@K{%s} ', color=color) % node.dag_hash(hlen) if show_types: types = set() @@ -4059,14 +4065,6 @@ class SpecParser(spack.parse.Parser): except spack.parse.ParseError as e: raise SpecParseError(e) - # If the spec has an os or a target and no platform, give it - # the default platform - platform_default = spack.architecture.platform().name - for spec in specs: - for s in spec.traverse(): - if s.architecture and not s.architecture.platform and \ - (s.architecture.os or s.architecture.target): - s._set_architecture(platform=platform_default) return specs def spec_from_file(self): @@ -4157,17 +4155,17 @@ class SpecParser(spack.parse.Parser): while self.next: if self.accept(AT): vlist = self.version_list() - spec.versions = VersionList() + spec.versions = vn.VersionList() for version in vlist: spec._add_version(version) elif self.accept(ON): name = self.variant() - spec.variants[name] = BoolValuedVariant(name, True) + spec.variants[name] = vt.BoolValuedVariant(name, True) elif self.accept(OFF): name = self.variant() - spec.variants[name] = BoolValuedVariant(name, False) + spec.variants[name] = vt.BoolValuedVariant(name, False) elif self.accept(PCT): spec._set_compiler(self.compiler()) @@ -4198,6 +4196,7 @@ class SpecParser(spack.parse.Parser): else: break + spec._add_default_platform() return spec def variant(self, name=None): @@ -4223,16 +4222,16 @@ class SpecParser(spack.parse.Parser): end = self.token.value elif start: # No colon, but there was a version. - return Version(start) + return vn.Version(start) else: # No colon and no id: invalid version. self.next_token_error("Invalid version specifier") if start: - start = Version(start) + start = vn.Version(start) if end: - end = Version(end) - return VersionRange(start, end) + end = vn.Version(end) + return vn.VersionRange(start, end) def version_list(self): vlist = [] @@ -4247,13 +4246,13 @@ class SpecParser(spack.parse.Parser): compiler = CompilerSpec.__new__(CompilerSpec) compiler.name = self.token.value - compiler.versions = VersionList() + compiler.versions = vn.VersionList() if self.accept(AT): vlist = self.version_list() for version in vlist: compiler._add_version(version) else: - compiler.versions = VersionList(':') + compiler.versions = vn.VersionList(':') return compiler def check_identifier(self, id=None): @@ -4309,10 +4308,10 @@ def base32_prefix_bits(hash_string, bits): % (bits, hash_string)) hash_bytes = base64.b32decode(hash_string, casefold=True) - return prefix_bits(hash_bytes, bits) + return spack.util.crypto.prefix_bits(hash_bytes, bits) -class SpecParseError(SpecError): +class SpecParseError(spack.error.SpecError): """Wrapper for ParseError for when we're parsing specs.""" def __init__(self, parse_error): super(SpecParseError, self).__init__(parse_error.message) @@ -4320,40 +4319,41 @@ class SpecParseError(SpecError): self.pos = parse_error.pos -class DuplicateDependencyError(SpecError): +class DuplicateDependencyError(spack.error.SpecError): """Raised when the same dependency occurs in a spec twice.""" -class DuplicateCompilerSpecError(SpecError): +class DuplicateCompilerSpecError(spack.error.SpecError): """Raised when the same compiler occurs in a spec twice.""" -class UnsupportedCompilerError(SpecError): +class UnsupportedCompilerError(spack.error.SpecError): """Raised when the user asks for a compiler spack doesn't know about.""" def __init__(self, compiler_name): super(UnsupportedCompilerError, self).__init__( "The '%s' compiler is not yet supported." % compiler_name) -class DuplicateArchitectureError(SpecError): +class DuplicateArchitectureError(spack.error.SpecError): """Raised when the same architecture occurs in a spec twice.""" -class InconsistentSpecError(SpecError): +class InconsistentSpecError(spack.error.SpecError): """Raised when two nodes in the same spec DAG have inconsistent constraints.""" -class InvalidDependencyError(SpecError): +class InvalidDependencyError(spack.error.SpecError): """Raised when a dependency in a spec is not actually a dependency of the package.""" def __init__(self, pkg, deps): self.invalid_deps = deps super(InvalidDependencyError, self).__init__( - 'Package {0} does not depend on {1}'.format(pkg, comma_or(deps))) + 'Package {0} does not depend on {1}'.format( + pkg, spack.util.string.comma_or(deps))) -class NoProviderError(SpecError): +class NoProviderError(spack.error.SpecError): """Raised when there is no package that provides a particular virtual dependency. """ @@ -4363,7 +4363,7 @@ class NoProviderError(SpecError): self.vpkg = vpkg -class MultipleProviderError(SpecError): +class MultipleProviderError(spack.error.SpecError): """Raised when there is no package that provides a particular virtual dependency. """ @@ -4376,42 +4376,42 @@ class MultipleProviderError(SpecError): self.providers = providers -class UnsatisfiableSpecNameError(UnsatisfiableSpecError): +class UnsatisfiableSpecNameError(spack.error.UnsatisfiableSpecError): """Raised when two specs aren't even for the same package.""" def __init__(self, provided, required): super(UnsatisfiableSpecNameError, self).__init__( provided, required, "name") -class UnsatisfiableVersionSpecError(UnsatisfiableSpecError): +class UnsatisfiableVersionSpecError(spack.error.UnsatisfiableSpecError): """Raised when a spec version conflicts with package constraints.""" def __init__(self, provided, required): super(UnsatisfiableVersionSpecError, self).__init__( provided, required, "version") -class UnsatisfiableCompilerSpecError(UnsatisfiableSpecError): +class UnsatisfiableCompilerSpecError(spack.error.UnsatisfiableSpecError): """Raised when a spec comiler conflicts with package constraints.""" def __init__(self, provided, required): super(UnsatisfiableCompilerSpecError, self).__init__( provided, required, "compiler") -class UnsatisfiableCompilerFlagSpecError(UnsatisfiableSpecError): +class UnsatisfiableCompilerFlagSpecError(spack.error.UnsatisfiableSpecError): """Raised when a spec variant conflicts with package constraints.""" def __init__(self, provided, required): super(UnsatisfiableCompilerFlagSpecError, self).__init__( provided, required, "compiler_flags") -class UnsatisfiableArchitectureSpecError(UnsatisfiableSpecError): +class UnsatisfiableArchitectureSpecError(spack.error.UnsatisfiableSpecError): """Raised when a spec architecture conflicts with package constraints.""" def __init__(self, provided, required): super(UnsatisfiableArchitectureSpecError, self).__init__( provided, required, "architecture") -class UnsatisfiableProviderSpecError(UnsatisfiableSpecError): +class UnsatisfiableProviderSpecError(spack.error.UnsatisfiableSpecError): """Raised when a provider is supplied but constraints don't match a vpkg requirement""" def __init__(self, provided, required): @@ -4421,14 +4421,14 @@ class UnsatisfiableProviderSpecError(UnsatisfiableSpecError): # TODO: get rid of this and be more specific about particular incompatible # dep constraints -class UnsatisfiableDependencySpecError(UnsatisfiableSpecError): +class UnsatisfiableDependencySpecError(spack.error.UnsatisfiableSpecError): """Raised when some dependency of constrained specs are incompatible""" def __init__(self, provided, required): super(UnsatisfiableDependencySpecError, self).__init__( provided, required, "dependency") -class AmbiguousHashError(SpecError): +class AmbiguousHashError(spack.error.SpecError): def __init__(self, msg, *specs): spec_fmt = '{namespace}.{name}{@version}{%compiler}{compiler_flags}' spec_fmt += '{variants}{arch=architecture}{/hash:7}' @@ -4437,21 +4437,21 @@ class AmbiguousHashError(SpecError): super(AmbiguousHashError, self).__init__(msg + specs_str) -class InvalidHashError(SpecError): +class InvalidHashError(spack.error.SpecError): def __init__(self, spec, hash): super(InvalidHashError, self).__init__( "The spec specified by %s does not match provided spec %s" % (hash, spec)) -class NoSuchHashError(SpecError): +class NoSuchHashError(spack.error.SpecError): def __init__(self, hash): super(NoSuchHashError, self).__init__( "No installed spec matches the hash: '%s'" % hash) -class SpecFilenameError(SpecError): +class SpecFilenameError(spack.error.SpecError): """Raised when a spec file name is invalid.""" @@ -4459,7 +4459,7 @@ class NoSuchSpecFileError(SpecFilenameError): """Raised when a spec file doesn't exist.""" -class RedundantSpecError(SpecError): +class RedundantSpecError(spack.error.SpecError): def __init__(self, spec, addition): super(RedundantSpecError, self).__init__( "Attempting to add %s to spec %s which is already concrete." @@ -4467,7 +4467,7 @@ class RedundantSpecError(SpecError): % (addition, spec)) -class SpecFormatStringError(SpecError): +class SpecFormatStringError(spack.error.SpecError): """Called for errors in Spec format strings.""" @@ -4479,7 +4479,7 @@ class SpecFormatSigilError(SpecFormatStringError): super(SpecFormatSigilError, self).__init__(msg) -class ConflictsInSpecError(SpecError, RuntimeError): +class ConflictsInSpecError(spack.error.SpecError, RuntimeError): def __init__(self, spec, matches): message = 'Conflicts in concretized spec "{0}"\n'.format( spec.short_spec @@ -4507,10 +4507,10 @@ class ConflictsInSpecError(SpecError, RuntimeError): super(ConflictsInSpecError, self).__init__(message, long_message) -class SpecDependencyNotFoundError(SpecError): +class SpecDependencyNotFoundError(spack.error.SpecError): """Raised when a failure is encountered writing the dependencies of a spec.""" -class SpecDeprecatedError(SpecError): +class SpecDeprecatedError(spack.error.SpecError): """Raised when a spec concretizes to a deprecated spec or dependency.""" diff --git a/lib/spack/spack/spec_list.py b/lib/spack/spack/spec_list.py index d9c1be2652..63bd29a7a9 100644 --- a/lib/spack/spack/spec_list.py +++ b/lib/spack/spack/spec_list.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index bf65ee0b01..917d20aa04 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -1,8 +1,10 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +from __future__ import print_function + import os import stat import sys @@ -269,7 +271,7 @@ class Stage(object): else: raise ValueError( "Can't construct Stage without url or fetch strategy") - self.fetcher.set_stage(self) + self.fetcher.stage = self # self.fetcher can change with mirrors. self.default_fetcher = self.fetcher self.search_fn = search_fn @@ -456,7 +458,7 @@ class Stage(object): for fetcher in generate_fetchers(): try: - fetcher.set_stage(self) + fetcher.stage = self self.fetcher = fetcher self.fetcher.fetch() break @@ -771,7 +773,7 @@ def get_checksums_for_versions( *spack.cmd.elide_list( ["{0:{1}} {2}".format(str(v), max_len, url_dict[v]) for v in sorted_versions])) - tty.msg('') + print() archives_to_fetch = tty.get_number( "How many would you like to checksum?", default=1, abort='q') @@ -818,7 +820,7 @@ def get_checksums_for_versions( ]) num_hash = len(version_hashes) - tty.msg("Checksummed {0} version{1} of {2}".format( + tty.msg("Checksummed {0} version{1} of {2}:".format( num_hash, '' if num_hash == 1 else 's', name)) return version_lines diff --git a/lib/spack/spack/store.py b/lib/spack/spack/store.py index a4f7596fc2..2b80e994c7 100644 --- a/lib/spack/spack/store.py +++ b/lib/spack/spack/store.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/tengine.py b/lib/spack/spack/tengine.py index 6aceb391cd..e1e059c6a6 100644 --- a/lib/spack/spack/tengine.py +++ b/lib/spack/spack/tengine.py @@ -1,11 +1,10 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) import itertools import textwrap -import jinja2 import llnl.util.lang import six @@ -13,9 +12,6 @@ import spack.config from spack.util.path import canonicalize_path -TemplateNotFound = jinja2.TemplateNotFound - - class ContextMeta(type): """Meta class for Context. It helps reducing the boilerplate in client code. @@ -77,6 +73,10 @@ def make_environment(dirs=None): dirs = [canonicalize_path(d) for d in itertools.chain(builtins, extensions)] + # avoid importing this at the top level as it's used infrequently and + # slows down startup a bit. + import jinja2 + # Loader for the templates loader = jinja2.FileSystemLoader(dirs) # Environment of the template engine diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py index 94f8ac4d9e..9f87532b85 100644 --- a/lib/spack/spack/test/__init__.py +++ b/lib/spack/spack/test/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py index 0a37ef9558..1f5ff28900 100644 --- a/lib/spack/spack/test/architecture.py +++ b/lib/spack/spack/test/architecture.py @@ -1,5 +1,5 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -176,7 +176,7 @@ def test_arch_spec_container_semantic(item, architecture_str): ('gcc@4.7.2', 'ivybridge', '-march=core-avx-i -mtune=core-avx-i'), # Check mixed toolchains ('clang@8.0.0', 'broadwell', ''), - ('clang@3.5', 'x86_64', '-march=x86-64 -mcpu=generic'), + ('clang@3.5', 'x86_64', '-march=x86-64 -mtune=generic'), # Check clang compilers with 'apple' suffix ('clang@9.1.0-apple', 'x86_64', '-march=x86-64') ]) diff --git a/lib/spack/spack/test/build_distribution.py b/lib/spack/spack/test/build_distribution.py new file mode 100644 index 0000000000..2d567aee14 --- /dev/null +++ b/lib/spack/spack/test/build_distribution.py @@ -0,0 +1,41 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import pytest + +import os +import os.path + +import spack.spec +import spack.binary_distribution + +install = spack.main.SpackCommand('install') + + +def test_build_tarball_overwrite( + install_mockery, mock_fetch, monkeypatch, tmpdir): + + with tmpdir.as_cwd(): + spec = spack.spec.Spec('trivial-install-test-package').concretized() + install(str(spec)) + + # Runs fine the first time, throws the second time + spack.binary_distribution.build_tarball(spec, '.', unsigned=True) + with pytest.raises(spack.binary_distribution.NoOverwriteException): + spack.binary_distribution.build_tarball(spec, '.', unsigned=True) + + # Should work fine with force=True + spack.binary_distribution.build_tarball( + spec, '.', force=True, unsigned=True) + + # Remove the tarball and try again. + # This must *also* throw, because of the existing .spec.yaml file + os.remove(os.path.join( + spack.binary_distribution.build_cache_prefix('.'), + spack.binary_distribution.tarball_directory_name(spec), + spack.binary_distribution.tarball_name(spec, '.spack'))) + + with pytest.raises(spack.binary_distribution.NoOverwriteException): + spack.binary_distribution.build_tarball(spec, '.', unsigned=True) diff --git a/lib/spack/spack/test/build_environment.py b/lib/spack/spack/test/build_environment.py index b6a0f4b441..a7a55af0ca 100644 --- a/lib/spack/spack/test/build_environment.py +++ b/lib/spack/spack/test/build_environment.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,10 +14,9 @@ import spack.spec from spack.paths import build_env_path from spack.build_environment import dso_suffix, _static_to_shared_library from spack.util.executable import Executable -from spack.util.spack_yaml import syaml_dict, syaml_str from spack.util.environment import EnvironmentModifications -from llnl.util.filesystem import LibraryList +from llnl.util.filesystem import LibraryList, HeaderList @pytest.fixture @@ -65,6 +64,18 @@ def build_environment(working_env): del os.environ[name] +@pytest.fixture +def ensure_env_variables(config, mock_packages, monkeypatch, working_env): + """Returns a function that takes a dictionary and updates os.environ + for the test lifetime accordingly. Plugs-in mock config and repo. + """ + def _ensure(env_mods): + for name, value in env_mods.items(): + monkeypatch.setenv(name, value) + + return _ensure + + def test_static_to_shared_library(build_environment): os.environ['SPACK_TEST_COMMAND'] = 'dump-args' @@ -119,79 +130,58 @@ def test_cc_not_changed_by_modules(monkeypatch, working_env): assert os.environ['ANOTHER_VAR'] == 'THIS_IS_SET' -@pytest.mark.usefixtures('config', 'mock_packages') -def test_compiler_config_modifications(monkeypatch, working_env): - s = spack.spec.Spec('cmake') - s.concretize() - pkg = s.package - - os.environ['SOME_VAR_STR'] = '' - os.environ['SOME_VAR_NUM'] = '0' - os.environ['PATH_LIST'] = '/path/third:/path/forth' - os.environ['EMPTY_PATH_LIST'] = '' - os.environ.pop('NEW_PATH_LIST', None) - - env_mod = syaml_dict() - set_cmd = syaml_dict() - env_mod[syaml_str('set')] = set_cmd - - set_cmd[syaml_str('SOME_VAR_STR')] = syaml_str('SOME_STR') - set_cmd[syaml_str('SOME_VAR_NUM')] = 1 - - monkeypatch.setattr(pkg.compiler, 'environment', env_mod) - spack.build_environment.setup_package(pkg, False) - assert os.environ['SOME_VAR_STR'] == 'SOME_STR' - assert os.environ['SOME_VAR_NUM'] == str(1) - - env_mod = syaml_dict() - unset_cmd = syaml_dict() - env_mod[syaml_str('unset')] = unset_cmd - - unset_cmd[syaml_str('SOME_VAR_STR')] = None - - monkeypatch.setattr(pkg.compiler, 'environment', env_mod) - assert 'SOME_VAR_STR' in os.environ - spack.build_environment.setup_package(pkg, False) - assert 'SOME_VAR_STR' not in os.environ - - env_mod = syaml_dict() - set_cmd = syaml_dict() - env_mod[syaml_str('set')] = set_cmd - append_cmd = syaml_dict() - env_mod[syaml_str('append-path')] = append_cmd - unset_cmd = syaml_dict() - env_mod[syaml_str('unset')] = unset_cmd - prepend_cmd = syaml_dict() - env_mod[syaml_str('prepend-path')] = prepend_cmd - - set_cmd[syaml_str('EMPTY_PATH_LIST')] = syaml_str('/path/middle') - - append_cmd[syaml_str('PATH_LIST')] = syaml_str('/path/last') - append_cmd[syaml_str('EMPTY_PATH_LIST')] = syaml_str('/path/last') - append_cmd[syaml_str('NEW_PATH_LIST')] = syaml_str('/path/last') - - unset_cmd[syaml_str('SOME_VAR_NUM')] = None +@pytest.mark.parametrize('initial,modifications,expected', [ + # Set and unset variables + ({'SOME_VAR_STR': '', 'SOME_VAR_NUM': '0'}, + {'set': {'SOME_VAR_STR': 'SOME_STR', 'SOME_VAR_NUM': 1}}, + {'SOME_VAR_STR': 'SOME_STR', 'SOME_VAR_NUM': '1'}), + ({'SOME_VAR_STR': ''}, + {'unset': ['SOME_VAR_STR']}, + {'SOME_VAR_STR': None}), + ({}, # Set a variable that was not defined already + {'set': {'SOME_VAR_STR': 'SOME_STR'}}, + {'SOME_VAR_STR': 'SOME_STR'}), + # Append and prepend to the same variable + ({'EMPTY_PATH_LIST': '/path/middle'}, + {'prepend_path': {'EMPTY_PATH_LIST': '/path/first'}, + 'append_path': {'EMPTY_PATH_LIST': '/path/last'}}, + {'EMPTY_PATH_LIST': '/path/first:/path/middle:/path/last'}), + # Append and prepend from empty variables + ({'EMPTY_PATH_LIST': '', 'SOME_VAR_STR': ''}, + {'prepend_path': {'EMPTY_PATH_LIST': '/path/first'}, + 'append_path': {'SOME_VAR_STR': '/path/last'}}, + {'EMPTY_PATH_LIST': '/path/first', 'SOME_VAR_STR': '/path/last'}), + ({}, # Same as before but on variables that were not defined + {'prepend_path': {'EMPTY_PATH_LIST': '/path/first'}, + 'append_path': {'SOME_VAR_STR': '/path/last'}}, + {'EMPTY_PATH_LIST': '/path/first', 'SOME_VAR_STR': '/path/last'}), + # Remove a path from a list + ({'EMPTY_PATH_LIST': '/path/first:/path/middle:/path/last'}, + {'remove_path': {'EMPTY_PATH_LIST': '/path/middle'}}, + {'EMPTY_PATH_LIST': '/path/first:/path/last'}), + ({'EMPTY_PATH_LIST': '/only/path'}, + {'remove_path': {'EMPTY_PATH_LIST': '/only/path'}}, + {'EMPTY_PATH_LIST': ''}), +]) +def test_compiler_config_modifications( + initial, modifications, expected, ensure_env_variables, monkeypatch +): + # Set the environment as per prerequisites + ensure_env_variables(initial) - prepend_cmd[syaml_str('PATH_LIST')] = syaml_str('/path/first:/path/second') - prepend_cmd[syaml_str('EMPTY_PATH_LIST')] = syaml_str('/path/first') - prepend_cmd[syaml_str('NEW_PATH_LIST')] = syaml_str('/path/first') - prepend_cmd[syaml_str('SOME_VAR_NUM')] = syaml_str('/8') + # Monkeypatch a pkg.compiler.environment with the required modifications + pkg = spack.spec.Spec('cmake').concretized().package + monkeypatch.setattr(pkg.compiler, 'environment', modifications) - assert 'SOME_VAR_NUM' in os.environ - monkeypatch.setattr(pkg.compiler, 'environment', env_mod) + # Trigger the modifications spack.build_environment.setup_package(pkg, False) - # Check that the order of modifications is respected and the - # variable was unset before it was prepended. - assert os.environ['SOME_VAR_NUM'] == '/8' - expected = '/path/first:/path/second:/path/third:/path/forth:/path/last' - assert os.environ['PATH_LIST'] == expected - - expected = '/path/first:/path/middle:/path/last' - assert os.environ['EMPTY_PATH_LIST'] == expected - - expected = '/path/first:/path/last' - assert os.environ['NEW_PATH_LIST'] == expected + # Check they were applied + for name, value in expected.items(): + if value is not None: + assert os.environ[name] == value + continue + assert name not in os.environ @pytest.mark.regression('9107') @@ -243,6 +233,18 @@ def test_set_build_environment_variables( variables. """ + # https://github.com/spack/spack/issues/13969 + cuda_headers = HeaderList([ + 'prefix/include/cuda_runtime.h', + 'prefix/include/cuda/atomic', + 'prefix/include/cuda/std/detail/libcxx/include/ctype.h']) + cuda_include_dirs = cuda_headers.directories + assert(os.path.join('prefix', 'include') + in cuda_include_dirs) + assert(os.path.join('prefix', 'include', 'cuda', 'std', 'detail', + 'libcxx', 'include') + not in cuda_include_dirs) + root = spack.spec.Spec('dt-diamond') root.concretize() diff --git a/lib/spack/spack/test/build_system_guess.py b/lib/spack/spack/test/build_system_guess.py index cd6216a907..76197e9e15 100644 --- a/lib/spack/spack/test/build_system_guess.py +++ b/lib/spack/spack/test/build_system_guess.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/build_systems.py b/lib/spack/spack/test/build_systems.py index 44a20ca56a..744821a04e 100644 --- a/lib/spack/spack/test/build_systems.py +++ b/lib/spack/spack/test/build_systems.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py index e3c962b9d7..c1e1db914f 100644 --- a/lib/spack/spack/test/cc.py +++ b/lib/spack/spack/test/cc.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/ci.py b/lib/spack/spack/test/ci.py new file mode 100644 index 0000000000..3143a938c2 --- /dev/null +++ b/lib/spack/spack/test/ci.py @@ -0,0 +1,158 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import os +import pytest +from six.moves.urllib.error import URLError + +import spack.ci as ci +import spack.main as spack_main +import spack.config as cfg +import spack.paths as spack_paths +import spack.spec as spec +import spack.util.web as web_util + + +@pytest.fixture +def tmp_scope(): + """Creates a temporary configuration scope""" + base_name = 'internal-testing-scope' + current_overrides = set( + x.name for x in + cfg.config.matching_scopes(r'^{0}'.format(base_name))) + + num_overrides = 0 + scope_name = base_name + while scope_name in current_overrides: + scope_name = '{0}{1}'.format(base_name, num_overrides) + num_overrides += 1 + + with cfg.override(cfg.InternalConfigScope(scope_name)): + yield scope_name + + +def test_urlencode_string(): + s = 'Spack Test Project' + + s_enc = ci.url_encode_string(s) + + assert(s_enc == 'Spack+Test+Project') + + +def test_import_signing_key(mock_gnupghome): + signing_key_dir = spack_paths.mock_gpg_keys_path + signing_key_path = os.path.join(signing_key_dir, 'package-signing-key') + with open(signing_key_path) as fd: + signing_key = fd.read() + + # Just make sure this does not raise any exceptions + ci.import_signing_key(signing_key) + + +def test_configure_compilers(mutable_config): + + def assert_missing(config): + assert('install_missing_compilers' not in config or + config['install_missing_compilers'] is False) + + def assert_present(config): + assert('install_missing_compilers' in config and + config['install_missing_compilers'] is True) + + original_config = cfg.get('config') + assert_missing(original_config) + + ci.configure_compilers('FIND_ANY', scope='site') + + second_config = cfg.get('config') + assert_missing(second_config) + + ci.configure_compilers('INSTALL_MISSING') + last_config = cfg.get('config') + assert_present(last_config) + + +def test_get_concrete_specs(config, mock_packages): + root_spec = ( + 'eJztkk1uwyAQhfc5BbuuYjWObSKuUlURYP5aDBjjBPv0RU7iRI6qpKuqUtnxzZvRwHud' + 'YxSt1oCMyuVoBdI5MN8paxDYZK/ZbkLYU3kqAuA0Dtz6BgGtTB8XdG87BCgzwXbwXArY' + 'CxYQiLtqXxUTpLZxSjN/mWlwwxAQlJ7v8wpFtsvK1UXSOUyTjvRKB2Um7LBPhZD0l1md' + 'xJ7VCATfszOiXGOR9np7vwDn7lCMS8SXQNf3RCtyBTVzzNTMUMXmfWrFeR+UngEAEncS' + 'ASjKwZcid7ERNldthBxjX46mMD2PsJnlYXDs2rye3l+vroOkJJ54SXgZPklLRQmx61sm' + 'cgKNVFRO0qlpf2pojq1Ro7OG56MY+Bgc1PkIo/WkaT8OVcrDYuvZkJdtBl/+XCZ+NQBJ' + 'oKg1h6X/VdXRoyE2OWeH6lCXZdHGrauUZAWFw/YJ/0/39OefN3F4Kle3cXjYsF684ZqG' + 'Tbap/uPwbRx+YPStIQ8bvgA7G6YE' + ) + + dep_builds = 'diffutils;libiconv' + spec_map = ci.get_concrete_specs(root_spec, 'bzip2', dep_builds, 'NONE') + + assert('root' in spec_map and 'deps' in spec_map) + + nonconc_root_spec = 'archive-files' + dep_builds = '' + spec_map = ci.get_concrete_specs( + nonconc_root_spec, 'archive-files', dep_builds, 'FIND_ANY') + + assert('root' in spec_map and 'deps' in spec_map) + assert('archive-files' in spec_map) + + +def test_register_cdash_build(): + build_name = 'Some pkg' + base_url = 'http://cdash.fake.org' + project = 'spack' + site = 'spacktests' + track = 'Experimental' + + with pytest.raises(URLError): + ci.register_cdash_build(build_name, base_url, project, site, track) + + +def test_relate_cdash_builds(config, mock_packages): + root_spec = ( + 'eJztkk1uwyAQhfc5BbuuYjWObSKuUlURYP5aDBjjBPv0RU7iRI6qpKuqUtnxzZvRwHud' + 'YxSt1oCMyuVoBdI5MN8paxDYZK/ZbkLYU3kqAuA0Dtz6BgGtTB8XdG87BCgzwXbwXArY' + 'CxYQiLtqXxUTpLZxSjN/mWlwwxAQlJ7v8wpFtsvK1UXSOUyTjvRKB2Um7LBPhZD0l1md' + 'xJ7VCATfszOiXGOR9np7vwDn7lCMS8SXQNf3RCtyBTVzzNTMUMXmfWrFeR+UngEAEncS' + 'ASjKwZcid7ERNldthBxjX46mMD2PsJnlYXDs2rye3l+vroOkJJ54SXgZPklLRQmx61sm' + 'cgKNVFRO0qlpf2pojq1Ro7OG56MY+Bgc1PkIo/WkaT8OVcrDYuvZkJdtBl/+XCZ+NQBJ' + 'oKg1h6X/VdXRoyE2OWeH6lCXZdHGrauUZAWFw/YJ/0/39OefN3F4Kle3cXjYsF684ZqG' + 'Tbap/uPwbRx+YPStIQ8bvgA7G6YE' + ) + + dep_builds = 'diffutils;libiconv' + spec_map = ci.get_concrete_specs(root_spec, 'bzip2', dep_builds, 'NONE') + cdash_api_url = 'http://cdash.fake.org' + job_build_id = '42' + cdash_project = 'spack' + cdashids_mirror_url = 'https://my.fake.mirror' + + with pytest.raises(web_util.SpackWebError): + ci.relate_cdash_builds(spec_map, cdash_api_url, job_build_id, + cdash_project, cdashids_mirror_url) + + # Just make sure passing None for build id doesn't throw exceptions + ci.relate_cdash_builds(spec_map, cdash_api_url, None, cdash_project, + cdashids_mirror_url) + + +def test_read_write_cdash_ids(config, tmp_scope, tmpdir, mock_packages): + working_dir = tmpdir.join('working_dir') + mirror_dir = working_dir.join('mirror') + mirror_url = 'file://{0}'.format(mirror_dir.strpath) + + mirror_cmd = spack_main.SpackCommand('mirror') + mirror_cmd('add', '--scope', tmp_scope, 'test_mirror', mirror_url) + + mock_spec = spec.Spec('archive-files').concretized() + orig_cdashid = '42' + + ci.write_cdashid_to_mirror(orig_cdashid, mock_spec, mirror_url) + + # Now read it back + read_cdashid = ci.read_cdashid_from_mirror(mock_spec, mirror_url) + + assert(str(read_cdashid) == orig_cdashid) diff --git a/lib/spack/spack/test/cmd/__init__.py b/lib/spack/spack/test/cmd/__init__.py new file mode 100644 index 0000000000..9f87532b85 --- /dev/null +++ b/lib/spack/spack/test/cmd/__init__.py @@ -0,0 +1,4 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/activate.py b/lib/spack/spack/test/cmd/activate.py index efe07255fe..a3546230f1 100644 --- a/lib/spack/spack/test/cmd/activate.py +++ b/lib/spack/spack/test/cmd/activate.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/arch.py b/lib/spack/spack/test/cmd/arch.py index 66c8f8e5dc..ec3c92a3d0 100644 --- a/lib/spack/spack/test/cmd/arch.py +++ b/lib/spack/spack/test/cmd/arch.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/blame.py b/lib/spack/spack/test/cmd/blame.py index f1ac2b0b3a..61bdf41084 100644 --- a/lib/spack/spack/test/cmd/blame.py +++ b/lib/spack/spack/test/cmd/blame.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/build_env.py b/lib/spack/spack/test/cmd/build_env.py index 379de521b2..b7de759a2e 100644 --- a/lib/spack/spack/test/cmd/build_env.py +++ b/lib/spack/spack/test/cmd/build_env.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/buildcache.py b/lib/spack/spack/test/cmd/buildcache.py index 2c4f351d86..064daeb063 100644 --- a/lib/spack/spack/test/cmd/buildcache.py +++ b/lib/spack/spack/test/cmd/buildcache.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,11 +8,19 @@ import platform import pytest import spack.main - +import spack.binary_distribution buildcache = spack.main.SpackCommand('buildcache') +@pytest.fixture() +def mock_get_specs(database, monkeypatch): + specs = database.query_local() + monkeypatch.setattr( + spack.binary_distribution, 'get_specs', lambda x, y: specs + ) + + @pytest.mark.skipif( platform.system().lower() != 'linux', reason='implementation for MacOS still missing' @@ -20,3 +28,16 @@ buildcache = spack.main.SpackCommand('buildcache') @pytest.mark.db def test_buildcache_preview_just_runs(database): buildcache('preview', 'mpileaks') + + +@pytest.mark.skipif( + platform.system().lower() != 'linux', + reason='implementation for MacOS still missing' +) +@pytest.mark.db +@pytest.mark.regression('13757') +def test_buildcache_list_duplicates(mock_get_specs, capsys): + with capsys.disabled(): + output = buildcache('list', 'mpileaks', '@2.3') + + assert output.count('mpileaks') == 3 diff --git a/lib/spack/spack/test/cmd/cd.py b/lib/spack/spack/test/cmd/cd.py index 356587b955..e3900c0d8f 100644 --- a/lib/spack/spack/test/cmd/cd.py +++ b/lib/spack/spack/test/cmd/cd.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/ci.py b/lib/spack/spack/test/cmd/ci.py new file mode 100644 index 0000000000..49663b3409 --- /dev/null +++ b/lib/spack/spack/test/cmd/ci.py @@ -0,0 +1,573 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import filecmp +import os +import pytest + +import llnl.util.filesystem as fs + +import spack +import spack.ci as ci +import spack.config +import spack.environment as ev +import spack.hash_types as ht +from spack.main import SpackCommand +import spack.paths as spack_paths +import spack.repo as repo +from spack.spec import Spec +from spack.test.conftest import MockPackage, MockPackageMultiRepo +import spack.util.executable as exe +import spack.util.spack_yaml as syaml + + +ci_cmd = SpackCommand('ci') +env_cmd = SpackCommand('env') +mirror_cmd = SpackCommand('mirror') +gpg_cmd = SpackCommand('gpg') +install_cmd = SpackCommand('install') +buildcache_cmd = SpackCommand('buildcache') +git = exe.which('git', required=True) + + +@pytest.fixture() +def env_deactivate(): + yield + spack.environment._active_environment = None + os.environ.pop('SPACK_ENV', None) + + +def initialize_new_repo(repo_path, initial_commit=False): + if not os.path.exists(repo_path): + os.makedirs(repo_path) + + with fs.working_dir(repo_path): + init_args = ['init', '.'] + # if not initial_commit: + # init_args.append('--bare') + + git(*init_args) + + if initial_commit: + readme_contents = "This is the project README\n" + readme_path = os.path.join(repo_path, 'README.md') + with open(readme_path, 'w') as fd: + fd.write(readme_contents) + git('add', '.') + git('commit', '-m', 'Project initial commit') + + +def get_repo_status(repo_path): + with fs.working_dir(repo_path): + output = git('rev-parse', '--abbrev-ref', 'HEAD', output=str) + current_branch = output.split()[0] + + output = git('rev-parse', 'HEAD', output=str) + current_sha = output.split()[0] + + return current_branch, current_sha + + +def set_env_var(key, val): + os.environ[key] = val + + +def test_specs_staging(config): + """Make sure we achieve the best possible staging for the following +spec DAG:: + + a + /| + c b + |\ + e d + |\ + f g + +In this case, we would expect 'c', 'e', 'f', and 'g' to be in the first stage, +and then 'd', 'b', and 'a' to be put in the next three stages, respectively. + +""" + default = ('build', 'link') + + g = MockPackage('g', [], []) + f = MockPackage('f', [], []) + e = MockPackage('e', [], []) + d = MockPackage('d', [f, g], [default, default]) + c = MockPackage('c', [], []) + b = MockPackage('b', [d, e], [default, default]) + a = MockPackage('a', [b, c], [default, default]) + + mock_repo = MockPackageMultiRepo([a, b, c, d, e, f, g]) + + with repo.swap(mock_repo): + spec_a = Spec('a') + spec_a.concretize() + + spec_a_label = ci.spec_deps_key_label(spec_a)[1] + spec_b_label = ci.spec_deps_key_label(spec_a['b'])[1] + spec_c_label = ci.spec_deps_key_label(spec_a['c'])[1] + spec_d_label = ci.spec_deps_key_label(spec_a['d'])[1] + spec_e_label = ci.spec_deps_key_label(spec_a['e'])[1] + spec_f_label = ci.spec_deps_key_label(spec_a['f'])[1] + spec_g_label = ci.spec_deps_key_label(spec_a['g'])[1] + + spec_labels, dependencies, stages = ci.stage_spec_jobs([spec_a]) + + assert (len(stages) == 4) + + assert (len(stages[0]) == 4) + assert (spec_c_label in stages[0]) + assert (spec_e_label in stages[0]) + assert (spec_f_label in stages[0]) + assert (spec_g_label in stages[0]) + + assert (len(stages[1]) == 1) + assert (spec_d_label in stages[1]) + + assert (len(stages[2]) == 1) + assert (spec_b_label in stages[2]) + + assert (len(stages[3]) == 1) + assert (spec_a_label in stages[3]) + + +def test_ci_generate_with_env(tmpdir, mutable_mock_env_path, env_deactivate, + install_mockery, mock_packages): + """Make sure we can get a .gitlab-ci.yml from an environment file + which has the gitlab-ci, cdash, and mirrors sections.""" + filename = str(tmpdir.join('spack.yaml')) + with open(filename, 'w') as f: + f.write("""\ +spack: + definitions: + - bootstrap: + - cmake@3.4.3 + - old-gcc-pkgs: + - archive-files + - callpath + - hypre@0.2.15 + specs: + - matrix: + - [$old-gcc-pkgs] + mirrors: + some-mirror: https://my.fake.mirror + gitlab-ci: + bootstrap: + - name: bootstrap + compiler-agnostic: true + mappings: + - match: + - arch=test-debian6-x86_64 + runner-attributes: + tags: + - donotcare + image: donotcare + final-stage-rebuild-index: + image: donotcare + tags: [donotcare] + cdash: + build-group: Not important + url: https://my.fake.cdash + project: Not used + site: Nothing +""") + with tmpdir.as_cwd(): + env_cmd('create', 'test', './spack.yaml') + outputfile = str(tmpdir.join('.gitlab-ci.yml')) + + with ev.read('test'): + ci_cmd('generate', '--output-file', outputfile) + + with open(outputfile) as f: + contents = f.read() + yaml_contents = syaml.load(contents) + found_spec = False + for ci_key in yaml_contents.keys(): + if '(bootstrap)' in ci_key: + found_spec = True + assert('cmake' in ci_key) + assert(found_spec) + assert('stages' in yaml_contents) + assert(len(yaml_contents['stages']) == 6) + assert(yaml_contents['stages'][0] == 'stage-0') + assert(yaml_contents['stages'][5] == 'stage-rebuild-index') + + +def test_ci_generate_with_env_missing_section(tmpdir, mutable_mock_env_path, + env_deactivate, install_mockery, + mock_packages): + """Make sure we get a reasonable message if we omit gitlab-ci section""" + filename = str(tmpdir.join('spack.yaml')) + with open(filename, 'w') as f: + f.write("""\ +spack: + specs: + - archive-files + mirrors: + some-mirror: https://my.fake.mirror +""") + + expect_out = 'Error: Environment yaml does not have "gitlab-ci" section' + + with tmpdir.as_cwd(): + env_cmd('create', 'test', './spack.yaml') + + with ev.read('test'): + output = ci_cmd('generate', fail_on_error=False, output=str) + assert(expect_out in output) + + +def test_ci_generate_with_cdash_token(tmpdir, mutable_mock_env_path, + env_deactivate, install_mockery, + mock_packages): + """Make sure we it doesn't break if we configure cdash""" + filename = str(tmpdir.join('spack.yaml')) + with open(filename, 'w') as f: + f.write("""\ +spack: + specs: + - archive-files + mirrors: + some-mirror: https://my.fake.mirror + gitlab-ci: + enable-artifacts-buildcache: True + enable-debug-messages: True + mappings: + - match: + - archive-files + runner-attributes: + tags: + - donotcare + image: donotcare + cdash: + build-group: Not important + url: https://my.fake.cdash + project: Not used + site: Nothing +""") + + with tmpdir.as_cwd(): + env_cmd('create', 'test', './spack.yaml') + + with ev.read('test'): + fake_token = 'notreallyatokenbutshouldnotmatter' + os.environ['SPACK_CDASH_AUTH_TOKEN'] = fake_token + copy_to_file = str(tmpdir.join('backup-ci.yml')) + output = ci_cmd('generate', '--copy-to', copy_to_file, output=str) + # That fake token should still have resulted in being unable to + # register build group with cdash, but the workload should + # still have been generated. + expect = 'Problem populating buildgroup' + assert(expect in output) + + dir_contents = os.listdir(tmpdir.strpath) + + print(dir_contents) + + assert('backup-ci.yml' in dir_contents) + + orig_file = str(tmpdir.join('.gitlab-ci.yml')) + + assert(filecmp.cmp(orig_file, copy_to_file) is True) + + +def test_ci_generate_with_external_pkg(tmpdir, mutable_mock_env_path, + env_deactivate, install_mockery, + mock_packages): + """Make sure we do not generate jobs for external pkgs""" + filename = str(tmpdir.join('spack.yaml')) + with open(filename, 'w') as f: + f.write("""\ +spack: + specs: + - archive-files + - externaltest + mirrors: + some-mirror: https://my.fake.mirror + gitlab-ci: + mappings: + - match: + - archive-files + - externaltest + runner-attributes: + tags: + - donotcare + image: donotcare +""") + + with tmpdir.as_cwd(): + env_cmd('create', 'test', './spack.yaml') + outputfile = str(tmpdir.join('.gitlab-ci.yml')) + + with ev.read('test'): + ci_cmd('generate', '--output-file', outputfile) + + with open(outputfile) as f: + contents = f.read() + print('generated contents: ') + print(contents) + yaml_contents = syaml.load(contents) + for ci_key in yaml_contents.keys(): + if 'externaltool' in ci_key: + print('Erroneously staged "externaltool" pkg') + assert(False) + + +def test_ci_generate_debug_with_custom_spack(tmpdir, mutable_mock_env_path, + env_deactivate, install_mockery, + mock_packages): + """Make sure we generate cloning of spack in job script if needed""" + filename = str(tmpdir.join('spack.yaml')) + with open(filename, 'w') as f: + f.write("""\ +spack: + specs: + - archive-files + mirrors: + some-mirror: https://my.fake.mirror + gitlab-ci: + enable-artifacts-buildcache: True + enable-debug-messages: True + mappings: + - match: + - archive-files + runner-attributes: + tags: + - donotcare + image: donotcare +""") + + with tmpdir.as_cwd(): + env_cmd('create', 'test', './spack.yaml') + outfile = str(tmpdir.join('.gitlab-ci.yml')) + + with ev.read('test'): + spack_repo = 'https://github.com/usera/spack.git' + spack_ref = 'custom-branch' + expected_clone_str = 'git clone "{0}"'.format(spack_repo) + + ci_cmd('generate', '--output-file', outfile, '--spack-repo', + spack_repo, '--spack-ref', spack_ref) + + with open(outfile) as f: + contents = f.read() + yaml_contents = syaml.load(contents) + for ci_key in yaml_contents.keys(): + if '(specs)' in ci_key: + next_job = yaml_contents[ci_key] + print(next_job) + assert('before_script' in next_job) + before_script = next_job['before_script'] + for step in before_script: + if expected_clone_str in step: + break + else: + msg = 'job "{0}" did not clone spack repo'.format( + ci_key) + print(msg) + assert(False) + + assert('script' in next_job) + script = next_job['script'] + for step in script: + if 'spack -d ci rebuild' in step: + break + else: + msg = 'job {0} missing rebuild command'.format( + ci_key) + print(msg) + assert(False) + + +def test_ci_rebuild_basic(tmpdir, mutable_mock_env_path, env_deactivate, + install_mockery, mock_packages, + mock_gnupghome): + working_dir = tmpdir.join('working_dir') + + mirror_dir = working_dir.join('mirror') + mirror_url = 'file://{0}'.format(mirror_dir.strpath) + + signing_key_dir = spack_paths.mock_gpg_keys_path + signing_key_path = os.path.join(signing_key_dir, 'package-signing-key') + with open(signing_key_path) as fd: + signing_key = fd.read() + + spack_yaml_contents = """ +spack: + definitions: + - packages: [archive-files] + specs: + - $packages + mirrors: + test-mirror: {0} + gitlab-ci: + enable-artifacts-buildcache: True + mappings: + - match: + - archive-files + runner-attributes: + tags: + - donotcare + image: donotcare + cdash: + build-group: Not important + url: https://my.fake.cdash + project: Not used + site: Nothing +""".format(mirror_url) + + print('spack.yaml:\n{0}\n'.format(spack_yaml_contents)) + + filename = str(tmpdir.join('spack.yaml')) + with open(filename, 'w') as f: + f.write(spack_yaml_contents) + + with tmpdir.as_cwd(): + env_cmd('create', 'test', './spack.yaml') + with ev.read('test'): + root_spec = ('eJyNjsGOwyAMRO/5Ct96alRFFK34ldUqcohJ6BJAQFHUry9Nk66' + 'UXNY3v5mxJ3qSojoDBjnqTGelDUVRQZlMIWpnBZya+nJa0Mv1Fg' + 'G8waRcmAQkimkHWxcF9NRptHyVEoaBkoD5i7ecLVC6yZd/YTtpc' + 'SIBg5Tr/mnA6mt9qTZL9CiLr7trk7StJyd/F81jKGoqoe2gVAaH' + '0uT7ZwPeH9A875HaA9MfidHdHxgxjgJuTGVtIrvfHGtynjkGyzi' + 'xRrkHy94t1lftvv1n4AkVK3kQ') + + # Create environment variables as gitlab would do it + set_env_var('CI_PROJECT_DIR', working_dir.strpath) + set_env_var('SPACK_SIGNING_KEY', signing_key) + set_env_var('SPACK_ROOT_SPEC', root_spec) + set_env_var('SPACK_JOB_SPEC_PKG_NAME', 'archive-files') + set_env_var('SPACK_COMPILER_ACTION', 'NONE') + set_env_var('SPACK_CDASH_BUILD_NAME', '(specs) archive-files') + set_env_var('SPACK_RELATED_BUILDS_CDASH', '') + + rebuild_output = ci_cmd( + 'rebuild', fail_on_error=False, output=str) + + print(rebuild_output) + + +def test_ci_pushyaml(tmpdir): + fake_yaml_contents = """generate ci jobs: + script: + - "./share/spack/qa/gitlab/generate-gitlab-ci-yml.sh" + tags: + - "spack-pre-ci" + artifacts: + paths: + - ci-generation + when: always + """ + local_repo_path = tmpdir.join('local_repo') + initialize_new_repo(local_repo_path.strpath, True) + + remote_repo_path = tmpdir.join('remote_repo') + initialize_new_repo(remote_repo_path.strpath) + + current_branch, current_sha = get_repo_status(local_repo_path.strpath) + + print('local repo info: {0}, {1}'.format(current_branch, current_sha)) + + local_jobs_yaml = local_repo_path.join('.gitlab-ci.yml') + with local_jobs_yaml.open('w') as f: + f.write(fake_yaml_contents) + + pushyaml_args = [ + 'pushyaml', + '--downstream-repo', remote_repo_path.strpath, + '--branch-name', current_branch, + '--commit-sha', current_sha, + ] + + with fs.working_dir(local_repo_path.strpath): + ci_cmd(*pushyaml_args) + + with fs.working_dir(remote_repo_path.strpath): + branch_to_checkout = 'multi-ci-{0}'.format(current_branch) + git('checkout', branch_to_checkout) + with open('.gitlab-ci.yml') as fd: + pushed_contents = fd.read() + assert pushed_contents == fake_yaml_contents + + +@pytest.mark.disable_clean_stage_check +def test_push_mirror_contents(tmpdir, mutable_mock_env_path, env_deactivate, + install_mockery, mock_packages, mock_fetch, + mock_stage, mock_gnupghome): + working_dir = tmpdir.join('working_dir') + + mirror_dir = working_dir.join('mirror') + mirror_url = 'file://{0}'.format(mirror_dir.strpath) + + signing_key_dir = spack_paths.mock_gpg_keys_path + signing_key_path = os.path.join(signing_key_dir, 'package-signing-key') + with open(signing_key_path) as fd: + signing_key = fd.read() + + ci.import_signing_key(signing_key) + + spack_yaml_contents = """ +spack: + definitions: + - packages: [patchelf] + specs: + - $packages + mirrors: + test-mirror: {0} +""".format(mirror_url) + + print('spack.yaml:\n{0}\n'.format(spack_yaml_contents)) + + filename = str(tmpdir.join('spack.yaml')) + with open(filename, 'w') as f: + f.write(spack_yaml_contents) + + with tmpdir.as_cwd(): + env_cmd('create', 'test', './spack.yaml') + with ev.read('test') as env: + spec_map = ci.get_concrete_specs( + 'patchelf', 'patchelf', '', 'FIND_ANY') + concrete_spec = spec_map['patchelf'] + spec_yaml = concrete_spec.to_yaml(hash=ht.build_hash) + yaml_path = str(tmpdir.join('spec.yaml')) + with open(yaml_path, 'w') as ypfd: + ypfd.write(spec_yaml) + + install_cmd('--keep-stage', yaml_path) + + # env, spec, yaml_path, mirror_url, build_id + ci.push_mirror_contents( + env, concrete_spec, yaml_path, mirror_url, '42') + + buildcache_list_output = buildcache_cmd('list', output=str) + + assert('patchelf' in buildcache_list_output) + + logs_dir = working_dir.join('logs_dir') + if not os.path.exists(logs_dir.strpath): + os.makedirs(logs_dir.strpath) + + ci.copy_stage_logs_to_artifacts(concrete_spec, logs_dir.strpath) + + logs_dir_list = os.listdir(logs_dir.strpath) + + assert('spack-build-env.txt' in logs_dir_list) + assert('spack-build-out.txt' in logs_dir_list) + + # Also just make sure that if something goes wrong with the + # stage logs copy, no exception is thrown + ci.copy_stage_logs_to_artifacts(None, logs_dir.strpath) + + dl_dir = working_dir.join('download_dir') + if not os.path.exists(dl_dir.strpath): + os.makedirs(dl_dir.strpath) + + buildcache_cmd('download', '--spec-yaml', yaml_path, '--path', + dl_dir.strpath, '--require-cdashid') + + dl_dir_list = os.listdir(dl_dir.strpath) + + assert(len(dl_dir_list) == 3) diff --git a/lib/spack/spack/test/cmd/clean.py b/lib/spack/spack/test/cmd/clean.py index a0e8d89aac..c3e9d79f23 100644 --- a/lib/spack/spack/test/cmd/clean.py +++ b/lib/spack/spack/test/cmd/clean.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/commands.py b/lib/spack/spack/test/cmd/commands.py index f0b80ea031..409dea7c51 100644 --- a/lib/spack/spack/test/cmd/commands.py +++ b/lib/spack/spack/test/cmd/commands.py @@ -1,15 +1,20 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import re -import pytest +import filecmp +import os +import shutil +import subprocess -from llnl.util.argparsewriter import ArgparseWriter +import pytest import spack.cmd +from spack.cmd.commands import _positional_to_subroutine import spack.main +import spack.paths + commands = spack.main.SpackCommand('commands') @@ -17,38 +22,64 @@ parser = spack.main.make_argument_parser() spack.main.add_all_commands(parser) -def test_commands_by_name(): +def test_names(): """Test default output of spack commands.""" - out = commands() - assert out.strip().split('\n') == sorted(spack.cmd.all_commands()) + out1 = commands().strip().split('\n') + assert out1 == spack.cmd.all_commands() + assert 'rm' not in out1 + + out2 = commands('--aliases').strip().split('\n') + assert out1 != out2 + assert 'rm' in out2 + + out3 = commands('--format=names').strip().split('\n') + assert out1 == out3 def test_subcommands(): """Test subcommand traversal.""" - out = commands('--format=subcommands') - assert 'spack mirror create' in out - assert 'spack buildcache list' in out - assert 'spack repo add' in out - assert 'spack pkg diff' in out - assert 'spack url parse' in out - assert 'spack view symlink' in out - - class Subcommands(ArgparseWriter): - def begin_command(self, prog): - assert prog in out + out1 = commands('--format=subcommands') + assert 'spack mirror create' in out1 + assert 'spack buildcache list' in out1 + assert 'spack repo add' in out1 + assert 'spack pkg diff' in out1 + assert 'spack url parse' in out1 + assert 'spack view symlink' in out1 + assert 'spack rm' not in out1 + assert 'spack compiler add' not in out1 - Subcommands().write(parser) + out2 = commands('--aliases', '--format=subcommands') + assert 'spack mirror create' in out2 + assert 'spack buildcache list' in out2 + assert 'spack repo add' in out2 + assert 'spack pkg diff' in out2 + assert 'spack url parse' in out2 + assert 'spack view symlink' in out2 + assert 'spack rm' in out2 + assert 'spack compiler add' in out2 def test_rst(): """Do some simple sanity checks of the rst writer.""" - out = commands('--format=rst') + out1 = commands('--format=rst') + assert 'spack mirror create' in out1 + assert 'spack buildcache list' in out1 + assert 'spack repo add' in out1 + assert 'spack pkg diff' in out1 + assert 'spack url parse' in out1 + assert 'spack view symlink' in out1 + assert 'spack rm' not in out1 + assert 'spack compiler add' not in out1 - class Subcommands(ArgparseWriter): - def begin_command(self, prog): - assert prog in out - assert re.sub(r' ', '-', prog) in out - Subcommands().write(parser) + out2 = commands('--aliases', '--format=rst') + assert 'spack mirror create' in out2 + assert 'spack buildcache list' in out2 + assert 'spack repo add' in out2 + assert 'spack pkg diff' in out2 + assert 'spack url parse' in out2 + assert 'spack view symlink' in out2 + assert 'spack rm' in out2 + assert 'spack compiler add' in out2 def test_rst_with_input_files(tmpdir): @@ -109,3 +140,126 @@ def test_rst_update(tmpdir): assert update_file.exists() with update_file.open() as f: assert f.read() == 'empty\n' + + +def test_update_with_header(tmpdir): + update_file = tmpdir.join('output') + + # not yet created when commands is run + commands('--update', str(update_file)) + assert update_file.exists() + with update_file.open() as f: + assert f.read() + fake_header = 'this is a header!\n\n' + + filename = tmpdir.join('header.txt') + with filename.open('w') as f: + f.write(fake_header) + + # created, newer than commands, but older than header + commands('--update', str(update_file), '--header', str(filename)) + + # newer than commands and header + commands('--update', str(update_file), '--header', str(filename)) + + +@pytest.mark.xfail +def test_no_pipe_error(): + """Make sure we don't see any pipe errors when piping output.""" + + proc = subprocess.Popen( + ['spack', 'commands', '--format=rst'], + stdout=subprocess.PIPE, stderr=subprocess.PIPE) + + # Call close() on stdout to cause a broken pipe + proc.stdout.close() + proc.wait() + stderr = proc.stderr.read().decode('utf-8') + + assert 'Broken pipe' not in stderr + + +def test_bash_completion(): + """Test the bash completion writer.""" + out1 = commands('--format=bash') + + # Make sure header not included + assert '_bash_completion_spack() {' not in out1 + assert '_all_packages() {' not in out1 + + # Make sure subcommands appear + assert '_spack_remove() {' in out1 + assert '_spack_compiler_find() {' in out1 + + # Make sure aliases don't appear + assert '_spack_rm() {' not in out1 + assert '_spack_compiler_add() {' not in out1 + + # Make sure options appear + assert '-h --help' in out1 + + # Make sure subcommands are called + for function in _positional_to_subroutine.values(): + assert function in out1 + + out2 = commands('--aliases', '--format=bash') + + # Make sure aliases appear + assert '_spack_rm() {' in out2 + assert '_spack_compiler_add() {' in out2 + + +def test_update_completion_arg(tmpdir, monkeypatch): + mock_infile = tmpdir.join("spack-completion.in") + mock_bashfile = tmpdir.join("spack-completion.bash") + + mock_args = { + "bash": { + "aliases": True, + "format": "bash", + "header": str(mock_infile), + "update": str(mock_bashfile), + }, + } + + # make a mock completion file missing the --update-completion argument + real_args = spack.cmd.commands.update_completion_args + shutil.copy(real_args['bash']['header'], mock_args['bash']['header']) + with open(real_args['bash']['update']) as old: + old_file = old.read() + with open(mock_args['bash']['update'], 'w') as mock: + mock.write(old_file.replace("--update-completion", "")) + mock_bashfile.setmtime(0) # ensure mtime triggers update + + monkeypatch.setattr( + spack.cmd.commands, 'update_completion_args', mock_args) + + # ensure things fail if --update-completion isn't specified alone + with pytest.raises(spack.main.SpackCommandError): + commands("--update-completion", "-a") + + # ensure arg is restored + assert "--update-completion" not in mock_bashfile.read() + commands("--update-completion") + assert "--update-completion" in mock_bashfile.read() + + +def test_updated_completion_scripts(tmpdir): + """Make sure our shell tab completion scripts remain up-to-date.""" + + msg = ("It looks like Spack's command-line interface has been modified. " + "Please update Spack's shell tab completion scripts by running:\n\n" + " spack commands --update-completion\n\n" + "and adding the changed files to your pull request.") + + for shell in ['bash']: # 'zsh', 'fish']: + header = os.path.join( + spack.paths.share_path, shell, 'spack-completion.in') + script = 'spack-completion.{0}'.format(shell) + old_script = os.path.join(spack.paths.share_path, script) + new_script = str(tmpdir.join(script)) + + commands('--aliases', '--format', shell, + '--header', header, '--update', new_script) + + assert filecmp.cmp(old_script, new_script), msg diff --git a/lib/spack/spack/test/cmd/common/__init__.py b/lib/spack/spack/test/cmd/common/__init__.py new file mode 100644 index 0000000000..9f87532b85 --- /dev/null +++ b/lib/spack/spack/test/cmd/common/__init__.py @@ -0,0 +1,4 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/common/arguments.py b/lib/spack/spack/test/cmd/common/arguments.py index 82ae495611..5117607a2e 100644 --- a/lib/spack/spack/test/cmd/common/arguments.py +++ b/lib/spack/spack/test/cmd/common/arguments.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/compiler_command.py b/lib/spack/spack/test/cmd/compiler_command.py index a4ceb63822..15949d08d4 100644 --- a/lib/spack/spack/test/cmd/compiler_command.py +++ b/lib/spack/spack/test/cmd/compiler_command.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/config.py b/lib/spack/spack/test/cmd/config.py index 0d6cc7ec40..82a9d814ea 100644 --- a/lib/spack/spack/test/cmd/config.py +++ b/lib/spack/spack/test/cmd/config.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,13 +14,13 @@ from spack.main import SpackCommand config = SpackCommand('config') -def test_get_config_scope(mock_config): +def test_get_config_scope(mock_low_high_config): assert config('get', 'compilers').strip() == 'compilers: {}' -def test_get_config_scope_merged(mock_config): - low_path = mock_config.scopes['low'].path - high_path = mock_config.scopes['high'].path +def test_get_config_scope_merged(mock_low_high_config): + low_path = mock_low_high_config.scopes['low'].path + high_path = mock_low_high_config.scopes['high'].path mkdirp(low_path) mkdirp(high_path) @@ -91,3 +91,9 @@ def test_config_edit_fails_correctly_with_no_env(mutable_mock_env_path): def test_config_get_fails_correctly_with_no_env(mutable_mock_env_path): output = config('get', fail_on_error=False) assert "requires a section argument or an active environment" in output + + +def test_config_list(): + output = config('list') + assert 'compilers' in output + assert 'packages' in output diff --git a/lib/spack/spack/test/cmd/create.py b/lib/spack/spack/test/cmd/create.py index 27d2b252bb..4262744317 100644 --- a/lib/spack/spack/test/cmd/create.py +++ b/lib/spack/spack/test/cmd/create.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -95,12 +95,16 @@ def test_create_template(parser, mock_test_repo, args, name, expected): (' ', 'name must be provided'), ('bad#name', 'name can only contain'), ]) -def test_create_template_bad_name(parser, mock_test_repo, name, expected): +def test_create_template_bad_name( + parser, mock_test_repo, name, expected, capsys): """Test template creation with bad name options.""" constr_args = parser.parse_args(['--skip-editor', '-n', name]) - with pytest.raises(SystemExit, matches=expected): + with pytest.raises(SystemExit): spack.cmd.create.create(parser, constr_args) + captured = capsys.readouterr() + assert expected in str(captured) + def test_build_system_guesser_no_stage(parser): """Test build system guesser when stage not provided.""" @@ -108,7 +112,7 @@ def test_build_system_guesser_no_stage(parser): # Ensure get the expected build system with pytest.raises(AttributeError, - matches="'NoneType' object has no attribute"): + match="'NoneType' object has no attribute"): guesser(None, '/the/url/does/not/matter') @@ -142,7 +146,7 @@ def test_get_name_urls(parser, url, expected): assert name == expected -def test_get_name_error(parser, monkeypatch): +def test_get_name_error(parser, monkeypatch, capsys): """Test get_name UndetectableNameError exception path.""" def _parse_name_offset(path, v): raise UndetectableNameError(path) @@ -152,5 +156,7 @@ def test_get_name_error(parser, monkeypatch): url = 'downloads.sourceforge.net/noapp/' args = parser.parse_args([url]) - with pytest.raises(SystemExit, matches="Couldn't guess a name"): + with pytest.raises(SystemExit): spack.cmd.create.get_name(args) + captured = capsys.readouterr() + assert "Couldn't guess a name" in str(captured) diff --git a/lib/spack/spack/test/cmd/debug.py b/lib/spack/spack/test/cmd/debug.py index aba46c2398..4a06276abf 100644 --- a/lib/spack/spack/test/cmd/debug.py +++ b/lib/spack/spack/test/cmd/debug.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/dependencies.py b/lib/spack/spack/test/cmd/dependencies.py index d38591e907..fc47069181 100644 --- a/lib/spack/spack/test/cmd/dependencies.py +++ b/lib/spack/spack/test/cmd/dependencies.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/dependents.py b/lib/spack/spack/test/cmd/dependents.py index 69c680a3c8..1001e8764f 100644 --- a/lib/spack/spack/test/cmd/dependents.py +++ b/lib/spack/spack/test/cmd/dependents.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/deprecate.py b/lib/spack/spack/test/cmd/deprecate.py index 6bc87fa5e3..7b38c177f5 100644 --- a/lib/spack/spack/test/cmd/deprecate.py +++ b/lib/spack/spack/test/cmd/deprecate.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/dev_build.py b/lib/spack/spack/test/cmd/dev_build.py index 835edac138..a007513067 100644 --- a/lib/spack/spack/test/cmd/dev_build.py +++ b/lib/spack/spack/test/cmd/dev_build.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py index 9b3ca6e66e..9e8c424ce0 100644 --- a/lib/spack/spack/test/cmd/env.py +++ b/lib/spack/spack/test/cmd/env.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,7 +26,7 @@ import spack.util.spack_json as sjson # everything here uses the mock_env_path pytestmark = pytest.mark.usefixtures( - 'mutable_mock_env_path', 'config', 'mutable_mock_packages') + 'mutable_mock_env_path', 'config', 'mutable_mock_repo') env = SpackCommand('env') install = SpackCommand('install') @@ -63,6 +63,27 @@ def test_add(): assert Spec('mpileaks') in e.user_specs +def test_env_add_virtual(): + env('create', 'test') + + e = ev.read('test') + e.add('mpi') + e.concretize() + + hashes = e.concretized_order + assert len(hashes) == 1 + spec = e.specs_by_hash[hashes[0]] + assert spec.satisfies('mpi') + + +def test_env_add_nonexistant_fails(): + env('create', 'test') + + e = ev.read('test') + with pytest.raises(ev.SpackEnvironmentError, match=r'no such package'): + e.add('thispackagedoesnotexist') + + def test_env_list(mutable_mock_env_path): env('create', 'foo') env('create', 'bar') @@ -382,13 +403,11 @@ env: mpileaks: version: [2.2] """ - spack.package_prefs.PackagePrefs.clear_caches() - _env_create('test', StringIO(test_config)) e = ev.read('test') - ev.prepare_config_scope(e) - e.concretize() + with e: + e.concretize() assert any(x.satisfies('mpileaks@2.2') for x in e._get_environment_specs()) @@ -402,8 +421,6 @@ env: specs: - mpileaks """ - spack.package_prefs.PackagePrefs.clear_caches() - _env_create('test', StringIO(test_config)) e = ev.read('test') @@ -414,8 +431,8 @@ packages: version: [2.2] """) - ev.prepare_config_scope(e) - e.concretize() + with e: + e.concretize() assert any(x.satisfies('mpileaks@2.2') for x in e._get_environment_specs()) @@ -431,7 +448,6 @@ env: - mpileaks """ % config_scope_path - spack.package_prefs.PackagePrefs.clear_caches() _env_create('test', StringIO(test_config)) e = ev.read('test') @@ -444,8 +460,8 @@ packages: version: [2.2] """) - ev.prepare_config_scope(e) - e.concretize() + with e: + e.concretize() assert any(x.satisfies('mpileaks@2.2') for x in e._get_environment_specs()) @@ -462,9 +478,6 @@ env: specs: - mpileaks """ - - spack.package_prefs.PackagePrefs.clear_caches() - _env_create('test', StringIO(test_config)) e = ev.read('test') @@ -477,8 +490,8 @@ packages: version: [0.8.11] """) - ev.prepare_config_scope(e) - e.concretize() + with e: + e.concretize() # ensure included scope took effect assert any( @@ -498,8 +511,6 @@ env: specs: - mpileaks """ - spack.package_prefs.PackagePrefs.clear_caches() - _env_create('test', StringIO(test_config)) e = ev.read('test') @@ -519,8 +530,8 @@ packages: version: [0.8.12] """) - ev.prepare_config_scope(e) - e.concretize() + with e: + e.concretize() assert any( x.satisfies('mpileaks@2.2') for x in e._get_environment_specs()) @@ -765,13 +776,13 @@ def test_indirect_build_dep(): @pytest.mark.usefixtures('config') def test_store_different_build_deps(): r"""Ensure that an environment can store two instances of a build-only -Dependency: + dependency:: - x y - /| (l) | (b) - (b) | y z2 - \| (b) # noqa: W605 - z1 + x y + /| (l) | (b) + (b) | y z2 + \| (b) + z1 """ default = ('build', 'link') @@ -1777,7 +1788,7 @@ def test_duplicate_packages_raise_when_concretizing_together(): def test_env_write_only_non_default(): - print(env('create', 'test')) + env('create', 'test') e = ev.read('test') with open(e.manifest_path, 'r') as f: diff --git a/lib/spack/spack/test/cmd/extensions.py b/lib/spack/spack/test/cmd/extensions.py index 544133698f..505573a7bc 100644 --- a/lib/spack/spack/test/cmd/extensions.py +++ b/lib/spack/spack/test/cmd/extensions.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/find.py b/lib/spack/spack/test/cmd/find.py index 45b065fce9..8516569592 100644 --- a/lib/spack/spack/test/cmd/find.py +++ b/lib/spack/spack/test/cmd/find.py @@ -1,20 +1,25 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) import argparse import json +import os import pytest import spack.cmd as cmd import spack.cmd.find +import spack.user_environment as uenv from spack.main import SpackCommand from spack.spec import Spec from spack.util.pattern import Bunch +import spack.environment as ev find = SpackCommand('find') +env = SpackCommand('env') +install = SpackCommand('install') base32_alphabet = 'abcdefghijklmnopqrstuvwxyz234567' @@ -302,3 +307,27 @@ def test_find_no_sections(database, config): def test_find_command_basic_usage(database): output = find() assert 'mpileaks' in output + + +@pytest.mark.regression('9875') +def test_find_prefix_in_env(mutable_mock_env_path, install_mockery, mock_fetch, + mock_packages, mock_archive, config): + """Test `find` formats requiring concrete specs work in environments.""" + env('create', 'test') + with ev.read('test'): + install('mpileaks') + find('-p') + find('-l') + find('-L') + # Would throw error on regression + + +def test_find_loaded(database, working_env): + output = find('--loaded', '--group') + assert output == '' # 0 packages installed printed separately + + os.environ[uenv.spack_loaded_hashes_var] = ':'.join( + [x.dag_hash() for x in spack.store.db.query()]) + output = find('--loaded') + expected = find() + assert output == expected diff --git a/lib/spack/spack/test/cmd/flake8.py b/lib/spack/spack/test/cmd/flake8.py index b95db93364..d4bfc5618d 100644 --- a/lib/spack/spack/test/cmd/flake8.py +++ b/lib/spack/spack/test/cmd/flake8.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -45,7 +45,7 @@ def flake8_package(): def test_changed_files(parser, flake8_package): - args = parser.parse_args() + args = parser.parse_args([]) # changed_files returns file paths relative to the root # directory of Spack. Convert to absolute file paths. diff --git a/lib/spack/spack/test/cmd/gc.py b/lib/spack/spack/test/cmd/gc.py new file mode 100644 index 0000000000..22c85a1d78 --- /dev/null +++ b/lib/spack/spack/test/cmd/gc.py @@ -0,0 +1,46 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import pytest + +import spack.environment as ev +import spack.spec +import spack.main + +gc = spack.main.SpackCommand('gc') + + +@pytest.mark.db +def test_no_packages_to_remove(config, mutable_database, capsys): + with capsys.disabled(): + output = gc('-y') + assert 'There are no unused specs.' in output + + +@pytest.mark.db +def test_packages_are_removed(config, mutable_database, capsys): + s = spack.spec.Spec('simple-inheritance') + s.concretize() + s.package.do_install(fake=True, explicit=True) + with capsys.disabled(): + output = gc('-y') + assert 'Successfully uninstalled cmake' in output + + +@pytest.mark.db +def test_gc_with_environment( + config, mutable_database, mutable_mock_env_path, capsys +): + s = spack.spec.Spec('simple-inheritance') + s.concretize() + s.package.do_install(fake=True, explicit=True) + + e = ev.create('test_gc') + e.add('cmake') + with e: + with capsys.disabled(): + output = gc('-y') + assert 'Restricting the garbage collection' in output + assert 'There are no unused specs' in output diff --git a/lib/spack/spack/test/cmd/gpg.py b/lib/spack/spack/test/cmd/gpg.py index f42282d72d..4333a38fe2 100644 --- a/lib/spack/spack/test/cmd/gpg.py +++ b/lib/spack/spack/test/cmd/gpg.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,37 +7,55 @@ import os import pytest +import llnl.util.filesystem as fs + +import spack.util.executable +import spack.util.gpg + from spack.paths import mock_gpg_data_path, mock_gpg_keys_path -import spack.util.gpg as gpg_util from spack.main import SpackCommand from spack.util.executable import ProcessError -@pytest.fixture(scope='function') -def testing_gpg_directory(tmpdir): - old_gpg_path = gpg_util.GNUPGHOME - gpg_util.GNUPGHOME = str(tmpdir.join('gpg')) - yield - gpg_util.GNUPGHOME = old_gpg_path +#: spack command used by tests below +gpg = SpackCommand('gpg') + +# test gpg command detection +@pytest.mark.parametrize('cmd_name,version', [ + ('gpg', 'undetectable'), # undetectable version + ('gpg', 'gpg (GnuPG) 1.3.4'), # insufficient version + ('gpg', 'gpg (GnuPG) 2.2.19'), # sufficient version + ('gpg2', 'gpg (GnuPG) 2.2.19'), # gpg2 command +]) +def test_find_gpg(cmd_name, version, tmpdir, mock_gnupghome, monkeypatch): + with tmpdir.as_cwd(): + with open(cmd_name, 'w') as f: + f.write("""\ +#!/bin/sh +echo "{version}" +""".format(version=version)) + fs.set_executable(cmd_name) -@pytest.fixture(scope='function') -def gpg(): - return SpackCommand('gpg') + monkeypatch.setitem(os.environ, "PATH", str(tmpdir)) + if version == 'undetectable' or version.endswith('1.3.4'): + with pytest.raises(spack.util.gpg.SpackGPGError): + exe = spack.util.gpg.Gpg.gpg() + else: + exe = spack.util.gpg.Gpg.gpg() + assert isinstance(exe, spack.util.executable.Executable) -def has_gnupg2(): - try: - gpg_util.Gpg.gpg()('--version', output=os.devnull) - return True - except Exception: - return False +def test_no_gpg_in_path(tmpdir, mock_gnupghome, monkeypatch): + monkeypatch.setitem(os.environ, "PATH", str(tmpdir)) + with pytest.raises(spack.util.gpg.SpackGPGError): + spack.util.gpg.Gpg.gpg() @pytest.mark.maybeslow -@pytest.mark.skipif(not has_gnupg2(), +@pytest.mark.skipif(not spack.util.gpg.Gpg.gpg(), reason='These tests require gnupg2') -def test_gpg(gpg, tmpdir, testing_gpg_directory): +def test_gpg(tmpdir, mock_gnupghome): # Verify a file with an empty keyring. with pytest.raises(ProcessError): gpg('verify', os.path.join(mock_gpg_data_path, 'content.txt')) @@ -77,7 +95,7 @@ def test_gpg(gpg, tmpdir, testing_gpg_directory): '--export', str(keypath), 'Spack testing 1', 'spack@googlegroups.com') - keyfp = gpg_util.Gpg.signing_keys()[0] + keyfp = spack.util.gpg.Gpg.signing_keys()[0] # List the keys. # TODO: Test the output here. diff --git a/lib/spack/spack/test/cmd/graph.py b/lib/spack/spack/test/cmd/graph.py index 0ddbc4f149..c402f35a9f 100644 --- a/lib/spack/spack/test/cmd/graph.py +++ b/lib/spack/spack/test/cmd/graph.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/help.py b/lib/spack/spack/test/cmd/help.py index c733474fda..00edfa187a 100644 --- a/lib/spack/spack/test/cmd/help.py +++ b/lib/spack/spack/test/cmd/help.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/info.py b/lib/spack/spack/test/cmd/info.py index 1928794560..b57ef3257b 100644 --- a/lib/spack/spack/test/cmd/info.py +++ b/lib/spack/spack/test/cmd/info.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/install.py b/lib/spack/spack/test/cmd/install.py index db8cf01f48..4c6c0860aa 100644 --- a/lib/spack/spack/test/cmd/install.py +++ b/lib/spack/spack/test/cmd/install.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,14 +30,6 @@ env = SpackCommand('env') add = SpackCommand('add') -@pytest.fixture(scope='module') -def parser(): - """Returns the parser for the module command""" - parser = argparse.ArgumentParser() - spack.cmd.install.setup_parser(parser) - return parser - - @pytest.fixture() def noop_install(monkeypatch): def noop(*args, **kwargs): @@ -115,7 +107,9 @@ def test_install_package_already_installed( (['--clean'], False), (['--dirty'], True), ]) -def test_install_dirty_flag(parser, arguments, expected): +def test_install_dirty_flag(arguments, expected): + parser = argparse.ArgumentParser() + spack.cmd.install.setup_parser(parser) args = parser.parse_args(arguments) assert args.dirty == expected @@ -664,3 +658,32 @@ def test_install_only_dependencies_of_all_in_env( assert not os.path.exists(root.prefix) for dep in root.traverse(root=False): assert os.path.exists(dep.prefix) + + +def test_install_help_does_not_show_cdash_options(capsys): + """Make sure `spack install --help` does not describe CDash arguments""" + with pytest.raises(SystemExit): + install('--help') + captured = capsys.readouterr() + assert 'CDash URL' not in captured.out + + +def test_install_help_cdash(capsys): + """Make sure `spack install --help-cdash` describes CDash arguments""" + install_cmd = SpackCommand('install') + out = install_cmd('--help-cdash') + assert 'CDash URL' in out + + +@pytest.mark.disable_clean_stage_check +def test_cdash_auth_token(tmpdir, install_mockery, capfd): + # capfd interferes with Spack's capturing + with tmpdir.as_cwd(): + with capfd.disabled(): + os.environ['SPACK_CDASH_AUTH_TOKEN'] = 'asdf' + out = install( + '-v', + '--log-file=cdash_reports', + '--log-format=cdash', + 'a') + assert 'Using CDash auth token from environment' in out diff --git a/lib/spack/spack/test/cmd/license.py b/lib/spack/spack/test/cmd/license.py index 630b93f68b..614d093c5f 100644 --- a/lib/spack/spack/test/cmd/license.py +++ b/lib/spack/spack/test/cmd/license.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,7 +31,7 @@ def test_verify(tmpdir): lgpl_header = source_dir.join('lgpl_header.py') with lgpl_header.open('w') as f: f.write("""\ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: LGPL-2.1-only @@ -48,7 +48,7 @@ def test_verify(tmpdir): correct_header = source_dir.join('correct_header.py') with correct_header.open('w') as f: f.write("""\ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/list.py b/lib/spack/spack/test/cmd/list.py index 6590b9ab2a..5d18787bc7 100644 --- a/lib/spack/spack/test/cmd/list.py +++ b/lib/spack/spack/test/cmd/list.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/load.py b/lib/spack/spack/test/cmd/load.py new file mode 100644 index 0000000000..a10b99d45b --- /dev/null +++ b/lib/spack/spack/test/cmd/load.py @@ -0,0 +1,125 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os +from spack.main import SpackCommand +import spack.spec +import spack.user_environment as uenv + +load = SpackCommand('load') +unload = SpackCommand('unload') +install = SpackCommand('install') +location = SpackCommand('location') + + +def test_load(install_mockery, mock_fetch, mock_archive, mock_packages): + """Test that the commands generated by load add the specified prefix + inspections. Also test that Spack records loaded specs by hash in the + user environment. + + CMAKE_PREFIX_PATH is the only prefix inspection guaranteed for fake + packages, since it keys on the prefix instead of a subdir.""" + install('mpileaks') + mpileaks_spec = spack.spec.Spec('mpileaks').concretized() + + sh_out = load('--sh', '--only', 'package', 'mpileaks') + csh_out = load('--csh', '--only', 'package', 'mpileaks') + + # Test prefix inspections + sh_out_test = 'export CMAKE_PREFIX_PATH=%s' % mpileaks_spec.prefix + csh_out_test = 'setenv CMAKE_PREFIX_PATH %s' % mpileaks_spec.prefix + assert sh_out_test in sh_out + assert csh_out_test in csh_out + + # Test hashes recorded properly + hash_test_replacements = (uenv.spack_loaded_hashes_var, + mpileaks_spec.dag_hash()) + sh_hash_test = 'export %s=%s' % hash_test_replacements + csh_hash_test = 'setenv %s %s' % hash_test_replacements + assert sh_hash_test in sh_out + assert csh_hash_test in csh_out + + +def test_load_recursive(install_mockery, mock_fetch, mock_archive, + mock_packages): + """Test that the '-r' option to the load command prepends dependency prefix + inspections in post-order""" + install('mpileaks') + mpileaks_spec = spack.spec.Spec('mpileaks').concretized() + + sh_out = load('--sh', 'mpileaks') + csh_out = load('--csh', 'mpileaks') + + # Test prefix inspections + prefix_test_replacement = ':'.join(reversed( + [s.prefix for s in mpileaks_spec.traverse(order='post')])) + + sh_prefix_test = 'export CMAKE_PREFIX_PATH=%s' % prefix_test_replacement + csh_prefix_test = 'setenv CMAKE_PREFIX_PATH %s' % prefix_test_replacement + assert sh_prefix_test in sh_out + assert csh_prefix_test in csh_out + + # Test spack records loaded hashes properly + hash_test_replacement = (uenv.spack_loaded_hashes_var, ':'.join(reversed( + [s.dag_hash() for s in mpileaks_spec.traverse(order='post')]))) + sh_hash_test = 'export %s=%s' % hash_test_replacement + csh_hash_test = 'setenv %s %s' % hash_test_replacement + assert sh_hash_test in sh_out + assert csh_hash_test in csh_out + + +def test_load_includes_run_env(install_mockery, mock_fetch, mock_archive, + mock_packages): + """Tests that environment changes from the package's + `setup_run_environment` method are added to the user environment in + addition to the prefix inspections""" + install('mpileaks') + + sh_out = load('--sh', 'mpileaks') + csh_out = load('--csh', 'mpileaks') + + assert 'export FOOBAR=mpileaks' in sh_out + assert 'setenv FOOBAR mpileaks' in csh_out + + +def test_load_fails_no_shell(install_mockery, mock_fetch, mock_archive, + mock_packages): + """Test that spack load prints an error message without a shell.""" + install('mpileaks') + + out = load('mpileaks', fail_on_error=False) + assert "To initialize spack's shell commands" in out + + +def test_unload(install_mockery, mock_fetch, mock_archive, mock_packages, + working_env): + """Tests that any variables set in the user environment are undone by the + unload command""" + install('mpileaks') + mpileaks_spec = spack.spec.Spec('mpileaks').concretized() + + # Set so unload has something to do + os.environ['FOOBAR'] = 'mpileaks' + os.environ[uenv.spack_loaded_hashes_var] = '%s:%s' % ( + mpileaks_spec.dag_hash(), 'garbage') + + sh_out = unload('--sh', 'mpileaks') + csh_out = unload('--csh', 'mpileaks') + + assert 'unset FOOBAR' in sh_out + assert 'unsetenv FOOBAR' in csh_out + + assert 'export %s=garbage' % uenv.spack_loaded_hashes_var in sh_out + assert 'setenv %s garbage' % uenv.spack_loaded_hashes_var in csh_out + + +def test_unload_fails_no_shell(install_mockery, mock_fetch, mock_archive, + mock_packages, working_env): + """Test that spack unload prints an error message without a shell.""" + install('mpileaks') + mpileaks_spec = spack.spec.Spec('mpileaks').concretized() + os.environ[uenv.spack_loaded_hashes_var] = mpileaks_spec.dag_hash() + + out = unload('mpileaks', fail_on_error=False) + assert "To initialize spack's shell commands" in out diff --git a/lib/spack/spack/test/cmd/location.py b/lib/spack/spack/test/cmd/location.py index f48cdb75e7..3977cba3e5 100644 --- a/lib/spack/spack/test/cmd/location.py +++ b/lib/spack/spack/test/cmd/location.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/maintainers.py b/lib/spack/spack/test/cmd/maintainers.py index 5ddf176c39..4c566c7513 100644 --- a/lib/spack/spack/test/cmd/maintainers.py +++ b/lib/spack/spack/test/cmd/maintainers.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/mirror.py b/lib/spack/spack/test/cmd/mirror.py index 889d81f98b..d62d7df432 100644 --- a/lib/spack/spack/test/cmd/mirror.py +++ b/lib/spack/spack/test/cmd/mirror.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ import pytest import os -from spack.main import SpackCommand +from spack.main import SpackCommand, SpackCommandError import spack.environment as ev import spack.config @@ -16,6 +16,25 @@ add = SpackCommand('add') concretize = SpackCommand('concretize') +@pytest.fixture +def tmp_scope(): + """Creates a temporary configuration scope""" + + base_name = 'internal-testing-scope' + current_overrides = set( + x.name for x in + spack.config.config.matching_scopes(r'^{0}'.format(base_name))) + + num_overrides = 0 + scope_name = base_name + while scope_name in current_overrides: + scope_name = '{0}{1}'.format(base_name, num_overrides) + num_overrides += 1 + + with spack.config.override(spack.config.InternalConfigScope(scope_name)): + yield scope_name + + @pytest.mark.disable_clean_stage_check @pytest.mark.regression('8083') def test_regression_8083(tmpdir, capfd, mock_packages, mock_fetch, config): @@ -45,3 +64,49 @@ def test_mirror_from_env(tmpdir, mock_packages, mock_fetch, config, mirror_res = os.listdir(os.path.join(mirror_dir, spec.name)) expected = ['%s.tar.gz' % spec.format('{name}-{version}')] assert mirror_res == expected + + +def test_mirror_crud(tmp_scope, capsys): + with capsys.disabled(): + mirror('add', '--scope', tmp_scope, 'mirror', 'http://spack.io') + + output = mirror('remove', '--scope', tmp_scope, 'mirror') + assert 'Removed mirror' in output + + mirror('add', '--scope', tmp_scope, 'mirror', 'http://spack.io') + + # no-op + output = mirror('set-url', '--scope', tmp_scope, + 'mirror', 'http://spack.io') + assert 'Url already set' in output + + output = mirror('set-url', '--scope', tmp_scope, + '--push', 'mirror', 's3://spack-public') + assert 'Changed (push) url' in output + + # no-op + output = mirror('set-url', '--scope', tmp_scope, + '--push', 'mirror', 's3://spack-public') + assert 'Url already set' in output + + output = mirror('remove', '--scope', tmp_scope, 'mirror') + assert 'Removed mirror' in output + + output = mirror('list', '--scope', tmp_scope) + assert 'No mirrors configured' in output + + +def test_mirror_nonexisting(tmp_scope): + with pytest.raises(SpackCommandError): + mirror('remove', '--scope', tmp_scope, 'not-a-mirror') + + with pytest.raises(SpackCommandError): + mirror('set-url', '--scope', tmp_scope, + 'not-a-mirror', 'http://spack.io') + + +def test_mirror_name_collision(tmp_scope): + mirror('add', '--scope', tmp_scope, 'first', '1') + + with pytest.raises(SpackCommandError): + mirror('add', '--scope', tmp_scope, 'first', '1') diff --git a/lib/spack/spack/test/cmd/module.py b/lib/spack/spack/test/cmd/module.py index 6f2ffcbf85..f9aeb4af66 100644 --- a/lib/spack/spack/test/cmd/module.py +++ b/lib/spack/spack/test/cmd/module.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,9 +10,21 @@ import pytest import spack.main import spack.modules +from spack.test.conftest import use_store, use_configuration, use_repo module = spack.main.SpackCommand('module') +#: make sure module files are generated for all the tests here +@pytest.fixture(scope='module', autouse=True) +def ensure_module_files_are_there( + mock_repo_path, mock_store, mock_configuration): + """Generate module files for module tests.""" + module = spack.main.SpackCommand('module') + with use_store(mock_store): + with use_configuration(mock_configuration): + with use_repo(mock_repo_path): + module('tcl', 'refresh', '-y') + def _module_files(module_type, *specs): specs = [spack.spec.Spec(x).concretized() for x in specs] @@ -20,11 +32,6 @@ def _module_files(module_type, *specs): return [writer_cls(spec).layout.filename for spec in specs] -@pytest.fixture(scope='module', autouse=True) -def ensure_module_files_are_there(database): - module('tcl', 'refresh', '-y') - - @pytest.fixture( params=[ ['rm', 'doesnotexist'], # Try to remove a non existing module diff --git a/lib/spack/spack/test/cmd/pkg.py b/lib/spack/spack/test/cmd/pkg.py index e7d1006cc1..fa324272bf 100644 --- a/lib/spack/spack/test/cmd/pkg.py +++ b/lib/spack/spack/test/cmd/pkg.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/print_shell_vars.py b/lib/spack/spack/test/cmd/print_shell_vars.py index e5522ea016..5f4f8164eb 100644 --- a/lib/spack/spack/test/cmd/print_shell_vars.py +++ b/lib/spack/spack/test/cmd/print_shell_vars.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/providers.py b/lib/spack/spack/test/cmd/providers.py index f10faeeb90..3d537c553f 100644 --- a/lib/spack/spack/test/cmd/providers.py +++ b/lib/spack/spack/test/cmd/providers.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/python.py b/lib/spack/spack/test/cmd/python.py index c4988f4269..074c295622 100644 --- a/lib/spack/spack/test/cmd/python.py +++ b/lib/spack/spack/test/cmd/python.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/reindex.py b/lib/spack/spack/test/cmd/reindex.py index 0ee36b3001..feb5545ae6 100644 --- a/lib/spack/spack/test/cmd/reindex.py +++ b/lib/spack/spack/test/cmd/reindex.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/release_jobs.py b/lib/spack/spack/test/cmd/release_jobs.py deleted file mode 100644 index 0dbe8c5d5c..0000000000 --- a/lib/spack/spack/test/cmd/release_jobs.py +++ /dev/null @@ -1,128 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -import os -import pytest -import re - -import spack -import spack.environment as ev -from spack import repo -from spack.cmd.release_jobs import stage_spec_jobs, spec_deps_key_label -from spack.main import SpackCommand -from spack.spec import Spec -from spack.test.conftest import MockPackage, MockPackageMultiRepo - - -env = SpackCommand('env') -release_jobs = SpackCommand('release-jobs') - - -@pytest.fixture() -def env_deactivate(): - yield - spack.environment._active_environment = None - os.environ.pop('SPACK_ENV', None) - - -def test_specs_staging(config): - """Make sure we achieve the best possible staging for the following -spec DAG:: - - a - /| - c b - |\ - e d - |\ - f g - -In this case, we would expect 'c', 'e', 'f', and 'g' to be in the first stage, -and then 'd', 'b', and 'a' to be put in the next three stages, respectively. - -""" - default = ('build', 'link') - - g = MockPackage('g', [], []) - f = MockPackage('f', [], []) - e = MockPackage('e', [], []) - d = MockPackage('d', [f, g], [default, default]) - c = MockPackage('c', [], []) - b = MockPackage('b', [d, e], [default, default]) - a = MockPackage('a', [b, c], [default, default]) - - mock_repo = MockPackageMultiRepo([a, b, c, d, e, f, g]) - - with repo.swap(mock_repo): - spec_a = Spec('a') - spec_a.concretize() - - spec_a_label = spec_deps_key_label(spec_a)[1] - spec_b_label = spec_deps_key_label(spec_a['b'])[1] - spec_c_label = spec_deps_key_label(spec_a['c'])[1] - spec_d_label = spec_deps_key_label(spec_a['d'])[1] - spec_e_label = spec_deps_key_label(spec_a['e'])[1] - spec_f_label = spec_deps_key_label(spec_a['f'])[1] - spec_g_label = spec_deps_key_label(spec_a['g'])[1] - - spec_labels, dependencies, stages = stage_spec_jobs([spec_a]) - - assert (len(stages) == 4) - - assert (len(stages[0]) == 4) - assert (spec_c_label in stages[0]) - assert (spec_e_label in stages[0]) - assert (spec_f_label in stages[0]) - assert (spec_g_label in stages[0]) - - assert (len(stages[1]) == 1) - assert (spec_d_label in stages[1]) - - assert (len(stages[2]) == 1) - assert (spec_b_label in stages[2]) - - assert (len(stages[3]) == 1) - assert (spec_a_label in stages[3]) - - -def test_release_jobs_with_env(tmpdir, mutable_mock_env_path, env_deactivate, - install_mockery, mock_packages): - """Make sure we can get a .gitlab-ci.yml from an environment file - which has the gitlab-ci, cdash, and mirrors sections.""" - filename = str(tmpdir.join('spack.yaml')) - with open(filename, 'w') as f: - f.write("""\ -spack: - definitions: - - packages: [archive-files] - specs: - - $packages - mirrors: - some-mirror: https://my.fake.mirror - gitlab-ci: - mappings: - - match: - - archive-files - runner-attributes: - tags: - - donotcare - image: donotcare - cdash: - build-group: Not important - url: https://my.fake.cdash - project: Not used - site: Nothing -""") - with tmpdir.as_cwd(): - env('create', 'test', './spack.yaml') - outputfile = str(tmpdir.join('.gitlab-ci.yml')) - - with ev.read('test'): - release_jobs('--output-file', outputfile) - - with open(outputfile) as f: - contents = f.read().replace(os.linesep, '') - assert('archive-files' in contents) - assert(re.search(r'stages:\s*\[\s*stage-0', contents)) diff --git a/lib/spack/spack/test/cmd/resource.py b/lib/spack/spack/test/cmd/resource.py index 62fa1c2d11..4fc5fd5c50 100644 --- a/lib/spack/spack/test/cmd/resource.py +++ b/lib/spack/spack/test/cmd/resource.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/spec.py b/lib/spack/spack/test/cmd/spec.py index 4637e14a1f..3c50a66ce7 100644 --- a/lib/spack/spack/test/cmd/spec.py +++ b/lib/spack/spack/test/cmd/spec.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,7 +9,7 @@ import pytest import spack.spec from spack.main import SpackCommand -pytestmark = pytest.mark.usefixtures('config', 'mutable_mock_packages') +pytestmark = pytest.mark.usefixtures('config', 'mutable_mock_repo') spec = SpackCommand('spec') diff --git a/lib/spack/spack/test/cmd/test.py b/lib/spack/spack/test/cmd/test.py new file mode 100644 index 0000000000..9a64209cfa --- /dev/null +++ b/lib/spack/spack/test/cmd/test.py @@ -0,0 +1,94 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.main import SpackCommand + +spack_test = SpackCommand('test') + + +def test_list(): + output = spack_test('--list') + assert "test.py" in output + assert "spec_semantics.py" in output + assert "test_list" not in output + + +def test_list_with_pytest_arg(): + output = spack_test('--list', 'cmd/test.py') + assert output.strip() == "cmd/test.py" + + +def test_list_with_keywords(): + output = spack_test('--list', '-k', 'cmd/test.py') + assert output.strip() == "cmd/test.py" + + +def test_list_long(capsys): + with capsys.disabled(): + output = spack_test('--list-long') + assert "test.py::\n" in output + assert "test_list" in output + assert "test_list_with_pytest_arg" in output + assert "test_list_with_keywords" in output + assert "test_list_long" in output + assert "test_list_long_with_pytest_arg" in output + assert "test_list_names" in output + assert "test_list_names_with_pytest_arg" in output + + assert "spec_dag.py::\n" in output + assert 'test_installed_deps' in output + assert 'test_test_deptype' in output + + +def test_list_long_with_pytest_arg(capsys): + with capsys.disabled(): + output = spack_test('--list-long', 'cmd/test.py') + assert "test.py::\n" in output + assert "test_list" in output + assert "test_list_with_pytest_arg" in output + assert "test_list_with_keywords" in output + assert "test_list_long" in output + assert "test_list_long_with_pytest_arg" in output + assert "test_list_names" in output + assert "test_list_names_with_pytest_arg" in output + + assert "spec_dag.py::\n" not in output + assert 'test_installed_deps' not in output + assert 'test_test_deptype' not in output + + +def test_list_names(): + output = spack_test('--list-names') + assert "test.py::test_list\n" in output + assert "test.py::test_list_with_pytest_arg\n" in output + assert "test.py::test_list_with_keywords\n" in output + assert "test.py::test_list_long\n" in output + assert "test.py::test_list_long_with_pytest_arg\n" in output + assert "test.py::test_list_names\n" in output + assert "test.py::test_list_names_with_pytest_arg\n" in output + + assert "spec_dag.py::test_installed_deps\n" in output + assert 'spec_dag.py::test_test_deptype\n' in output + + +def test_list_names_with_pytest_arg(): + output = spack_test('--list-names', 'cmd/test.py') + assert "test.py::test_list\n" in output + assert "test.py::test_list_with_pytest_arg\n" in output + assert "test.py::test_list_with_keywords\n" in output + assert "test.py::test_list_long\n" in output + assert "test.py::test_list_long_with_pytest_arg\n" in output + assert "test.py::test_list_names\n" in output + assert "test.py::test_list_names_with_pytest_arg\n" in output + + assert "spec_dag.py::test_installed_deps\n" not in output + assert 'spec_dag.py::test_test_deptype\n' not in output + + +def test_pytest_help(): + output = spack_test('--pytest-help') + assert "-k EXPRESSION" in output + assert "pytest-warnings:" in output + assert "--collect-only" in output diff --git a/lib/spack/spack/test/cmd/test_compiler_cmd.py b/lib/spack/spack/test/cmd/test_compiler_cmd.py index 381ff12ae9..3c34f720ec 100644 --- a/lib/spack/spack/test/cmd/test_compiler_cmd.py +++ b/lib/spack/spack/test/cmd/test_compiler_cmd.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/uninstall.py b/lib/spack/spack/test/cmd/uninstall.py index c9a23c48cf..882f075ec7 100644 --- a/lib/spack/spack/test/cmd/uninstall.py +++ b/lib/spack/spack/test/cmd/uninstall.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/url.py b/lib/spack/spack/test/cmd/url.py index 6593c94d98..54ef3d55cf 100644 --- a/lib/spack/spack/test/cmd/url.py +++ b/lib/spack/spack/test/cmd/url.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/verify.py b/lib/spack/spack/test/cmd/verify.py index 4896cb05c8..dda992fe49 100644 --- a/lib/spack/spack/test/cmd/verify.py +++ b/lib/spack/spack/test/cmd/verify.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/versions.py b/lib/spack/spack/test/cmd/versions.py index 07761be1d4..1e2bcbedb3 100644 --- a/lib/spack/spack/test/cmd/versions.py +++ b/lib/spack/spack/test/cmd/versions.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd/view.py b/lib/spack/spack/test/cmd/view.py index f7375d8903..c52cd12325 100644 --- a/lib/spack/spack/test/cmd/view.py +++ b/lib/spack/spack/test/cmd/view.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/cmd_extensions.py b/lib/spack/spack/test/cmd_extensions.py index bb018eedb5..486ac925cf 100644 --- a/lib/spack/spack/test/cmd_extensions.py +++ b/lib/spack/spack/test/cmd_extensions.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/compilers.py b/lib/spack/spack/test/compilers.py index ac107170b0..9395ddba80 100644 --- a/lib/spack/spack/test/compilers.py +++ b/lib/spack/spack/test/compilers.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -348,6 +348,14 @@ def test_fj_flags(): ('clang version 8.0.0-3~ubuntu18.04.1 (tags/RELEASE_800/final)\n' 'Target: x86_64-pc-linux-gnu\n' 'Thread model: posix\n' + 'InstalledDir: /usr/bin\n', '8.0.0'), + ('clang version 9.0.1-+201911131414230800840845a1eea-1~exp1~20191113231141.78\n' # noqa + 'Target: x86_64-pc-linux-gnu\n' + 'Thread model: posix\n' + 'InstalledDir: /usr/bin\n', '9.0.1'), + ('clang version 8.0.0-3 (tags/RELEASE_800/final)\n' + 'Target: aarch64-unknown-linux-gnu\n' + 'Thread model: posix\n' 'InstalledDir: /usr/bin\n', '8.0.0') ]) def test_clang_version_detection(version_str, expected_version): diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py index 4b17e755ed..72092a956f 100644 --- a/lib/spack/spack/test/concretize.py +++ b/lib/spack/spack/test/concretize.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,9 +11,9 @@ import spack.concretize import spack.repo from spack.concretize import find_spec, NoValidVersionError +from spack.error import SpecError from spack.package_prefs import PackagePrefs -from spack.spec import Spec, CompilerSpec -from spack.spec import ConflictsInSpecError, SpecError +from spack.spec import Spec, CompilerSpec, ConflictsInSpecError from spack.version import ver from spack.test.conftest import MockPackage, MockPackageMultiRepo import spack.compilers @@ -276,7 +276,7 @@ class TestConcretize(object): Spec('hypre').concretize() def test_concretize_two_virtuals_with_one_bound( - self, mutable_mock_packages + self, mutable_mock_repo ): """Test a package with multiple virtual dependencies and one preset.""" Spec('hypre ^openblas').concretize() @@ -302,7 +302,7 @@ class TestConcretize(object): with pytest.raises(spack.spec.MultipleProviderError): s.concretize() - def test_no_matching_compiler_specs(self, mock_config): + def test_no_matching_compiler_specs(self, mock_low_high_config): # only relevant when not building compilers as needed with spack.concretize.enable_compiler_existence_check(): s = Spec('a %gcc@0.0.0') diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py index e5fa4a851d..0d0d870506 100644 --- a/lib/spack/spack/test/concretize_preferences.py +++ b/lib/spack/spack/test/concretize_preferences.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,6 +11,7 @@ import spack.repo import spack.util.spack_yaml as syaml from spack.config import ConfigScope, ConfigError from spack.spec import Spec +from spack.version import Version @pytest.fixture() @@ -23,7 +24,6 @@ def concretize_scope(config, tmpdir): yield config.pop_scope() - spack.package_prefs.PackagePrefs.clear_caches() spack.repo.path._provider_index = None @@ -60,7 +60,6 @@ def update_packages(pkgname, section, value): """Update config and reread package list""" conf = {pkgname: {section: value}} spack.config.set('packages', conf, scope='concretize') - spack.package_prefs.PackagePrefs.clear_caches() def assert_variant_values(spec, **variants): @@ -85,7 +84,7 @@ class TestConcretizePreferences(object): 'mpileaks', debug=True, opt=True, shared=False, static=False ) - def test_preferred_compilers(self, mutable_mock_packages): + def test_preferred_compilers(self, mutable_mock_repo): """Test preferred compilers are applied correctly """ update_packages('mpileaks', 'compiler', ['clang@3.3']) @@ -96,7 +95,7 @@ class TestConcretizePreferences(object): spec = concretize('mpileaks') assert spec.compiler == spack.spec.CompilerSpec('gcc@4.5.0') - def test_preferred_target(self, mutable_mock_packages): + def test_preferred_target(self, mutable_mock_repo): """Test preferred compilers are applied correctly """ spec = concretize('mpich') @@ -121,16 +120,16 @@ class TestConcretizePreferences(object): """ update_packages('mpileaks', 'version', ['2.3']) spec = concretize('mpileaks') - assert spec.version == spack.spec.Version('2.3') + assert spec.version == Version('2.3') update_packages('mpileaks', 'version', ['2.2']) spec = concretize('mpileaks') - assert spec.version == spack.spec.Version('2.2') + assert spec.version == Version('2.2') def test_preferred_versions_mixed_version_types(self): update_packages('mixedversions', 'version', ['2.0']) spec = concretize('mixedversions') - assert spec.version == spack.spec.Version('2.0') + assert spec.version == Version('2.0') def test_preferred_providers(self): """Test preferred providers of virtual packages are @@ -148,35 +147,35 @@ class TestConcretizePreferences(object): """"Test packages with some version marked as preferred=True""" spec = Spec('preferred-test') spec.concretize() - assert spec.version == spack.spec.Version('0.2.15') + assert spec.version == Version('0.2.15') # now add packages.yaml with versions other than preferred # ensure that once config is in place, non-preferred version is used update_packages('preferred-test', 'version', ['0.2.16']) spec = Spec('preferred-test') spec.concretize() - assert spec.version == spack.spec.Version('0.2.16') + assert spec.version == Version('0.2.16') def test_develop(self): """Test concretization with develop-like versions""" spec = Spec('develop-test') spec.concretize() - assert spec.version == spack.spec.Version('0.2.15') + assert spec.version == Version('0.2.15') spec = Spec('develop-test2') spec.concretize() - assert spec.version == spack.spec.Version('0.2.15') + assert spec.version == Version('0.2.15') # now add packages.yaml with develop-like versions # ensure that once config is in place, develop-like version is used update_packages('develop-test', 'version', ['develop']) spec = Spec('develop-test') spec.concretize() - assert spec.version == spack.spec.Version('develop') + assert spec.version == Version('develop') update_packages('develop-test2', 'version', ['0.2.15.develop']) spec = Spec('develop-test2') spec.concretize() - assert spec.version == spack.spec.Version('0.2.15.develop') + assert spec.version == Version('0.2.15.develop') def test_no_virtuals_in_packages_yaml(self): """Verify that virtuals are not allowed in packages.yaml.""" @@ -204,7 +203,6 @@ all: spack.config.set('packages', conf, scope='concretize') # should be no error for 'all': - spack.package_prefs.PackagePrefs.clear_caches() spack.package_prefs.get_packages_config() def test_external_mpi(self): diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py index 605c37d468..feb2b9cae4 100644 --- a/lib/spack/spack/test/config.py +++ b/lib/spack/spack/test/config.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -203,7 +203,7 @@ def compiler_specs(): return CompilerSpecs(a=a, b=b) -def test_write_key_in_memory(mock_config, compiler_specs): +def test_write_key_in_memory(mock_low_high_config, compiler_specs): # Write b_comps "on top of" a_comps. spack.config.set('compilers', a_comps['compilers'], scope='low') spack.config.set('compilers', b_comps['compilers'], scope='high') @@ -213,7 +213,7 @@ def test_write_key_in_memory(mock_config, compiler_specs): check_compiler_config(b_comps['compilers'], *compiler_specs.b) -def test_write_key_to_disk(mock_config, compiler_specs): +def test_write_key_to_disk(mock_low_high_config, compiler_specs): # Write b_comps "on top of" a_comps. spack.config.set('compilers', a_comps['compilers'], scope='low') spack.config.set('compilers', b_comps['compilers'], scope='high') @@ -226,7 +226,7 @@ def test_write_key_to_disk(mock_config, compiler_specs): check_compiler_config(b_comps['compilers'], *compiler_specs.b) -def test_write_to_same_priority_file(mock_config, compiler_specs): +def test_write_to_same_priority_file(mock_low_high_config, compiler_specs): # Write b_comps in the same file as a_comps. spack.config.set('compilers', a_comps['compilers'], scope='low') spack.config.set('compilers', b_comps['compilers'], scope='low') @@ -247,7 +247,7 @@ repos_high = {'repos': ["/some/other/path"]} # repos -def test_write_list_in_memory(mock_config): +def test_write_list_in_memory(mock_low_high_config): spack.config.set('repos', repos_low['repos'], scope='low') spack.config.set('repos', repos_high['repos'], scope='high') @@ -255,7 +255,7 @@ def test_write_list_in_memory(mock_config): assert config == repos_high['repos'] + repos_low['repos'] -def test_substitute_config_variables(mock_config): +def test_substitute_config_variables(mock_low_high_config): prefix = spack.paths.prefix.lstrip('/') assert os.path.join( @@ -315,7 +315,7 @@ packages_merge_high = { @pytest.mark.regression('7924') -def test_merge_with_defaults(mock_config, write_config_file): +def test_merge_with_defaults(mock_low_high_config, write_config_file): """This ensures that specified preferences merge with defaults as expected. Originally all defaults were initialized with the exact same object, which led to aliasing problems. Therefore @@ -331,14 +331,14 @@ def test_merge_with_defaults(mock_config, write_config_file): assert cfg['baz']['version'] == ['c'] -def test_substitute_user(mock_config): +def test_substitute_user(mock_low_high_config): user = getpass.getuser() assert '/foo/bar/' + user + '/baz' == canonicalize_path( '/foo/bar/$user/baz' ) -def test_substitute_tempdir(mock_config): +def test_substitute_tempdir(mock_low_high_config): tempdir = tempfile.gettempdir() assert tempdir == canonicalize_path('$tempdir') assert tempdir + '/foo/bar/baz' == canonicalize_path( @@ -346,12 +346,12 @@ def test_substitute_tempdir(mock_config): ) -def test_read_config(mock_config, write_config_file): +def test_read_config(mock_low_high_config, write_config_file): write_config_file('config', config_low, 'low') assert spack.config.get('config') == config_low['config'] -def test_read_config_override_all(mock_config, write_config_file): +def test_read_config_override_all(mock_low_high_config, write_config_file): write_config_file('config', config_low, 'low') write_config_file('config', config_override_all, 'high') assert spack.config.get('config') == { @@ -359,7 +359,7 @@ def test_read_config_override_all(mock_config, write_config_file): } -def test_read_config_override_key(mock_config, write_config_file): +def test_read_config_override_key(mock_low_high_config, write_config_file): write_config_file('config', config_low, 'low') write_config_file('config', config_override_key, 'high') assert spack.config.get('config') == { @@ -368,7 +368,7 @@ def test_read_config_override_key(mock_config, write_config_file): } -def test_read_config_merge_list(mock_config, write_config_file): +def test_read_config_merge_list(mock_low_high_config, write_config_file): write_config_file('config', config_low, 'low') write_config_file('config', config_merge_list, 'high') assert spack.config.get('config') == { @@ -377,7 +377,7 @@ def test_read_config_merge_list(mock_config, write_config_file): } -def test_read_config_override_list(mock_config, write_config_file): +def test_read_config_override_list(mock_low_high_config, write_config_file): write_config_file('config', config_low, 'low') write_config_file('config', config_override_list, 'high') assert spack.config.get('config') == { @@ -386,33 +386,34 @@ def test_read_config_override_list(mock_config, write_config_file): } -def test_internal_config_update(mock_config, write_config_file): +def test_internal_config_update(mock_low_high_config, write_config_file): write_config_file('config', config_low, 'low') - before = mock_config.get('config') + before = mock_low_high_config.get('config') assert before['install_tree'] == 'install_tree_path' # add an internal configuration scope scope = spack.config.InternalConfigScope('command_line') assert 'InternalConfigScope' in repr(scope) - mock_config.push_scope(scope) + mock_low_high_config.push_scope(scope) - command_config = mock_config.get('config', scope='command_line') + command_config = mock_low_high_config.get('config', scope='command_line') command_config['install_tree'] = 'foo/bar' - mock_config.set('config', command_config, scope='command_line') + mock_low_high_config.set('config', command_config, scope='command_line') - after = mock_config.get('config') + after = mock_low_high_config.get('config') assert after['install_tree'] == 'foo/bar' -def test_internal_config_filename(mock_config, write_config_file): +def test_internal_config_filename(mock_low_high_config, write_config_file): write_config_file('config', config_low, 'low') - mock_config.push_scope(spack.config.InternalConfigScope('command_line')) + mock_low_high_config.push_scope( + spack.config.InternalConfigScope('command_line')) with pytest.raises(NotImplementedError): - mock_config.get_config_filename('command_line', 'config') + mock_low_high_config.get_config_filename('command_line', 'config') def test_mark_internal(): @@ -585,7 +586,7 @@ mirrors: assert "mirrors.yaml:5" in str(e) -def test_bad_config_section(mock_config): +def test_bad_config_section(mock_low_high_config): """Test that getting or setting a bad section gives an error.""" with pytest.raises(spack.config.ConfigSectionError): spack.config.set('foobar', 'foobar') @@ -595,7 +596,7 @@ def test_bad_config_section(mock_config): @pytest.mark.skipif(os.getuid() == 0, reason='user is root') -def test_bad_command_line_scopes(tmpdir, mock_config): +def test_bad_command_line_scopes(tmpdir, mock_low_high_config): cfg = spack.config.Configuration() with tmpdir.as_cwd(): @@ -844,7 +845,7 @@ compilers: @pytest.mark.regression('13045') def test_dotkit_in_config_does_not_raise( - mock_config, write_config_file, capsys + mock_low_high_config, write_config_file, capsys ): write_config_file('config', {'config': {'module_roots': {'dotkit': '/some/path'}}}, diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py index 969e2471e4..97bbb69b52 100644 --- a/lib/spack/spack/test/conftest.py +++ b/lib/spack/spack/test/conftest.py @@ -1,16 +1,17 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) import collections -import copy +import contextlib import errno import inspect import itertools import os import os.path import shutil +import tempfile import xml.etree.ElementTree import ordereddict_backport @@ -33,6 +34,8 @@ import spack.platforms.test import spack.repo import spack.stage import spack.util.executable +import spack.util.gpg + from spack.util.pattern import Bunch from spack.dependency import Dependency from spack.package import PackageBase @@ -167,7 +170,7 @@ def ignore_stage_files(): Used to track which leftover files in the stage have been seen. """ # to start with, ignore the .lock file at the stage root. - return set(['.lock', spack.stage._source_path_subdir]) + return set(['.lock', spack.stage._source_path_subdir, 'build_cache']) def remove_whatever_it_is(path): @@ -240,9 +243,6 @@ def mock_fetch_cache(monkeypatch): return MockCacheFetcher() class MockCacheFetcher(object): - def set_stage(self, stage): - pass - def fetch(self): raise FetchError('Mock cache always fails for tests') @@ -273,31 +273,75 @@ def _skip_if_missing_executables(request): spack.architecture.real_platform = spack.architecture.platform spack.architecture.platform = lambda: spack.platforms.test.Test() -########## -# Test-specific fixtures -########## + +# +# Context managers used by fixtures +# +# Because these context managers modify global state, they should really +# ONLY be used persistently (i.e., around yield statements) in +# function-scoped fixtures, OR in autouse session- or module-scoped +# fixtures. +# +# If they're used in regular tests or in module-scoped fixtures that are +# then injected as function arguments, weird things can happen, because +# the original state won't be restored until *after* the fixture is +# destroyed. This makes sense for an autouse fixture, where you know +# everything in the module/session is going to need the modified +# behavior, but modifying global state for one function in a way that +# won't be restored until after the module or session is done essentially +# leaves garbage behind for other tests. +# +# In general, we should module- or session-scope the *STATE* required for +# these global objects, but we shouldn't module- or session-scope their +# *USE*, or things can get really confusing. +# + +@contextlib.contextmanager +def use_configuration(config): + """Context manager to swap out the global Spack configuration.""" + saved = spack.config.config + spack.config.config = config + yield + spack.config.config = saved +@contextlib.contextmanager +def use_store(store): + """Context manager to swap out the global Spack store.""" + saved = spack.store.store + spack.store.store = store + yield + spack.store.store = saved + + +@contextlib.contextmanager +def use_repo(repo): + """Context manager to swap out the global Spack repo path.""" + with spack.repo.swap(repo): + yield + + +# +# Test-specific fixtures +# @pytest.fixture(scope='session') -def repo_path(): - """Session scoped RepoPath object pointing to the mock repository""" - return spack.repo.RepoPath(spack.paths.mock_packages_path) +def mock_repo_path(): + yield spack.repo.RepoPath(spack.paths.mock_packages_path) -@pytest.fixture(scope='module') -def mock_packages(repo_path): +@pytest.fixture(scope='function') +def mock_packages(mock_repo_path): """Use the 'builtin.mock' repository instead of 'builtin'""" - mock_repo = copy.deepcopy(repo_path) - with spack.repo.swap(mock_repo): - yield + with use_repo(mock_repo_path): + yield mock_repo_path @pytest.fixture(scope='function') -def mutable_mock_packages(mock_packages, repo_path): +def mutable_mock_repo(mock_repo_path): """Function-scoped mock packages, for tests that need to modify them.""" - mock_repo = copy.deepcopy(repo_path) - with spack.repo.swap(mock_repo): - yield + mock_repo_path = spack.repo.RepoPath(spack.paths.mock_packages_path) + with use_repo(mock_repo_path): + yield mock_repo_path @pytest.fixture(scope='session') @@ -322,23 +366,16 @@ def configuration_dir(tmpdir_factory, linux_os): """ tmpdir = tmpdir_factory.mktemp('configurations') - # Name of the yaml files in the test/data folder - test_path = py.path.local(spack.paths.test_path) - compilers_yaml = test_path.join('data', 'compilers.yaml') - packages_yaml = test_path.join('data', 'packages.yaml') - config_yaml = test_path.join('data', 'config.yaml') - repos_yaml = test_path.join('data', 'repos.yaml') + # <test_path>/data/config has mock config yaml files in it + # copy these to the site config. + test_config = py.path.local(spack.paths.test_path).join('data', 'config') + test_config.copy(tmpdir.join('site')) - # Create temporary 'site' and 'user' folders - tmpdir.ensure('site', dir=True) + # Create temporary 'defaults', 'site' and 'user' folders tmpdir.ensure('user', dir=True) - # Copy the configurations that don't need further work - packages_yaml.copy(tmpdir.join('site', 'packages.yaml')) - config_yaml.copy(tmpdir.join('site', 'config.yaml')) - repos_yaml.copy(tmpdir.join('site', 'repos.yaml')) - - # Write the one that needs modifications + # Slightly modify compilers.yaml to look like Linux + compilers_yaml = test_config.join('compilers.yaml') content = ''.join(compilers_yaml.read()).format(linux_os) t = tmpdir.join('site', 'compilers.yaml') t.write(content) @@ -348,14 +385,9 @@ def configuration_dir(tmpdir_factory, linux_os): shutil.rmtree(str(tmpdir)) -@pytest.fixture(scope='module') -def config(configuration_dir): - """Hooks the mock configuration files into spack.config""" - # Set up a mock config scope - spack.package_prefs.PackagePrefs.clear_caches() - - real_configuration = spack.config.config - +@pytest.fixture(scope='session') +def mock_configuration(configuration_dir): + """Create a persistent Configuration object from the configuration_dir.""" defaults = spack.config.InternalConfigScope( '_builtin', spack.config.config_defaults ) @@ -365,48 +397,43 @@ def config(configuration_dir): for name in ['site', 'system', 'user']] test_scopes.append(spack.config.InternalConfigScope('command_line')) - spack.config.config = spack.config.Configuration(*test_scopes) + yield spack.config.Configuration(*test_scopes) - yield spack.config.config - spack.config.config = real_configuration - spack.package_prefs.PackagePrefs.clear_caches() +@pytest.fixture(scope='function') +def config(mock_configuration): + """This fixture activates/deactivates the mock configuration.""" + with use_configuration(mock_configuration): + yield mock_configuration @pytest.fixture(scope='function') def mutable_config(tmpdir_factory, configuration_dir, monkeypatch): """Like config, but tests can modify the configuration.""" - spack.package_prefs.PackagePrefs.clear_caches() - mutable_dir = tmpdir_factory.mktemp('mutable_config').join('tmp') configuration_dir.copy(mutable_dir) cfg = spack.config.Configuration( *[spack.config.ConfigScope(name, str(mutable_dir)) for name in ['site', 'system', 'user']]) - monkeypatch.setattr(spack.config, 'config', cfg) # This is essential, otherwise the cache will create weird side effects # that will compromise subsequent tests if compilers.yaml is modified monkeypatch.setattr(spack.compilers, '_cache_config_file', []) - yield spack.config.config - - spack.package_prefs.PackagePrefs.clear_caches() + with use_configuration(cfg): + yield cfg @pytest.fixture() -def mock_config(tmpdir): +def mock_low_high_config(tmpdir): """Mocks two configuration scopes: 'low' and 'high'.""" - real_configuration = spack.config.config - - spack.config.config = spack.config.Configuration( + config = spack.config.Configuration( *[spack.config.ConfigScope(name, str(tmpdir.join(name))) for name in ['low', 'high']]) - yield spack.config.config - - spack.config.config = real_configuration + with use_configuration(config): + yield config def _populate(mock_db): @@ -453,30 +480,41 @@ def _store_dir_and_cache(tmpdir_factory): return store, cache -@pytest.fixture(scope='module') -def database(tmpdir_factory, mock_packages, config, _store_dir_and_cache): +@pytest.fixture(scope='session') +def mock_store(tmpdir_factory, mock_repo_path, mock_configuration, + _store_dir_and_cache): """Creates a read-only mock database with some packages installed note that the ref count for dyninst here will be 3, as it's recycled across each install. + + This does not actually activate the store for use by Spack -- see the + ``database`` fixture for that. + """ - real_store = spack.store.store store_path, store_cache = _store_dir_and_cache - - mock_store = spack.store.Store(str(store_path)) - spack.store.store = mock_store + store = spack.store.Store(str(store_path)) # If the cache does not exist populate the store and create it if not os.path.exists(str(store_cache.join('.spack-db'))): - _populate(mock_store.db) + with use_configuration(mock_configuration): + with use_store(store): + with use_repo(mock_repo_path): + _populate(store.db) store_path.copy(store_cache, mode=True, stat=True) - # Make the database read-only to ensure we can't modify entries + # Make the DB filesystem read-only to ensure we can't modify entries store_path.join('.spack-db').chmod(mode=0o555, rec=1) - yield mock_store.db + yield store store_path.join('.spack-db').chmod(mode=0o755, rec=1) - spack.store.store = real_store + + +@pytest.fixture(scope='function') +def database(mock_store, mock_packages, config): + """This activates the mock store, packages, AND config.""" + with use_store(mock_store): + yield mock_store.db @pytest.fixture(scope='function') @@ -612,15 +650,21 @@ def module_configuration(monkeypatch, request): with open(file) as f: configuration = yaml.load(f) + def mock_config_function(): + return configuration + + def writer_key_function(): + return mock_config_function()[writer_key] + monkeypatch.setattr( spack.modules.common, 'configuration', - configuration + mock_config_function ) monkeypatch.setattr( writer_mod, 'configuration', - configuration[writer_key] + writer_key_function ) monkeypatch.setattr( writer_mod, @@ -629,6 +673,22 @@ def module_configuration(monkeypatch, request): ) return _impl + +@pytest.fixture() +def mock_gnupghome(monkeypatch): + # GNU PGP can't handle paths longer than 108 characters (wtf!@#$) so we + # have to make our own tmpdir with a shorter name than pytest's. + # This comes up because tmp paths on macOS are already long-ish, and + # pytest makes them longer. + short_name_tmpdir = tempfile.mkdtemp() + monkeypatch.setattr(spack.util.gpg, 'GNUPGHOME', short_name_tmpdir) + monkeypatch.setattr(spack.util.gpg.Gpg, '_gpg', None) + + yield + + # clean up, since we are doing this manually + shutil.rmtree(short_name_tmpdir) + ########## # Fake archives and repositories ########## @@ -684,11 +744,31 @@ def mock_archive(request, tmpdir_factory): @pytest.fixture(scope='session') def mock_git_repository(tmpdir_factory): - """Creates a very simple git repository with two branches and - two commits. + """Creates a simple git repository with two branches, + two commits and two submodules. Each submodule has one commit. """ git = spack.util.executable.which('git', required=True) + suburls = [] + for submodule_count in range(2): + tmpdir = tmpdir_factory.mktemp('mock-git-repo-submodule-dir-{0}' + .format(submodule_count)) + tmpdir.ensure(spack.stage._source_path_subdir, dir=True) + repodir = tmpdir.join(spack.stage._source_path_subdir) + suburls.append((submodule_count, 'file://' + str(repodir))) + + # Initialize the repository + with repodir.as_cwd(): + git('init') + git('config', 'user.name', 'Spack') + git('config', 'user.email', 'spack@spack.io') + + # r0 is just the first commit + submodule_file = 'r0_file_{0}'.format(submodule_count) + repodir.ensure(submodule_file) + git('add', submodule_file) + git('commit', '-m', 'mock-git-repo r0 {0}'.format(submodule_count)) + tmpdir = tmpdir_factory.mktemp('mock-git-repo-dir') tmpdir.ensure(spack.stage._source_path_subdir, dir=True) repodir = tmpdir.join(spack.stage._source_path_subdir) @@ -699,6 +779,9 @@ def mock_git_repository(tmpdir_factory): git('config', 'user.name', 'Spack') git('config', 'user.email', 'spack@spack.io') url = 'file://' + str(repodir) + for number, suburl in suburls: + git('submodule', 'add', suburl, + 'third_party/submodule{0}'.format(number)) # r0 is just the first commit r0_file = 'r0_file' diff --git a/lib/spack/spack/test/container/cli.py b/lib/spack/spack/test/container/cli.py new file mode 100644 index 0000000000..8e5403f072 --- /dev/null +++ b/lib/spack/spack/test/container/cli.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import llnl.util.filesystem as fs +import spack.main + + +containerize = spack.main.SpackCommand('containerize') + + +def test_command(configuration_dir, capsys): + with capsys.disabled(): + with fs.working_dir(configuration_dir): + output = containerize() + assert 'FROM spack/ubuntu-bionic' in output diff --git a/lib/spack/spack/test/container/conftest.py b/lib/spack/spack/test/container/conftest.py new file mode 100644 index 0000000000..802b34c5f8 --- /dev/null +++ b/lib/spack/spack/test/container/conftest.py @@ -0,0 +1,43 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import pytest + +import spack.util.spack_yaml as syaml + + +@pytest.fixture() +def minimal_configuration(): + return { + 'spack': { + 'specs': [ + 'gromacs', + 'mpich', + 'fftw precision=float' + ], + 'container': { + 'format': 'docker', + 'base': { + 'image': 'ubuntu:18.04', + 'spack': 'develop' + } + } + } + } + + +@pytest.fixture() +def config_dumper(tmpdir): + """Function that dumps an environment config in a temporary folder.""" + def dumper(configuration): + content = syaml.dump(configuration, default_flow_style=False) + config_file = tmpdir / 'spack.yaml' + config_file.write(content) + return str(tmpdir) + return dumper + + +@pytest.fixture() +def configuration_dir(minimal_configuration, config_dumper): + return config_dumper(minimal_configuration) diff --git a/lib/spack/spack/test/container/docker.py b/lib/spack/spack/test/container/docker.py new file mode 100644 index 0000000000..fbdc085828 --- /dev/null +++ b/lib/spack/spack/test/container/docker.py @@ -0,0 +1,74 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import spack.container.writers as writers + + +def test_manifest(minimal_configuration): + writer = writers.create(minimal_configuration) + manifest_str = writer.manifest + for line in manifest_str.split('\n'): + assert 'echo' in line + + +def test_build_and_run_images(minimal_configuration): + writer = writers.create(minimal_configuration) + + # Test the output of run property + run = writer.run + assert run.image == 'ubuntu:18.04' + + # Test the output of the build property + build = writer.build + assert build.image == 'spack/ubuntu-bionic' + assert build.tag == 'latest' + + +def test_packages(minimal_configuration): + # In this minimal configuration we don't have packages + writer = writers.create(minimal_configuration) + assert writer.os_packages is None + + # If we add them a list should be returned + pkgs = ['libgomp1'] + minimal_configuration['spack']['container']['os_packages'] = pkgs + writer = writers.create(minimal_configuration) + p = writer.os_packages + assert p.update + assert p.install + assert p.clean + assert p.list == pkgs + + +def test_ensure_render_works(minimal_configuration): + # Here we just want to ensure that nothing is raised + writer = writers.create(minimal_configuration) + writer() + + +def test_strip_is_set_from_config(minimal_configuration): + writer = writers.create(minimal_configuration) + assert writer.strip is True + + minimal_configuration['spack']['container']['strip'] = False + writer = writers.create(minimal_configuration) + assert writer.strip is False + + +def test_extra_instructions_is_set_from_config(minimal_configuration): + writer = writers.create(minimal_configuration) + assert writer.extra_instructions == (None, None) + + test_line = 'RUN echo Hello world!' + e = minimal_configuration['spack']['container'] + e['extra_instructions'] = {} + e['extra_instructions']['build'] = test_line + writer = writers.create(minimal_configuration) + assert writer.extra_instructions == (test_line, None) + + e['extra_instructions']['final'] = test_line + del e['extra_instructions']['build'] + writer = writers.create(minimal_configuration) + assert writer.extra_instructions == (None, test_line) diff --git a/lib/spack/spack/test/container/images.py b/lib/spack/spack/test/container/images.py new file mode 100644 index 0000000000..808676c39a --- /dev/null +++ b/lib/spack/spack/test/container/images.py @@ -0,0 +1,58 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os.path + +import pytest + +import spack.container + + +@pytest.mark.parametrize('image,spack_version,expected', [ + ('ubuntu:18.04', 'develop', ('spack/ubuntu-bionic', 'latest')), + ('ubuntu:18.04', '0.14.0', ('spack/ubuntu-bionic', '0.14.0')), +]) +def test_build_info(image, spack_version, expected): + output = spack.container.images.build_info(image, spack_version) + assert output == expected + + +@pytest.mark.parametrize('image,spack_version', [ + ('ubuntu:18.04', 'doesnotexist') +]) +def test_build_info_error(image, spack_version): + with pytest.raises(ValueError, match=r"has no tag for"): + spack.container.images.build_info(image, spack_version) + + +@pytest.mark.parametrize('image', [ + 'ubuntu:18.04' +]) +def test_package_info(image): + update, install, clean = spack.container.images.package_info(image) + assert update + assert install + assert clean + + +@pytest.mark.parametrize('extra_config,expected_msg', [ + ({'modules': {'enable': ['tcl']}}, 'the subsection "modules" in'), + ({'concretization': 'separately'}, 'the "concretization" attribute'), + ({'config': {'install_tree': '/some/dir'}}, + 'the "config:install_tree" attribute has been set'), + ({'view': '/some/dir'}, 'the "view" attribute has been set') +]) +def test_validate( + extra_config, expected_msg, minimal_configuration, config_dumper +): + minimal_configuration['spack'].update(extra_config) + spack_yaml_dir = config_dumper(minimal_configuration) + spack_yaml = os.path.join(spack_yaml_dir, 'spack.yaml') + + with pytest.warns(UserWarning) as w: + spack.container.validate(spack_yaml) + + # Tests are designed to raise only one warning + assert len(w) == 1 + assert expected_msg in str(w.pop().message) diff --git a/lib/spack/spack/test/container/schema.py b/lib/spack/spack/test/container/schema.py new file mode 100644 index 0000000000..3f33a3f9f7 --- /dev/null +++ b/lib/spack/spack/test/container/schema.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import spack.container +import spack.schema.container + + +def test_images_in_schema(): + properties = spack.schema.container.container_schema['properties'] + allowed_images = set( + properties['base']['properties']['image']['enum'] + ) + images_in_json = set(x for x in spack.container.images.data()) + assert images_in_json == allowed_images diff --git a/lib/spack/spack/test/container/singularity.py b/lib/spack/spack/test/container/singularity.py new file mode 100644 index 0000000000..445a119f6c --- /dev/null +++ b/lib/spack/spack/test/container/singularity.py @@ -0,0 +1,42 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import pytest + +import spack.container.writers as writers + + +@pytest.fixture +def singularity_configuration(minimal_configuration): + minimal_configuration['spack']['container']['format'] = 'singularity' + return minimal_configuration + + +def test_ensure_render_works(singularity_configuration): + container_config = singularity_configuration['spack']['container'] + assert container_config['format'] == 'singularity' + # Here we just want to ensure that nothing is raised + writer = writers.create(singularity_configuration) + writer() + + +@pytest.mark.parametrize('properties,expected', [ + ({'runscript': '/opt/view/bin/h5ls'}, + {'runscript': '/opt/view/bin/h5ls', + 'startscript': '', + 'test': '', + 'help': ''}) +]) +def test_singularity_specific_properties( + properties, expected, singularity_configuration +): + # Set the property in the configuration + container_config = singularity_configuration['spack']['container'] + for name, value in properties.items(): + container_config.setdefault('singularity', {})[name] = value + + # Assert the properties return the expected values + writer = writers.create(singularity_configuration) + for name, value in expected.items(): + assert getattr(writer, name) == value diff --git a/lib/spack/spack/test/data/compilers.yaml b/lib/spack/spack/test/data/config/compilers.yaml index 7aec138473..7aec138473 100644 --- a/lib/spack/spack/test/data/compilers.yaml +++ b/lib/spack/spack/test/data/config/compilers.yaml diff --git a/lib/spack/spack/test/data/config.yaml b/lib/spack/spack/test/data/config/config.yaml index 2d2c2e356a..0cf0d32cb0 100644 --- a/lib/spack/spack/test/data/config.yaml +++ b/lib/spack/spack/test/data/config/config.yaml @@ -11,4 +11,6 @@ config: misc_cache: ~/.spack/cache verify_ssl: true checksum: true - dirty: True + dirty: false + module_roots: + tcl: $spack/share/spack/modules diff --git a/lib/spack/spack/test/data/packages.yaml b/lib/spack/spack/test/data/config/packages.yaml index c7256ddb33..c7256ddb33 100644 --- a/lib/spack/spack/test/data/packages.yaml +++ b/lib/spack/spack/test/data/config/packages.yaml diff --git a/lib/spack/spack/test/data/repos.yaml b/lib/spack/spack/test/data/config/repos.yaml index 4fbbfe9d62..4fbbfe9d62 100644 --- a/lib/spack/spack/test/data/repos.yaml +++ b/lib/spack/spack/test/data/config/repos.yaml diff --git a/lib/spack/spack/test/data/sourceme_first.sh b/lib/spack/spack/test/data/sourceme_first.sh index 5d6b705e22..8fa1774b17 100644 --- a/lib/spack/spack/test/data/sourceme_first.sh +++ b/lib/spack/spack/test/data/sourceme_first.sh @@ -1,6 +1,6 @@ #!/usr/bin/env bash # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/data/sourceme_parameters.sh b/lib/spack/spack/test/data/sourceme_parameters.sh index bfe2c0c480..d11590d224 100644 --- a/lib/spack/spack/test/data/sourceme_parameters.sh +++ b/lib/spack/spack/test/data/sourceme_parameters.sh @@ -1,6 +1,6 @@ #!/usr/bin/env bash # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/data/sourceme_second.sh b/lib/spack/spack/test/data/sourceme_second.sh index 0cb0f45eb5..3f16153627 100644 --- a/lib/spack/spack/test/data/sourceme_second.sh +++ b/lib/spack/spack/test/data/sourceme_second.sh @@ -1,6 +1,6 @@ #!/usr/bin/env bash # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/data/sourceme_unicode.sh b/lib/spack/spack/test/data/sourceme_unicode.sh index cc3f59c4e3..d819126bb6 100644 --- a/lib/spack/spack/test/data/sourceme_unicode.sh +++ b/lib/spack/spack/test/data/sourceme_unicode.sh @@ -1,6 +1,6 @@ #!/usr/bin/env bash # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/data/sourceme_unset.sh b/lib/spack/spack/test/data/sourceme_unset.sh index e14aeb3f89..0366833838 100644 --- a/lib/spack/spack/test/data/sourceme_unset.sh +++ b/lib/spack/spack/test/data/sourceme_unset.sh @@ -1,6 +1,6 @@ #!/usr/bin/env bash # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/data/targets/linux-centos7-cascadelake b/lib/spack/spack/test/data/targets/linux-centos7-cascadelake new file mode 100644 index 0000000000..e409c3d07a --- /dev/null +++ b/lib/spack/spack/test/data/targets/linux-centos7-cascadelake @@ -0,0 +1,20 @@ +processor : 0 +vendor_id : GenuineIntel +cpu family : 6 +model : 85 +model name : Intel(R) Xeon(R) Platinum 8260M CPU @ 2.40GHz +stepping : 7 +microcode : 0x5000024 +cpu MHz : 2400.000 +cache size : 36608 KB +physical id : 0 +siblings : 48 +core id : 0 +cpu cores : 24 +apicid : 0 +initial apicid : 0 +fpu : yes +fpu_exception : yes +cpuid level : 22 +wp : yes +flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_ppin intel_pt ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke avx512_vnni md_clear spec_ctrl intel_stibp flush_l1d arch_capabilities
\ No newline at end of file diff --git a/lib/spack/spack/test/data/targets/linux-centos7-thunderx2 b/lib/spack/spack/test/data/targets/linux-centos7-thunderx2 new file mode 100644 index 0000000000..2447306bac --- /dev/null +++ b/lib/spack/spack/test/data/targets/linux-centos7-thunderx2 @@ -0,0 +1,8 @@ +processor : 0 +BogoMIPS : 400.00 +Features : fp asimd evtstrm aes pmull sha1 sha2 crc32 atomics cpuid asimdrdm +CPU implementer : 0x43 +CPU architecture: 8 +CPU variant : 0x1 +CPU part : 0x0af +CPU revision : 1 diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py index 06ddc83a47..a2b9677ec6 100644 --- a/lib/spack/spack/test/database.py +++ b/lib/spack/spack/test/database.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -41,10 +41,11 @@ def test_store(tmpdir): @pytest.fixture() def upstream_and_downstream_db(tmpdir_factory, gen_mock_layout): mock_db_root = str(tmpdir_factory.mktemp('mock_db_root')) - upstream_db = spack.database.Database(mock_db_root) + upstream_write_db = spack.database.Database(mock_db_root) + upstream_db = spack.database.Database(mock_db_root, is_upstream=True) # Generate initial DB file to avoid reindex - with open(upstream_db._index_path, 'w') as db_file: - upstream_db._write_to_file(db_file) + with open(upstream_write_db._index_path, 'w') as db_file: + upstream_write_db._write_to_file(db_file) upstream_layout = gen_mock_layout('/a/') downstream_db_root = str( @@ -55,13 +56,14 @@ def upstream_and_downstream_db(tmpdir_factory, gen_mock_layout): downstream_db._write_to_file(db_file) downstream_layout = gen_mock_layout('/b/') - yield upstream_db, upstream_layout, downstream_db, downstream_layout + yield upstream_write_db, upstream_db, upstream_layout,\ + downstream_db, downstream_layout @pytest.mark.usefixtures('config') def test_installed_upstream(upstream_and_downstream_db): - upstream_db, upstream_layout, downstream_db, downstream_layout = ( - upstream_and_downstream_db) + upstream_write_db, upstream_db, upstream_layout,\ + downstream_db, downstream_layout = (upstream_and_downstream_db) default = ('build', 'link') x = MockPackage('x', [], []) @@ -75,7 +77,14 @@ def test_installed_upstream(upstream_and_downstream_db): spec.concretize() for dep in spec.traverse(root=False): - upstream_db.add(dep, upstream_layout) + upstream_write_db.add(dep, upstream_layout) + upstream_db._read() + + for dep in spec.traverse(root=False): + record = downstream_db.get_by_hash(dep.dag_hash()) + assert record is not None + with pytest.raises(spack.database.ForbiddenLockError): + record = upstream_db.get_by_hash(dep.dag_hash()) new_spec = spack.spec.Spec('w') new_spec.concretize() @@ -96,8 +105,8 @@ def test_installed_upstream(upstream_and_downstream_db): @pytest.mark.usefixtures('config') def test_removed_upstream_dep(upstream_and_downstream_db): - upstream_db, upstream_layout, downstream_db, downstream_layout = ( - upstream_and_downstream_db) + upstream_write_db, upstream_db, upstream_layout,\ + downstream_db, downstream_layout = (upstream_and_downstream_db) default = ('build', 'link') z = MockPackage('z', [], []) @@ -108,13 +117,15 @@ def test_removed_upstream_dep(upstream_and_downstream_db): spec = spack.spec.Spec('y') spec.concretize() - upstream_db.add(spec['z'], upstream_layout) + upstream_write_db.add(spec['z'], upstream_layout) + upstream_db._read() new_spec = spack.spec.Spec('y') new_spec.concretize() downstream_db.add(new_spec, downstream_layout) - upstream_db.remove(new_spec['z']) + upstream_write_db.remove(new_spec['z']) + upstream_db._read() new_downstream = spack.database.Database( downstream_db.root, upstream_dbs=[upstream_db]) @@ -129,8 +140,8 @@ def test_add_to_upstream_after_downstream(upstream_and_downstream_db): DB. When a package is recorded as installed in both, the results should refer to the downstream DB. """ - upstream_db, upstream_layout, downstream_db, downstream_layout = ( - upstream_and_downstream_db) + upstream_write_db, upstream_db, upstream_layout,\ + downstream_db, downstream_layout = (upstream_and_downstream_db) x = MockPackage('x', [], []) mock_repo = MockPackageMultiRepo([x]) @@ -141,7 +152,8 @@ def test_add_to_upstream_after_downstream(upstream_and_downstream_db): downstream_db.add(spec, downstream_layout) - upstream_db.add(spec, upstream_layout) + upstream_write_db.add(spec, upstream_layout) + upstream_db._read() upstream, record = downstream_db.query_by_spec_hash(spec.dag_hash()) # Even though the package is recorded as installed in the upstream DB, @@ -706,3 +718,14 @@ def test_uninstall_by_spec(mutable_database): else: mutable_database.remove(spec) assert len(mutable_database.query()) == 0 + + +def test_query_unused_specs(mutable_database): + # This spec installs a fake cmake as a build only dependency + s = spack.spec.Spec('simple-inheritance') + s.concretize() + s.package.do_install(fake=True, explicit=True) + + unused = spack.store.db.unused_specs + assert len(unused) == 1 + assert unused[0].name == 'cmake' diff --git a/lib/spack/spack/test/directives.py b/lib/spack/spack/test/directives.py index 2f2e4d55a8..ae1b6b7e2a 100644 --- a/lib/spack/spack/test/directives.py +++ b/lib/spack/spack/test/directives.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/directory_layout.py b/lib/spack/spack/test/directory_layout.py index 619b617bab..c9ef68b3cf 100644 --- a/lib/spack/spack/test/directory_layout.py +++ b/lib/spack/spack/test/directory_layout.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/environment_modifications.py b/lib/spack/spack/test/environment_modifications.py index 1e1759ddbc..9983594a84 100644 --- a/lib/spack/spack/test/environment_modifications.py +++ b/lib/spack/spack/test/environment_modifications.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/fetch_strategy.py b/lib/spack/spack/test/fetch_strategy.py new file mode 100644 index 0000000000..5470d88c13 --- /dev/null +++ b/lib/spack/spack/test/fetch_strategy.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import pytest + +from spack.fetch_strategy import from_url_scheme + + +def test_fetchstrategy_bad_url_scheme(): + """Ensure that trying to make a fetch strategy from a URL with an + unsupported scheme fails as expected.""" + + with pytest.raises(ValueError): + fetcher = from_url_scheme( # noqa: F841 + 'bogus-scheme://example.com/a/b/c') diff --git a/lib/spack/spack/test/flag_handlers.py b/lib/spack/spack/test/flag_handlers.py index 094afe595a..6c7651ad19 100644 --- a/lib/spack/spack/test/flag_handlers.py +++ b/lib/spack/spack/test/flag_handlers.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/git_fetch.py b/lib/spack/spack/test/git_fetch.py index ae1e027752..8dc57da793 100644 --- a/lib/spack/spack/test/git_fetch.py +++ b/lib/spack/spack/test/git_fetch.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,7 +19,6 @@ from spack.version import ver from spack.fetch_strategy import GitFetchStrategy from spack.util.executable import which - pytestmark = pytest.mark.skipif( not which('git'), reason='requires git to be installed') @@ -88,7 +87,7 @@ def test_fetch(type_of_test, secure, mock_git_repository, config, - mutable_mock_packages, + mutable_mock_repo, git_version): """Tries to: @@ -137,7 +136,7 @@ def test_fetch(type_of_test, @pytest.mark.parametrize("type_of_test", ['branch', 'commit']) -def test_debug_fetch(type_of_test, mock_git_repository, config): +def test_debug_fetch(mock_packages, type_of_test, mock_git_repository, config): """Fetch the repo with debug enabled.""" # Retrieve the right test parameters t = mock_git_repository.checks[type_of_test] @@ -169,14 +168,14 @@ def test_git_extra_fetch(tmpdir): def test_needs_stage(): """Trigger a NoStageError when attempt a fetch without a stage.""" with pytest.raises(spack.fetch_strategy.NoStageError, - matches=_mock_transport_error): + match=r"set_stage.*before calling fetch"): fetcher = GitFetchStrategy(git='file:///not-a-real-git-repo') fetcher.fetch() @pytest.mark.parametrize("get_full_repo", [True, False]) def test_get_full_repo(get_full_repo, git_version, mock_git_repository, - config, mutable_mock_packages): + config, mutable_mock_repo): """Ensure that we can clone a full repository.""" if git_version < ver('1.7.1'): @@ -217,3 +216,59 @@ def test_get_full_repo(get_full_repo, git_version, mock_git_repository, else: assert(nbranches == 2) assert(ncommits == 1) + + +@pytest.mark.disable_clean_stage_check +@pytest.mark.parametrize("submodules", [True, False]) +def test_gitsubmodule(submodules, mock_git_repository, config, + mutable_mock_repo): + """ + Test GitFetchStrategy behavior with submodules + """ + type_of_test = 'tag-branch' + t = mock_git_repository.checks[type_of_test] + + # Construct the package under test + spec = Spec('git-test') + spec.concretize() + pkg = spack.repo.get(spec) + args = copy.copy(t.args) + args['submodules'] = submodules + pkg.versions[ver('git')] = args + pkg.do_stage() + with working_dir(pkg.stage.source_path): + for submodule_count in range(2): + file_path = os.path.join(pkg.stage.source_path, + 'third_party/submodule{0}/r0_file_{0}' + .format(submodule_count)) + if submodules: + assert os.path.isfile(file_path) + else: + assert not os.path.isfile(file_path) + + +@pytest.mark.disable_clean_stage_check +def test_gitsubmodules_delete(mock_git_repository, config, mutable_mock_repo): + """ + Test GitFetchStrategy behavior with submodules_delete + """ + type_of_test = 'tag-branch' + t = mock_git_repository.checks[type_of_test] + + # Construct the package under test + spec = Spec('git-test') + spec.concretize() + pkg = spack.repo.get(spec) + args = copy.copy(t.args) + args['submodules'] = True + args['submodules_delete'] = ['third_party/submodule0', + 'third_party/submodule1'] + pkg.versions[ver('git')] = args + pkg.do_stage() + with working_dir(pkg.stage.source_path): + file_path = os.path.join(pkg.stage.source_path, + 'third_party/submodule0') + assert not os.path.isdir(file_path) + file_path = os.path.join(pkg.stage.source_path, + 'third_party/submodule1') + assert not os.path.isdir(file_path) diff --git a/lib/spack/spack/test/graph.py b/lib/spack/spack/test/graph.py index 57e7d54933..7ad1a75a90 100644 --- a/lib/spack/spack/test/graph.py +++ b/lib/spack/spack/test/graph.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/hg_fetch.py b/lib/spack/spack/test/hg_fetch.py index 109e3d9d59..2cdeace3e4 100644 --- a/lib/spack/spack/test/hg_fetch.py +++ b/lib/spack/spack/test/hg_fetch.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -29,7 +29,7 @@ def test_fetch( secure, mock_hg_repository, config, - mutable_mock_packages + mutable_mock_repo ): """Tries to: diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py index 4bed12456a..914ae527a0 100644 --- a/lib/spack/spack/test/install.py +++ b/lib/spack/spack/test/install.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,6 +10,7 @@ import shutil from llnl.util.filesystem import mkdirp, touch, working_dir from spack.package import InstallError, PackageBase, PackageStillNeededError +import spack.error import spack.patch import spack.repo import spack.store @@ -128,7 +129,7 @@ def test_dont_add_patches_to_installed_package(install_mockery, mock_fetch): def test_installed_dependency_request_conflicts( - install_mockery, mock_fetch, mutable_mock_packages): + install_mockery, mock_fetch, mutable_mock_repo): dependency = Spec('dependency-install') dependency.concretize() dependency.package.do_install() @@ -136,12 +137,12 @@ def test_installed_dependency_request_conflicts( dependency_hash = dependency.dag_hash() dependent = Spec( 'conflicting-dependent ^/' + dependency_hash) - with pytest.raises(spack.spec.UnsatisfiableSpecError): + with pytest.raises(spack.error.UnsatisfiableSpecError): dependent.concretize() def test_install_dependency_symlinks_pkg( - install_mockery, mock_fetch, mutable_mock_packages): + install_mockery, mock_fetch, mutable_mock_repo): """Test dependency flattening/symlinks mock package.""" spec = Spec('flatten-deps') spec.concretize() @@ -154,7 +155,7 @@ def test_install_dependency_symlinks_pkg( def test_flatten_deps( - install_mockery, mock_fetch, mutable_mock_packages): + install_mockery, mock_fetch, mutable_mock_repo): """Explicitly test the flattening code for coverage purposes.""" # Unfortunately, executing the 'flatten-deps' spec's installation does # not affect code coverage results, so be explicit here. @@ -315,14 +316,14 @@ def test_uninstall_by_spec_errors(mutable_database): """Test exceptional cases with the uninstall command.""" # Try to uninstall a spec that has not been installed - rec = mutable_database.get_record('zmpi') - with pytest.raises(InstallError, matches="not installed"): - PackageBase.uninstall_by_spec(rec.spec) + spec = Spec('dependent-install') + spec.concretize() + with pytest.raises(InstallError, match="is not installed"): + PackageBase.uninstall_by_spec(spec) # Try an unforced uninstall of a spec with dependencies rec = mutable_database.get_record('mpich') - - with pytest.raises(PackageStillNeededError, matches="cannot uninstall"): + with pytest.raises(PackageStillNeededError, match="Cannot uninstall"): PackageBase.uninstall_by_spec(rec.spec) diff --git a/lib/spack/spack/test/link_paths.py b/lib/spack/spack/test/link_paths.py index 5f26a272c6..27e42d2194 100644 --- a/lib/spack/spack/test/link_paths.py +++ b/lib/spack/spack/test/link_paths.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/llnl/util/__init__.py b/lib/spack/spack/test/llnl/util/__init__.py new file mode 100644 index 0000000000..9f87532b85 --- /dev/null +++ b/lib/spack/spack/test/llnl/util/__init__.py @@ -0,0 +1,4 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/llnl/util/argparsewriter.py b/lib/spack/spack/test/llnl/util/argparsewriter.py new file mode 100644 index 0000000000..127149bbaa --- /dev/null +++ b/lib/spack/spack/test/llnl/util/argparsewriter.py @@ -0,0 +1,37 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +"""Tests for ``llnl/util/argparsewriter.py`` + +These tests are fairly minimal, and ArgparseWriter is more extensively +tested in ``cmd/commands.py``. +""" + +import pytest + +import llnl.util.argparsewriter as aw + +import spack.main + + +parser = spack.main.make_argument_parser() +spack.main.add_all_commands(parser) + + +def test_format_not_overridden(): + writer = aw.ArgparseWriter('spack') + + with pytest.raises(NotImplementedError): + writer.write(parser) + + +def test_completion_format_not_overridden(): + writer = aw.ArgparseCompletionWriter('spack') + + assert writer.positionals([]) == '' + assert writer.optionals([]) == '' + assert writer.subcommands([]) == '' + + writer.write(parser) diff --git a/lib/spack/spack/test/llnl/util/cpu.py b/lib/spack/spack/test/llnl/util/cpu.py index f75c02f4b0..319d9e684e 100644 --- a/lib/spack/spack/test/llnl/util/cpu.py +++ b/lib/spack/spack/test/llnl/util/cpu.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -32,6 +32,8 @@ from llnl.util.cpu import Microarchitecture # noqa 'linux-scientific7-piledriver', 'linux-rhel6-piledriver', 'linux-centos7-power8le', + 'linux-centos7-thunderx2', + 'linux-centos7-cascadelake', 'darwin-mojave-ivybridge', 'darwin-mojave-haswell', 'darwin-mojave-skylake', @@ -86,6 +88,7 @@ def supported_target(request): return request.param +@pytest.mark.regression('13803') def test_target_detection(expected_target): detected_target = llnl.util.cpu.host() assert detected_target == expected_target @@ -121,6 +124,8 @@ def test_equality(supported_target): ('piledriver <= steamroller', True), ('zen2 >= zen', True), ('zen >= zen', True), + ('aarch64 <= thunderx2', True), + ('aarch64 <= a64fx', True), # Test unrelated microarchitectures ('power8 < skylake', False), ('power8 <= skylake', False), @@ -205,12 +210,16 @@ def test_target_json_schema(): ('nehalem', 'gcc', '4.9.3', '-march=nehalem -mtune=nehalem'), ('nehalem', 'gcc', '4.8.5', '-march=corei7 -mtune=corei7'), ('sandybridge', 'gcc', '4.8.5', '-march=corei7-avx -mtune=corei7-avx'), + ('thunderx2', 'gcc', '4.8.5', '-march=armv8-a'), + ('thunderx2', 'gcc', '4.9.3', '-march=armv8-a+crc+crypto'), # Test Clang / LLVM - ('sandybridge', 'clang', '3.9.0', '-march=x86-64 -mcpu=sandybridge'), - ('icelake', 'clang', '6.0.0', '-march=x86-64 -mcpu=icelake'), - ('icelake', 'clang', '8.0.0', '-march=x86-64 -mcpu=icelake-client'), - ('zen2', 'clang', '9.0.0', '-march=x86-64 -mcpu=znver2'), - ('power9le', 'clang', '8.0.0', '-march=ppc64le -mcpu=pwr9'), + ('sandybridge', 'clang', '3.9.0', '-march=sandybridge -mtune=sandybridge'), + ('icelake', 'clang', '6.0.0', '-march=icelake -mtune=icelake'), + ('icelake', 'clang', '8.0.0', + '-march=icelake-client -mtune=icelake-client'), + ('zen2', 'clang', '9.0.0', '-march=znver2 -mtune=znver2'), + ('power9le', 'clang', '8.0.0', '-mcpu=power9 -mtune=power9'), + ('thunderx2', 'clang', '6.0.0', '-mcpu=thunderx2t99'), # Test Intel on Intel CPUs ('sandybridge', 'intel', '17.0.2', '-march=corei7-avx -mtune=corei7-avx'), ('sandybridge', 'intel', '18.0.5', @@ -236,7 +245,7 @@ def test_unsupported_optimization_flags(target_name, compiler, version): target = llnl.util.cpu.targets[target_name] with pytest.raises( llnl.util.cpu.UnsupportedMicroarchitecture, - matches='cannot produce optimized binary' + match='cannot produce optimized binary' ): target.optimization_flags(compiler, version) @@ -269,3 +278,14 @@ def test_version_components(version, expected_number, expected_suffix): number, suffix = llnl.util.cpu.version_components(version) assert number == expected_number assert suffix == expected_suffix + + +def test_invalid_family(): + targets = llnl.util.cpu.targets + multi_parents = Microarchitecture( + name='chimera', parents=[targets['pentium4'], targets['power7']], + vendor='Imagination', features=[], compilers={}, generation=0 + ) + with pytest.raises(AssertionError, + match='a target is expected to belong'): + multi_parents.family diff --git a/lib/spack/spack/test/llnl/util/file_list.py b/lib/spack/spack/test/llnl/util/file_list.py index a43c8b2b44..e4036fe492 100644 --- a/lib/spack/spack/test/llnl/util/file_list.py +++ b/lib/spack/spack/test/llnl/util/file_list.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/llnl/util/filesystem.py b/lib/spack/spack/test/llnl/util/filesystem.py index 6c26c5fb43..b48abb4fc6 100644 --- a/lib/spack/spack/test/llnl/util/filesystem.py +++ b/lib/spack/spack/test/llnl/util/filesystem.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -116,13 +116,13 @@ class TestCopyTree: # Make sure we get the right error if we try to copy a parent into # a descendent directory. - with pytest.raises(ValueError, matches="Cannot copy"): + with pytest.raises(ValueError, match="Cannot copy"): with fs.working_dir(str(stage)): fs.copy_tree('source', 'source/sub/directory') # Only point with this check is to make sure we don't try to perform # the copy. - with pytest.raises(IOError, matches="No such file or directory"): + with pytest.raises(IOError, match="No such file or directory"): with fs.working_dir(str(stage)): fs.copy_tree('foo/ba', 'foo/bar') diff --git a/lib/spack/spack/test/llnl/util/lang.py b/lib/spack/spack/test/llnl/util/lang.py index cbc24b51db..b285d8d0b2 100644 --- a/lib/spack/spack/test/llnl/util/lang.py +++ b/lib/spack/spack/test/llnl/util/lang.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/llnl/util/link_tree.py b/lib/spack/spack/test/llnl/util/link_tree.py index 6b00afb3fe..bebb3da805 100644 --- a/lib/spack/spack/test/llnl/util/link_tree.py +++ b/lib/spack/spack/test/llnl/util/link_tree.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/llnl/util/lock.py b/lib/spack/spack/test/llnl/util/lock.py index ca879cdc0b..63f2b91782 100644 --- a/lib/spack/spack/test/llnl/util/lock.py +++ b/lib/spack/spack/test/llnl/util/lock.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/llnl/util/log.py b/lib/spack/spack/test/llnl/util/log.py index 5a57c8bb96..1eae1ccf69 100644 --- a/lib/spack/spack/test/llnl/util/log.py +++ b/lib/spack/spack/test/llnl/util/log.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/main.py b/lib/spack/spack/test/main.py new file mode 100644 index 0000000000..c35a6e195b --- /dev/null +++ b/lib/spack/spack/test/main.py @@ -0,0 +1,63 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import os + +import llnl.util.filesystem as fs + +import spack.paths +from spack.main import get_version, main + + +def test_get_version_no_match_git(tmpdir, working_env): + git = str(tmpdir.join("git")) + with open(git, "w") as f: + f.write("""#!/bin/sh +echo v0.13.3 +""") + fs.set_executable(git) + + os.environ["PATH"] = str(tmpdir) + assert spack.spack_version == get_version() + + +def test_get_version_match_git(tmpdir, working_env): + git = str(tmpdir.join("git")) + with open(git, "w") as f: + f.write("""#!/bin/sh +echo v0.13.3-912-g3519a1762 +""") + fs.set_executable(git) + + os.environ["PATH"] = str(tmpdir) + assert "0.13.3-912-3519a1762" == get_version() + + +def test_get_version_no_repo(tmpdir, monkeypatch): + monkeypatch.setattr(spack.paths, "prefix", str(tmpdir)) + assert spack.spack_version == get_version() + + +def test_get_version_no_git(tmpdir, working_env): + os.environ["PATH"] = str(tmpdir) + assert spack.spack_version == get_version() + + +def test_main_calls_get_version(tmpdir, capsys, working_env): + os.environ["PATH"] = str(tmpdir) + main(["-V"]) + assert spack.spack_version == capsys.readouterr()[0].strip() + + +def test_get_version_bad_git(tmpdir, working_env): + bad_git = str(tmpdir.join("git")) + with open(bad_git, "w") as f: + f.write("""#!/bin/sh +exit 1 +""") + fs.set_executable(bad_git) + + os.environ["PATH"] = str(tmpdir) + assert spack.spack_version == get_version() diff --git a/lib/spack/spack/test/make_executable.py b/lib/spack/spack/test/make_executable.py index d945593dde..f554fd038c 100644 --- a/lib/spack/spack/test/make_executable.py +++ b/lib/spack/spack/test/make_executable.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py index e1b31695e3..08b32f74f1 100644 --- a/lib/spack/spack/test/mirror.py +++ b/lib/spack/spack/test/mirror.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ from spack.util.executable import which from llnl.util.filesystem import resolve_link_target_relative_to_the_link -pytestmark = pytest.mark.usefixtures('config', 'mutable_mock_packages') +pytestmark = pytest.mark.usefixtures('config', 'mutable_mock_repo') # paths in repos that shouldn't be in the mirror tarballs. exclude = ['.hg', '.git', '.svn'] diff --git a/lib/spack/spack/test/module_parsing.py b/lib/spack/spack/test/module_parsing.py index 95a65ab33f..bbe18b1ad0 100644 --- a/lib/spack/spack/test/module_parsing.py +++ b/lib/spack/spack/test/module_parsing.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/modules/__init__.py b/lib/spack/spack/test/modules/__init__.py new file mode 100644 index 0000000000..9f87532b85 --- /dev/null +++ b/lib/spack/spack/test/modules/__init__.py @@ -0,0 +1,4 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/modules/common.py b/lib/spack/spack/test/modules/common.py index fdaf898daf..cc2eb61d0b 100644 --- a/lib/spack/spack/test/modules/common.py +++ b/lib/spack/spack/test/modules/common.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/modules/conftest.py b/lib/spack/spack/test/modules/conftest.py index b49d8cd535..4ba25bd073 100644 --- a/lib/spack/spack/test/modules/conftest.py +++ b/lib/spack/spack/test/modules/conftest.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/modules/lmod.py b/lib/spack/spack/test/modules/lmod.py index 34ba63c373..12b6d71aa5 100644 --- a/lib/spack/spack/test/modules/lmod.py +++ b/lib/spack/spack/test/modules/lmod.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/modules/tcl.py b/lib/spack/spack/test/modules/tcl.py index 7bb058cd13..70eee24461 100644 --- a/lib/spack/spack/test/modules/tcl.py +++ b/lib/spack/spack/test/modules/tcl.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/multimethod.py b/lib/spack/spack/test/multimethod.py index 5e50006e86..0e5bd5dad5 100644 --- a/lib/spack/spack/test/multimethod.py +++ b/lib/spack/spack/test/multimethod.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/namespace_trie.py b/lib/spack/spack/test/namespace_trie.py index a24a75deac..2bf83c59f2 100644 --- a/lib/spack/spack/test/namespace_trie.py +++ b/lib/spack/spack/test/namespace_trie.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/operating_system.py b/lib/spack/spack/test/operating_system.py index e1a34e8436..221712e5ef 100644 --- a/lib/spack/spack/test/operating_system.py +++ b/lib/spack/spack/test/operating_system.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/optional_deps.py b/lib/spack/spack/test/optional_deps.py index e663ee70f4..d9268e7e14 100644 --- a/lib/spack/spack/test/optional_deps.py +++ b/lib/spack/spack/test/optional_deps.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/package_class.py b/lib/spack/spack/test/package_class.py index 9502be08c9..b3351ffb49 100644 --- a/lib/spack/spack/test/package_class.py +++ b/lib/spack/spack/test/package_class.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,14 +10,14 @@ etc.). Only methods like ``possible_dependencies()`` that deal with the static DSL metadata for packages. """ +import pytest import spack.repo -def test_possible_dependencies(mock_packages): - mpileaks = spack.repo.get('mpileaks') +@pytest.fixture +def mpileaks_possible_deps(mock_packages): mpi_names = [spec.name for spec in spack.repo.path.providers_for('mpi')] - - assert mpileaks.possible_dependencies(expand_virtuals=True) == { + possible = { 'callpath': set(['dyninst'] + mpi_names), 'dyninst': set(['libdwarf', 'libelf']), 'fake': set(), @@ -29,6 +29,13 @@ def test_possible_dependencies(mock_packages): 'multi-provider-mpi': set(), 'zmpi': set(['fake']), } + return possible + + +def test_possible_dependencies(mock_packages, mpileaks_possible_deps): + mpileaks = spack.repo.get('mpileaks') + assert (mpileaks.possible_dependencies(expand_virtuals=True) == + mpileaks_possible_deps) assert mpileaks.possible_dependencies(expand_virtuals=False) == { 'callpath': set(['dyninst']), @@ -40,6 +47,15 @@ def test_possible_dependencies(mock_packages): } +def test_possible_dependencies_missing(mock_packages): + md = spack.repo.get("missing-dependency") + missing = {} + md.possible_dependencies(transitive=True, missing=missing) + assert missing["missing-dependency"] == set([ + "this-is-a-missing-dependency" + ]) + + def test_possible_dependencies_with_deptypes(mock_packages): dtbuild1 = spack.repo.get('dtbuild1') @@ -59,3 +75,17 @@ def test_possible_dependencies_with_deptypes(mock_packages): 'dtbuild1': set(['dtlink2']), 'dtlink2': set(), } + + +def test_possible_dependencies_with_multiple_classes( + mock_packages, mpileaks_possible_deps): + pkgs = ['dt-diamond', 'mpileaks'] + expected = mpileaks_possible_deps.copy() + expected.update({ + 'dt-diamond': set(['dt-diamond-left', 'dt-diamond-right']), + 'dt-diamond-left': set(['dt-diamond-bottom']), + 'dt-diamond-right': set(['dt-diamond-bottom']), + 'dt-diamond-bottom': set(), + }) + + assert spack.package.possible_dependencies(*pkgs) == expected diff --git a/lib/spack/spack/test/package_hash.py b/lib/spack/spack/test/package_hash.py index 61da62bb7e..a8a160d96e 100644 --- a/lib/spack/spack/test/package_hash.py +++ b/lib/spack/spack/test/package_hash.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py index bbf63881a7..25494e1ab2 100644 --- a/lib/spack/spack/test/package_sanity.py +++ b/lib/spack/spack/test/package_sanity.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,6 +10,7 @@ import re import pytest import spack.fetch_strategy +import spack.package import spack.paths import spack.repo import spack.util.executable as executable @@ -141,7 +142,6 @@ def test_all_packages_use_sha256_checksums(): assert [] == errors -@pytest.mark.xfail def test_api_for_build_and_run_environment(): """Ensure that every package uses the correct API to set build and run environment, and not the old one. @@ -154,7 +154,7 @@ def test_api_for_build_and_run_environment(): failing.append(pkg) msg = ('there are {0} packages using the old API to set build ' - 'and run environment [{1}], for further information see' + 'and run environment [{1}], for further information see ' 'https://github.com/spack/spack/pull/11115') assert not failing, msg.format( len(failing), ','.join(x.name for x in failing) @@ -182,7 +182,24 @@ def test_prs_update_old_api(): if failed: failing.append(name) - msg = 'there are {0} packages still using old APIs in this PR [{1}]' + msg = ('there are {0} packages using the old API to set build ' + 'and run environment [{1}], for further information see ' + 'https://github.com/spack/spack/pull/11115') assert not failing, msg.format( len(failing), ','.join(failing) ) + + +def test_all_dependencies_exist(): + """Make sure no packages have nonexisting dependencies.""" + missing = {} + pkgs = [pkg for pkg in spack.repo.path.all_package_names()] + spack.package.possible_dependencies( + *pkgs, transitive=True, missing=missing) + + lines = [ + "%s: [%s]" % (name, ", ".join(deps)) for name, deps in missing.items() + ] + assert not missing, "These packages have missing dependencies:\n" + ( + "\n".join(lines) + ) diff --git a/lib/spack/spack/test/packages.py b/lib/spack/spack/test/packages.py index 186b0d0007..c811f9040e 100644 --- a/lib/spack/spack/test/packages.py +++ b/lib/spack/spack/test/packages.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,6 +16,11 @@ from spack.version import VersionChecksumError import spack.directives +def _generate_content_strip_name(spec): + content = package_content(spec) + return content.replace(spec.package.__class__.__name__, '') + + @pytest.mark.usefixtures('config', 'mock_packages') class TestPackage(object): def test_load_package(self): @@ -53,38 +58,43 @@ class TestPackage(object): assert '_3db' == mod_to_class('3db') def test_content_hash_all_same_but_patch_contents(self): - spec1 = Spec("hash-test1@1.1") - spec2 = Spec("hash-test2@1.1") - spec1.concretize() - spec2.concretize() - content1 = package_content(spec1) - content1 = content1.replace(spec1.package.__class__.__name__, '') - content2 = package_content(spec2) - content2 = content2.replace(spec2.package.__class__.__name__, '') + spec1 = Spec("hash-test1@1.1").concretized() + spec2 = Spec("hash-test2@1.1").concretized() + content1 = _generate_content_strip_name(spec1) + content2 = _generate_content_strip_name(spec2) assert spec1.package.content_hash(content=content1) != \ spec2.package.content_hash(content=content2) def test_content_hash_different_variants(self): - spec1 = Spec("hash-test1@1.2 +variantx") - spec2 = Spec("hash-test2@1.2 ~variantx") - spec1.concretize() - spec2.concretize() - content1 = package_content(spec1) - content1 = content1.replace(spec1.package.__class__.__name__, '') - content2 = package_content(spec2) - content2 = content2.replace(spec2.package.__class__.__name__, '') + spec1 = Spec("hash-test1@1.2 +variantx").concretized() + spec2 = Spec("hash-test2@1.2 ~variantx").concretized() + content1 = _generate_content_strip_name(spec1) + content2 = _generate_content_strip_name(spec2) assert spec1.package.content_hash(content=content1) == \ spec2.package.content_hash(content=content2) + def test_content_hash_cannot_get_details_from_ast(self): + """Packages hash-test1 and hash-test3 would be considered the same + except that hash-test3 conditionally executes a phase based on + a "when" directive that Spack cannot evaluate by examining the + AST. This test ensures that Spack can compute a content hash + for hash-test3. If Spack cannot determine when a phase applies, + it adds it by default, so the test also ensures that the hashes + differ where Spack includes a phase on account of AST-examination + failure. + """ + spec3 = Spec("hash-test1@1.7").concretized() + spec4 = Spec("hash-test3@1.7").concretized() + content3 = _generate_content_strip_name(spec3) + content4 = _generate_content_strip_name(spec4) + assert(spec3.package.content_hash(content=content3) != + spec4.package.content_hash(content=content4)) + def test_all_same_but_archive_hash(self): - spec1 = Spec("hash-test1@1.3") - spec2 = Spec("hash-test2@1.3") - spec1.concretize() - spec2.concretize() - content1 = package_content(spec1) - content1 = content1.replace(spec1.package.__class__.__name__, '') - content2 = package_content(spec2) - content2 = content2.replace(spec2.package.__class__.__name__, '') + spec1 = Spec("hash-test1@1.3").concretized() + spec2 = Spec("hash-test2@1.3").concretized() + content1 = _generate_content_strip_name(spec1) + content2 = _generate_content_strip_name(spec2) assert spec1.package.content_hash(content=content1) != \ spec2.package.content_hash(content=content2) @@ -172,7 +182,7 @@ def test_urls_for_versions(mock_packages, config): assert url == 'http://www.doesnotexist.org/url_override-0.8.1.tar.gz' -def test_url_for_version_with_no_urls(): +def test_url_for_version_with_no_urls(mock_packages, config): pkg = spack.repo.get('git-test') with pytest.raises(spack.package.NoURLError): pkg.url_for_version('1.0') diff --git a/lib/spack/spack/test/packaging.py b/lib/spack/spack/test/packaging.py index 9c0396ef5e..edad8e29fa 100644 --- a/lib/spack/spack/test/packaging.py +++ b/lib/spack/spack/test/packaging.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,10 +19,10 @@ import spack.repo import spack.store import spack.binary_distribution as bindist import spack.cmd.buildcache as buildcache +import spack.util.gpg from spack.spec import Spec from spack.paths import mock_gpg_keys_path from spack.fetch_strategy import URLFetchStrategy, FetchStrategyComposite -from spack.util.executable import ProcessError from spack.relocate import needs_binary_relocation, needs_text_relocation from spack.relocate import strings_contains_installroot from spack.relocate import get_patchelf, relocate_text, relocate_links @@ -31,22 +31,6 @@ from spack.relocate import macho_replace_paths, macho_make_paths_relative from spack.relocate import modify_macho_object, macho_get_paths -@pytest.fixture(scope='function') -def testing_gpg_directory(tmpdir): - old_gpg_path = spack.util.gpg.GNUPGHOME - spack.util.gpg.GNUPGHOME = str(tmpdir.join('gpg')) - yield - spack.util.gpg.GNUPGHOME = old_gpg_path - - -def has_gnupg2(): - try: - spack.util.gpg.Gpg.gpg()('--version', output=os.devnull) - return True - except ProcessError: - return False - - def fake_fetchify(url, pkg): """Fake the URL for a package so it downloads from a file.""" fetcher = FetchStrategyComposite() @@ -54,7 +38,7 @@ def fake_fetchify(url, pkg): pkg.fetcher = fetcher -@pytest.mark.usefixtures('install_mockery', 'testing_gpg_directory') +@pytest.mark.usefixtures('install_mockery', 'mock_gnupghome') def test_buildcache(mock_archive, tmpdir): # tweak patchelf to only do a download spec = Spec("patchelf") @@ -107,7 +91,7 @@ echo $PATH""" buildcache.setup_parser(parser) # Create a private key to sign package with if gpg2 available - if has_gnupg2(): + if spack.util.gpg.Gpg.gpg(): spack.util.gpg.Gpg.create(name='test key 1', expires='0', email='spack@googlegroups.com', comment='Spack test key') @@ -230,7 +214,7 @@ echo $PATH""" stage.destroy() # Remove cached binary specs since we deleted the mirror - bindist._cached_specs = None + bindist._cached_specs = set() def test_relocate_text(tmpdir): diff --git a/lib/spack/spack/test/patch.py b/lib/spack/spack/test/patch.py index b705d01e42..2dc781538a 100644 --- a/lib/spack/spack/test/patch.py +++ b/lib/spack/spack/test/patch.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,6 +24,7 @@ from spack.spec import Spec foo_sha256 = 'b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c' bar_sha256 = '7d865e959b2466918c9863afca942d0fb89d7c9ac0c99bafc3749504ded97730' baz_sha256 = 'bf07a7fbb825fc0aae7bf4a1177b2b31fcf8a3feeaf7092761e18c859ee52a9c' +biz_sha256 = 'a69b288d7393261e613c276c6d38a01461028291f6e381623acc58139d01f54d' # url patches url1_sha256 = 'abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234abcd1234' @@ -105,6 +106,20 @@ def test_patch_in_spec(mock_packages, config): tuple(spec.variants['patches']._patches_in_order_of_appearance)) +def test_patch_mixed_versions_subset_constraint(mock_packages, config): + """If we have a package with mixed x.y and x.y.z versions, make sure that + a patch applied to a version range of x.y.z versions is not applied to + an x.y version. + """ + spec1 = Spec('patch@1.0.1') + spec1.concretize() + assert biz_sha256 in spec1.variants['patches'].value + + spec2 = Spec('patch@1.0') + spec2.concretize() + assert biz_sha256 not in spec2.variants['patches'].value + + def test_patch_order(mock_packages, config): spec = Spec('dep-diamond-patch-top') spec.concretize() diff --git a/lib/spack/spack/test/pattern.py b/lib/spack/spack/test/pattern.py index 5481bfc0ea..582ece3d51 100644 --- a/lib/spack/spack/test/pattern.py +++ b/lib/spack/spack/test/pattern.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/permissions.py b/lib/spack/spack/test/permissions.py index b233c7a0fa..fa83eb37ff 100644 --- a/lib/spack/spack/test/permissions.py +++ b/lib/spack/spack/test/permissions.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/provider_index.py b/lib/spack/spack/test/provider_index.py index 84ffcc3092..0855ac50ec 100644 --- a/lib/spack/spack/test/provider_index.py +++ b/lib/spack/spack/test/provider_index.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/python_version.py b/lib/spack/spack/test/python_version.py deleted file mode 100644 index 6875aa4655..0000000000 --- a/lib/spack/spack/test/python_version.py +++ /dev/null @@ -1,159 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -"""Check that Spack complies with minimum supported python versions. - -We ensure that all Spack files work with Python2 >= 2.6 and Python3 >= 3.0. - -We'd like to drop 2.6 support at some point, but there are still many HPC -systems that ship with RHEL6/CentOS 6, which have Python 2.6 as the -default version. Once those go away, we can likely drop 2.6 and increase -the minimum supported Python 3 version, as well. -""" -from __future__ import print_function - -import os -import sys -import re - -import pytest - -import llnl.util.tty as tty - -import spack.paths -from spack.paths import lib_path as spack_lib_path - - -# -# This test uses pyqver, by Greg Hewgill, which is a dual-source module. -# That means we need to do different checks depending on whether we're -# running Python 2 or Python 3. -# -if sys.version_info[0] < 3: - import pyqver2 as pyqver - spack_min_supported = (2, 6) - - # Exclude Python 3 versions of dual-source modules when using Python 2 - exclude_paths = [ - # Jinja 2 has some 'async def' functions that are not treated correctly - # by pyqver.py - os.path.join(spack_lib_path, 'external', 'jinja2', 'asyncfilters.py'), - os.path.join(spack_lib_path, 'external', 'jinja2', 'asyncsupport.py'), - os.path.join(spack_lib_path, 'external', 'yaml', 'lib3'), - os.path.join(spack_lib_path, 'external', 'pyqver3.py'), - # Uses importlib - os.path.join(spack_lib_path, 'spack', 'test', 'schema.py') - ] - -else: - import pyqver3 as pyqver - spack_min_supported = (3, 0) - - # Exclude Python 2 versions of dual-source modules when using Python 3 - exclude_paths = [ - # Jinja 2 has some 'async def' functions that are not treated correctly - # by pyqver.py - os.path.join(spack_lib_path, 'external', 'jinja2', 'asyncfilters.py'), - os.path.join(spack_lib_path, 'external', 'jinja2', 'asyncsupport.py'), - os.path.join(spack_lib_path, 'external', 'yaml', 'lib'), - os.path.join(spack_lib_path, 'external', 'pyqver2.py'), - # Uses importlib - os.path.join(spack_lib_path, 'spack', 'test', 'schema.py') - ] - - -def pyfiles(search_paths, exclude=()): - """Generator that yields all the python files in the search paths. - - Args: - search_paths (list of str): list of paths to search for python files - exclude (list of str): file paths to exclude from search - - Yields: - python files in the search path. - """ - # first file is the spack script. - yield spack.paths.spack_script - - # Iterate through the whole spack source tree. - for path in search_paths: - for root, dirnames, filenames in os.walk(path): - for filename in filenames: - realpath = os.path.realpath(os.path.join(root, filename)) - if any(realpath.startswith(p) for p in exclude): - continue - - if re.match(r'^[^.#].*\.py$', filename): - yield os.path.join(root, filename) - - -def check_python_versions(files): - """Check that a set of Python files works with supported Ptyhon versions""" - # This is a dict dict mapping: - # version -> filename -> reasons - # - # Reasons are tuples of (lineno, string), where the string is the - # cause for a version incompatibility. - all_issues = {} - - # Parse files and run pyqver on each file. - for path in files: - with open(path) as pyfile: - full_text = pyfile.read() - versions = pyqver.get_versions(full_text, path) - - for ver, reasons in versions.items(): - if ver <= spack_min_supported: - continue - - # Record issues. Mark exceptions with '# nopyqver' comment - for lineno, cause in reasons: - lines = full_text.split('\n') - if not re.search(r'#\s*nopyqver\s*$', lines[lineno - 1]): - all_issues.setdefault(ver, {})[path] = reasons - - # Print a message if there are are issues - if all_issues: - tty.msg("Spack must remain compatible with Python version %d.%d" - % spack_min_supported) - - # Print out a table showing which files/linenos require which - # python version, and a string describing why. - for v in sorted(all_issues.keys(), reverse=True): - messages = [] - for path in sorted(all_issues[v].keys()): - short_path = path - if path.startswith(spack.paths.prefix): - short_path = path[len(spack.paths.prefix):] - - reasons = [r for r in set(all_issues[v][path]) if r] - for lineno, cause in reasons: - file_line = "%s:%s" % (short_path.lstrip('/'), lineno) - messages.append((file_line, cause)) - - print() - tty.msg("These files require version %d.%d:" % v) - maxlen = max(len(f) for f, prob in messages) - fmt = "%%-%ds%%s" % (maxlen + 3) - print(fmt % ('File', 'Reason')) - print(fmt % ('-' * (maxlen), '-' * 20)) - for msg in messages: - print(fmt % msg) - - # Fail this test if there were issues. - assert not all_issues - - -@pytest.mark.maybeslow -def test_core_module_compatibility(): - """Test that all core spack modules work with supported Python versions.""" - check_python_versions( - pyfiles([spack_lib_path], exclude=exclude_paths)) - - -@pytest.mark.maybeslow -def test_package_module_compatibility(): - """Test that all spack packages work with supported Python versions.""" - check_python_versions(pyfiles([spack.paths.packages_path])) diff --git a/lib/spack/spack/test/relocate.py b/lib/spack/spack/test/relocate.py index f070e150c7..113bdcf66a 100644 --- a/lib/spack/spack/test/relocate.py +++ b/lib/spack/spack/test/relocate.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -60,6 +60,15 @@ def test_file_is_relocatable(source_file, is_relocatable): assert spack.relocate.file_is_relocatable(executable) is is_relocatable +@pytest.mark.requires_executables( + 'patchelf', 'strings', 'file' +) +def test_patchelf_is_relocatable(): + patchelf = spack.relocate.get_patchelf() + assert llnl.util.filesystem.is_exe(patchelf) + assert spack.relocate.file_is_relocatable(patchelf) + + @pytest.mark.skipif( platform.system().lower() != 'linux', reason='implementation for MacOS still missing' diff --git a/lib/spack/spack/test/repo.py b/lib/spack/spack/test/repo.py index e171dbca68..2cd1c0fa4a 100644 --- a/lib/spack/spack/test/repo.py +++ b/lib/spack/spack/test/repo.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,14 +10,6 @@ import spack.repo import spack.paths -# Unlike the repo_path fixture defined in conftest, this has a test-level -# scope rather than a session level scope, since we want to edit the -# given RepoPath -@pytest.fixture() -def repo_for_test(): - return spack.repo.RepoPath(spack.paths.mock_packages_path) - - @pytest.fixture() def extra_repo(tmpdir_factory): repo_namespace = 'extra_test_repo' @@ -32,31 +24,31 @@ repo: return spack.repo.Repo(str(repo_dir)) -def test_repo_getpkg(repo_for_test): - repo_for_test.get('a') - repo_for_test.get('builtin.mock.a') +def test_repo_getpkg(mutable_mock_repo): + mutable_mock_repo.get('a') + mutable_mock_repo.get('builtin.mock.a') -def test_repo_multi_getpkg(repo_for_test, extra_repo): - repo_for_test.put_first(extra_repo) - repo_for_test.get('a') - repo_for_test.get('builtin.mock.a') +def test_repo_multi_getpkg(mutable_mock_repo, extra_repo): + mutable_mock_repo.put_first(extra_repo) + mutable_mock_repo.get('a') + mutable_mock_repo.get('builtin.mock.a') -def test_repo_multi_getpkgclass(repo_for_test, extra_repo): - repo_for_test.put_first(extra_repo) - repo_for_test.get_pkg_class('a') - repo_for_test.get_pkg_class('builtin.mock.a') +def test_repo_multi_getpkgclass(mutable_mock_repo, extra_repo): + mutable_mock_repo.put_first(extra_repo) + mutable_mock_repo.get_pkg_class('a') + mutable_mock_repo.get_pkg_class('builtin.mock.a') -def test_repo_pkg_with_unknown_namespace(repo_for_test): +def test_repo_pkg_with_unknown_namespace(mutable_mock_repo): with pytest.raises(spack.repo.UnknownNamespaceError): - repo_for_test.get('unknown.a') + mutable_mock_repo.get('unknown.a') -def test_repo_unknown_pkg(repo_for_test): +def test_repo_unknown_pkg(mutable_mock_repo): with pytest.raises(spack.repo.UnknownPackageError): - repo_for_test.get('builtin.mock.nonexistentpackage') + mutable_mock_repo.get('builtin.mock.nonexistentpackage') @pytest.mark.maybeslow @@ -66,7 +58,7 @@ def test_repo_last_mtime(): assert spack.repo.path.last_mtime() == latest_mtime -def test_repo_invisibles(repo_for_test, extra_repo): +def test_repo_invisibles(mutable_mock_repo, extra_repo): with open(os.path.join(extra_repo.root, 'packages', '.invisible'), 'w'): pass extra_repo.all_package_names() diff --git a/lib/spack/spack/test/s3_fetch.py b/lib/spack/spack/test/s3_fetch.py new file mode 100644 index 0000000000..682f1a2842 --- /dev/null +++ b/lib/spack/spack/test/s3_fetch.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import pytest + +import spack.fetch_strategy as spack_fs +import spack.stage as spack_stage + + +def test_s3fetchstrategy_sans_url(): + """Ensure constructor with no URL fails.""" + with pytest.raises(ValueError): + spack_fs.S3FetchStrategy(None) + + +def test_s3fetchstrategy_bad_url(tmpdir): + """Ensure fetch with bad URL fails as expected.""" + testpath = str(tmpdir) + + fetcher = spack_fs.S3FetchStrategy(url='file:///does-not-exist') + assert fetcher is not None + + with spack_stage.Stage(fetcher, path=testpath) as stage: + assert stage is not None + assert fetcher.archive_file is None + with pytest.raises(spack_fs.FetchError): + fetcher.fetch() diff --git a/lib/spack/spack/test/sbang.py b/lib/spack/spack/test/sbang.py index 94c732e6ec..ade6b08a97 100644 --- a/lib/spack/spack/test/sbang.py +++ b/lib/spack/spack/test/sbang.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/schema.py b/lib/spack/spack/test/schema.py index 9149b77b37..a6e9986a01 100644 --- a/lib/spack/spack/test/schema.py +++ b/lib/spack/spack/test/schema.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -107,7 +107,7 @@ def test_module_suffixes(module_suffixes_schema): 'repos' ]) def test_schema_validation(meta_schema, config_name): - import importlib + import importlib # novm module_name = 'spack.schema.{0}'.format(config_name) module = importlib.import_module(module_name) schema = getattr(module, 'schema') diff --git a/lib/spack/spack/test/spack_yaml.py b/lib/spack/spack/test/spack_yaml.py index 2166d294e9..fb4abbf1d8 100644 --- a/lib/spack/spack/test/spack_yaml.py +++ b/lib/spack/spack/test/spack_yaml.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py index 628f67948f..419a39968e 100644 --- a/lib/spack/spack/test/spec_dag.py +++ b/lib/spack/spack/test/spec_dag.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -189,7 +189,7 @@ def test_conditional_dep_with_user_constraints(): assert ('y@3' in spec) -@pytest.mark.usefixtures('mutable_mock_packages') +@pytest.mark.usefixtures('mutable_mock_repo') class TestSpecDag(object): def test_conflicting_package_constraints(self, set_dependency): diff --git a/lib/spack/spack/test/spec_list.py b/lib/spack/spack/test/spec_list.py index e52608ce5c..9bbbc435e2 100644 --- a/lib/spack/spack/test/spec_list.py +++ b/lib/spack/spack/test/spec_list.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/spec_semantics.py b/lib/spack/spack/test/spec_semantics.py index a183742e65..b55fa27ae1 100644 --- a/lib/spack/spack/test/spec_semantics.py +++ b/lib/spack/spack/test/spec_semantics.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,11 @@ import sys import pytest -from spack.spec import Spec, UnsatisfiableSpecError, SpecError -from spack.spec import substitute_abstract_variants -from spack.spec import SpecFormatSigilError, SpecFormatStringError -from spack.variant import InvalidVariantValueError +from spack.error import SpecError, UnsatisfiableSpecError +from spack.spec import Spec, SpecFormatSigilError, SpecFormatStringError +from spack.variant import InvalidVariantValueError, UnknownVariantError from spack.variant import MultipleValuesInExclusiveVariantError +from spack.variant import substitute_abstract_variants import spack.architecture import spack.directives @@ -981,3 +981,9 @@ class TestSpecSematics(object): def test_target_constraints(self, spec, constraint, expected_result): s = Spec(spec) assert s.satisfies(constraint) is expected_result + + @pytest.mark.regression('13124') + def test_error_message_unknown_variant(self): + s = Spec('mpileaks +unknown') + with pytest.raises(UnknownVariantError, match=r'package has no such'): + s.concretize() diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py index a87fa5188d..a5f7b6fdb0 100644 --- a/lib/spack/spack/test/spec_syntax.py +++ b/lib/spack/spack/test/spec_syntax.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,9 +17,10 @@ from spack.parse import Token from spack.spec import Spec from spack.spec import SpecParseError, RedundantSpecError from spack.spec import AmbiguousHashError, InvalidHashError, NoSuchHashError -from spack.spec import DuplicateArchitectureError, DuplicateVariantError +from spack.spec import DuplicateArchitectureError from spack.spec import DuplicateDependencyError, DuplicateCompilerSpecError from spack.spec import SpecFilenameError, NoSuchSpecFileError +from spack.variant import DuplicateVariantError # Sample output for a complex lexing. diff --git a/lib/spack/spack/test/spec_yaml.py b/lib/spack/spack/test/spec_yaml.py index 96bed17b78..f9b41df19a 100644 --- a/lib/spack/spack/test/spec_yaml.py +++ b/lib/spack/spack/test/spec_yaml.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -68,7 +68,7 @@ def test_concrete_spec(config, mock_packages): check_yaml_round_trip(spec) -def test_yaml_multivalue(): +def test_yaml_multivalue(config, mock_packages): spec = Spec('multivalue_variant foo="bar,baz"') spec.concretize() check_yaml_round_trip(spec) diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py index cc4f944867..9cf50b8da2 100644 --- a/lib/spack/spack/test/stage.py +++ b/lib/spack/spack/test/stage.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -927,8 +927,11 @@ def test_stage_create_replace_path(tmp_build_stage_dir): assert os.path.isdir(stage.path) -def test_cannot_access(): +def test_cannot_access(capsys): """Ensure can_access dies with the expected error.""" - with pytest.raises(SystemExit, matches='Insufficient permissions'): + with pytest.raises(SystemExit): # It's far more portable to use a non-existent filename. spack.stage.ensure_access('/no/such/file') + + captured = capsys.readouterr() + assert 'Insufficient permissions' in str(captured) diff --git a/lib/spack/spack/test/svn_fetch.py b/lib/spack/spack/test/svn_fetch.py index eb0d22ee7c..f435b07db2 100644 --- a/lib/spack/spack/test/svn_fetch.py +++ b/lib/spack/spack/test/svn_fetch.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,7 +30,7 @@ def test_fetch( secure, mock_svn_repository, config, - mutable_mock_packages + mutable_mock_repo ): """Tries to: diff --git a/lib/spack/spack/test/tengine.py b/lib/spack/spack/test/tengine.py index 5cacc3cf66..01f2d65780 100644 --- a/lib/spack/spack/test/tengine.py +++ b/lib/spack/spack/test/tengine.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/test_activations.py b/lib/spack/spack/test/test_activations.py index 11de2e5431..eaac98f318 100644 --- a/lib/spack/spack/test/test_activations.py +++ b/lib/spack/spack/test/test_activations.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/url_fetch.py b/lib/spack/spack/test/url_fetch.py index 8047d5e26e..71a122455f 100644 --- a/lib/spack/spack/test/url_fetch.py +++ b/lib/spack/spack/test/url_fetch.py @@ -1,8 +1,9 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import collections import os import pytest @@ -10,8 +11,7 @@ from llnl.util.filesystem import working_dir, is_exe import spack.repo import spack.config -from spack.fetch_strategy import FailedDownloadError -from spack.fetch_strategy import from_list_url, URLFetchStrategy +import spack.fetch_strategy as fs from spack.spec import Spec from spack.stage import Stage from spack.version import ver @@ -23,10 +23,30 @@ def checksum_type(request): return request.param +@pytest.fixture +def pkg_factory(): + Pkg = collections.namedtuple( + 'Pkg', ['url_for_version', 'urls', 'url', 'versions'] + ) + + def factory(url, urls): + + def fn(v): + main_url = url or urls.pop(0) + return spack.url.substitute_version(main_url, v) + + return Pkg( + url_for_version=fn, url=url, urls=urls, + versions=collections.defaultdict(dict) + ) + + return factory + + def test_urlfetchstrategy_sans_url(): """Ensure constructor with no URL fails.""" with pytest.raises(ValueError): - with URLFetchStrategy(None): + with fs.URLFetchStrategy(None): pass @@ -34,8 +54,8 @@ def test_urlfetchstrategy_bad_url(tmpdir): """Ensure fetch with bad URL fails as expected.""" testpath = str(tmpdir) - with pytest.raises(FailedDownloadError): - fetcher = URLFetchStrategy(url='file:///does-not-exist') + with pytest.raises(fs.FailedDownloadError): + fetcher = fs.URLFetchStrategy(url='file:///does-not-exist') assert fetcher is not None with Stage(fetcher, path=testpath) as stage: @@ -55,7 +75,7 @@ def test_fetch( secure, checksum_type, config, - mutable_mock_packages + mutable_mock_repo ): """Fetch an archive and make sure we can checksum it.""" mock_archive.url @@ -106,8 +126,8 @@ def test_from_list_url(mock_packages, config, spec, url, digest): """ specification = Spec(spec).concretized() pkg = spack.repo.get(specification) - fetch_strategy = from_list_url(pkg) - assert isinstance(fetch_strategy, URLFetchStrategy) + fetch_strategy = fs.from_list_url(pkg) + assert isinstance(fetch_strategy, fs.URLFetchStrategy) assert os.path.basename(fetch_strategy.url) == url assert fetch_strategy.digest == digest @@ -118,8 +138,8 @@ def test_from_list_url_unspecified(mock_packages, config): spec = Spec('url-list-test @2.0.0').concretized() pkg = spack.repo.get(spec) - fetch_strategy = from_list_url(pkg) - assert isinstance(fetch_strategy, URLFetchStrategy) + fetch_strategy = fs.from_list_url(pkg) + assert isinstance(fetch_strategy, fs.URLFetchStrategy) assert os.path.basename(fetch_strategy.url) == 'foo-2.0.0.tar.gz' assert fetch_strategy.digest is None @@ -128,7 +148,7 @@ def test_nosource_from_list_url(mock_packages, config): """This test confirms BundlePackages do not have list url.""" pkg = spack.repo.get('nosource') - fetch_strategy = from_list_url(pkg) + fetch_strategy = fs.from_list_url(pkg) assert fetch_strategy is None @@ -148,9 +168,26 @@ def test_url_extra_fetch(tmpdir, mock_archive): """Ensure a fetch after downloading is effectively a no-op.""" testpath = str(tmpdir) - fetcher = URLFetchStrategy(mock_archive.url) + fetcher = fs.URLFetchStrategy(mock_archive.url) with Stage(fetcher, path=testpath) as stage: assert fetcher.archive_file is None stage.fetch() assert fetcher.archive_file is not None fetcher.fetch() + + +@pytest.mark.parametrize('url,urls,version,expected', [ + (None, + ['https://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz', + 'https://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz'], + '2.62', + ['https://ftpmirror.gnu.org/autoconf/autoconf-2.62.tar.gz', + 'https://ftp.gnu.org/gnu/autoconf/autoconf-2.62.tar.gz']) +]) +def test_candidate_urls(pkg_factory, url, urls, version, expected): + """Tests that candidate urls include mirrors and that they go through + pattern matching and substitution for versions. + """ + pkg = pkg_factory(url, urls) + f = fs._from_merged_attrs(fs.URLFetchStrategy, pkg, version) + assert f.candidate_urls == expected diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py index c557f78405..0651562007 100644 --- a/lib/spack/spack/test/url_parse.py +++ b/lib/spack/spack/test/url_parse.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -60,6 +60,8 @@ from spack.version import Version ('cppad-20170114.gpl', 'cppad-20170114'), # Arch ('pcraster-4.1.0_x86-64', 'pcraster-4.1.0'), + ('dislin-11.0.linux.i586_64', 'dislin-11.0'), + ('PAGIT.V1.01.64bit', 'PAGIT.V1.01'), # OS - linux ('astyle_2.04_linux', 'astyle_2.04'), # OS - unix @@ -72,6 +74,8 @@ from spack.version import Version ('numpy-1.12.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl', 'numpy-1.12.0'), # noqa # PyPI - exe ('PyYAML-3.12.win-amd64-py3.5.exe', 'PyYAML-3.12'), + # Combinations of multiple patterns - bin, release + ('rocketmq-all-4.5.2-bin-release', 'rocketmq-all-4.5.2'), # Combinations of multiple patterns - all ('p7zip_9.04_src_all', 'p7zip_9.04'), # Combinations of multiple patterns - run @@ -85,20 +89,31 @@ from spack.version import Version # Combinations of multiple patterns - darwin ('ghc-7.0.4-x86_64-apple-darwin', 'ghc-7.0.4'), ('ghc-7.0.4-i386-apple-darwin', 'ghc-7.0.4'), + # Combinations of multiple patterns - centos + ('sratoolkit.2.8.2-1-centos_linux64', 'sratoolkit.2.8.2-1'), # Combinations of multiple patterns - arch ('VizGlow_v2.2alpha17-R21November2016-Linux-x86_64-Install', 'VizGlow_v2.2alpha17-R21November2016'), ('jdk-8u92-linux-x64', 'jdk-8u92'), ('cuda_6.5.14_linux_64.run', 'cuda_6.5.14'), + ('Mathematica_12.0.0_LINUX.sh', 'Mathematica_12.0.0'), + ('trf407b.linux64', 'trf407b'), # Combinations of multiple patterns - with ('mafft-7.221-with-extensions-src', 'mafft-7.221'), ('spark-2.0.0-bin-without-hadoop', 'spark-2.0.0'), + ('conduit-v0.3.0-src-with-blt', 'conduit-v0.3.0'), + # Combinations of multiple patterns - rock + ('bitlib-23-2.src.rock', 'bitlib-23-2'), # Combinations of multiple patterns - public ('dakota-6.3-public.src', 'dakota-6.3'), # Combinations of multiple patterns - universal ('synergy-1.3.6p2-MacOSX-Universal', 'synergy-1.3.6p2'), # Combinations of multiple patterns - dynamic ('snptest_v2.5.2_linux_x86_64_dynamic', 'snptest_v2.5.2'), + # Combinations of multiple patterns - other + ('alglib-3.11.0.cpp.gpl', 'alglib-3.11.0'), + ('hpcviewer-2019.08-linux.gtk.x86_64', 'hpcviewer-2019.08'), + ('apache-mxnet-src-1.3.0-incubating', 'apache-mxnet-src-1.3.0'), ]) def test_url_strip_version_suffixes(url, expected): stripped = strip_version_suffixes(url) @@ -109,24 +124,40 @@ def test_url_strip_version_suffixes(url, expected): # No suffix ('rgb-1.0.6', '1.0.6', 'rgb'), ('nauty26r7', '26r7', 'nauty'), + ('PAGIT.V1.01', '1.01', 'PAGIT'), + ('AmpliconNoiseV1.29', '1.29', 'AmpliconNoise'), # Download type - install ('converge_install_2.3.16', '2.3.16', 'converge'), # Download type - src ('jpegsrc.v9b', '9b', 'jpeg'), + ('blatSrc35', '35', 'blat'), + # Download type - open + ('RepeatMasker-open-4-0-7', '4-0-7', 'RepeatMasker'), # Download type - archive ('coinhsl-archive-2014.01.17', '2014.01.17', 'coinhsl'), # Download type - std ('ghostscript-fonts-std-8.11', '8.11', 'ghostscript-fonts'), + # Download type - bin + ('GapCloser-bin-v1.12-r6', '1.12-r6', 'GapCloser'), + # Download type - software + ('orthomclSoftware-v2.0.9', '2.0.9', 'orthomcl'), # Download version - release ('cbench_release_1.3.0.tar.gz', '1.3.0', 'cbench'), # Download version - snapshot ('gts-snapshot-121130', '121130', 'gts'), # Download version - distrib ('zoltan_distrib_v3.83', '3.83', 'zoltan'), + # Download version - latest + ('Platypus-latest', 'N/A', 'Platypus'), + # Download version - complex + ('qt-everywhere-opensource-src-5.7.0', '5.7.0', 'qt'), + # Arch + ('VESTA-x86_64', '3.4.6', 'VESTA'), # VCS - bazaar ('libvterm-0+bzr681', '681', 'libvterm'), # License - gpl - ('PyQt-x11-gpl-4.11.3', '4.11.3', 'PyQt-x11') + ('PyQt-x11-gpl-4.11.3', '4.11.3', 'PyQt'), + ('PyQt4_gpl_x11-4.12.3', '4.12.3', 'PyQt4'), ]) def test_url_strip_name_suffixes(url, version, expected): stripped = strip_name_suffixes(url, version) @@ -182,6 +213,7 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): @pytest.mark.parametrize('name,version,url', [ # Common Repositories - github downloads + # name/archive/ver.ver ('nco', '4.6.2', 'https://github.com/nco/nco/archive/4.6.2.tar.gz'), # name/archive/vver.ver ('vim', '8.0.0134', 'https://github.com/vim/vim/archive/v8.0.0134.tar.gz'), @@ -257,6 +289,15 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): # Common Tarball Formats + # 1st Pass: Simplest case + # Assume name contains no digits and version contains no letters + + # name-ver.ver + ('libpng', '1.6.37', 'http://download.sourceforge.net/libpng/libpng-1.6.37.tar.gz'), + + # 2nd Pass: Version only + # Assume version contains no letters + # ver.ver ('eigen', '3.2.7', 'https://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2'), # ver.ver-ver @@ -266,10 +307,17 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): # vver_ver ('luafilesystem', '1_6_3', 'https://github.com/keplerproject/luafilesystem/archive/v1_6_3.tar.gz'), - # No separators + # 3rd Pass: No separator characters are used + # Assume name contains no digits + + # namever ('turbolinux', '702', 'file://{0}/turbolinux702.tar.gz'.format(os.getcwd())), ('nauty', '26r7', 'http://pallini.di.uniroma1.it/nauty26r7.tar.gz'), - # Dashes only + + # 4th Pass: A single separator character is used + # Assume name contains no digits + + # name-name-ver-ver ('Trilinos', '12-10-1', 'https://github.com/trilinos/Trilinos/archive/trilinos-release-12-10-1.tar.gz'), ('panda', '2016-03-07', @@ -278,7 +326,7 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): 'http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz'), ('cdd', '061a', 'http://www.cs.mcgill.ca/~fukuda/download/cdd/cdd-061a.tar.gz'), - # Only underscores + # name_name_ver_ver ('tinyxml', '2_6_2', 'https://sourceforge.net/projects/tinyxml/files/tinyxml/2.6.2/tinyxml_2_6_2.tar.gz'), ('boost', '1_55_0', @@ -287,9 +335,6 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): 'https://github.com/dhmunro/yorick/archive/y_2_2_04.tar.gz'), ('tbb', '44_20160413', 'https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz'), - - # Only dots - # name.name.ver.ver ('prank', '150803', 'http://wasabiapp.org/download/prank/prank.source.150803.tgz'), ('jpeg', '9b', 'http://www.ijg.org/files/jpegsrc.v9b.tar.gz'), @@ -302,61 +347,51 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): ('geant', '4.10.01.p03', 'http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz'), ('tcl', '8.6.5', 'http://prdownloads.sourceforge.net/tcl/tcl8.6.5-src.tar.gz'), - # Dash and dots + # 5th Pass: Two separator characters are used + # Name may contain digits, version may contain letters # name-name-ver.ver - # digit in name ('m4', '1.4.17', 'https://ftp.gnu.org/gnu/m4/m4-1.4.17.tar.gz'), - # letter in version ('gmp', '6.0.0a', 'https://gmplib.org/download/gmp/gmp-6.0.0a.tar.bz2'), - # version starts with 'v' ('LaunchMON', '1.0.2', 'https://github.com/LLNL/LaunchMON/releases/download/v1.0.2/launchmon-v1.0.2.tar.gz'), # name-ver-ver.ver ('libedit', '20150325-3.1', 'http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz'), - - # Dash and unserscores - # name-name-ver_ver ('icu4c', '57_1', 'http://download.icu-project.org/files/icu4c/57.1/icu4c-57_1-src.tgz'), - - # Underscores and dots - # name_name_ver.ver ('superlu_dist', '4.1', 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz'), ('pexsi', '0.9.0', 'https://math.berkeley.edu/~linlin/pexsi/download/pexsi_v0.9.0.tar.gz'), # name_name.ver.ver ('fer', '696', 'ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.v696.tar.gz'), - - # Dash dot dah dot - + # name_name_ver-ver + ('Bridger', '2014-12-01', + 'https://downloads.sourceforge.net/project/rnaseqassembly/Bridger_r2014-12-01.tar.gz'), # name-name-ver.ver-ver.ver ('sowing', '1.1.23-p1', 'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/sowing-1.1.23-p1.tar.gz'), ('bib2xhtml', '3.0-15-gf506', 'http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-15-gf506.tar.gz'), # namever.ver-ver.ver ('go', '1.4-bootstrap-20161024', 'https://storage.googleapis.com/golang/go1.4-bootstrap-20161024.tar.gz'), - # Underscore dash dot + # 6th Pass: All three separator characters are used + # Name may contain digits, version may contain letters # name_name-ver.ver ('the_silver_searcher', '0.32.0', 'http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz'), ('sphinx_rtd_theme', '0.1.10a0', 'https://pypi.python.org/packages/source/s/sphinx_rtd_theme/sphinx_rtd_theme-0.1.10a0.tar.gz'), - - # Dot underscore dot dash dot - # name.name_ver.ver-ver.ver ('TH.data', '1.0-8', 'https://cran.r-project.org/src/contrib/TH.data_1.0-8.tar.gz'), ('XML', '3.98-1.4', 'https://cran.r-project.org/src/contrib/XML_3.98-1.4.tar.gz'), - - # Dash dot underscore dot - # name-name-ver.ver_ver.ver ('pypar', '2.1.5_108', 'https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/pypar/pypar-2.1.5_108.tgz'), # name-namever.ver_ver.ver ('STAR-CCM+', '11.06.010_02', 'file://{0}/STAR-CCM+11.06.010_02_linux-x86_64.tar.gz'.format(os.getcwd())), + # name-name_name-ver.ver + ('PerlIO-utf8_strict', '0.002', + 'http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/PerlIO-utf8_strict-0.002.tar.gz'), # Various extensions # .tar.gz @@ -399,18 +434,61 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): # .txz ('kim-api', '2.1.0', 'https://s3.openkim.org/kim-api/kim-api-2.1.0.txz'), - # Weird URLS + # 8th Pass: Query strings - # github.com/repo/name/releases/download/name-vver/name - ('nextflow', '0.20.1', 'https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow'), # suffix queries ('swiftsim', '0.3.0', 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'), - ('swiftsim', '0.3.0', 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'), + ('swiftsim', '0.3.0', + 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'), ('sionlib', '1.7.1', 'http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1'), + ('jube2', '2.2.2', 'https://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=2.2.2'), + ('archive', '1.0.0', 'https://code.ornl.gov/eck/papyrus/repository/archive.tar.bz2?ref=v1.0.0'), + ('VecGeom', '0.3.rc', + 'https://gitlab.cern.ch/api/v4/projects/VecGeom%2FVecGeom/repository/archive.tar.gz?sha=v0.3.rc'), + ('parsplice', '1.1', + 'https://gitlab.com/api/v4/projects/exaalt%2Fparsplice/repository/archive.tar.gz?sha=v1.1'), + ('busco', '2.0.1', 'https://gitlab.com/api/v4/projects/ezlab%2Fbusco/repository/archive.tar.gz?sha=2.0.1'), + ('libaec', '1.0.2', + 'https://gitlab.dkrz.de/api/v4/projects/k202009%2Flibaec/repository/archive.tar.gz?sha=v1.0.2'), + ('icet', '2.1.1', + 'https://gitlab.kitware.com/api/v4/projects/icet%2Ficet/repository/archive.tar.bz2?sha=IceT-2.1.1'), + ('vtk-m', '1.3.0', + 'https://gitlab.kitware.com/api/v4/projects/vtk%2Fvtk-m/repository/archive.tar.gz?sha=v1.3.0'), + ('GATK', '3.8-1-0-gf15c1c3ef', + 'https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef'), # stem queries ('slepc', '3.6.2', 'http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz'), ('otf', '1.12.5salmon', 'http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz'), + ('eospac', '6.4.0beta.1', + 'http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz'), + ('vampirtrace', '5.14.4', + 'http://wwwpub.zih.tu-dresden.de/~mlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz'), + # (we don't actually look for these, they are picked up + # during the preliminary stem parsing) + ('octopus', '6.0', 'http://octopus-code.org/down.php?file=6.0/octopus-6.0.tar.gz'), + ('cloog', '0.18.1', 'http://www.bastoul.net/cloog/pages/download/count.php3?url=./cloog-0.18.1.tar.gz'), + ('libxc', '2.2.2', 'http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz'), + ('cistem', '1.0.0-beta', + 'https://cistem.org/system/tdf/upload3/cistem-1.0.0-beta-source-code.tar.gz?file=1&type=cistem_details&id=37&force=0'), + ('Magics', '4.1.0', + 'https://confluence.ecmwf.int/download/attachments/3473464/Magics-4.1.0-Source.tar.gz?api=v2'), + ('grib_api', '1.17.0', + 'https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz?api=v2'), + ('eccodes', '2.2.0', + 'https://software.ecmwf.int/wiki/download/attachments/45757960/eccodes-2.2.0-Source.tar.gz?api=v2'), + ('SWFFT', '1.0', + 'https://xgitlab.cels.anl.gov/api/v4/projects/hacc%2FSWFFT/repository/archive.tar.gz?sha=v1.0'), + + # 9th Pass: Version in path + + # github.com/repo/name/releases/download/name-vver/name + ('nextflow', '0.20.1', 'https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow'), + # ver/name + ('ncbi', '2.2.26', 'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ncbi.tar.gz'), + + # Other tests for corner cases + # single character name ('R', '3.3.2', 'https://cloud.r-project.org/src/base/R-3/R-3.3.2.tar.gz'), # name starts with digit diff --git a/lib/spack/spack/test/url_substitution.py b/lib/spack/spack/test/url_substitution.py index 281c62e99f..08a3b99a4a 100644 --- a/lib/spack/spack/test/url_substitution.py +++ b/lib/spack/spack/test/url_substitution.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/__init__.py b/lib/spack/spack/test/util/__init__.py new file mode 100644 index 0000000000..9f87532b85 --- /dev/null +++ b/lib/spack/spack/test/util/__init__.py @@ -0,0 +1,4 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/editor.py b/lib/spack/spack/test/util/editor.py index 2bb30cd1a2..e1495a70cc 100644 --- a/lib/spack/spack/test/util/editor.py +++ b/lib/spack/spack/test/util/editor.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/environment.py b/lib/spack/spack/test/util/environment.py index e34fc95f33..a555c35c9c 100644 --- a/lib/spack/spack/test/util/environment.py +++ b/lib/spack/spack/test/util/environment.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/executable.py b/lib/spack/spack/test/util/executable.py index 054cdbfccd..26719e94d1 100644 --- a/lib/spack/spack/test/util/executable.py +++ b/lib/spack/spack/test/util/executable.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,6 +8,7 @@ import sys import llnl.util.filesystem as fs import spack.util.executable as ex +from spack.hooks.sbang import filter_shebangs_in_directory def test_read_unicode(tmpdir): @@ -28,6 +29,7 @@ print(u'\\xc3') # make it executable fs.set_executable(script_name) + filter_shebangs_in_directory('.', [script_name]) # read the unicode back in and see whether things work script = ex.Executable('./%s' % script_name) diff --git a/lib/spack/spack/test/util/file_cache.py b/lib/spack/spack/test/util/file_cache.py index 0a82ae9f51..0fec1a5dc9 100644 --- a/lib/spack/spack/test/util/file_cache.py +++ b/lib/spack/spack/test/util/file_cache.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/log_parser.py b/lib/spack/spack/test/util/log_parser.py index 9025eb0741..0f829082b6 100644 --- a/lib/spack/spack/test/util/log_parser.py +++ b/lib/spack/spack/test/util/log_parser.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/prefix.py b/lib/spack/spack/test/util/prefix.py index 1d905eb13b..cee3ad028b 100644 --- a/lib/spack/spack/test/util/prefix.py +++ b/lib/spack/spack/test/util/prefix.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/spack_lock_wrapper.py b/lib/spack/spack/test/util/spack_lock_wrapper.py index c64af82e37..d7819c84cb 100644 --- a/lib/spack/spack/test/util/spack_lock_wrapper.py +++ b/lib/spack/spack/test/util/spack_lock_wrapper.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/spack_yaml.py b/lib/spack/spack/test/util/spack_yaml.py index 5e8c803774..ed7ba789c0 100644 --- a/lib/spack/spack/test/util/spack_yaml.py +++ b/lib/spack/spack/test/util/spack_yaml.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/util_gpg.py b/lib/spack/spack/test/util/util_gpg.py index a0d9d4d807..4a243985db 100644 --- a/lib/spack/spack/test/util/util_gpg.py +++ b/lib/spack/spack/test/util/util_gpg.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/util_string.py b/lib/spack/spack/test/util/util_string.py index 396c6abc0e..bcaa7d6211 100644 --- a/lib/spack/spack/test/util/util_string.py +++ b/lib/spack/spack/test/util/util_string.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/util/util_url.py b/lib/spack/spack/test/util/util_url.py index 24b40ac63c..5d0d9fa4eb 100644 --- a/lib/spack/spack/test/util/util_url.py +++ b/lib/spack/spack/test/util/util_url.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,6 +6,7 @@ """Test Spack's URL handling utility functions.""" import os import os.path +import spack.paths import spack.util.url as url_util @@ -41,7 +42,7 @@ def test_url_parse(): assert(parsed.netloc == 'path') assert(parsed.path == '/to/resource') - spack_root = os.path.abspath(os.environ['SPACK_ROOT']) + spack_root = spack.paths.spack_root parsed = url_util.parse('$spack') assert(parsed.scheme == 'file') assert(parsed.netloc == '') @@ -56,7 +57,7 @@ def test_url_parse(): def test_url_local_file_path(): - spack_root = os.path.abspath(os.environ['SPACK_ROOT']) + spack_root = spack.paths.spack_root lfp = url_util.local_file_path('/a/b/c.txt') assert(lfp == '/a/b/c.txt') @@ -171,7 +172,7 @@ def test_url_join_local_paths(): 'https://mirror.spack.io/build_cache/my-package') # file:// URL path components are *NOT* canonicalized - spack_root = os.path.abspath(os.environ['SPACK_ROOT']) + spack_root = spack.paths.spack_root join_result = url_util.join('/a/b/c', '$spack') assert(join_result == 'file:///a/b/c/$spack') # not canonicalized diff --git a/lib/spack/spack/test/variant.py b/lib/spack/spack/test/variant.py index 4a76b4824e..d1657b71b7 100644 --- a/lib/spack/spack/test/variant.py +++ b/lib/spack/spack/test/variant.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/verification.py b/lib/spack/spack/test/verification.py index dbc76e6268..009f407186 100644 --- a/lib/spack/spack/test/verification.py +++ b/lib/spack/spack/test/verification.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/versions.py b/lib/spack/spack/test/versions.py index b39da0c698..315788f7f3 100644 --- a/lib/spack/spack/test/versions.py +++ b/lib/spack/spack/test/versions.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -266,6 +266,8 @@ def test_contains(): assert_in('1.3.5-7', '1.2:1.4') assert_not_in('1.1', '1.2:1.4') assert_not_in('1.5', '1.2:1.4') + assert_not_in('1.5', '1.5.1:1.6') + assert_not_in('1.5', '1.5.1:') assert_in('1.4.2', '1.2:1.4') assert_not_in('1.4.2', '1.2:1.4.0') diff --git a/lib/spack/spack/test/views.py b/lib/spack/spack/test/views.py index 52ecb91e73..e1dcec4c5c 100644 --- a/lib/spack/spack/test/views.py +++ b/lib/spack/spack/test/views.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/test/web.py b/lib/spack/spack/test/web.py index c80e29b523..ae62301319 100644 --- a/lib/spack/spack/test/web.py +++ b/lib/spack/spack/test/web.py @@ -1,13 +1,16 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) """Tests for web.py.""" import os +import pytest + +from ordereddict_backport import OrderedDict import spack.paths -from spack.util.web import spider, find_versions_of_archive +import spack.util.web as web_util from spack.version import ver @@ -23,7 +26,7 @@ page_4 = 'file://' + os.path.join(web_data_path, '4.html') def test_spider_0(): - pages, links = spider(root, depth=0) + pages, links = web_util.spider(root, depth=0) assert root in pages assert page_1 not in pages @@ -41,7 +44,7 @@ def test_spider_0(): def test_spider_1(): - pages, links = spider(root, depth=1) + pages, links = web_util.spider(root, depth=1) assert root in pages assert page_1 in pages @@ -60,7 +63,7 @@ def test_spider_1(): def test_spider_2(): - pages, links = spider(root, depth=2) + pages, links = web_util.spider(root, depth=2) assert root in pages assert page_1 in pages @@ -81,7 +84,7 @@ def test_spider_2(): def test_spider_3(): - pages, links = spider(root, depth=3) + pages, links = web_util.spider(root, depth=3) assert root in pages assert page_1 in pages @@ -104,31 +107,36 @@ def test_spider_3(): def test_find_versions_of_archive_0(): - versions = find_versions_of_archive(root_tarball, root, list_depth=0) + versions = web_util.find_versions_of_archive( + root_tarball, root, list_depth=0) assert ver('0.0.0') in versions def test_find_versions_of_archive_1(): - versions = find_versions_of_archive(root_tarball, root, list_depth=1) + versions = web_util.find_versions_of_archive( + root_tarball, root, list_depth=1) assert ver('0.0.0') in versions assert ver('1.0.0') in versions def test_find_versions_of_archive_2(): - versions = find_versions_of_archive(root_tarball, root, list_depth=2) + versions = web_util.find_versions_of_archive( + root_tarball, root, list_depth=2) assert ver('0.0.0') in versions assert ver('1.0.0') in versions assert ver('2.0.0') in versions def test_find_exotic_versions_of_archive_2(): - versions = find_versions_of_archive(root_tarball, root, list_depth=2) + versions = web_util.find_versions_of_archive( + root_tarball, root, list_depth=2) # up for grabs to make this better. assert ver('2.0.0b2') in versions def test_find_versions_of_archive_3(): - versions = find_versions_of_archive(root_tarball, root, list_depth=3) + versions = web_util.find_versions_of_archive( + root_tarball, root, list_depth=3) assert ver('0.0.0') in versions assert ver('1.0.0') in versions assert ver('2.0.0') in versions @@ -137,7 +145,49 @@ def test_find_versions_of_archive_3(): def test_find_exotic_versions_of_archive_3(): - versions = find_versions_of_archive(root_tarball, root, list_depth=3) + versions = web_util.find_versions_of_archive( + root_tarball, root, list_depth=3) assert ver('2.0.0b2') in versions assert ver('3.0a1') in versions assert ver('4.5-rc5') in versions + + +def test_get_header(): + headers = { + 'Content-type': 'text/plain' + } + + # looking up headers should just work like a plain dict + # lookup when there is an entry with the right key + assert(web_util.get_header(headers, 'Content-type') == 'text/plain') + + # looking up headers should still work if there is a fuzzy match + assert(web_util.get_header(headers, 'contentType') == 'text/plain') + + # ...unless there is an exact match for the "fuzzy" spelling. + headers['contentType'] = 'text/html' + assert(web_util.get_header(headers, 'contentType') == 'text/html') + + # If lookup has to fallback to fuzzy matching and there are more than one + # fuzzy match, the result depends on the internal ordering of the given + # mapping + headers = OrderedDict() + headers['Content-type'] = 'text/plain' + headers['contentType'] = 'text/html' + + assert(web_util.get_header(headers, 'CONTENT_TYPE') == 'text/plain') + del headers['Content-type'] + assert(web_util.get_header(headers, 'CONTENT_TYPE') == 'text/html') + + # Same as above, but different ordering + headers = OrderedDict() + headers['contentType'] = 'text/html' + headers['Content-type'] = 'text/plain' + + assert(web_util.get_header(headers, 'CONTENT_TYPE') == 'text/html') + del headers['contentType'] + assert(web_util.get_header(headers, 'CONTENT_TYPE') == 'text/plain') + + # If there isn't even a fuzzy match, raise KeyError + with pytest.raises(KeyError): + web_util.get_header(headers, 'ContentLength') diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py index 11b289a0b1..a728c46a71 100644 --- a/lib/spack/spack/url.py +++ b/lib/spack/spack/url.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -153,13 +153,14 @@ def strip_version_suffixes(path): r'[Ii]nstall', r'all', r'code', - r'src(_0)?', r'[Ss]ources?', r'file', r'full', r'single', - r'public', r'with[a-zA-Z_-]+', + r'rock', + r'src(_0)?', + r'public', r'bin', r'binary', r'run', @@ -174,6 +175,7 @@ def strip_version_suffixes(path): # Download version r'release', + r'bin', r'stable', r'[Ff]inal', r'rel', @@ -189,15 +191,24 @@ def strip_version_suffixes(path): r'ia32', r'intel', r'amd64', + r'linux64', r'x64', + r'64bit', r'x86[_-]64', + r'i586_64', r'x86', r'i[36]86', r'ppc64(le)?', r'armv?(7l|6l|64)', + # Other + r'cpp', + r'gtk', + r'incubating', + # OS r'[Ll]inux(_64)?', + r'LINUX', r'[Uu]ni?x', r'[Ss]un[Oo][Ss]', r'[Mm]ac[Oo][Ss][Xx]?', @@ -208,14 +219,18 @@ def strip_version_suffixes(path): r'[Ww]in(64|32)?', r'[Cc]ygwin(64|32)?', r'[Mm]ingw', + r'centos', # Arch # Needs to come before and after OS, appears in both orders r'ia32', r'intel', r'amd64', + r'linux64', r'x64', + r'64bit', r'x86[_-]64', + r'i586_64', r'x86', r'i[36]86', r'ppc64(le)?', @@ -270,31 +285,41 @@ def strip_name_suffixes(path, version): # name-ver # name_ver # name.ver - r'[._-]v?' + str(version) + '.*', + r'[._-][rvV]?' + str(version) + '.*', # namever - str(version) + '.*', + r'V?' + str(version) + '.*', # Download type r'install', - r'src', + r'[Ss]rc', r'(open)?[Ss]ources?', + r'[._-]open', r'[._-]archive', r'[._-]std', + r'[._-]bin', + r'Software', # Download version r'release', r'snapshot', r'distrib', + r'everywhere', + r'latest', # Arch - r'Linux64', + r'Linux(64)?', + r'x86_64', # VCS r'0\+bzr', # License r'gpl', + + # Needs to come before and after gpl, appears in both orders + r'[._-]x11', + r'gpl', ] for regex in suffix_regexes: @@ -407,7 +432,7 @@ def parse_version_offset(path): # 3. names can contain A-Z, a-z, 0-9, '+', separators # 4. versions can contain A-Z, a-z, 0-9, separators # 5. versions always start with a digit - # 6. versions are often prefixed by a 'v' character + # 6. versions are often prefixed by a 'v' or 'r' character # 7. separators are most reliable to determine name/version boundaries # List of the following format: @@ -450,7 +475,7 @@ def parse_version_offset(path): (r'^[a-zA-Z+-]*(\d[\da-zA-Z-]*)$', stem), # name_name_ver_ver - # e.g. tinyxml_2_6_2, boost_1_55_0, tbb2017_20161128, v1_6_3 + # e.g. tinyxml_2_6_2, boost_1_55_0, tbb2017_20161128 (r'^[a-zA-Z+_]*(\d[\da-zA-Z_]*)$', stem), # name.name.ver.ver @@ -476,6 +501,10 @@ def parse_version_offset(path): # e.g. fer_source.v696 (r'^[a-zA-Z\d+_]+\.v?(\d[\da-zA-Z.]*)$', stem), + # name_ver-ver + # e.g. Bridger_r2014-12-01 + (r'^[a-zA-Z\d+]+_r?(\d[\da-zA-Z-]*)$', stem), + # name-name-ver.ver-ver.ver # e.g. sowing-1.1.23-p1, bib2xhtml-v3.0-15-gf506, 4.6.3-alpha04 (r'^(?:[a-zA-Z\d+-]+-)?v?(\d[\da-zA-Z.-]*)$', stem), @@ -507,19 +536,17 @@ def parse_version_offset(path): # e.g. STAR-CCM+11.06.010_02 (r'^[a-zA-Z+-]+(\d[\da-zA-Z._]*)$', stem), + # name-name_name-ver.ver + # e.g. PerlIO-utf8_strict-0.002 + (r'^[a-zA-Z\d+_-]+-v?(\d[\da-zA-Z.]*)$', stem), + # 7th Pass: Specific VCS # bazaar # e.g. libvterm-0+bzr681 (r'bzr(\d[\da-zA-Z._-]*)$', stem), - # 8th Pass: Version in path - - # github.com/repo/name/releases/download/vver/name - # e.g. https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow - (r'github\.com/[^/]+/[^/]+/releases/download/[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)/', path), # noqa - - # 9th Pass: Query strings + # 8th Pass: Query strings # e.g. https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0 (r'\?sha=[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)$', suffix), @@ -528,13 +555,24 @@ def parse_version_offset(path): (r'\?ref=[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)$', suffix), # e.g. http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1 - (r'\?version=v?(\d[\da-zA-Z._-]*)$', suffix), + # e.g. https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef + (r'[?&]version=v?(\d[\da-zA-Z._-]*)$', suffix), # e.g. http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz - (r'\?filename=[a-zA-Z\d+-]+-v?(\d[\da-zA-Z.]*)$', stem), + # e.g. http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz + (r'[?&]filename=[a-zA-Z\d+-]+[_-]v?(\d[\da-zA-Z.]*)', stem), # e.g. http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz - (r'\?package=[a-zA-Z\d+-]+&get=[a-zA-Z\d+-]+-v?(\d[\da-zA-Z.]*)$', stem), # noqa + (r'&get=[a-zA-Z\d+-]+-v?(\d[\da-zA-Z.]*)$', stem), # noqa + + # 9th Pass: Version in path + + # github.com/repo/name/releases/download/vver/name + # e.g. https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow + (r'github\.com/[^/]+/[^/]+/releases/download/[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)/', path), # noqa + + # e.g. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ncbi.tar.gz + (r'(\d[\da-zA-Z._-]*)/[^/]+$', path), ] for i, version_regex in enumerate(version_regexes): @@ -662,6 +700,9 @@ def parse_name_offset(path, v=None): # e.g. http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz (r'\?package=([A-Za-z\d+-]+)', stem), + # ?package=name-version + (r'\?package=([A-Za-z\d]+)', suffix), + # download.php # e.g. http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1 (r'([^/]+)/download.php$', path), diff --git a/lib/spack/spack/user_environment.py b/lib/spack/spack/user_environment.py new file mode 100644 index 0000000000..4c9fdc3d67 --- /dev/null +++ b/lib/spack/spack/user_environment.py @@ -0,0 +1,91 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import sys +import os + +import spack.util.prefix as prefix +import spack.util.environment as environment +import spack.build_environment as build_env + +#: Environment variable name Spack uses to track individually loaded packages +spack_loaded_hashes_var = 'SPACK_LOADED_HASHES' + + +def prefix_inspections(platform): + """Get list of prefix inspections for platform + + Arguments: + platform (string): the name of the platform to consider. The platform + determines what environment variables Spack will use for some + inspections. + + Returns: + A dictionary mapping subdirectory names to lists of environment + variables to modify with that directory if it exists. + """ + inspections = { + 'bin': ['PATH'], + 'lib': ['LD_LIBRARY_PATH', 'LIBRARY_PATH'], + 'lib64': ['LD_LIBRARY_PATH', 'LIBRARY_PATH'], + 'man': ['MANPATH'], + 'share/man': ['MANPATH'], + 'share/aclocal': ['ACLOCAL_PATH'], + 'include': ['CPATH'], + 'lib/pkgconfig': ['PKG_CONFIG_PATH'], + 'lib64/pkgconfig': ['PKG_CONFIG_PATH'], + '': ['CMAKE_PREFIX_PATH'] + } + + if platform == 'darwin': + for subdir in ('lib', 'lib64'): + inspections[subdir].append('DYLD_LIBRARY_PATH') + + return inspections + + +def unconditional_environment_modifications(view): + """List of environment (shell) modifications to be processed for view. + + This list does not depend on the specs in this environment""" + env = environment.EnvironmentModifications() + + for subdir, vars in prefix_inspections(sys.platform).items(): + full_subdir = os.path.join(view.root, subdir) + for var in vars: + env.prepend_path(var, full_subdir) + + return env + + +def environment_modifications_for_spec(spec, view=None): + """List of environment (shell) modifications to be processed for spec. + + This list is specific to the location of the spec or its projection in + the view.""" + spec = spec.copy() + if view: + spec.prefix = prefix.Prefix(view.view().get_projection_for_spec(spec)) + + # generic environment modifications determined by inspecting the spec + # prefix + env = environment.inspect_path( + spec.prefix, + prefix_inspections(spec.platform), + exclude=environment.is_system_path + ) + + # Let the extendee/dependency modify their extensions/dependents + # before asking for package-specific modifications + env.extend( + build_env.modifications_from_dependencies( + spec, context='run' + ) + ) + + # Package specific modifications + build_env.set_module_variables_for_package(spec.package) + spec.package.setup_run_environment(env) + + return env diff --git a/lib/spack/spack/util/__init__.py b/lib/spack/spack/util/__init__.py index 94f8ac4d9e..9f87532b85 100644 --- a/lib/spack/spack/util/__init__.py +++ b/lib/spack/spack/util/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/compression.py b/lib/spack/spack/util/compression.py index 0ad80457ec..d617954ab1 100644 --- a/lib/spack/spack/util/compression.py +++ b/lib/spack/spack/util/compression.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/crypto.py b/lib/spack/spack/util/crypto.py index 523878106e..566e99da21 100644 --- a/lib/spack/spack/util/crypto.py +++ b/lib/spack/spack/util/crypto.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/debug.py b/lib/spack/spack/util/debug.py index 8fcb50973f..1ff74f24cf 100644 --- a/lib/spack/spack/util/debug.py +++ b/lib/spack/spack/util/debug.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/editor.py b/lib/spack/spack/util/editor.py index ce5010d99f..00a095252e 100644 --- a/lib/spack/spack/util/editor.py +++ b/lib/spack/spack/util/editor.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py index bfd6300ec8..248a6d3c8c 100644 --- a/lib/spack/spack/util/environment.py +++ b/lib/spack/spack/util/environment.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/executable.py b/lib/spack/spack/util/executable.py index e383a533af..ce30e18f42 100644 --- a/lib/spack/spack/util/executable.py +++ b/lib/spack/spack/util/executable.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/file_cache.py b/lib/spack/spack/util/file_cache.py index 0227edf155..9342f9772b 100644 --- a/lib/spack/spack/util/file_cache.py +++ b/lib/spack/spack/util/file_cache.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/file_permissions.py b/lib/spack/spack/util/file_permissions.py index c732aad0ab..d94b74f51e 100644 --- a/lib/spack/spack/util/file_permissions.py +++ b/lib/spack/spack/util/file_permissions.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/gpg.py b/lib/spack/spack/util/gpg.py index a7d1a3d8fa..29b2add852 100644 --- a/lib/spack/spack/util/gpg.py +++ b/lib/spack/spack/util/gpg.py @@ -1,13 +1,17 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) import os +import re +import spack.error import spack.paths -from spack.util.executable import Executable +import spack.version +from spack.util.executable import which +_gnupg_version_re = r"^gpg \(GnuPG\) (.*)$" GNUPGHOME = spack.paths.gpg_path @@ -28,15 +32,39 @@ def parse_keys_output(output): class Gpg(object): + _gpg = None + @staticmethod def gpg(): # TODO: Support loading up a GPG environment from a built gpg. - gpg = Executable('gpg2') - if not os.path.exists(GNUPGHOME): - os.makedirs(GNUPGHOME) - os.chmod(GNUPGHOME, 0o700) - gpg.add_default_env('GNUPGHOME', GNUPGHOME) - return gpg + if Gpg._gpg is None: + gpg = which('gpg2', 'gpg') + + if not gpg: + raise SpackGPGError("Spack requires gpg version 2 or higher.") + + # ensure that the version is actually >= 2 if we find 'gpg' + if gpg.name == 'gpg': + output = gpg('--version', output=str) + match = re.search(_gnupg_version_re, output, re.M) + + if not match: + raise SpackGPGError("Couldn't determine version of gpg") + + v = spack.version.Version(match.group(1)) + if v < spack.version.Version('2'): + raise SpackGPGError("Spack requires GPG version >= 2") + + # make the GNU PG path if we need to + # TODO: does this need to be in the spack directory? + # we should probably just use GPG's regular conventions + if not os.path.exists(GNUPGHOME): + os.makedirs(GNUPGHOME) + os.chmod(GNUPGHOME, 0o700) + gpg.add_default_env('GNUPGHOME', GNUPGHOME) + + Gpg._gpg = gpg + return Gpg._gpg @classmethod def create(cls, **kwargs): @@ -112,3 +140,7 @@ class Gpg(object): cls.gpg()('--list-public-keys') if signing: cls.gpg()('--list-secret-keys') + + +class SpackGPGError(spack.error.SpackError): + """Class raised when GPG errors are detected.""" diff --git a/lib/spack/spack/util/imp/__init__.py b/lib/spack/spack/util/imp/__init__.py index e06b83492a..27e2b00f9f 100644 --- a/lib/spack/spack/util/imp/__init__.py +++ b/lib/spack/spack/util/imp/__init__.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/imp/imp_importer.py b/lib/spack/spack/util/imp/imp_importer.py index 523926e469..810e1d01a3 100644 --- a/lib/spack/spack/util/imp/imp_importer.py +++ b/lib/spack/spack/util/imp/imp_importer.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/imp/importlib_importer.py b/lib/spack/spack/util/imp/importlib_importer.py index 33c50cb601..c230f4c50a 100644 --- a/lib/spack/spack/util/imp/importlib_importer.py +++ b/lib/spack/spack/util/imp/importlib_importer.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,7 +7,7 @@ ``importlib`` is only fully implemented in Python 3. """ -from importlib.machinery import SourceFileLoader +from importlib.machinery import SourceFileLoader # novm class PrependFileLoader(SourceFileLoader): diff --git a/lib/spack/spack/util/lock.py b/lib/spack/spack/util/lock.py index 59202528e2..b748aa056a 100644 --- a/lib/spack/spack/util/lock.py +++ b/lib/spack/spack/util/lock.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/log_parse.py b/lib/spack/spack/util/log_parse.py index 467f9eb45f..4b01c18c91 100644 --- a/lib/spack/spack/util/log_parse.py +++ b/lib/spack/spack/util/log_parse.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/module_cmd.py b/lib/spack/spack/util/module_cmd.py index d203670769..0edf7e6102 100644 --- a/lib/spack/spack/util/module_cmd.py +++ b/lib/spack/spack/util/module_cmd.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/naming.py b/lib/spack/spack/util/naming.py index 618c21e8bd..1cc6d6109f 100644 --- a/lib/spack/spack/util/naming.py +++ b/lib/spack/spack/util/naming.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/package_hash.py b/lib/spack/spack/util/package_hash.py index 2a3ee80fd5..f689aa9710 100644 --- a/lib/spack/spack/util/package_hash.py +++ b/lib/spack/spack/util/package_hash.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -69,8 +69,17 @@ class TagMultiMethods(ast.NodeVisitor): if node.decorator_list: dec = node.decorator_list[0] if isinstance(dec, ast.Call) and dec.func.id == 'when': - cond = dec.args[0].s - nodes.append((node, self.spec.satisfies(cond, strict=True))) + try: + cond = dec.args[0].s + nodes.append( + (node, self.spec.satisfies(cond, strict=True))) + except AttributeError: + # In this case the condition for the 'when' decorator is + # not a string literal (for example it may be a Python + # variable name). Therefore the function is added + # unconditionally since we don't know whether the + # constraint applies or not. + nodes.append((node, None)) else: nodes.append((node, None)) diff --git a/lib/spack/spack/util/path.py b/lib/spack/spack/util/path.py index 20b1d8b41f..9d5413c609 100644 --- a/lib/spack/spack/util/path.py +++ b/lib/spack/spack/util/path.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/pattern.py b/lib/spack/spack/util/pattern.py index 8ba6c54d71..f467e2d18e 100644 --- a/lib/spack/spack/util/pattern.py +++ b/lib/spack/spack/util/pattern.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/prefix.py b/lib/spack/spack/util/prefix.py index b4c0a63ce8..804790c1d3 100644 --- a/lib/spack/spack/util/prefix.py +++ b/lib/spack/spack/util/prefix.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/s3.py b/lib/spack/spack/util/s3.py index ee6b3d56cf..c9ed22f72c 100644 --- a/lib/spack/spack/util/s3.py +++ b/lib/spack/spack/util/s3.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/spack_json.py b/lib/spack/spack/util/spack_json.py index 4a966de46c..01f773058b 100644 --- a/lib/spack/spack/util/spack_json.py +++ b/lib/spack/spack/util/spack_json.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/spack_yaml.py b/lib/spack/spack/util/spack_yaml.py index 1d92d59ad2..46e8e35543 100644 --- a/lib/spack/spack/util/spack_yaml.py +++ b/lib/spack/spack/util/spack_yaml.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/string.py b/lib/spack/spack/util/string.py index 1c28dbe6c3..7284cef2d3 100644 --- a/lib/spack/spack/util/string.py +++ b/lib/spack/spack/util/string.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/util/url.py b/lib/spack/spack/util/url.py index 7ac12e7b81..ab5503229f 100644 --- a/lib/spack/spack/util/url.py +++ b/lib/spack/spack/util/url.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,6 +9,7 @@ Utility functions for parsing, formatting, and manipulating URLs. import itertools import os.path +import re from six import string_types import six.moves.urllib.parse as urllib_parse @@ -69,8 +70,7 @@ def parse(url, scheme='file'): if scheme == 'file': path = spack.util.path.canonicalize_path(netloc + path) - while path.startswith('//'): - path = path[1:] + path = re.sub(r'^/+', '/', path) netloc = '' return urllib_parse.ParseResult(scheme=scheme, diff --git a/lib/spack/spack/util/web.py b/lib/spack/spack/util/web.py index 1fe58d6415..4fb8c5a591 100644 --- a/lib/spack/spack/util/web.py +++ b/lib/spack/spack/util/web.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,16 +15,13 @@ import ssl import sys import traceback -from itertools import product - -import six from six.moves.urllib.request import urlopen, Request from six.moves.urllib.error import URLError import multiprocessing.pool try: # Python 2 had these in the HTMLParser package. - from HTMLParser import HTMLParser, HTMLParseError + from HTMLParser import HTMLParser, HTMLParseError # novm except ImportError: # In Python 3, things moved to html.parser from html.parser import HTMLParser @@ -50,30 +47,6 @@ from spack.util.compression import ALLOWED_ARCHIVE_TYPES # Timeout in seconds for web requests _timeout = 10 -# See docstring for standardize_header_names() -_separators = ('', ' ', '_', '-') -HTTP_HEADER_NAME_ALIASES = { - "Accept-ranges": set( - ''.join((A, 'ccept', sep, R, 'anges')) - for A, sep, R in product('Aa', _separators, 'Rr')), - - "Content-length": set( - ''.join((C, 'ontent', sep, L, 'ength')) - for C, sep, L in product('Cc', _separators, 'Ll')), - - "Content-type": set( - ''.join((C, 'ontent', sep, T, 'ype')) - for C, sep, T in product('Cc', _separators, 'Tt')), - - "Date": set(('Date', 'date')), - - "Last-modified": set( - ''.join((L, 'ast', sep, M, 'odified')) - for L, sep, M in product('Ll', _separators, 'Mm')), - - "Server": set(('Server', 'server')) -} - class LinkParser(HTMLParser): """This parser just takes an HTML page and strips out the hrefs on the @@ -107,7 +80,7 @@ if sys.version_info[0] < 3: Process = NonDaemonProcess else: - class NonDaemonContext(type(multiprocessing.get_context())): + class NonDaemonContext(type(multiprocessing.get_context())): # novm Process = NonDaemonProcess class NonDaemonPool(multiprocessing.pool.Pool): @@ -155,7 +128,7 @@ def read_from_url(url, accept_content_type=None): warn_no_ssl_cert_checking() else: # User wants SSL verification, and it *can* be provided. - context = ssl.create_default_context() + context = ssl.create_default_context() # novm else: # User has explicitly indicated that they do not want SSL # verification. @@ -173,7 +146,7 @@ def read_from_url(url, accept_content_type=None): req.get_method = lambda: "HEAD" resp = _urlopen(req, timeout=_timeout, context=context) - content_type = resp.headers.get('Content-type') + content_type = get_header(resp.headers, 'Content-type') # Do the real GET request when we know it's just HTML. req.get_method = lambda: "GET" @@ -185,7 +158,7 @@ def read_from_url(url, accept_content_type=None): ERROR=str(err))) if accept_content_type and not is_web_url: - content_type = response.headers.get('Content-type') + content_type = get_header(response.headers, 'Content-type') reject_content_type = ( accept_content_type and ( @@ -208,9 +181,8 @@ def warn_no_ssl_cert_checking(): "your Python to enable certificate verification.") -def push_to_url(local_file_path, remote_path, **kwargs): - keep_original = kwargs.get('keep_original', True) - +def push_to_url( + local_file_path, remote_path, keep_original=True, extra_args=None): remote_url = url_util.parse(remote_path) verify_ssl = spack.config.get('config:verify_ssl') @@ -235,7 +207,8 @@ def push_to_url(local_file_path, remote_path, **kwargs): os.remove(local_file_path) elif remote_url.scheme == 's3': - extra_args = kwargs.get('extra_args', {}) + if extra_args is None: + extra_args = {} remote_path = remote_url.path while remote_path.startswith('/'): @@ -290,16 +263,31 @@ def remove_url(url): if url.scheme == 's3': s3 = s3_util.create_s3_session(url) - s3.delete_object(Bucket=url.s3_bucket, Key=url.path) + s3.delete_object(Bucket=url.netloc, Key=url.path) return # Don't even try for other URL schemes. -def _list_s3_objects(client, url, num_entries, start_after=None): +def _iter_s3_contents(contents, prefix): + for entry in contents: + key = entry['Key'] + + if not key.startswith('/'): + key = '/' + key + + key = os.path.relpath(key, prefix) + + if key == '.': + continue + + yield key + + +def _list_s3_objects(client, bucket, prefix, num_entries, start_after=None): list_args = dict( - Bucket=url.netloc, - Prefix=url.path, + Bucket=bucket, + Prefix=prefix[1:], MaxKeys=num_entries) if start_after is not None: @@ -311,21 +299,19 @@ def _list_s3_objects(client, url, num_entries, start_after=None): if result['IsTruncated']: last_key = result['Contents'][-1]['Key'] - iter = (key for key in - ( - os.path.relpath(entry['Key'], url.path) - for entry in result['Contents'] - ) - if key != '.') + iter = _iter_s3_contents(result['Contents'], prefix) return iter, last_key def _iter_s3_prefix(client, url, num_entries=1024): key = None + bucket = url.netloc + prefix = re.sub(r'^/*', '/', url.path) + while True: contents, key = _list_s3_objects( - client, url, num_entries, start_after=key) + client, bucket, prefix, num_entries, start_after=key) for x in contents: yield x @@ -577,106 +563,34 @@ def find_versions_of_archive(archive_urls, list_url=None, list_depth=0): return versions -def standardize_header_names(headers): - """Replace certain header names with standardized spellings. - - Standardizes the spellings of the following header names: - - Accept-ranges - - Content-length - - Content-type - - Date - - Last-modified - - Server - - Every name considered is translated to one of the above names if the only - difference between the two is how the first letters of each word are - capitalized; whether words are separated; or, if separated, whether they - are so by a dash (-), underscore (_), or space ( ). Header names that - cannot be mapped as described above are returned unaltered. - - For example: The standard spelling of "Content-length" would be substituted - for any of the following names: - - Content-length - - content_length - - contentlength - - content_Length - - contentLength - - content Length - - ... and any other header name, such as "Content-encoding", would not be - altered, regardless of spelling. - - If headers is a string, then it (or an appropriate substitute) is returned. - - If headers is a non-empty tuple, headers[0] is a string, and there exists a - standardized spelling for header[0] that differs from it, then a new tuple - is returned. This tuple has the same elements as headers, except the first - element is the standardized spelling for headers[0]. - - If headers is a sequence, then a new list is considered, where each element - is its corresponding element in headers, but mapped as above if a string or - tuple. This new list is returned if at least one of its elements differ - from their corrsponding element in headers. - - If headers is a mapping, then a new dict is considered, where the key in - each item is the key of its corresponding item in headers, mapped as above - if a string or tuple. The value is taken from the corresponding item. If - the keys of multiple items in headers map to the same key after being - standardized, then the value for the resulting item is undefined. The new - dict is returned if at least one of its items has a key that differs from - that of their corresponding item in headers, or if the keys of multiple - items in headers map to the same key after being standardized. - - In all other cases headers is returned unaltered. - """ - if isinstance(headers, six.string_types): - for standardized_spelling, other_spellings in ( - HTTP_HEADER_NAME_ALIASES.items()): - if headers in other_spellings: - if headers == standardized_spelling: - return headers - return standardized_spelling - return headers - - if isinstance(headers, tuple): - if not headers: - return headers - old = headers[0] - if isinstance(old, six.string_types): - new = standardize_header_names(old) - if old is not new: - return (new,) + headers[1:] - return headers - - try: - changed = False - new_dict = {} - for key, value in headers.items(): - if isinstance(key, (tuple, six.string_types)): - old_key, key = key, standardize_header_names(key) - changed = changed or key is not old_key - - new_dict[key] = value +def get_header(headers, header_name): + """Looks up a dict of headers for the given header value. - return new_dict if changed else headers - except (AttributeError, TypeError, ValueError): - pass + Looks up a dict of headers, [headers], for a header value given by + [header_name]. Returns headers[header_name] if header_name is in headers. + Otherwise, the first fuzzy match is returned, if any. - try: - changed = False - new_list = [] - for item in headers: - if isinstance(item, (tuple, six.string_types)): - old_item, item = item, standardize_header_names(item) - changed = changed or item is not old_item + This fuzzy matching is performed by discarding word separators and + capitalization, so that for example, "Content-length", "content_length", + "conTENtLength", etc., all match. In the case of multiple fuzzy-matches, + the returned value is the "first" such match given the underlying mapping's + ordering, or unspecified if no such ordering is defined. - new_list.append(item) + If header_name is not in headers, and no such fuzzy match exists, then a + KeyError is raised. + """ - return new_list if changed else headers - except TypeError: - pass + def unfuzz(header): + return re.sub(r'[ _-]', '', header).lower() - return headers + try: + return headers[header_name] + except KeyError: + unfuzzed_header_name = unfuzz(header_name) + for header, value in headers.items(): + if unfuzz(header) == unfuzzed_header_name: + return value + raise class SpackWebError(spack.error.SpackError): diff --git a/lib/spack/spack/variant.py b/lib/spack/spack/variant.py index 7eea243b06..3915fe00fa 100644 --- a/lib/spack/spack/variant.py +++ b/lib/spack/spack/variant.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,7 +21,7 @@ import spack.directives import spack.error as error try: - from collections.abc import Sequence + from collections.abc import Sequence # novm except ImportError: from collections import Sequence @@ -600,7 +600,9 @@ def substitute_abstract_variants(spec): for name, v in spec.variants.items(): if name in spack.directives.reserved_names: continue - pkg_variant = spec.package_class.variants[name] + pkg_variant = spec.package_class.variants.get(name, None) + if not pkg_variant: + raise UnknownVariantError(spec, [name]) new_variant = pkg_variant.make_variant(v._original_value) pkg_variant.validate_or_raise(new_variant, spec.package_class) spec.variants.substitute(new_variant) @@ -778,12 +780,13 @@ class DuplicateVariantError(error.SpecError): class UnknownVariantError(error.SpecError): """Raised when an unknown variant occurs in a spec.""" - - def __init__(self, pkg, variants): + def __init__(self, spec, variants): self.unknown_variants = variants - super(UnknownVariantError, self).__init__( - 'Package {0} has no variant {1}!'.format(pkg, comma_or(variants)) - ) + variant_str = 'variant' if len(variants) == 1 else 'variants' + msg = ('trying to set {0} "{1}" in package "{2}", but the package' + ' has no such {0} [happened during concretization of {3}]') + msg = msg.format(variant_str, comma_or(variants), spec.name, spec.root) + super(UnknownVariantError, self).__init__(msg) class InconsistentValidationError(error.SpecError): diff --git a/lib/spack/spack/verify.py b/lib/spack/spack/verify.py index 88b89cf17c..08e6270a4a 100644 --- a/lib/spack/spack/verify.py +++ b/lib/spack/spack/verify.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py index 0bb5a767e7..bb7a79772e 100644 --- a/lib/spack/spack/version.py +++ b/lib/spack/spack/version.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/bash/spack-completion.in b/share/spack/bash/spack-completion.in new file mode 100755 index 0000000000..ca15b8dfb2 --- /dev/null +++ b/share/spack/bash/spack-completion.in @@ -0,0 +1,309 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +# NOTE: spack-completion.bash is auto-generated by: +# +# $ spack commands --aliases --format=bash +# --header=bash/spack-completion.in --update=spack-completion.bash +# +# Please do not manually modify this file. + + +# The following global variables are set by Bash programmable completion: +# +# COMP_CWORD: An index into ${COMP_WORDS} of the word containing the +# current cursor position +# COMP_KEY: The key (or final key of a key sequence) used to invoke +# the current completion function +# COMP_LINE: The current command line +# COMP_POINT: The index of the current cursor position relative to the +# beginning of the current command +# COMP_TYPE: Set to an integer value corresponding to the type of +# completion attempted that caused a completion function +# to be called +# COMP_WORDBREAKS: The set of characters that the readline library treats +# as word separators when performing word completion +# COMP_WORDS: An array variable consisting of the individual words in +# the current command line +# +# The following global variable is used by Bash programmable completion: +# +# COMPREPLY: An array variable from which bash reads the possible +# completions generated by a shell function invoked by the +# programmable completion facility +# +# See `man bash` for more details. + +# Bash programmable completion for Spack +_bash_completion_spack() { + # In all following examples, let the cursor be denoted by brackets, i.e. [] + + # For our purposes, flags should not affect tab completion. For instance, + # `spack install []` and `spack -d install --jobs 8 []` should both give the same + # possible completions. Therefore, we need to ignore any flags in COMP_WORDS. + local COMP_WORDS_NO_FLAGS=() + local index=0 + while [[ "$index" -lt "$COMP_CWORD" ]] + do + if [[ "${COMP_WORDS[$index]}" == [a-z]* ]] + then + COMP_WORDS_NO_FLAGS+=("${COMP_WORDS[$index]}") + fi + let index++ + done + + # Options will be listed by a subfunction named after non-flag arguments. + # For example, `spack -d install []` will call _spack_install + # and `spack compiler add []` will call _spack_compiler_add + local subfunction=$(IFS='_'; echo "_${COMP_WORDS_NO_FLAGS[*]}") + + # Translate dashes to underscores, as dashes are not permitted in + # compatibility mode. See https://github.com/spack/spack/pull/4079 + subfunction=${subfunction//-/_} + + # However, the word containing the current cursor position needs to be + # added regardless of whether or not it is a flag. This allows us to + # complete something like `spack install --keep-st[]` + COMP_WORDS_NO_FLAGS+=("${COMP_WORDS[$COMP_CWORD]}") + + # Since we have removed all words after COMP_CWORD, we can safely assume + # that COMP_CWORD_NO_FLAGS is simply the index of the last element + local COMP_CWORD_NO_FLAGS=$((${#COMP_WORDS_NO_FLAGS[@]} - 1)) + + # There is no guarantee that the cursor is at the end of the command line + # when tab completion is envoked. For example, in the following situation: + # `spack -d [] install` + # if the user presses the TAB key, a list of valid flags should be listed. + # Note that we cannot simply ignore everything after the cursor. In the + # previous scenario, the user should expect to see a list of flags, but + # not of other subcommands. Obviously, `spack -d list install` would be + # invalid syntax. To accomplish this, we use the variable list_options + # which is true if the current word starts with '-' or if the cursor is + # not at the end of the line. + local list_options=false + if [[ "${COMP_WORDS[$COMP_CWORD]}" == -* || "$COMP_POINT" -ne "${#COMP_LINE}" ]] + then + list_options=true + fi + + # In general, when envoking tab completion, the user is not expecting to + # see optional flags mixed in with subcommands or package names. Tab + # completion is used by those who are either lazy or just bad at spelling. + # If someone doesn't remember what flag to use, seeing single letter flags + # in their results won't help them, and they should instead consult the + # documentation. However, if the user explicitly declares that they are + # looking for a flag, we can certainly help them out. + # `spack install -[]` + # and + # `spack install --[]` + # should list all flags and long flags, respectively. Furthermore, if a + # subcommand has no non-flag completions, such as `spack arch []`, it + # should list flag completions. + + local cur=${COMP_WORDS_NO_FLAGS[$COMP_CWORD_NO_FLAGS]} + + # If the cursor is in the middle of the line, like: + # `spack -d [] install` + # COMP_WORDS will not contain the empty character, so we have to add it. + if [[ "${COMP_LINE:$COMP_POINT:1}" == " " ]] + then + cur="" + fi + + # Uncomment this line to enable logging + #_test_vars >> temp + + # Make sure function exists before calling it + if [[ "$(type -t $subfunction)" == "function" ]] + then + $subfunction + COMPREPLY=($(compgen -W "$SPACK_COMPREPLY" -- "$cur")) + fi +} + +# Helper functions for subcommands +# Results of each query are cached via environment variables + +_subcommands() { + if [[ -z "${SPACK_SUBCOMMANDS:-}" ]] + then + SPACK_SUBCOMMANDS="$(spack commands)" + fi + SPACK_COMPREPLY="$SPACK_SUBCOMMANDS" +} + +_all_packages() { + if [[ -z "${SPACK_ALL_PACKAGES:-}" ]] + then + SPACK_ALL_PACKAGES="$(spack list)" + fi + SPACK_COMPREPLY="$SPACK_ALL_PACKAGES" +} + +_all_resource_hashes() { + if [[ -z "${SPACK_ALL_RESOURCES_HASHES:-}" ]] + then + SPACK_ALL_RESOURCE_HASHES="$(spack resource list --only-hashes)" + fi + SPACK_COMPREPLY="$SPACK_ALL_RESOURCE_HASHES" +} + +_installed_packages() { + if [[ -z "${SPACK_INSTALLED_PACKAGES:-}" ]] + then + SPACK_INSTALLED_PACKAGES="$(spack --color=never find --no-groups)" + fi + SPACK_COMPREPLY="$SPACK_INSTALLED_PACKAGES" +} + +_installed_compilers() { + if [[ -z "${SPACK_INSTALLED_COMPILERS:-}" ]] + then + SPACK_INSTALLED_COMPILERS="$(spack compilers | egrep -v "^(-|=)")" + fi + SPACK_COMPREPLY="$SPACK_INSTALLED_COMPILERS" +} + +_providers() { + if [[ -z "${SPACK_PROVIDERS:-}" ]] + then + SPACK_PROVIDERS="$(spack providers)" + fi + SPACK_COMPREPLY="$SPACK_PROVIDERS" +} + +_mirrors() { + if [[ -z "${SPACK_MIRRORS:-}" ]] + then + SPACK_MIRRORS="$(spack mirror list | awk '{print $1}')" + fi + SPACK_COMPREPLY="$SPACK_MIRRORS" +} + +_repos() { + if [[ -z "${SPACK_REPOS:-}" ]] + then + SPACK_REPOS="$(spack repo list | awk '{print $1}')" + fi + SPACK_COMPREPLY="$SPACK_REPOS" +} + +_tests() { + if [[ -z "${SPACK_TESTS:-}" ]] + then + SPACK_TESTS="$(spack test -l)" + fi + SPACK_COMPREPLY="$SPACK_TESTS" +} + +_environments() { + if [[ -z "${SPACK_ENVIRONMENTS:-}" ]] + then + SPACK_ENVIRONMENTS="$(spack env list)" + fi + SPACK_COMPREPLY="$SPACK_ENVIRONMENTS" +} + +_keys() { + if [[ -z "${SPACK_KEYS:-}" ]] + then + SPACK_KEYS="$(spack gpg list)" + fi + SPACK_COMPREPLY="$SPACK_KEYS" +} + +_config_sections() { + if [[ -z "${SPACK_CONFIG_SECTIONS:-}" ]] + then + SPACK_CONFIG_SECTIONS="$(spack config list)" + fi + SPACK_COMPREPLY="$SPACK_CONFIG_SECTIONS" +} + +_extensions() { + if [[ -z "${SPACK_EXTENSIONS:-}" ]] + then + SPACK_EXTENSIONS="aspell go-bootstrap go icedtea jdk kim-api lua matlab mofem-cephas octave openjdk perl python r ruby rust tcl yorick" + fi + SPACK_COMPREPLY="$SPACK_EXTENSIONS" +} + +# Testing functions + +# Function for unit testing tab completion +# Syntax: _spack_completions spack install py- +_spack_completions() { + local COMP_CWORD COMP_KEY COMP_LINE COMP_POINT COMP_TYPE COMP_WORDS COMPREPLY + + # Set each variable the way bash would + COMP_LINE="$*" + COMP_POINT=${#COMP_LINE} + COMP_WORDS=("$@") + if [[ ${COMP_LINE: -1} == ' ' ]] + then + COMP_WORDS+=('') + fi + COMP_CWORD=$((${#COMP_WORDS[@]} - 1)) + COMP_KEY=9 # ASCII 09: Horizontal Tab + COMP_TYPE=64 # ASCII 64: '@', to list completions if the word is not unmodified + + # Run Spack's tab completion function + _bash_completion_spack + + # Return the result + echo "${COMPREPLY[@]:-}" +} + +# Log the environment variables used +# Syntax: _test_vars >> temp +_test_vars() { + echo "-----------------------------------------------------" + echo "Variables set by bash:" + echo + echo "COMP_LINE: '$COMP_LINE'" + echo "# COMP_LINE: '${#COMP_LINE}'" + echo "COMP_WORDS: $(_pretty_print COMP_WORDS[@])" + echo "# COMP_WORDS: '${#COMP_WORDS[@]}'" + echo "COMP_CWORD: '$COMP_CWORD'" + echo "COMP_KEY: '$COMP_KEY'" + echo "COMP_POINT: '$COMP_POINT'" + echo "COMP_TYPE: '$COMP_TYPE'" + echo "COMP_WORDBREAKS: '$COMP_WORDBREAKS'" + echo + echo "Intermediate variables:" + echo + echo "COMP_WORDS_NO_FLAGS: $(_pretty_print COMP_WORDS_NO_FLAGS[@])" + echo "# COMP_WORDS_NO_FLAGS: '${#COMP_WORDS_NO_FLAGS[@]}'" + echo "COMP_CWORD_NO_FLAGS: '$COMP_CWORD_NO_FLAGS'" + echo + echo "Subfunction: '$subfunction'" + if $list_options + then + echo "List options: 'True'" + else + echo "List options: 'False'" + fi + echo "Current word: '$cur'" +} + +# Pretty-prints one or more arrays +# Syntax: _pretty_print array1[@] ... +_pretty_print() { + for arg in $@ + do + local array=("${!arg}") + printf "$arg: [" + printf "'%s'" "${array[0]}" + printf ", '%s'" "${array[@]:1}" + echo "]" + done +} + +complete -o bashdefault -o default -F _bash_completion_spack spack + +# Spack commands +# +# Everything below here is auto-generated. diff --git a/share/spack/csh/pathadd.csh b/share/spack/csh/pathadd.csh index 5a69d10d6b..4390a788d0 100644 --- a/share/spack/csh/pathadd.csh +++ b/share/spack/csh/pathadd.csh @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/csh/spack.csh b/share/spack/csh/spack.csh index ac893d72b1..b4d963ae10 100644 --- a/share/spack/csh/spack.csh +++ b/share/spack/csh/spack.csh @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,6 +27,16 @@ # avoids the need to come up with a user-friendly naming scheme for # spack module files. ######################################################################## +# Store LD_LIBRARY_PATH variables from spack shell function +# This is necessary because MacOS System Integrity Protection clears +# (DY?)LD_LIBRARY_PATH variables on process start. +if ( ${?LD_LIBRARY_PATH} ) then + setenv SPACK_LD_LIBRARY_PATH $LD_LIBRARY_PATH +endif +if ( ${?DYLD_LIBRARY_PATH} ) then + setenv SPACK_DYLD_LIBRARY_PATH $DYLD_LIBRARY_PATH +endif + # accumulate initial flags for main spack command set _sp_flags = "" while ( $#_sp_args > 0 ) @@ -47,8 +57,7 @@ set _sp_spec="" [ $#_sp_args -gt 0 ] && set _sp_subcommand = ($_sp_args[1]) [ $#_sp_args -gt 1 ] && set _sp_spec = ($_sp_args[2-]) -# Figure out what type of module we're running here. -set _sp_modtype = "" +# Run subcommand switch ($_sp_subcommand) case cd: shift _sp_args # get rid of 'cd' @@ -106,35 +115,17 @@ case env: endif case load: case unload: - set _sp_module_args="""" - if ( "$_sp_spec" =~ "-*" ) then - set _sp_module_args = $_sp_spec[1] - shift _sp_spec - set _sp_spec = ($_sp_spec) + # Space in `-h` portion is important for differentiating -h option + # from variants that begin with "h" or packages with "-h" in name + if ( "$_sp_spec" =~ "*--sh*" || "$_sp_spec" =~ "*--csh*" || \ + " $_sp_spec" =~ "* -h*" || "$_sp_spec" =~ "*--help*") then + # IF a shell is given, print shell output + \spack $_sp_flags $_sp_subcommand $_sp_spec + else + # otherwise eval with csh + eval `\spack $_sp_flags $_sp_subcommand --csh $_sp_spec || \ + echo "exit 1"` endif - - # Here the user has run load or unload with a spec. Find a matching - # spec using 'spack module find', then use the appropriate module - # tool's commands to add/remove the result from the environment. - switch ($_sp_subcommand) - case "load": - # _sp_module_args may be "-r" for recursive spec retrieval - set _sp_full_spec = ( "`\spack $_sp_flags module tcl find $_sp_module_args $_sp_spec`" ) - if ( "$_sp_module_args" == "-r" ) then - # module load can handle the list of modules to load and "-r" is not a valid option - set _sp_module_args = "" - endif - if ( $? == 0 ) then - module load $_sp_module_args $_sp_full_spec - endif - breaksw - case "unload": - set _sp_full_spec = ( "`\spack $_sp_flags module tcl find $_sp_spec`" ) - if ( $? == 0 ) then - module unload $_sp_module_args $_sp_full_spec - endif - breaksw - endsw breaksw default: @@ -143,6 +134,5 @@ default: endsw _sp_end: -unset _sp_args _sp_full_spec _sp_modtype _sp_module_args -unset _sp_sh_cmd _sp_spec _sp_subcommand _sp_flags +unset _sp_args _sp_full_spec _sp_sh_cmd _sp_spec _sp_subcommand _sp_flags unset _sp_arg _sp_env_arg diff --git a/share/spack/docker/entrypoint.bash b/share/spack/docker/entrypoint.bash index 1393cbb0bf..775747d904 100755 --- a/share/spack/docker/entrypoint.bash +++ b/share/spack/docker/entrypoint.bash @@ -1,6 +1,6 @@ #! /usr/bin/env bash -e # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/docker/handle-prompt.sh b/share/spack/docker/handle-prompt.sh index 1f44deb61e..a01047463e 100644 --- a/share/spack/docker/handle-prompt.sh +++ b/share/spack/docker/handle-prompt.sh @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/docker/handle-ssh.sh b/share/spack/docker/handle-ssh.sh index a4587a1f9f..18e5ae259d 100644 --- a/share/spack/docker/handle-ssh.sh +++ b/share/spack/docker/handle-ssh.sh @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/docker/package-index/Dockerfile b/share/spack/docker/package-index/Dockerfile new file mode 100644 index 0000000000..3ffafe90e8 --- /dev/null +++ b/share/spack/docker/package-index/Dockerfile @@ -0,0 +1,30 @@ +# prepare the package index in form of JSON files +FROM ubuntu:18.04 AS build-env + +ENV SPACK_ROOT=/opt/spack \ + DEBIAN_FRONTEND=noninteractive + +COPY bin $SPACK_ROOT/bin +COPY etc $SPACK_ROOT/etc +COPY lib $SPACK_ROOT/lib +COPY share $SPACK_ROOT/share +COPY var $SPACK_ROOT/var + +RUN apt-get -yqq update \ + && apt-get -yqq install \ + bash jq python \ + && rm -rf /var/lib/apt/lists/* + +WORKDIR /build +# single, large index file +RUN $SPACK_ROOT/bin/spack list --format version_json > packages.json +# individual packages split into a tree of :firstLetter/:packageName.json +RUN $SPACK_ROOT/share/spack/docker/package-index/split.sh + +# nginx web service +FROM nginx:mainline-alpine +MAINTAINER Spack Maintainers <maintainers@spack.io> +COPY --from=build-env --chown=nginx:nginx /build/packages /build/packages.json /usr/share/nginx/html/api/ +COPY share/spack/docker/package-index/cors-header.conf /etc/nginx/conf.d/ + +CMD ["nginx", "-g", "daemon off;"] diff --git a/share/spack/docker/package-index/README.rst b/share/spack/docker/package-index/README.rst new file mode 100644 index 0000000000..af5cde8025 --- /dev/null +++ b/share/spack/docker/package-index/README.rst @@ -0,0 +1,45 @@ +============================================ +The packages.spack.io Package Index REST API +============================================ + +This directory provides the docker recipe for the Spack package index on https://packages.spack.io + +On each merge to ``develop``, DockerHub builds a new image ``spack/packages.spack.io`` which is configured in: + https://cloud.docker.com/u/spack/repository/docker/spack/packages.spack.io/builds/edit + +------------ +The REST API +------------ + +The API is a simple, file-based JSON index. +A specific package can be queried via the URI syntax: +``https://packages.spack.io/api/:firstLetter/:packageName.json`` +which will return a HTTP status code ``200`` with a JSON file for all valid packages (content from ``spack list --format version_json``) and HTTP status code ``404`` for all other package names. + +Examples: + +- https://packages.spack.io/api/a/adios2.json +- https://packages.spack.io/api/p/py-pandas.json + +There is also the full index available at once under https://packages.spack.io/api/packages.json + +Current down-stream dependencies are, e.g. the https://shields.io service: + +- https://shields.io/category/version +- https://github.com/badges/shields/pull/3536 + +-------------------- +Local Build and Test +-------------------- + +Execute in your local Spack source root directory: + +.. code-block:: bash + + docker build -t spack/packages.spack.io:latest -f share/spack/docker/package-index/Dockerfile . + +Startup a local HTTP server on http://localhost:8080 via: + +.. code-block:: bash + + docker run -p 8080:80 spack/packages.spack.io:latest diff --git a/share/spack/packages/cors-header.conf b/share/spack/docker/package-index/cors-header.conf index 77e34b60a4..77e34b60a4 100644 --- a/share/spack/packages/cors-header.conf +++ b/share/spack/docker/package-index/cors-header.conf diff --git a/share/spack/packages/split.sh b/share/spack/docker/package-index/split.sh index 2c499926cb..c82d8045f6 100755 --- a/share/spack/packages/split.sh +++ b/share/spack/docker/package-index/split.sh @@ -1,6 +1,6 @@ #!/usr/bin/env bash # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/docker/ubuntu-1604.dockerfile b/share/spack/docker/ubuntu-1604.dockerfile index eb30ab8a8d..7d57f76c7f 100644 --- a/share/spack/docker/ubuntu-1604.dockerfile +++ b/share/spack/docker/ubuntu-1604.dockerfile @@ -17,16 +17,36 @@ COPY share $SPACK_ROOT/share COPY var $SPACK_ROOT/var RUN mkdir -p $SPACK_ROOT/opt/spack -RUN apt-get -yqq update \ - && apt-get -yqq install \ - build-essential ca-certificates curl g++ \ - gcc gfortran git gnupg2 \ - iproute2 lmod lua-posix make \ - openssh-server python python-pip tcl \ - unzip \ - && pip install boto3 \ +RUN apt-get -yqq update \ + && apt-get -yqq install --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + file \ + g++ \ + gcc \ + gfortran \ + git \ + gnupg2 \ + iproute2 \ + lmod \ + locales \ + lua-posix \ + make \ + openssh-server \ + python3 \ + python3-pip \ + tcl \ + unzip \ + && locale-gen en_US.UTF-8 \ + && pip3 install boto3 \ && rm -rf /var/lib/apt/lists/* +# Add LANG default to en_US.UTF-8 +ENV LANGUAGE en_US.UTF-8 +ENV LANG en_US.UTF-8 +ENV LC_ALL en_US.UTF-8 + RUN ( echo ". /usr/share/lmod/lmod/init/bash" \ && echo ". \$SPACK_ROOT/share/spack/setup-env.sh" \ && echo "if [ \"\$CURRENTLY_BUILDING_DOCKER_IMAGE\" '!=' '1' ]" \ diff --git a/share/spack/docker/ubuntu-1804.dockerfile b/share/spack/docker/ubuntu-1804.dockerfile index e8447b7daa..9b3be21bec 100644 --- a/share/spack/docker/ubuntu-1804.dockerfile +++ b/share/spack/docker/ubuntu-1804.dockerfile @@ -17,16 +17,36 @@ COPY share $SPACK_ROOT/share COPY var $SPACK_ROOT/var RUN mkdir -p $SPACK_ROOT/opt/spack -RUN apt-get -yqq update \ - && apt-get -yqq install \ - build-essential ca-certificates curl g++ \ - gcc gfortran git gnupg2 \ - iproute2 lmod lua-posix make \ - openssh-server python python-pip tcl \ - unzip \ - && pip install boto3 \ +RUN apt-get -yqq update \ + && apt-get -yqq install --no-install-recommends \ + build-essential \ + ca-certificates \ + curl \ + file \ + g++ \ + gcc \ + gfortran \ + git \ + gnupg2 \ + iproute2 \ + lmod \ + locales \ + lua-posix \ + make \ + openssh-server \ + python3 \ + python3-pip \ + tcl \ + unzip \ + && locale-gen en_US.UTF-8 \ + && pip3 install boto3 \ && rm -rf /var/lib/apt/lists/* +# Add LANG default to en_US.UTF-8 +ENV LANGUAGE en_US.UTF-8 +ENV LANG en_US.UTF-8 +ENV LC_ALL en_US.UTF-8 + RUN ( echo ". /usr/share/lmod/lmod/init/bash" \ && echo ". \$SPACK_ROOT/share/spack/setup-env.sh" \ && echo "if [ \"\$CURRENTLY_BUILDING_DOCKER_IMAGE\" '!=' '1' ]" \ diff --git a/share/spack/docs/docker/module-file-tutorial/spack.sh b/share/spack/docs/docker/module-file-tutorial/spack.sh index 40c2afb5b3..b025bda979 100644 --- a/share/spack/docs/docker/module-file-tutorial/spack.sh +++ b/share/spack/docs/docker/module-file-tutorial/spack.sh @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/packages/Dockerfile b/share/spack/packages/Dockerfile deleted file mode 100644 index 3b9bd89ec2..0000000000 --- a/share/spack/packages/Dockerfile +++ /dev/null @@ -1,12 +0,0 @@ -FROM ubuntu:18.04 AS build-env -WORKDIR /build -RUN apt-get update && apt-get install -y jq -COPY packages.json ./ -COPY split.sh ./ -RUN /build/split.sh - -FROM nginx:mainline-alpine -COPY --from=build-env --chown=nginx:nginx /build/packages /build/packages.json /usr/share/nginx/html/api/ -COPY cors-header.conf /etc/nginx/conf.d/ - -CMD ["nginx", "-g", "daemon off;"] diff --git a/share/spack/packages/build-image.sh b/share/spack/packages/build-image.sh deleted file mode 100755 index adde5842ab..0000000000 --- a/share/spack/packages/build-image.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env bash -# -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -script="$( basename "$0" )" -cd "$( dirname "$0" )" - -export IMAGE="spack/packages.spack.io:latest" - -if [ "$script" '=' 'push-image.sh' ] ; then - docker push "${IMAGE}" -else - docker build --no-cache --force-rm -t "${IMAGE}" . -fi diff --git a/share/spack/packages/push-image.sh b/share/spack/packages/push-image.sh deleted file mode 120000 index b3fd71be24..0000000000 --- a/share/spack/packages/push-image.sh +++ /dev/null @@ -1 +0,0 @@ -build-image.sh
\ No newline at end of file diff --git a/share/spack/qa/completion-test.sh b/share/spack/qa/completion-test.sh new file mode 100755 index 0000000000..5b326b4a6d --- /dev/null +++ b/share/spack/qa/completion-test.sh @@ -0,0 +1,89 @@ +#!/bin/sh +# +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +# +# This script tests that Spack's tab completion scripts work. +# +# The tests are portable to bash, zsh, and bourne shell, and can be run +# in any of these shells. +# + +export QA_DIR=$(dirname "$0") +export SHARE_DIR=$(cd "$QA_DIR/.." && pwd) +export SPACK_ROOT=$(cd "$QA_DIR/../../.." && pwd) + +. "$QA_DIR/test-framework.sh" + +# Fail on undefined variables +set -u + +# Source setup-env.sh before tests +. "$SHARE_DIR/setup-env.sh" +. "$SHARE_DIR/spack-completion.$_sp_shell" + +title "Testing spack-completion.$_sp_shell with $_sp_shell" + +# Spack command is now available +succeeds which spack + +title 'Testing all subcommands' +while IFS= read -r line +do + # Test that completion with no args works + succeeds _spack_completions ${line[*]} '' + + # Test that completion with flags works + contains '-h --help' _spack_completions ${line[*]} - +done <<- EOF + $(spack commands --aliases --format=subcommands) +EOF + +title 'Testing for correct output' +contains 'compiler' _spack_completions spack '' +contains 'install' _spack_completions spack inst +contains 'find' _spack_completions spack help '' +contains 'hdf5' _spack_completions spack list '' +contains 'py-numpy' _spack_completions spack list py- +contains 'mpi' _spack_completions spack providers '' +contains 'builtin' _spack_completions spack repo remove '' +contains 'packages' _spack_completions spack config edit '' +contains 'python' _spack_completions spack extensions '' +contains 'hdf5' _spack_completions spack -d install --jobs 8 '' +contains 'hdf5' _spack_completions spack install -v '' + +# XFAIL: Fails for Python 2.6 because pkg_resources not found? +#contains 'compilers.py' _spack_completions spack test '' + +title 'Testing debugging functions' + +# This is a particularly tricky case that involves the following situation: +# `spack -d [] install ` +# Here, [] represents the cursor, which is in the middle of the line. +# We should tab-complete optional flags for `spack`, not optional flags for +# `spack install` or package names. +COMP_LINE='spack -d install ' +COMP_POINT=9 +COMP_WORDS=(spack -d install) +COMP_CWORD=2 +COMP_KEY=9 +COMP_TYPE=64 + +_bash_completion_spack +contains "--all-help" echo "${COMPREPLY[@]}" + +contains "['spack', '-d', 'install', '']" _pretty_print COMP_WORDS[@] + +# Set the rest of the intermediate variables manually +COMP_WORDS_NO_FLAGS=(spack install) +COMP_CWORD_NO_FLAGS=1 +subfunction=_spack +cur= + +list_options=true +contains "'True'" _test_vars +list_options=false +contains "'False'" _test_vars diff --git a/share/spack/qa/configuration/packages.yaml b/share/spack/qa/configuration/packages.yaml index fad3489d3b..076095a7ca 100644 --- a/share/spack/qa/configuration/packages.yaml +++ b/share/spack/qa/configuration/packages.yaml @@ -2,12 +2,25 @@ packages: cmake: buildable: False paths: - cmake@2.8.12.2: /usr + cmake@3.12.4: /usr r: buildable: False paths: - r@3.0.2: /usr + r@3.4.4: /usr perl: buildable: False paths: - perl@5.18.2: /usr + perl@5.26.1: /usr + findutils: + buildable: False + paths: + findutils@4.6.0: /usr + openssl: + buildable: False + paths: + openssl@1.1.1: /usr + libpciaccess: + buildable: False + paths: + libpciaccess@0.13.5: /usr + diff --git a/share/spack/qa/run-bootstrap-tests b/share/spack/qa/run-bootstrap-tests index 346122c529..9532d2d801 100755 --- a/share/spack/qa/run-bootstrap-tests +++ b/share/spack/qa/run-bootstrap-tests @@ -1,6 +1,6 @@ #!/bin/bash -e # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/qa/run-build-tests b/share/spack/qa/run-build-tests index 99a66db49c..c714c59440 100755 --- a/share/spack/qa/run-build-tests +++ b/share/spack/qa/run-build-tests @@ -1,6 +1,6 @@ #!/bin/bash -e # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/qa/run-doc-tests b/share/spack/qa/run-doc-tests index 2a4930bf29..eeba12d8d6 100755 --- a/share/spack/qa/run-doc-tests +++ b/share/spack/qa/run-doc-tests @@ -1,6 +1,6 @@ #!/bin/bash -e # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/qa/run-docker-tests b/share/spack/qa/run-docker-tests deleted file mode 100755 index 769384c90e..0000000000 --- a/share/spack/qa/run-docker-tests +++ /dev/null @@ -1,45 +0,0 @@ -#!/bin/bash -e -# -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -# -# Description: -# Runs Spack docker tests. This builds a docker image for each of the -# configurations in share/spack/docker/config. -# -# Usage: -# run-docker-tests -# - -__login_attempted=0 -__login_success=1 -ensure_docker_login() { - if [ "$__login_attempted" '!=' '0' ] ; then - return $__login_success - fi - - echo "$DOCKER_PASSWORD" | \ - docker login -u "$DOCKER_USERNAME" --password-stdin - - if [ $? '=' '0' ] ; then - __login_success=0 - fi - - __login_attempted=1 - return $__login_success -} - -this_dir=$(cd $(dirname $0) && pwd) -SPACK_BIN="${this_dir}/../../../bin/spack" - -# packages.spack.io service -${SPACK_BIN} list --format version_json > ${this_dir}/../packages/packages.json -./share/spack/packages/build-image.sh -if [ "$TEST_SUITE" '=' "docker" -a \ - "$TRAVIS_EVENT_TYPE" != "pull_request" ] && ensure_docker_login ; then - ./share/spack/packages/push-image.sh -fi - diff --git a/share/spack/qa/run-flake8-tests b/share/spack/qa/run-flake8-tests index 33946868ef..d6077fceb8 100755 --- a/share/spack/qa/run-flake8-tests +++ b/share/spack/qa/run-flake8-tests @@ -1,6 +1,6 @@ #!/bin/bash -e # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/qa/run-unit-tests b/share/spack/qa/run-unit-tests index 11f3ac1fcb..52748dacdf 100755 --- a/share/spack/qa/run-unit-tests +++ b/share/spack/qa/run-unit-tests @@ -1,6 +1,6 @@ #!/bin/bash -e # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,7 +23,7 @@ ORIGINAL_PATH="$PATH" . "$(dirname $0)/setup.sh" -check_dependencies ${coverage} git hg svn +check_dependencies $coverage git hg svn # Move to root directory of Spack # Allows script to be run from anywhere @@ -46,7 +46,7 @@ extra_args="" if [[ -n "$@" ]]; then extra_args="-k $@" fi -${coverage_run} bin/spack test -x --verbose "$extra_args" +$coverage_run bin/spack test -x --verbose "$extra_args" #----------------------------------------------------------- # Run tests for setup-env.sh @@ -57,15 +57,18 @@ export PATH="$ORIGINAL_PATH" unset spack # start in the spack root directory -cd $SPACK_ROOT +cd "$SPACK_ROOT" # Run bash tests with coverage enabled, but pipe output to /dev/null # because it seems that kcov seems to undo the script's redirection if [ "$BASH_COVERAGE" = true ]; then - ${QA_DIR}/bashcov ${QA_DIR}/setup-env-test.sh &> /dev/null + "$QA_DIR/bashcov" "$QA_DIR/setup-env-test.sh" &> /dev/null + "$QA_DIR/bashcov" "$QA_DIR/completion-test.sh" &> /dev/null fi # run the test scripts for their output (these will print nicely) -bash ${QA_DIR}/setup-env-test.sh -zsh ${QA_DIR}/setup-env-test.sh -dash ${QA_DIR}/setup-env-test.sh +bash "$QA_DIR/setup-env-test.sh" +zsh "$QA_DIR/setup-env-test.sh" +dash "$QA_DIR/setup-env-test.sh" + +bash "$QA_DIR/completion-test.sh" diff --git a/share/spack/qa/setup-env-test.sh b/share/spack/qa/setup-env-test.sh index e16e31fffb..da4fb9657d 100755 --- a/share/spack/qa/setup-env-test.sh +++ b/share/spack/qa/setup-env-test.sh @@ -1,6 +1,6 @@ #!/bin/sh # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,159 +12,11 @@ # in any of these shells. # -# ------------------------------------------------------------------------ -# Functions for color output. -# ------------------------------------------------------------------------ - -# Colors for output -red='\033[1;31m' -cyan='\033[1;36m' -green='\033[1;32m' -reset='\033[0m' - -echo_red() { - printf "${red}$*${reset}\n" -} - -echo_green() { - printf "${green}$*${reset}\n" -} - -echo_msg() { - printf "${cyan}$*${reset}\n" -} - -# ------------------------------------------------------------------------ -# Generic functions for testing shell code. -# ------------------------------------------------------------------------ - -# counts of test successes and failures. -success=0 -errors=0 - -# Print out a header for a group of tests. -title() { - echo - echo_msg "$@" - echo_msg "---------------------------------" -} - -# echo FAIL in red text; increment failures -fail() { - echo_red FAIL - errors=$((errors+1)) -} - -# -# Echo SUCCESS in green; increment successes -# -pass() { - echo_green SUCCESS - success=$((success+1)) -} - -# -# Run a command and suppress output unless it fails. -# On failure, echo the exit code and output. -# -succeeds() { - printf "'%s' succeeds ... " "$*" - output=$($* 2>&1) - err="$?" - - if [ "$err" != 0 ]; then - fail - echo_red "Command failed with error $err." - if [ -n "$output" ]; then - echo_msg "Output:" - echo "$output" - else - echo_msg "No output." - fi - else - pass - fi -} - -# -# Run a command and suppress output unless it succeeds. -# If the command succeeds, echo the output. -# -fails() { - printf "'%s' fails ... " "$*" - output=$("$@" 2>&1) - err="$?" - - if [ "$err" = 0 ]; then - fail - echo_red "Command failed with error $err." - if [ -n "$output" ]; then - echo_msg "Output:" - echo "$output" - else - echo_msg "No output." - fi - else - pass - fi -} - -# -# Ensure that a string is in the output of a command. -# Suppresses output on success. -# On failure, echo the exit code and output. -# -contains() { - string="$1" - shift - - printf "'%s' output contains '$string' ... " "$*" - output=$("$@" 2>&1) - err="$?" - - if [ "${output#*$string}" = "${output}" ]; then - fail - echo_red "Command exited with error $err." - echo_red "'$string' was not in output." - if [ -n "$output" ]; then - echo_msg "Output:" - echo "$output" - else - echo_msg "No output." - fi - else - pass - fi -} - -# -# Ensure that a variable is set. -# -is_set() { - printf "'%s' is set ... " "$1" - if eval "[ -z \${${1:-}+x} ]"; then - fail - echo_msg "$1 was not set!" - else - pass - fi -} - -# -# Ensure that a variable is not set. -# Fails and prints the value of the variable if it is set. -# -is_not_set() { - printf "'%s' is not set ... " "$1" - if eval "[ ! -z \${${1:-}+x} ]"; then - fail - echo_msg "$1 was set:" - echo " $1" - else - pass - fi -} +export QA_DIR=$(dirname "$0") +export SHARE_DIR=$(cd "$QA_DIR/.." && pwd) +export SPACK_ROOT=$(cd "$QA_DIR/../../.." && pwd) +. "$QA_DIR/test-framework.sh" # ----------------------------------------------------------------------- # Instead of invoking the module commands, we print the @@ -184,28 +36,28 @@ module() { # Make sure no environment is active unset SPACK_ENV -# fail on undefined variables +# Fail on undefined variables set -u # Source setup-env.sh before tests -. share/spack/setup-env.sh +. "$SHARE_DIR/setup-env.sh" -# bash should expand aliases even when non-interactive +# Bash should expand aliases even when non-interactive if [ -n "${BASH:-}" ]; then shopt -s expand_aliases fi title "Testing setup-env.sh with $_sp_shell" -# spack command is now avaialble +# Spack command is now available succeeds which spack -# mock cd command (intentionally define only AFTER setup-env.sh) +# Mock cd command (intentionally define only AFTER setup-env.sh) cd() { echo cd "$@" } -# create a fake mock package install and store its location for later +# Create a fake mock package install and store its location for later title "Setup" echo "Creating a mock package installation" spack -m install --fake a @@ -215,44 +67,21 @@ a_module=$(spack -m module tcl find a) b_install=$(spack location -i b) b_module=$(spack -m module tcl find b) -# create a test environment for tesitng environment commands +# Create a test environment for testing environment commands echo "Creating a mock environment" spack env create spack_test_env test_env_location=$(spack location -e spack_test_env) -# ensure that we uninstall b on exit +# Ensure that we uninstall b on exit cleanup() { - if [ "$?" != 0 ]; then - trapped_error=true - else - trapped_error=false - fi - echo "Removing test environment before exiting." - spack env deactivate 2>1 > /dev/null + spack env deactivate 2>&1 > /dev/null spack env rm -y spack_test_env title "Cleanup" echo "Removing test packages before exiting." spack -m uninstall -yf b a - - echo - echo "$success tests succeeded." - echo "$errors tests failed." - - if [ "$trapped_error" = true ]; then - echo "Exited due to an error." - fi - - if [ "$errors" = 0 ] && [ "$trapped_error" = false ]; then - pass - exit 0 - else - fail - exit 1 - fi } -trap cleanup EXIT # ----------------------------------------------------------------------- # Test all spack commands with special env support @@ -275,20 +104,25 @@ contains "usage: spack module " spack -m module --help contains "usage: spack module " spack -m module title 'Testing `spack load`' -contains "module load $b_module" spack -m load b +contains "export LD_LIBRARY_PATH=$(spack -m location -i b)/lib" spack -m load --only package --sh b +succeeds spack -m load b fails spack -m load -l -contains "module load -l --arg $b_module" spack -m load -l --arg b -contains "module load $b_module $a_module" spack -m load -r a -contains "module load $b_module $a_module" spack -m load --dependencies a +# test a variable MacOS clears and one it doesn't for recursive loads +contains "export LD_LIBRARY_PATH=$(spack -m location -i a)/lib:$(spack -m location -i b)/lib" spack -m load --sh a +contains "export LIBRARY_PATH=$(spack -m location -i a)/lib:$(spack -m location -i b)/lib" spack -m load --sh a +succeeds spack -m load --only dependencies a +succeeds spack -m load --only package a fails spack -m load d contains "usage: spack load " spack -m load -h contains "usage: spack load " spack -m load -h d contains "usage: spack load " spack -m load --help title 'Testing `spack unload`' -contains "module unload $b_module" spack -m unload b +spack -m load b a # setup +succeeds spack -m unload b +succeeds spack -m unload --all +spack -m unload --all # cleanup fails spack -m unload -l -contains "module unload -l --arg $b_module" spack -m unload -l --arg b fails spack -m unload d contains "usage: spack unload " spack -m unload -h contains "usage: spack unload " spack -m unload -h d diff --git a/share/spack/qa/setup.sh b/share/spack/qa/setup.sh index 3ff226d057..61fb2a7706 100755 --- a/share/spack/qa/setup.sh +++ b/share/spack/qa/setup.sh @@ -1,6 +1,6 @@ #!/bin/bash -e # -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/qa/test-framework.sh b/share/spack/qa/test-framework.sh new file mode 100755 index 0000000000..14b58bbecf --- /dev/null +++ b/share/spack/qa/test-framework.sh @@ -0,0 +1,195 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +# +# A testing framework for any POSIX-compatible shell. +# + +# ------------------------------------------------------------------------ +# Functions for color output. +# ------------------------------------------------------------------------ + +# Colors for output +red='\033[1;31m' +cyan='\033[1;36m' +green='\033[1;32m' +reset='\033[0m' + +echo_red() { + printf "${red}$*${reset}\n" +} + +echo_green() { + printf "${green}$*${reset}\n" +} + +echo_msg() { + printf "${cyan}$*${reset}\n" +} + +# ------------------------------------------------------------------------ +# Generic functions for testing shell code. +# ------------------------------------------------------------------------ + +# counts of test successes and failures. +success=0 +errors=0 + +# Print out a header for a group of tests. +title() { + echo + echo_msg "$@" + echo_msg "---------------------------------" +} + +# echo FAIL in red text; increment failures +fail() { + echo_red FAIL + errors=$((errors+1)) +} + +# +# Echo SUCCESS in green; increment successes +# +pass() { + echo_green SUCCESS + success=$((success+1)) +} + +# +# Run a command and suppress output unless it fails. +# On failure, echo the exit code and output. +# +succeeds() { + printf "'%s' succeeds ... " "$*" + output=$("$@" 2>&1) + err="$?" + + if [ "$err" != 0 ]; then + fail + echo_red "Command failed with error $err." + if [ -n "$output" ]; then + echo_msg "Output:" + echo "$output" + else + echo_msg "No output." + fi + else + pass + fi +} + +# +# Run a command and suppress output unless it succeeds. +# If the command succeeds, echo the output. +# +fails() { + printf "'%s' fails ... " "$*" + output=$("$@" 2>&1) + err="$?" + + if [ "$err" = 0 ]; then + fail + echo_red "Command failed with error $err." + if [ -n "$output" ]; then + echo_msg "Output:" + echo "$output" + else + echo_msg "No output." + fi + else + pass + fi +} + +# +# Ensure that a string is in the output of a command. +# Suppresses output on success. +# On failure, echo the exit code and output. +# +contains() { + string="$1" + shift + + printf "'%s' output contains '$string' ... " "$*" + output=$("$@" 2>&1) + err="$?" + + if [ "${output#*$string}" = "${output}" ]; then + fail + echo_red "Command exited with error $err." + echo_red "'$string' was not in output." + if [ -n "$output" ]; then + echo_msg "Output:" + echo "$output" + else + echo_msg "No output." + fi + else + pass + fi +} + +# +# Ensure that a variable is set. +# +is_set() { + printf "'%s' is set ... " "$1" + if eval "[ -z \${${1:-}+x} ]"; then + fail + echo_msg "$1 was not set!" + else + pass + fi +} + +# +# Ensure that a variable is not set. +# Fails and prints the value of the variable if it is set. +# +is_not_set() { + printf "'%s' is not set ... " "$1" + if eval "[ ! -z \${${1:-}+x} ]"; then + fail + echo_msg "$1 was set:" + echo " $1" + else + pass + fi +} + +# +# Report the number of tests that succeeded and failed on exit. +# +teardown() { + if [ "$?" != 0 ]; then + trapped_error=true + else + trapped_error=false + fi + + if type cleanup &> /dev/null + then + cleanup + fi + + echo + echo "$success tests succeeded." + echo "$errors tests failed." + + if [ "$trapped_error" = true ]; then + echo "Exited due to an error." + fi + + if [ "$errors" = 0 ] && [ "$trapped_error" = false ]; then + pass + exit 0 + else + fail + exit 1 + fi +} + +trap teardown EXIT diff --git a/share/spack/setup-env.csh b/share/spack/setup-env.csh index b49597918c..67357c94e4 100755 --- a/share/spack/setup-env.csh +++ b/share/spack/setup-env.csh @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index d5cad059a6..207e9c4a80 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -40,6 +40,16 @@ ######################################################################## spack() { + # Store LD_LIBRARY_PATH variables from spack shell function + # This is necessary because MacOS System Integrity Protection clears + # (DY?)LD_LIBRARY_PATH variables on process start. + if [ -n "${LD_LIBRARY_PATH-}" ]; then + export SPACK_LD_LIBRARY_PATH=$LD_LIBRARY_PATH + fi + if [ -n "${DYLD_LIBRARY_PATH-}" ]; then + export SPACK_DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH + fi + # Zsh does not do word splitting by default, this enables it for this # function only if [ -n "${ZSH_VERSION:-}" ]; then @@ -141,41 +151,22 @@ spack() { return ;; "load"|"unload") - # Shift any other args for use off before parsing spec. - _sp_subcommand_args="" - _sp_module_args="" - while [ "${1#-}" != "${1}" ]; do - if [ "$1" = "-h" ] || [ "$1" = "--help" ]; then - command spack $_sp_flags $_sp_subcommand $_sp_subcommand_args "$@" - return - elif [ "$1" = "-r" ] || [ "$1" = "--dependencies" ]; then - _sp_subcommand_args="$_sp_subcommand_args $1" - else - _sp_module_args="$_sp_module_args $1" - fi - shift - done - - # Here the user has run use or unuse with a spec. Find a matching - # spec using 'spack module find', then use the appropriate module - # tool's commands to add/remove the result from the environment. - # If spack module command comes back with an error, do nothing. - case $_sp_subcommand in - "load") - if _sp_full_spec=$(command spack $_sp_flags module tcl find $_sp_subcommand_args "$@"); then - module load $_sp_module_args $_sp_full_spec - else - $(exit 1) - fi - ;; - "unload") - if _sp_full_spec=$(command spack $_sp_flags module tcl find $_sp_subcommand_args "$@"); then - module unload $_sp_module_args $_sp_full_spec - else - $(exit 1) - fi - ;; - esac + # get --sh, --csh, --help, or -h arguments + # space is important for -h case to differentiate between `-h` + # argument and specs with "-h" in package name or variant settings + _a=" $@" + if [ "${_a#* --sh}" != "$_a" ] || \ + [ "${_a#* --csh}" != "$_a" ] || \ + [ "${_a#* -h}" != "$_a" ] || \ + [ "${_a#* --help}" != "$_a" ]; + then + # just execute the command if --sh or --csh are provided + # or if the -h or --help arguments are provided + command spack $_sp_flags $_sp_subcommand "$@" + else + eval $(command spack $_sp_flags $_sp_subcommand --sh "$@" || \ + echo "return 1") # return 1 if spack command fails + fi ;; *) command spack $_sp_flags $_sp_subcommand "$@" @@ -215,11 +206,14 @@ _spack_pathadd() { } -# # Determine which shell is being used -# _spack_determine_shell() { - if [ -n "${BASH:-}" ]; then + if [ -f "/proc/$$/exe" ]; then + # If procfs is present this seems a more reliable + # way to detect the current shell + _sp_exe=$(readlink /proc/$$/exe) + basename ${_sp_exe} + elif [ -n "${BASH:-}" ]; then echo bash elif [ -n "${ZSH_NAME:-}" ]; then echo zsh @@ -333,7 +327,7 @@ fi; _sp_multi_pathadd() { local IFS=':' if [ "$_sp_shell" = zsh ]; then - setopt sh_word_split + emulate -L sh fi for pth in $2; do for systype in ${_sp_compatible_sys_types}; do diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash index 8597cd3d7e..e6b7529452 100755 --- a/share/spack/spack-completion.bash +++ b/share/spack/spack-completion.bash @@ -1,19 +1,44 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -# The following global variables are used/set by Bash programmable completion -# COMP_CWORD: An index into ${COMP_WORDS} of the word containing the -# current cursor position -# COMP_LINE: The current command line -# COMP_WORDS: an array containing individual command arguments typed so far -# COMPREPLY: an array containing possible completions as a result of your -# function +# NOTE: spack-completion.bash is auto-generated by: +# +# $ spack commands --aliases --format=bash +# --header=bash/spack-completion.in --update=spack-completion.bash +# +# Please do not manually modify this file. + + +# The following global variables are set by Bash programmable completion: +# +# COMP_CWORD: An index into ${COMP_WORDS} of the word containing the +# current cursor position +# COMP_KEY: The key (or final key of a key sequence) used to invoke +# the current completion function +# COMP_LINE: The current command line +# COMP_POINT: The index of the current cursor position relative to the +# beginning of the current command +# COMP_TYPE: Set to an integer value corresponding to the type of +# completion attempted that caused a completion function +# to be called +# COMP_WORDBREAKS: The set of characters that the readline library treats +# as word separators when performing word completion +# COMP_WORDS: An array variable consisting of the individual words in +# the current command line +# +# The following global variable is used by Bash programmable completion: +# +# COMPREPLY: An array variable from which bash reads the possible +# completions generated by a shell function invoked by the +# programmable completion facility +# +# See `man bash` for more details. # Bash programmable completion for Spack -function _bash_completion_spack { +_bash_completion_spack() { # In all following examples, let the cursor be denoted by brackets, i.e. [] # For our purposes, flags should not affect tab completion. For instance, @@ -46,7 +71,7 @@ function _bash_completion_spack { # Since we have removed all words after COMP_CWORD, we can safely assume # that COMP_CWORD_NO_FLAGS is simply the index of the last element - local COMP_CWORD_NO_FLAGS=$(( ${#COMP_WORDS_NO_FLAGS[@]} - 1 )) + local COMP_CWORD_NO_FLAGS=$((${#COMP_WORDS_NO_FLAGS[@]} - 1)) # There is no guarantee that the cursor is at the end of the command line # when tab completion is envoked. For example, in the following situation: @@ -59,8 +84,7 @@ function _bash_completion_spack { # which is true if the current word starts with '-' or if the cursor is # not at the end of the line. local list_options=false - if [[ "${COMP_WORDS[$COMP_CWORD]}" == -* || \ - "$COMP_CWORD" -ne "${#COMP_WORDS[@]}-1" ]] + if [[ "${COMP_WORDS[$COMP_CWORD]}" == -* || "$COMP_POINT" -ne "${#COMP_LINE}" ]] then list_options=true fi @@ -80,1347 +104,1496 @@ function _bash_completion_spack { # should list flag completions. local cur=${COMP_WORDS_NO_FLAGS[$COMP_CWORD_NO_FLAGS]} - local prev=${COMP_WORDS_NO_FLAGS[$COMP_CWORD_NO_FLAGS-1]} - #_test_vars + # If the cursor is in the middle of the line, like: + # `spack -d [] install` + # COMP_WORDS will not contain the empty character, so we have to add it. + if [[ "${COMP_LINE:$COMP_POINT:1}" == " " ]] + then + cur="" + fi + + # Uncomment this line to enable logging + #_test_vars >> temp # Make sure function exists before calling it if [[ "$(type -t $subfunction)" == "function" ]] then - COMPREPLY=($($subfunction)) + $subfunction + COMPREPLY=($(compgen -W "$SPACK_COMPREPLY" -- "$cur")) + fi +} + +# Helper functions for subcommands +# Results of each query are cached via environment variables + +_subcommands() { + if [[ -z "${SPACK_SUBCOMMANDS:-}" ]] + then + SPACK_SUBCOMMANDS="$(spack commands)" + fi + SPACK_COMPREPLY="$SPACK_SUBCOMMANDS" +} + +_all_packages() { + if [[ -z "${SPACK_ALL_PACKAGES:-}" ]] + then + SPACK_ALL_PACKAGES="$(spack list)" + fi + SPACK_COMPREPLY="$SPACK_ALL_PACKAGES" +} + +_all_resource_hashes() { + if [[ -z "${SPACK_ALL_RESOURCES_HASHES:-}" ]] + then + SPACK_ALL_RESOURCE_HASHES="$(spack resource list --only-hashes)" + fi + SPACK_COMPREPLY="$SPACK_ALL_RESOURCE_HASHES" +} + +_installed_packages() { + if [[ -z "${SPACK_INSTALLED_PACKAGES:-}" ]] + then + SPACK_INSTALLED_PACKAGES="$(spack --color=never find --no-groups)" + fi + SPACK_COMPREPLY="$SPACK_INSTALLED_PACKAGES" +} + +_installed_compilers() { + if [[ -z "${SPACK_INSTALLED_COMPILERS:-}" ]] + then + SPACK_INSTALLED_COMPILERS="$(spack compilers | egrep -v "^(-|=)")" + fi + SPACK_COMPREPLY="$SPACK_INSTALLED_COMPILERS" +} + +_providers() { + if [[ -z "${SPACK_PROVIDERS:-}" ]] + then + SPACK_PROVIDERS="$(spack providers)" + fi + SPACK_COMPREPLY="$SPACK_PROVIDERS" +} + +_mirrors() { + if [[ -z "${SPACK_MIRRORS:-}" ]] + then + SPACK_MIRRORS="$(spack mirror list | awk '{print $1}')" + fi + SPACK_COMPREPLY="$SPACK_MIRRORS" +} + +_repos() { + if [[ -z "${SPACK_REPOS:-}" ]] + then + SPACK_REPOS="$(spack repo list | awk '{print $1}')" + fi + SPACK_COMPREPLY="$SPACK_REPOS" +} + +_tests() { + if [[ -z "${SPACK_TESTS:-}" ]] + then + SPACK_TESTS="$(spack test -l)" + fi + SPACK_COMPREPLY="$SPACK_TESTS" +} + +_environments() { + if [[ -z "${SPACK_ENVIRONMENTS:-}" ]] + then + SPACK_ENVIRONMENTS="$(spack env list)" + fi + SPACK_COMPREPLY="$SPACK_ENVIRONMENTS" +} + +_keys() { + if [[ -z "${SPACK_KEYS:-}" ]] + then + SPACK_KEYS="$(spack gpg list)" + fi + SPACK_COMPREPLY="$SPACK_KEYS" +} + +_config_sections() { + if [[ -z "${SPACK_CONFIG_SECTIONS:-}" ]] + then + SPACK_CONFIG_SECTIONS="$(spack config list)" + fi + SPACK_COMPREPLY="$SPACK_CONFIG_SECTIONS" +} + +_extensions() { + if [[ -z "${SPACK_EXTENSIONS:-}" ]] + then + SPACK_EXTENSIONS="aspell go-bootstrap go icedtea jdk kim-api lua matlab mofem-cephas octave openjdk perl python r ruby rust tcl yorick" + fi + SPACK_COMPREPLY="$SPACK_EXTENSIONS" +} + +# Testing functions + +# Function for unit testing tab completion +# Syntax: _spack_completions spack install py- +_spack_completions() { + local COMP_CWORD COMP_KEY COMP_LINE COMP_POINT COMP_TYPE COMP_WORDS COMPREPLY + + # Set each variable the way bash would + COMP_LINE="$*" + COMP_POINT=${#COMP_LINE} + COMP_WORDS=("$@") + if [[ ${COMP_LINE: -1} == ' ' ]] + then + COMP_WORDS+=('') + fi + COMP_CWORD=$((${#COMP_WORDS[@]} - 1)) + COMP_KEY=9 # ASCII 09: Horizontal Tab + COMP_TYPE=64 # ASCII 64: '@', to list completions if the word is not unmodified + + # Run Spack's tab completion function + _bash_completion_spack + + # Return the result + echo "${COMPREPLY[@]:-}" +} + +# Log the environment variables used +# Syntax: _test_vars >> temp +_test_vars() { + echo "-----------------------------------------------------" + echo "Variables set by bash:" + echo + echo "COMP_LINE: '$COMP_LINE'" + echo "# COMP_LINE: '${#COMP_LINE}'" + echo "COMP_WORDS: $(_pretty_print COMP_WORDS[@])" + echo "# COMP_WORDS: '${#COMP_WORDS[@]}'" + echo "COMP_CWORD: '$COMP_CWORD'" + echo "COMP_KEY: '$COMP_KEY'" + echo "COMP_POINT: '$COMP_POINT'" + echo "COMP_TYPE: '$COMP_TYPE'" + echo "COMP_WORDBREAKS: '$COMP_WORDBREAKS'" + echo + echo "Intermediate variables:" + echo + echo "COMP_WORDS_NO_FLAGS: $(_pretty_print COMP_WORDS_NO_FLAGS[@])" + echo "# COMP_WORDS_NO_FLAGS: '${#COMP_WORDS_NO_FLAGS[@]}'" + echo "COMP_CWORD_NO_FLAGS: '$COMP_CWORD_NO_FLAGS'" + echo + echo "Subfunction: '$subfunction'" + if $list_options + then + echo "List options: 'True'" + else + echo "List options: 'False'" fi + echo "Current word: '$cur'" +} + +# Pretty-prints one or more arrays +# Syntax: _pretty_print array1[@] ... +_pretty_print() { + for arg in $@ + do + local array=("${!arg}") + printf "$arg: [" + printf "'%s'" "${array[0]}" + printf ", '%s'" "${array[@]:1}" + echo "]" + done } +complete -o bashdefault -o default -F _bash_completion_spack spack + # Spack commands +# +# Everything below here is auto-generated. -function _spack { +_spack() { if $list_options then - compgen -W "-h --help -H --all-help --color -C --config-scope - -d --debug --timestamp --pdb -e --env -D --env-dir - -E --no-env --use-env-repo -k --insecure - -l --enable-locks -L --disable-locks -m --mock - -p --profile --sorted-profile --lines -v --verbose - --stacktrace -V --version --print-shell-vars" -- "$cur" + SPACK_COMPREPLY="-h --help -H --all-help --color -C --config-scope -d --debug --timestamp --pdb -e --env -D --env-dir -E --no-env --use-env-repo -k --insecure -l --enable-locks -L --disable-locks -m --mock -p --profile --sorted-profile --lines -v --verbose --stacktrace -V --version --print-shell-vars" else - compgen -W "$(_subcommands)" -- "$cur" + SPACK_COMPREPLY="activate add arch blame bootstrap build build-env buildcache cd checksum ci clean clone commands compiler compilers concretize config configure containerize create deactivate debug dependencies dependents deprecate dev-build diy docs edit env extensions fetch find flake8 gc gpg graph help info install license list load location log-parse maintainers mirror module patch pkg providers pydoc python reindex remove rm repo resource restage setup spec stage test uninstall unload upload-s3 url verify versions view" fi } -function _spack_activate { +_spack_activate() { if $list_options then - compgen -W "-h --help -f --force -v --view" -- "$cur" + SPACK_COMPREPLY="-h --help -f --force -v --view" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_add { +_spack_add() { if $list_options then - compgen -W "-h --help -l --list-name" -- "$cur" + SPACK_COMPREPLY="-h --help -l --list-name" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_arch { - compgen -W "-h --help --known-targets -p --platform - -o --operating-system -t --target -f --frontend - -b --backend" -- "$cur" +_spack_arch() { + SPACK_COMPREPLY="-h --help --known-targets -p --platform -o --operating-system -t --target -f --frontend -b --backend" } -function _spack_blame { +_spack_blame() { if $list_options then - compgen -W "-h --help -t --time -p --percent -g --git" -- "$cur" + SPACK_COMPREPLY="-h --help -t --time -p --percent -g --git" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_bootstrap { - compgen -W "-h --help -j --jobs --keep-prefix --keep-stage - -n --no-checksum -v --verbose --use-cache --no-cache - --cache-only --clean --dirty" -- "$cur" +_spack_bootstrap() { + SPACK_COMPREPLY="-h --help -j --jobs --keep-prefix --keep-stage -n --no-checksum -v --verbose --use-cache --no-cache --cache-only --clean --dirty" } -function _spack_build { +_spack_build() { if $list_options then - compgen -W "-h --help -v --verbose" -- "$cur" + SPACK_COMPREPLY="-h --help -v --verbose" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_build_env { +_spack_build_env() { if $list_options then - compgen -W "-h --help --clean --dirty --dump --pickle" -- "$cur" + SPACK_COMPREPLY="-h --help --clean --dirty --dump --pickle" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_buildcache { +_spack_buildcache() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "create install list keys preview check download - get-buildcache-name save-yaml copy update-index" -- "$cur" + SPACK_COMPREPLY="create install list keys preview check download get-buildcache-name save-yaml copy update-index" fi } -function _spack_buildcache_create { +_spack_buildcache_create() { if $list_options then - compgen -W "-h --help -r --rel -f --force -u --unsigned - -a --allow-root -k --key -d --directory - --no-rebuild-index -y --spec-yaml --no-deps" -- "$cur" + SPACK_COMPREPLY="-h --help -r --rel -f --force -u --unsigned -a --allow-root -k --key -d --directory --no-rebuild-index -y --spec-yaml --no-deps" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_buildcache_install { +_spack_buildcache_install() { if $list_options then - compgen -W "-h --help -f --force -m --multiple -a --allow-root - -u --unsigned" -- "$cur" + SPACK_COMPREPLY="-h --help -f --force -m --multiple -a --allow-root -u --unsigned" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_buildcache_list { +_spack_buildcache_list() { if $list_options then - compgen -W "-h --help -l --long -L --very-long -v --variants - -f --force" -- "$cur" + SPACK_COMPREPLY="-h --help -l --long -L --very-long -v --variants -f --force -a --allarch" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_buildcache_keys { - compgen -W "-h --help -i --install -t --trust -f --force" -- "$cur" +_spack_buildcache_keys() { + SPACK_COMPREPLY="-h --help -i --install -t --trust -f --force" } -function _spack_buildcache_preview { +_spack_buildcache_preview() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_buildcache_check { - compgen -W "-h --help -m --mirror-url -o --output-file --scope - -s --spec -y --spec-yaml --rebuild-on-error" -- "$cur" +_spack_buildcache_check() { + SPACK_COMPREPLY="-h --help -m --mirror-url -o --output-file --scope -s --spec -y --spec-yaml --rebuild-on-error" } -function _spack_buildcache_download { - compgen -W "-h --help -s --spec -y --spec-yaml -p --path - -c --require-cdashid" -- "$cur" +_spack_buildcache_download() { + SPACK_COMPREPLY="-h --help -s --spec -y --spec-yaml -p --path -c --require-cdashid" } -function _spack_buildcache_get_buildcache_name { - compgen -W "-h --help -s --spec -y --spec-yaml" -- "$cur" +_spack_buildcache_get_buildcache_name() { + SPACK_COMPREPLY="-h --help -s --spec -y --spec-yaml" } -function _spack_buildcache_save_yaml { - compgen -W "-h --help --root-spec --root-spec-yaml -s --specs - -y --yaml-dir" -- "$cur" +_spack_buildcache_save_yaml() { + SPACK_COMPREPLY="-h --help --root-spec --root-spec-yaml -s --specs -y --yaml-dir" } -function _spack_buildcache_copy { - compgen -W "-h --help --base-dir --spec-yaml --destination-url" -- "$cur" +_spack_buildcache_copy() { + SPACK_COMPREPLY="-h --help --base-dir --spec-yaml --destination-url" } -function _spack_buildcache_update_index { - compgen -W "-h --help -d --mirror-url" -- "$cur" +_spack_buildcache_update_index() { + SPACK_COMPREPLY="-h --help -d --mirror-url" } -function _spack_cd { +_spack_cd() { if $list_options then - compgen -W "-h --help -m --module-dir -r --spack-root -i --install-dir - -p --package-dir -P --packages -s --stage-dir -S --stages - -b --build-dir -e --env" -- "$cur" + SPACK_COMPREPLY="-h --help -m --module-dir -r --spack-root -i --install-dir -p --package-dir -P --packages -s --stage-dir -S --stages -b --build-dir -e --env" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_checksum { +_spack_checksum() { if $list_options then - compgen -W "-h --help --keep-stage" -- "$cur" + SPACK_COMPREPLY="-h --help --keep-stage" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_clean { +_spack_ci() { if $list_options then - compgen -W "-h --help -s --stage -d --downloads - -m --misc-cache -p --python-cache -a --all" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "$(_all_packages)" -- "$cur" + SPACK_COMPREPLY="start generate pushyaml rebuild" fi } -function _spack_clone { +_spack_ci_start() { + SPACK_COMPREPLY="-h --help --output-file --copy-to --spack-repo --spack-ref --downstream-repo --branch-name --commit-sha" +} + +_spack_ci_generate() { + SPACK_COMPREPLY="-h --help --output-file --copy-to --spack-repo --spack-ref" +} + +_spack_ci_pushyaml() { + SPACK_COMPREPLY="-h --help --downstream-repo --branch-name --commit-sha" +} + +_spack_ci_rebuild() { + SPACK_COMPREPLY="-h --help" +} + +_spack_clean() { if $list_options then - compgen -W "-h --help -r --remote" -- "$cur" + SPACK_COMPREPLY="-h --help -s --stage -d --downloads -m --misc-cache -p --python-cache -a --all" + else + _all_packages fi } -function _spack_commands { +_spack_clone() { if $list_options then - compgen -W "-h --help --format --header --update" -- "$cur" + SPACK_COMPREPLY="-h --help -r --remote" + else + SPACK_COMPREPLY="" fi } -function _spack_compiler { +_spack_commands() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help --update-completion -a --aliases --format --header --update" else - compgen -W "find add remove rm list info" -- "$cur" + SPACK_COMPREPLY="" fi } -function _spack_compiler_find { +_spack_compiler() { if $list_options then - compgen -W "-h --help --scope" -- "$cur" + SPACK_COMPREPLY="-h --help" + else + SPACK_COMPREPLY="find add remove rm list info" fi } -function _spack_compiler_add { - # Alias to `spack compiler find` - _spack_compiler_find +_spack_compiler_find() { + if $list_options + then + SPACK_COMPREPLY="-h --help --scope" + else + SPACK_COMPREPLY="" + fi } -function _spack_compiler_remove { +_spack_compiler_add() { if $list_options then - compgen -W "-h --help -a --all --scope" -- "$cur" + SPACK_COMPREPLY="-h --help --scope" else - compgen -W "$(_installed_compilers)" -- "$cur" + SPACK_COMPREPLY="" fi } -function _spack_compiler_rm { - # Alias to `spack compiler remove` - _spack_compiler_remove +_spack_compiler_remove() { + if $list_options + then + SPACK_COMPREPLY="-h --help -a --all --scope" + else + _installed_compilers + fi +} + +_spack_compiler_rm() { + if $list_options + then + SPACK_COMPREPLY="-h --help -a --all --scope" + else + _installed_compilers + fi } -function _spack_compiler_list { - compgen -W "-h --help --scope" -- "$cur" +_spack_compiler_list() { + SPACK_COMPREPLY="-h --help --scope" } -function _spack_compiler_info { +_spack_compiler_info() { if $list_options then - compgen -W "-h --help --scope" -- "$cur" + SPACK_COMPREPLY="-h --help --scope" else - compgen -W "$(_installed_compilers)" -- "$cur" + _installed_compilers fi } -function _spack_compilers { - # Alias to `spack compiler list` - _spack_compiler_list +_spack_compilers() { + SPACK_COMPREPLY="-h --help --scope" } -function _spack_concretize { - compgen -W "-h --help -f --force" -- "$cur" +_spack_concretize() { + SPACK_COMPREPLY="-h --help -f --force" } -function _spack_config { +_spack_config() { if $list_options then - compgen -W "-h --help --scope" -- "$cur" + SPACK_COMPREPLY="-h --help --scope" else - compgen -W "get blame edit" -- "$cur" + SPACK_COMPREPLY="get blame edit list" fi } -function _spack_config_get { +_spack_config_get() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "compilers mirrors repos packages modules config - upstreams" -- "$cur" + _config_sections fi } -function _spack_config_blame { +_spack_config_blame() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "compilers mirrors repos packages modules config - upstreams" -- "$cur" + _config_sections fi } -function _spack_config_edit { +_spack_config_edit() { if $list_options then - compgen -W "-h --help --print-file" -- "$cur" + SPACK_COMPREPLY="-h --help --print-file" else - compgen -W "compilers mirrors repos packages modules config - upstreams" -- "$cur" + _config_sections fi } -function _spack_configure { +_spack_config_list() { + SPACK_COMPREPLY="-h --help" +} + +_spack_configure() { if $list_options then - compgen -W "-h --help -v --verbose" -- "$cur" + SPACK_COMPREPLY="-h --help -v --verbose" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_create { +_spack_containerize() { + SPACK_COMPREPLY="-h --help" +} + +_spack_create() { if $list_options then - compgen -W "-h --help --keep-stage -n --name -t --template -r --repo - -N --namespace -f --force --skip-editor" -- "$cur" + SPACK_COMPREPLY="-h --help --keep-stage -n --name -t --template -r --repo -N --namespace -f --force --skip-editor" + else + SPACK_COMPREPLY="" fi } -function _spack_deactivate { +_spack_deactivate() { if $list_options then - compgen -W "-h --help -f --force -v --view -a --all" -- "$cur" + SPACK_COMPREPLY="-h --help -f --force -v --view -a --all" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_debug { +_spack_debug() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "create-db-tarball" -- "$cur" + SPACK_COMPREPLY="create-db-tarball" fi } -function _spack_debug_create_db_tarball { - compgen -W "-h --help" -- "$cur" +_spack_debug_create_db_tarball() { + SPACK_COMPREPLY="-h --help" } -function _spack_dependencies { +_spack_dependencies() { if $list_options then - compgen -W "-h --help -i --installed -t --transitive - --deptype -V --no-expand-virtuals" -- "$cur" + SPACK_COMPREPLY="-h --help -i --installed -t --transitive --deptype -V --no-expand-virtuals" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_dependents { +_spack_dependents() { if $list_options then - compgen -W "-h --help -i --installed -t --transitive" -- "$cur" + SPACK_COMPREPLY="-h --help -i --installed -t --transitive" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_deprecate { +_spack_deprecate() { if $list_options then - compgen -W "-h --help -y --yes-to-all -d --dependencies - -D --no-dependencies -i --install-deprecator - -I --no-install-deprecator -l --link-type" -- "$cur" + SPACK_COMPREPLY="-h --help -y --yes-to-all -d --dependencies -D --no-dependencies -i --install-deprecator -I --no-install-deprecator -l --link-type" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_dev_build { +_spack_dev_build() { if $list_options then - compgen -W "-h --help -j --jobs -d --source-path - -i --ignore-dependencies -n --no-checksum - --keep-prefix --skip-patch -q --quiet -u --until - --clean --dirty" -- "$cur" + SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet -u --until --clean --dirty" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_diy { +_spack_diy() { if $list_options then - compgen -W "-h --help -j --jobs -d --source-path - -i --ignore-dependencies -n --no-checksum - --keep-prefix --skip-patch -q --quiet -u --until - --clean --dirty" -- "$cur" + SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet -u --until --clean --dirty" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_docs { - compgen -W "-h --help" -- "$cur" +_spack_docs() { + SPACK_COMPREPLY="-h --help" } -function _spack_edit { +_spack_edit() { if $list_options then - compgen -W "-h --help -b --build-system -c --command -d --docs - -t --test -m --module -r --repo -N --namespace" -- "$cur" + SPACK_COMPREPLY="-h --help -b --build-system -c --command -d --docs -t --test -m --module -r --repo -N --namespace" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_env { +_spack_env() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "activate deactivate create remove rm list ls - status st loads view" -- "$cur" + SPACK_COMPREPLY="activate deactivate create remove rm list ls status st loads view" fi } -function _spack_env_activate { +_spack_env_activate() { if $list_options then - compgen -W "-h --help --sh --csh -v --with-view - -V --without-view -d --dir -p --prompt" -- "$cur" + SPACK_COMPREPLY="-h --help --sh --csh -v --with-view -V --without-view -d --dir -p --prompt" else - compgen -W "$(_environments)" -- "$cur" + _environments fi } -function _spack_env_deactivate { - compgen -W "-h --help --sh --csh" -- "$cur" +_spack_env_deactivate() { + SPACK_COMPREPLY="-h --help --sh --csh" } -function _spack_env_create { +_spack_env_create() { if $list_options then - compgen -W "-h --help -d --dir --without-view --with-view" -- "$cur" + SPACK_COMPREPLY="-h --help -d --dir --without-view --with-view" + else + _environments fi } -function _spack_env_remove { +_spack_env_remove() { if $list_options then - compgen -W "-h --help -y --yes-to-all" -- "$cur" + SPACK_COMPREPLY="-h --help -y --yes-to-all" else - compgen -W "$(_environments)" -- "$cur" + _environments fi } -function _spack_env_rm { - # Alias to `spack env remove` - _spack_env_remove +_spack_env_rm() { + if $list_options + then + SPACK_COMPREPLY="-h --help -y --yes-to-all" + else + _environments + fi } -function _spack_env_list { - compgen -W "-h --help" -- "$cur" +_spack_env_list() { + SPACK_COMPREPLY="-h --help" } -function _spack_env_ls { - # Alias to `spack env list` - _spack_env_list +_spack_env_ls() { + SPACK_COMPREPLY="-h --help" } -function _spack_env_status { - compgen -W "-h --help" -- "$cur" +_spack_env_status() { + SPACK_COMPREPLY="-h --help" } -function _spack_env_st { - # Alias to `spack env status` - _spack_env_status +_spack_env_st() { + SPACK_COMPREPLY="-h --help" } -function _spack_env_loads { +_spack_env_loads() { if $list_options then - compgen -W "-h --help -m --module-type --input-only -p --prefix - -x --exclude -r --dependencies" -- "$cur" + SPACK_COMPREPLY="-h --help -m --module-type --input-only -p --prefix -x --exclude -r --dependencies" else - compgen -W "$(_environments)" -- "$cur" + _environments fi } -function _spack_env_view { +_spack_env_view() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "regenerate enable disable" -- "$cur" + SPACK_COMPREPLY="" fi } -function _spack_extensions { +_spack_extensions() { if $list_options then - compgen -W "-h --help -l --long -L --very-long -d --deps - -p --paths -s --show -v --view" -- "$cur" + SPACK_COMPREPLY="-h --help -l --long -L --very-long -d --deps -p --paths -s --show -v --view" else - compgen -W "aspell go-bootstrap go icedtea jdk kim-api lua - matlab mofem-cephas octave openjdk perl python r - ruby rust tcl yorick" -- "$cur" + _extensions fi } -function _spack_fetch { +_spack_fetch() { if $list_options then - compgen -W "-h --help -n --no-checksum -m --missing - -D --dependencies" -- "$cur" + SPACK_COMPREPLY="-h --help -n --no-checksum -m --missing -D --dependencies" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_find { +_spack_find() { if $list_options then - compgen -W "-h --help --format --json -d --deps -p --paths - --groups --no-groups -l --long -L --very-long - -t --tags -c --show-concretized -f --show-flags - --show-full-compiler -x --explicit -X --implicit - -u --unknown -m --missing -v --variants - -M --only-missing --deprecated --only-deprecated - -N --namespace --start-date --end-date" -- "$cur" + SPACK_COMPREPLY="-h --help --format --json -d --deps -p --paths --groups --no-groups -l --long -L --very-long -t --tags -c --show-concretized -f --show-flags --show-full-compiler -x --explicit -X --implicit -u --unknown -m --missing -v --variants --loaded -M --only-missing --deprecated --only-deprecated -N --namespace --start-date --end-date" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_flake8 { +_spack_flake8() { if $list_options then - compgen -W "-h --help -b --base -k --keep-temp -a --all -o --output - -r --root-relative -U --no-untracked" -- "$cur" + SPACK_COMPREPLY="-h --help -b --base -k --keep-temp -a --all -o --output -r --root-relative -U --no-untracked" + else + SPACK_COMPREPLY="" fi } -function _spack_gpg { +_spack_gc() { + SPACK_COMPREPLY="-h --help -y --yes-to-all" +} + +_spack_gpg() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "verify trust untrust sign create list init - export" -- "$cur" + SPACK_COMPREPLY="verify trust untrust sign create list init export" fi } -function _spack_gpg_verify { +_spack_gpg_verify() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "$(installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_gpg_trust { +_spack_gpg_trust() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" + else + SPACK_COMPREPLY="" fi } -function _spack_gpg_untrust { +_spack_gpg_untrust() { if $list_options then - compgen -W "-h --help --signing" -- "$cur" + SPACK_COMPREPLY="-h --help --signing" else - compgen -W "$(_keys)" -- "$cur" + _keys fi } -function _spack_gpg_sign { +_spack_gpg_sign() { if $list_options then - compgen -W "-h --help --output --key --clearsign" -- "$cur" + SPACK_COMPREPLY="-h --help --output --key --clearsign" else - compgen -W "$(installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_gpg_create { +_spack_gpg_create() { if $list_options then - compgen -W "-h --help --comment --expires --export" -- "$cur" + SPACK_COMPREPLY="-h --help --comment --expires --export" + else + SPACK_COMPREPLY="" fi } -function _spack_gpg_list { - compgen -W "-h --help --trusted --signing" -- "$cur" +_spack_gpg_list() { + SPACK_COMPREPLY="-h --help --trusted --signing" } -function _spack_gpg_init { - compgen -W "-h --help" -- "$cur" +_spack_gpg_init() { + SPACK_COMPREPLY="-h --help --from" } -function _spack_gpg_export { +_spack_gpg_export() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "$(_keys)" -- "$cur" + _keys fi } -function _spack_graph { +_spack_graph() { if $list_options then - compgen -W "-h --help -a --ascii -d --dot -s --static - -i --installed --deptype" -- "$cur" + SPACK_COMPREPLY="-h --help -a --ascii -d --dot -s --static -i --installed --deptype" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_help { +_spack_help() { if $list_options then - compgen -W "-h --help -a --all --spec" -- "$cur" + SPACK_COMPREPLY="-h --help -a --all --spec" else - compgen -W "$(_subcommands)" -- "$cur" + _subcommands fi } -function _spack_info { +_spack_info() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_install { +_spack_install() { if $list_options then - compgen -W "-h --help --only -u --until -j --jobs --overwrite - --keep-prefix --keep-stage --dont-restage --use-cache - --no-cache --cache-only --show-log-on-error --source - -n --no-checksum -v --verbose --fake --only-concrete - -f --file --clean --dirty --test --run-tests - --log-format --log-file -y --yes-to-all - --cdash-upload-url --cdash-build --cdash-site - --cdash-track --cdash-buildstamp" -- "$cur" + SPACK_COMPREPLY="-h --help --only -u --until -j --jobs --overwrite --keep-prefix --keep-stage --dont-restage --use-cache --no-cache --cache-only --no-check-signature --show-log-on-error --source -n --no-checksum -v --verbose --fake --only-concrete -f --file --clean --dirty --test --run-tests --log-format --log-file --help-cdash --cdash-upload-url --cdash-build --cdash-site --cdash-track --cdash-buildstamp -y --yes-to-all" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_license { +_spack_license() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "list-files verify" -- "$cur" + SPACK_COMPREPLY="list-files verify" fi } -function _spack_license_list_files { - compgen -W "-h --help" -- "$cur" +_spack_license_list_files() { + SPACK_COMPREPLY="-h --help" } -function _spack_license_verify { - compgen -W "-h --help --root" -- "$cur" +_spack_license_verify() { + SPACK_COMPREPLY="-h --help --root" } -function _spack_list { +_spack_list() { if $list_options then - compgen -W "-h --help -d --search-description --format --update - -t --tags" -- "$cur" + SPACK_COMPREPLY="-h --help -d --search-description --format --update -t --tags" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_load { +_spack_load() { if $list_options then - compgen -W "-h --help -r --dependencies" -- "$cur" + SPACK_COMPREPLY="-h --help -r --dependencies --sh --csh --only" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_location { +_spack_location() { if $list_options then - compgen -W "-h --help -m --module-dir -r --spack-root -i --install-dir - -p --package-dir -P --packages -s --stage-dir -S --stages - -b --build-dir -e --env" -- "$cur" + SPACK_COMPREPLY="-h --help -m --module-dir -r --spack-root -i --install-dir -p --package-dir -P --packages -s --stage-dir -S --stages -b --build-dir -e --env" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_log_parse { +_spack_log_parse() { if $list_options then - compgen -W "-h --help --show -c --context -p --profile -w --width - -j --jobs" -- "$cur" + SPACK_COMPREPLY="-h --help --show -c --context -p --profile -w --width -j --jobs" + else + SPACK_COMPREPLY="" fi } -function _spack_maintainers { +_spack_maintainers() { if $list_options then - compgen -W "-h --help --maintained --unmaintained -a --all - --by-user" -- "$cur" + SPACK_COMPREPLY="-h --help --maintained --unmaintained -a --all --by-user" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_mirror { +_spack_mirror() { if $list_options then - compgen -W "-h --help -n --no-checksum" -- "$cur" + SPACK_COMPREPLY="-h --help -n --no-checksum" else - compgen -W "create add remove rm set-url list" -- "$cur" + SPACK_COMPREPLY="create add remove rm set-url list" fi } -function _spack_mirror_create { +_spack_mirror_create() { if $list_options then - compgen -W "-h --help -d --directory -a --all -f --file - -D --dependencies -n --versions-per-spec" -- "$cur" + SPACK_COMPREPLY="-h --help -d --directory -a --all -f --file -D --dependencies -n --versions-per-spec" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_mirror_add { +_spack_mirror_add() { if $list_options then - compgen -W "-h --help --scope" -- "$cur" + SPACK_COMPREPLY="-h --help --scope" + else + _mirrors fi } -function _spack_mirror_remove { +_spack_mirror_remove() { if $list_options then - compgen -W "-h --help --scope" -- "$cur" + SPACK_COMPREPLY="-h --help --scope" else - compgen -W "$(_mirrors)" -- "$cur" + _mirrors fi } -function _spack_mirror_rm { - # Alias to `spack mirror remove` - _spack_mirror_remove +_spack_mirror_rm() { + if $list_options + then + SPACK_COMPREPLY="-h --help --scope" + else + _mirrors + fi } -function _spack_mirror_set_url { +_spack_mirror_set_url() { if $list_options then - compgen -W "-h --help --push --scope" -- "$cur" + SPACK_COMPREPLY="-h --help --push --scope" else - compgen -W "$(_mirrors)" -- "$cur" + _mirrors fi } -function _spack_mirror_list { - compgen -W "-h --help --scope" -- "$cur" +_spack_mirror_list() { + SPACK_COMPREPLY="-h --help --scope" } -function _spack_module { +_spack_module() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "lmod tcl" -- "$cur" + SPACK_COMPREPLY="lmod tcl" fi } -function _spack_module_lmod { +_spack_module_lmod() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "refresh find rm loads setdefault" -- "$cur" + SPACK_COMPREPLY="refresh find rm loads setdefault" fi } -function _spack_module_lmod_refresh { +_spack_module_lmod_refresh() { if $list_options then - compgen -W "-h --help --delete-tree --upstream-modules - -y --yes-to-all" -- "$cur" + SPACK_COMPREPLY="-h --help --delete-tree --upstream-modules -y --yes-to-all" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_module_lmod_find { +_spack_module_lmod_find() { if $list_options then - compgen -W "-h --help --full-path -r --dependencies" -- "$cur" + SPACK_COMPREPLY="-h --help --full-path -r --dependencies" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_module_lmod_rm { +_spack_module_lmod_rm() { if $list_options then - compgen -W "-h --help -y --yes-to-all" -- "$cur" + SPACK_COMPREPLY="-h --help -y --yes-to-all" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_module_lmod_loads { +_spack_module_lmod_loads() { if $list_options then - compgen -W "-h --help --input-only -p --prefix -x --exclude - -r --dependencies" -- "$cur" + SPACK_COMPREPLY="-h --help --input-only -p --prefix -x --exclude -r --dependencies" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi - } -function _spack_module_lmod_setdefault { +_spack_module_lmod_setdefault() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_module_tcl { +_spack_module_tcl() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "refresh find rm loads" -- "$cur" + SPACK_COMPREPLY="refresh find rm loads" fi } -function _spack_module_tcl_refresh { +_spack_module_tcl_refresh() { if $list_options then - compgen -W "-h --help --delete-tree --upstream-modules - -y --yes-to-all" -- "$cur" + SPACK_COMPREPLY="-h --help --delete-tree --upstream-modules -y --yes-to-all" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_module_tcl_find { +_spack_module_tcl_find() { if $list_options then - compgen -W "-h --help --full-path -r --dependencies" -- "$cur" + SPACK_COMPREPLY="-h --help --full-path -r --dependencies" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_module_tcl_rm { +_spack_module_tcl_rm() { if $list_options then - compgen -W "-h --help -y --yes-to-all" -- "$cur" + SPACK_COMPREPLY="-h --help -y --yes-to-all" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_module_tcl_loads { +_spack_module_tcl_loads() { if $list_options then - compgen -W "-h --help --input-only -p --prefix -x --exclude - -r --dependencies" -- "$cur" + SPACK_COMPREPLY="-h --help --input-only -p --prefix -x --exclude -r --dependencies" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_patch { +_spack_patch() { if $list_options then - compgen -W "-h --help -n --no-checksum" -- "$cur" + SPACK_COMPREPLY="-h --help -n --no-checksum" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_pkg { +_spack_pkg() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "add list diff added changed removed" -- "$cur" + SPACK_COMPREPLY="add list diff added changed removed" fi } -function _spack_pkg_add { +_spack_pkg_add() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_pkg_list { - # FIXME: How to list git revisions? +_spack_pkg_list() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" + else + SPACK_COMPREPLY="" fi } -function _spack_pkg_diff { - # FIXME: How to list git revisions? +_spack_pkg_diff() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" + else + SPACK_COMPREPLY="" fi } -function _spack_pkg_added { - # FIXME: How to list git revisions? +_spack_pkg_added() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" + else + SPACK_COMPREPLY="" fi } -function _spack_pkg_changed { - # FIXME: How to list git revisions? +_spack_pkg_changed() { if $list_options then - compgen -W "-h --help -t --type" -- "$cur" + SPACK_COMPREPLY="-h --help -t --type" + else + SPACK_COMPREPLY="" fi } -function _spack_pkg_removed { - # FIXME: How to list git revisions? +_spack_pkg_removed() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" + else + SPACK_COMPREPLY="" fi } -function _spack_providers { +_spack_providers() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "$(_providers)" -- "$cur" + _providers fi } -function _spack_pydoc { +_spack_pydoc() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" + else + SPACK_COMPREPLY="" fi } -function _spack_python { +_spack_python() { if $list_options then - compgen -W "-h --help -c" -- "$cur" + SPACK_COMPREPLY="-h --help -c" + else + SPACK_COMPREPLY="" fi } -function _spack_reindex { - compgen -W "-h --help" -- "$cur" +_spack_reindex() { + SPACK_COMPREPLY="-h --help" } -function _spack_release_jobs { - compgen -W "-h --help -o --output-file -p --print-summary - --cdash-credentials" -- "$cur" +_spack_remove() { + if $list_options + then + SPACK_COMPREPLY="-h --help -a --all -l --list-name -f --force" + else + _all_packages + fi } -function _spack_remove { +_spack_rm() { if $list_options then - compgen -W "-h --help -a --all -l --list-name -f --force" -- "$cur" + SPACK_COMPREPLY="-h --help -a --all -l --list-name -f --force" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_repo { +_spack_repo() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "create list add remove rm" -- "$cur" + SPACK_COMPREPLY="create list add remove rm" fi } -function _spack_repo_create { +_spack_repo_create() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" + else + _repos fi } -function _spack_repo_list { - compgen -W "-h --help --scope" -- "$cur" +_spack_repo_list() { + SPACK_COMPREPLY="-h --help --scope" } -function _spack_repo_add { +_spack_repo_add() { if $list_options then - compgen -W "-h --help --scope" -- "$cur" + SPACK_COMPREPLY="-h --help --scope" + else + SPACK_COMPREPLY="" fi } -function _spack_repo_remove { +_spack_repo_remove() { if $list_options then - compgen -W "-h --help --scope" -- "$cur" + SPACK_COMPREPLY="-h --help --scope" else - compgen -W "$(_repos)" -- "$cur" + _repos fi } -function _spack_repo_rm { - # Alias to `spack repo remove` - _spack_repo_remove +_spack_repo_rm() { + if $list_options + then + SPACK_COMPREPLY="-h --help --scope" + else + _repos + fi } -function _spack_resource { +_spack_resource() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "list show" -- "$cur" + SPACK_COMPREPLY="list show" fi } -function _spack_resource_list { - compgen -W "-h --help --only-hashes" -- "$cur" +_spack_resource_list() { + SPACK_COMPREPLY="-h --help --only-hashes" } -function _spack_resource_show { +_spack_resource_show() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "$(_all_resource_hashes)" -- "$cur" + _all_resource_hashes fi } -function _spack_restage { +_spack_restage() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_setup { +_spack_setup() { if $list_options then - compgen -W "-h --help -i --ignore-dependencies -n --no-checksum - -v --verbose --clean --dirty" -- "$cur" + SPACK_COMPREPLY="-h --help -i --ignore-dependencies -n --no-checksum -v --verbose --clean --dirty" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_spec { +_spack_spec() { if $list_options then - compgen -W "-h --help -l --long -L --very-long -I --install-status - -y --yaml -j --json -c --cover -N --namespaces - -t --types" -- "$cur" + SPACK_COMPREPLY="-h --help -l --long -L --very-long -I --install-status -y --yaml -j --json -c --cover -N --namespaces -t --types" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_stage { +_spack_stage() { if $list_options then - compgen -W "-h --help -n --no-checksum -p --path" -- "$cur" + SPACK_COMPREPLY="-h --help -n --no-checksum -p --path" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_test { +_spack_test() { if $list_options then - compgen -W "-h --help -H --pytest-help -l --list - -L --long-list" -- "$cur" + SPACK_COMPREPLY="-h --help -H --pytest-help -l --list -L --list-long -N --list-names --extension -s -k --showlocals" else - compgen -W "$(_tests)" -- "$cur" + _tests fi } -function _spack_uninstall { +_spack_uninstall() { if $list_options then - compgen -W "-h --help -f --force -R --dependents - -y --yes-to-all -a --all" -- "$cur" + SPACK_COMPREPLY="-h --help -f --force -R --dependents -y --yes-to-all -a --all" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_unload { +_spack_unload() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help --sh --csh -a --all" else - compgen -W "$(_installed_packages)" -- "$cur" + _installed_packages fi } -function _spack_upload_s3 { +_spack_upload_s3() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "spec index" -- "$cur" + SPACK_COMPREPLY="spec index" fi } -function _spack_upload_s3_spec { - compgen -W "-h --help -s --spec -y --spec-yaml -b --base-dir - -e --endpoint-url" -- "$cur" +_spack_upload_s3_spec() { + SPACK_COMPREPLY="-h --help -s --spec -y --spec-yaml -b --base-dir -e --endpoint-url" } -function _spack_upload_s3_index { - compgen -W "-h --help -e --endpoint-url" -- "$cur" +_spack_upload_s3_index() { + SPACK_COMPREPLY="-h --help -e --endpoint-url" } -function _spack_url { +_spack_url() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help" else - compgen -W "parse list summary stats" -- "$cur" + SPACK_COMPREPLY="parse list summary stats" fi } -function _spack_url_parse { +_spack_url_parse() { if $list_options then - compgen -W "-h --help -s --spider" -- "$cur" + SPACK_COMPREPLY="-h --help -s --spider" + else + SPACK_COMPREPLY="" fi } -function _spack_url_list { - compgen -W "-h --help -c --color -e --extrapolation - -n --incorrect-name -N --correct-name - -v --incorrect-version -V --correct-version" -- "$cur" +_spack_url_list() { + SPACK_COMPREPLY="-h --help -c --color -e --extrapolation -n --incorrect-name -N --correct-name -v --incorrect-version -V --correct-version" } -function _spack_url_summary { - compgen -W "-h --help" -- "$cur" +_spack_url_summary() { + SPACK_COMPREPLY="-h --help" } -function _spack_url_stats { - compgen -W "-h --help" -- "$cur" +_spack_url_stats() { + SPACK_COMPREPLY="-h --help" } -function _spack_verify { +_spack_verify() { if $list_options then - compgen -W "-h --help -l --local -j --json -a --all -s --specs - -f --files" -- "$cur" + SPACK_COMPREPLY="-h --help -l --local -j --json -a --all -s --specs -f --files" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_versions { +_spack_versions() { if $list_options then - compgen -W "-h --help -s --safe-only" -- "$cur" + SPACK_COMPREPLY="-h --help -s --safe-only" else - compgen -W "$(_all_packages)" -- "$cur" + _all_packages fi } -function _spack_view { +_spack_view() { if $list_options then - compgen -W "-h --help -v --verbose -e --exclude - -d --dependencies" -- "$cur" + SPACK_COMPREPLY="-h --help -v --verbose -e --exclude -d --dependencies" else - compgen -W "symlink add soft hardlink hard remove rm statlink - status check" -- "$cur" + SPACK_COMPREPLY="symlink add soft hardlink hard remove rm statlink status check" fi } -function _spack_view_symlink { +_spack_view_symlink() { if $list_options then - compgen -W "-h --help --projection-file - -i --ignore-conflicts" -- "$cur" + SPACK_COMPREPLY="-h --help --projection-file -i --ignore-conflicts" + else + _all_packages fi } -function _spack_view_add { - # Alias for `spack view symlink` - _spack_view_symlink -} - -function _spack_view_soft { - # Alias for `spack view symlink` - _spack_view_symlink -} - -function _spack_view_hardlink { +_spack_view_add() { if $list_options then - compgen -W "-h --help --projection-file - -i --ignore-conflicts" -- "$cur" + SPACK_COMPREPLY="-h --help --projection-file -i --ignore-conflicts" + else + _all_packages fi } -function _spack_view_hard { - # Alias for `spack view hardlink` - _spack_view_hardlink -} - -function _spack_view_remove { +_spack_view_soft() { if $list_options then - compgen -W "-h --help --no-remove-dependents -a --all" -- "$cur" + SPACK_COMPREPLY="-h --help --projection-file -i --ignore-conflicts" + else + _all_packages fi } -function _spack_view_rm { - # Alias for `spack view remove` - _spack_view_remove -} - -function _spack_view_statlink { +_spack_view_hardlink() { if $list_options then - compgen -W "-h --help" -- "$cur" + SPACK_COMPREPLY="-h --help --projection-file -i --ignore-conflicts" + else + _all_packages fi } -function _spack_view_status { - # Alias for `spack view statlink` - _spack_view_statlink -} - -function _spack_view_check { - # Alias for `spack view statlink` - _spack_view_statlink -} - -# Helper functions for subcommands - -function _subcommands { - spack commands -} - -function _all_packages { - spack list -} - -function _all_resource_hashes { - spack resource list --only-hashes -} - -function _installed_packages { - spack --color=never find --no-groups -} - -function _installed_compilers { - spack compilers | egrep -v "^(-|=)" -} - -function _providers { - spack providers -} - -function _mirrors { - spack mirror list | awk '{print $1}' -} - -function _repos { - spack repo list | awk '{print $1}' +_spack_view_hard() { + if $list_options + then + SPACK_COMPREPLY="-h --help --projection-file -i --ignore-conflicts" + else + _all_packages + fi } -function _tests { - spack test -l +_spack_view_remove() { + if $list_options + then + SPACK_COMPREPLY="-h --help --no-remove-dependents -a --all" + else + _all_packages + fi } -function _environments { - spack env list +_spack_view_rm() { + if $list_options + then + SPACK_COMPREPLY="-h --help --no-remove-dependents -a --all" + else + _all_packages + fi } -function _keys { - spack gpg list +_spack_view_statlink() { + if $list_options + then + SPACK_COMPREPLY="-h --help" + else + _all_packages + fi } -# Testing functions - -function _test_vars { - echo "-----------------------------------------------------" >> temp - echo "Full line: '$COMP_LINE'" >> temp - echo >> temp - echo "Word list w/ flags: $(_pretty_print COMP_WORDS[@])" >> temp - echo "# words w/ flags: '${#COMP_WORDS[@]}'" >> temp - echo "Cursor index w/ flags: '$COMP_CWORD'" >> temp - echo >> temp - echo "Word list w/out flags: $(_pretty_print COMP_WORDS_NO_FLAGS[@])" >> temp - echo "# words w/out flags: '${#COMP_WORDS_NO_FLAGS[@]}'" >> temp - echo "Cursor index w/out flags: '$COMP_CWORD_NO_FLAGS'" >> temp - echo >> temp - echo "Subfunction: '$subfunction'" >> temp +_spack_view_status() { if $list_options then - echo "List options: 'True'" >> temp + SPACK_COMPREPLY="-h --help" else - echo "List options: 'False'" >> temp + _all_packages fi - echo "Current word: '$cur'" >> temp - echo "Previous word: '$prev'" >> temp } -# Pretty-prints one or more arrays -# Syntax: _pretty_print array1[@] ... -function _pretty_print { - for arg in $@ - do - local array=("${!arg}") - echo -n "$arg: [" - printf "'%s'" "${array[0]}" - printf ", '%s'" "${array[@]:1}" - echo "]" - done +_spack_view_check() { + if $list_options + then + SPACK_COMPREPLY="-h --help" + else + _all_packages + fi } - -complete -o default -F _bash_completion_spack spack diff --git a/share/spack/templates/container/Dockerfile b/share/spack/templates/container/Dockerfile new file mode 100644 index 0000000000..740f46e9ee --- /dev/null +++ b/share/spack/templates/container/Dockerfile @@ -0,0 +1,51 @@ +# Build stage with Spack pre-installed and ready to be used +FROM {{ build.image }}:{{ build.tag }} as builder + +# What we want to install and how we want to install it +# is specified in a manifest file (spack.yaml) +RUN mkdir {{ paths.environment }} \ +{{ manifest }} > {{ paths.environment }}/spack.yaml + +# Install the software, remove unecessary deps +RUN cd {{ paths.environment }} && spack install && spack gc -y +{% if strip %} + +# Strip all the binaries +RUN find -L {{ paths.view }}/* -type f -exec readlink -f '{}' \; | \ + xargs file -i | \ + grep 'charset=binary' | \ + grep 'x-executable\|x-archive\|x-sharedlib' | \ + awk -F: '{print $1}' | xargs strip -s +{% endif %} + +# Modifications to the environment that are necessary to run +RUN cd {{ paths.environment }} && \ + spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh + +{% if extra_instructions.build %} +{{ extra_instructions.build }} +{% endif %} + +# Bare OS image to run the installed executables +FROM {{ run.image }} + +COPY --from=builder {{ paths.environment }} {{ paths.environment }} +COPY --from=builder {{ paths.store }} {{ paths.store }} +COPY --from=builder {{ paths.view }} {{ paths.view }} +COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh + +{% if os_packages %} +RUN {{ os_packages.update }} \ + && {{ os_packages.install }}{% for pkg in os_packages.list %} {{ pkg }}{% endfor %} \ + && {{ os_packages.clean }} +{% endif %} + +{% if extra_instructions.final %} +{{ extra_instructions.final }} +{% endif %} + +{% for label, value in labels.items() %} +LABEL "{{ label }}"="{{ value }}" +{% endfor %} + +ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"] diff --git a/share/spack/templates/container/singularity.def b/share/spack/templates/container/singularity.def new file mode 100644 index 0000000000..616e677f96 --- /dev/null +++ b/share/spack/templates/container/singularity.def @@ -0,0 +1,90 @@ +Bootstrap: docker +From: {{ build.image }}:{{ build.tag }} +Stage: build + +%post + # Create the manifest file for the installation in /opt/spack-environment + mkdir {{ paths.environment }} && cd {{ paths.environment }} + cat << EOF > spack.yaml +{{ manifest }} +EOF + + # Install all the required software + . /opt/spack/share/spack/setup-env.sh + spack install + spack gc -y + spack env activate --sh -d . >> {{ paths.environment }}/environment_modifications.sh +{% if strip %} + + # Strip the binaries to reduce the size of the image + find -L {{ paths.view }}/* -type f -exec readlink -f '{}' \; | \ + xargs file -i | \ + grep 'charset=binary' | \ + grep 'x-executable\|x-archive\|x-sharedlib' | \ + awk -F: '{print $1}' | xargs strip -s +{% endif %} +{% if extra_instructions.build %} +{{ extra_instructions.build }} +{% endif %} + + +{% if apps %} +{% for application, help_text in apps.items() %} + +%apprun {{ application }} + exec /opt/view/bin/{{ application }} "$@" + +%apphelp {{ application }} + {{help_text }} +{% endfor %} +{% endif %} + +Bootstrap: docker +From: {{ run.image }} +Stage: final + +%files from build + {{ paths.environment }} /opt + {{ paths.store }} /opt + {{ paths.view }} /opt + {{ paths.environment }}/environment_modifications.sh {{ paths.environment }}/environment_modifications.sh + +%post +{% if os_packages.list %} + # Update, install and cleanup of system packages + {{ os_packages.update }} + {{ os_packages.install }} {{ os_packages.list | join | replace('\n', ' ') }} + {{ os_packages.clean }} +{% endif %} + # Modify the environment without relying on sourcing shell specific files at startup + cat {{ paths.environment }}/environment_modifications.sh >> $SINGULARITY_ENVIRONMENT +{% if extra_instructions.final %} +{{ extra_instructions.final }} +{% endif %} + +{% if runscript %} +%runscript +{{ runscript }} +{% endif %} + +{% if startscript %} +%startscript +{{ startscript }} +{% endif %} + +{% if test %} +%test +{{ test }} +{% endif %} + +{% if help %} +%help +{{ help }} +{% endif %} + +{% if labels %} +%labels +{% for label, value in labels.items() %} + {{ label }} {{ value }} +{% endfor %} +{% endif %}
\ No newline at end of file diff --git a/share/spack/templates/misc/coconcretization.pyt b/share/spack/templates/misc/coconcretization.pyt index eddab6a70c..56f671cb73 100644 --- a/share/spack/templates/misc/coconcretization.pyt +++ b/share/spack/templates/misc/coconcretization.pyt @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/gpg.mock/keys/package-signing-key b/var/spack/gpg.mock/keys/package-signing-key new file mode 100644 index 0000000000..43d5c4ed66 --- /dev/null +++ b/var/spack/gpg.mock/keys/package-signing-key @@ -0,0 +1 @@ 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
\ No newline at end of file diff --git a/var/spack/repos/builtin.mock/packages/a/package.py b/var/spack/repos/builtin.mock/packages/a/package.py index 951e633d78..3eae25366a 100644 --- a/var/spack/repos/builtin.mock/packages/a/package.py +++ b/var/spack/repos/builtin.mock/packages/a/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/archive-files/package.py b/var/spack/repos/builtin.mock/packages/archive-files/package.py index 1e41fa83f2..a2c008efb4 100644 --- a/var/spack/repos/builtin.mock/packages/archive-files/package.py +++ b/var/spack/repos/builtin.mock/packages/archive-files/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/b/package.py b/var/spack/repos/builtin.mock/packages/b/package.py index 2f295e29de..5fabc274d2 100644 --- a/var/spack/repos/builtin.mock/packages/b/package.py +++ b/var/spack/repos/builtin.mock/packages/b/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/boost/package.py b/var/spack/repos/builtin.mock/packages/boost/package.py index d65fa66de8..f946191f47 100644 --- a/var/spack/repos/builtin.mock/packages/boost/package.py +++ b/var/spack/repos/builtin.mock/packages/boost/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/build-error/package.py b/var/spack/repos/builtin.mock/packages/build-error/package.py index 20beb682d6..04e1b147c6 100644 --- a/var/spack/repos/builtin.mock/packages/build-error/package.py +++ b/var/spack/repos/builtin.mock/packages/build-error/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/build-warnings/package.py b/var/spack/repos/builtin.mock/packages/build-warnings/package.py index e4063631cf..02254ef801 100644 --- a/var/spack/repos/builtin.mock/packages/build-warnings/package.py +++ b/var/spack/repos/builtin.mock/packages/build-warnings/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/c/package.py b/var/spack/repos/builtin.mock/packages/c/package.py index b3d3f3aa06..9942a297eb 100644 --- a/var/spack/repos/builtin.mock/packages/c/package.py +++ b/var/spack/repos/builtin.mock/packages/c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/callpath/package.py b/var/spack/repos/builtin.mock/packages/callpath/package.py index dba61b51e1..42bf277786 100644 --- a/var/spack/repos/builtin.mock/packages/callpath/package.py +++ b/var/spack/repos/builtin.mock/packages/callpath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/canfail/package.py b/var/spack/repos/builtin.mock/packages/canfail/package.py index 02adde4ef2..79ded75a55 100644 --- a/var/spack/repos/builtin.mock/packages/canfail/package.py +++ b/var/spack/repos/builtin.mock/packages/canfail/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py index 40e1c9f9ed..286ee08086 100644 --- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py +++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/cmake/package.py b/var/spack/repos/builtin.mock/packages/cmake/package.py index 76ef41fcfa..4815032e66 100644 --- a/var/spack/repos/builtin.mock/packages/cmake/package.py +++ b/var/spack/repos/builtin.mock/packages/cmake/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/conflict-parent/package.py b/var/spack/repos/builtin.mock/packages/conflict-parent/package.py index 9fa729d85e..8e8e148b88 100644 --- a/var/spack/repos/builtin.mock/packages/conflict-parent/package.py +++ b/var/spack/repos/builtin.mock/packages/conflict-parent/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/conflict/package.py b/var/spack/repos/builtin.mock/packages/conflict/package.py index 9d18bcc3e4..d7598aa84d 100644 --- a/var/spack/repos/builtin.mock/packages/conflict/package.py +++ b/var/spack/repos/builtin.mock/packages/conflict/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py b/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py index 9fadbb9985..8fa6c67d6e 100644 --- a/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py +++ b/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dep-diamond-patch-mid1/package.py b/var/spack/repos/builtin.mock/packages/dep-diamond-patch-mid1/package.py index f4ec1554fa..291fd887a6 100644 --- a/var/spack/repos/builtin.mock/packages/dep-diamond-patch-mid1/package.py +++ b/var/spack/repos/builtin.mock/packages/dep-diamond-patch-mid1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dep-diamond-patch-mid2/package.py b/var/spack/repos/builtin.mock/packages/dep-diamond-patch-mid2/package.py index 2aea75f307..fa53466440 100644 --- a/var/spack/repos/builtin.mock/packages/dep-diamond-patch-mid2/package.py +++ b/var/spack/repos/builtin.mock/packages/dep-diamond-patch-mid2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dep-diamond-patch-top/package.py b/var/spack/repos/builtin.mock/packages/dep-diamond-patch-top/package.py index 21388011c5..c966045952 100644 --- a/var/spack/repos/builtin.mock/packages/dep-diamond-patch-top/package.py +++ b/var/spack/repos/builtin.mock/packages/dep-diamond-patch-top/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dependency-install/package.py b/var/spack/repos/builtin.mock/packages/dependency-install/package.py index d0298293ae..37cb3edd61 100644 --- a/var/spack/repos/builtin.mock/packages/dependency-install/package.py +++ b/var/spack/repos/builtin.mock/packages/dependency-install/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dependent-install/package.py b/var/spack/repos/builtin.mock/packages/dependent-install/package.py index 54c60ce99e..84b6331e78 100644 --- a/var/spack/repos/builtin.mock/packages/dependent-install/package.py +++ b/var/spack/repos/builtin.mock/packages/dependent-install/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dev-build-test-install/package.py b/var/spack/repos/builtin.mock/packages/dev-build-test-install/package.py index 0eb9648941..a2c979691f 100644 --- a/var/spack/repos/builtin.mock/packages/dev-build-test-install/package.py +++ b/var/spack/repos/builtin.mock/packages/dev-build-test-install/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/develop-test/package.py b/var/spack/repos/builtin.mock/packages/develop-test/package.py index a8ebe974c7..4a2fde701e 100644 --- a/var/spack/repos/builtin.mock/packages/develop-test/package.py +++ b/var/spack/repos/builtin.mock/packages/develop-test/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/develop-test2/package.py b/var/spack/repos/builtin.mock/packages/develop-test2/package.py index 762a82f838..464219f603 100644 --- a/var/spack/repos/builtin.mock/packages/develop-test2/package.py +++ b/var/spack/repos/builtin.mock/packages/develop-test2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/direct-mpich/package.py b/var/spack/repos/builtin.mock/packages/direct-mpich/package.py index 5df0f6ebc1..4db94c66c2 100644 --- a/var/spack/repos/builtin.mock/packages/direct-mpich/package.py +++ b/var/spack/repos/builtin.mock/packages/direct-mpich/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py index af1e31d5d8..85f661a485 100644 --- a/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py +++ b/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py index 3929420edd..d0ed4efaeb 100644 --- a/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py +++ b/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py index 6dd6120ac9..c7842ead47 100644 --- a/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py +++ b/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond/package.py index 8033b05cbc..9a441a953b 100644 --- a/var/spack/repos/builtin.mock/packages/dt-diamond/package.py +++ b/var/spack/repos/builtin.mock/packages/dt-diamond/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtbuild1/package.py b/var/spack/repos/builtin.mock/packages/dtbuild1/package.py index aa50029f42..07e86bb3e0 100644 --- a/var/spack/repos/builtin.mock/packages/dtbuild1/package.py +++ b/var/spack/repos/builtin.mock/packages/dtbuild1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtbuild2/package.py b/var/spack/repos/builtin.mock/packages/dtbuild2/package.py index 8babe7a695..752a34c900 100644 --- a/var/spack/repos/builtin.mock/packages/dtbuild2/package.py +++ b/var/spack/repos/builtin.mock/packages/dtbuild2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtbuild3/package.py b/var/spack/repos/builtin.mock/packages/dtbuild3/package.py index 1206e143ca..23fd06bcb9 100644 --- a/var/spack/repos/builtin.mock/packages/dtbuild3/package.py +++ b/var/spack/repos/builtin.mock/packages/dtbuild3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtlink1/package.py b/var/spack/repos/builtin.mock/packages/dtlink1/package.py index ceefbcf3a2..0235591381 100644 --- a/var/spack/repos/builtin.mock/packages/dtlink1/package.py +++ b/var/spack/repos/builtin.mock/packages/dtlink1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtlink2/package.py b/var/spack/repos/builtin.mock/packages/dtlink2/package.py index 89e97cba1a..1f629d3d6b 100644 --- a/var/spack/repos/builtin.mock/packages/dtlink2/package.py +++ b/var/spack/repos/builtin.mock/packages/dtlink2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtlink3/package.py b/var/spack/repos/builtin.mock/packages/dtlink3/package.py index b77c871a0a..dc0d2532ec 100644 --- a/var/spack/repos/builtin.mock/packages/dtlink3/package.py +++ b/var/spack/repos/builtin.mock/packages/dtlink3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtlink4/package.py b/var/spack/repos/builtin.mock/packages/dtlink4/package.py index b535828a0e..2ec4ddd7e2 100644 --- a/var/spack/repos/builtin.mock/packages/dtlink4/package.py +++ b/var/spack/repos/builtin.mock/packages/dtlink4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtlink5/package.py b/var/spack/repos/builtin.mock/packages/dtlink5/package.py index 405779917e..cb191f32f0 100644 --- a/var/spack/repos/builtin.mock/packages/dtlink5/package.py +++ b/var/spack/repos/builtin.mock/packages/dtlink5/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtrun1/package.py b/var/spack/repos/builtin.mock/packages/dtrun1/package.py index cefa6e2c76..fcc26022ca 100644 --- a/var/spack/repos/builtin.mock/packages/dtrun1/package.py +++ b/var/spack/repos/builtin.mock/packages/dtrun1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtrun2/package.py b/var/spack/repos/builtin.mock/packages/dtrun2/package.py index a8ff2bea32..f455af1bb7 100644 --- a/var/spack/repos/builtin.mock/packages/dtrun2/package.py +++ b/var/spack/repos/builtin.mock/packages/dtrun2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtrun3/package.py b/var/spack/repos/builtin.mock/packages/dtrun3/package.py index 253617c449..c884ef6b46 100644 --- a/var/spack/repos/builtin.mock/packages/dtrun3/package.py +++ b/var/spack/repos/builtin.mock/packages/dtrun3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dttop/package.py b/var/spack/repos/builtin.mock/packages/dttop/package.py index ac44aa59f9..225af9fee4 100644 --- a/var/spack/repos/builtin.mock/packages/dttop/package.py +++ b/var/spack/repos/builtin.mock/packages/dttop/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dtuse/package.py b/var/spack/repos/builtin.mock/packages/dtuse/package.py index af2607fd86..083cb1ba76 100644 --- a/var/spack/repos/builtin.mock/packages/dtuse/package.py +++ b/var/spack/repos/builtin.mock/packages/dtuse/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/dyninst/package.py b/var/spack/repos/builtin.mock/packages/dyninst/package.py index bfc9e6d27e..2cf84f94ab 100644 --- a/var/spack/repos/builtin.mock/packages/dyninst/package.py +++ b/var/spack/repos/builtin.mock/packages/dyninst/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/e/package.py b/var/spack/repos/builtin.mock/packages/e/package.py index 7dcdf025aa..c85c78e137 100644 --- a/var/spack/repos/builtin.mock/packages/e/package.py +++ b/var/spack/repos/builtin.mock/packages/e/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/extendee/package.py b/var/spack/repos/builtin.mock/packages/extendee/package.py index 42cbad9199..0a17848806 100644 --- a/var/spack/repos/builtin.mock/packages/extendee/package.py +++ b/var/spack/repos/builtin.mock/packages/extendee/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/extension1/package.py b/var/spack/repos/builtin.mock/packages/extension1/package.py index 7786710528..73847753cc 100644 --- a/var/spack/repos/builtin.mock/packages/extension1/package.py +++ b/var/spack/repos/builtin.mock/packages/extension1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/extension2/package.py b/var/spack/repos/builtin.mock/packages/extension2/package.py index 84e869640e..29f3c9423e 100644 --- a/var/spack/repos/builtin.mock/packages/extension2/package.py +++ b/var/spack/repos/builtin.mock/packages/extension2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/externalmodule/package.py b/var/spack/repos/builtin.mock/packages/externalmodule/package.py index 156e15bf13..f871762c7e 100644 --- a/var/spack/repos/builtin.mock/packages/externalmodule/package.py +++ b/var/spack/repos/builtin.mock/packages/externalmodule/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/externalprereq/package.py b/var/spack/repos/builtin.mock/packages/externalprereq/package.py index d5f48650d5..866df9f838 100644 --- a/var/spack/repos/builtin.mock/packages/externalprereq/package.py +++ b/var/spack/repos/builtin.mock/packages/externalprereq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/externaltest/package.py b/var/spack/repos/builtin.mock/packages/externaltest/package.py index 80593200f2..f76863a37b 100644 --- a/var/spack/repos/builtin.mock/packages/externaltest/package.py +++ b/var/spack/repos/builtin.mock/packages/externaltest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/externaltool/package.py b/var/spack/repos/builtin.mock/packages/externaltool/package.py index 5a8727aa18..2d6caef35d 100644 --- a/var/spack/repos/builtin.mock/packages/externaltool/package.py +++ b/var/spack/repos/builtin.mock/packages/externaltool/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py index f893a83ec7..e16997dbd8 100644 --- a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py +++ b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/failing-build/package.py b/var/spack/repos/builtin.mock/packages/failing-build/package.py index f07c8765cb..e95795dcf0 100644 --- a/var/spack/repos/builtin.mock/packages/failing-build/package.py +++ b/var/spack/repos/builtin.mock/packages/failing-build/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/fake/package.py b/var/spack/repos/builtin.mock/packages/fake/package.py index b155a7d9c8..e022af1766 100644 --- a/var/spack/repos/builtin.mock/packages/fake/package.py +++ b/var/spack/repos/builtin.mock/packages/fake/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/flake8/package.py b/var/spack/repos/builtin.mock/packages/flake8/package.py index 67a5b43290..2de7bd8e12 100644 --- a/var/spack/repos/builtin.mock/packages/flake8/package.py +++ b/var/spack/repos/builtin.mock/packages/flake8/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/flatten-deps/package.py b/var/spack/repos/builtin.mock/packages/flatten-deps/package.py index 6696e8d529..a272dfc53c 100644 --- a/var/spack/repos/builtin.mock/packages/flatten-deps/package.py +++ b/var/spack/repos/builtin.mock/packages/flatten-deps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/git-svn-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-svn-top-level/package.py index ac0189a980..72e7b1fe89 100644 --- a/var/spack/repos/builtin.mock/packages/git-svn-top-level/package.py +++ b/var/spack/repos/builtin.mock/packages/git-svn-top-level/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/git-test/package.py b/var/spack/repos/builtin.mock/packages/git-test/package.py index 77b245df61..a5aa428664 100644 --- a/var/spack/repos/builtin.mock/packages/git-test/package.py +++ b/var/spack/repos/builtin.mock/packages/git-test/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/git-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-top-level/package.py index 2271aafe5f..1e511628f3 100644 --- a/var/spack/repos/builtin.mock/packages/git-top-level/package.py +++ b/var/spack/repos/builtin.mock/packages/git-top-level/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/git-url-svn-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-url-svn-top-level/package.py index 9bc7296888..e1c7476e3b 100644 --- a/var/spack/repos/builtin.mock/packages/git-url-svn-top-level/package.py +++ b/var/spack/repos/builtin.mock/packages/git-url-svn-top-level/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/git-url-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-url-top-level/package.py index ac34475ecd..2eacba15b7 100644 --- a/var/spack/repos/builtin.mock/packages/git-url-top-level/package.py +++ b/var/spack/repos/builtin.mock/packages/git-url-top-level/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/hash-test1/package.py b/var/spack/repos/builtin.mock/packages/hash-test1/package.py index 879e08147e..db3616145b 100644 --- a/var/spack/repos/builtin.mock/packages/hash-test1/package.py +++ b/var/spack/repos/builtin.mock/packages/hash-test1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,6 +19,9 @@ class HashTest1(Package): version('1.2', 'b' * 32) version('1.3', 'c' * 32) version('1.4', 'd' * 32) + version('1.5', 'd' * 32) + version('1.6', 'e' * 32) + version('1.7', 'f' * 32) patch('patch1.patch', when="@1.1") patch('patch2.patch', when="@1.4") @@ -34,6 +37,10 @@ class HashTest1(Package): print("install 1") os.listdir(os.getcwd()) - @when('@1.5') + @when('@1.5:') def install(self, spec, prefix): os.listdir(os.getcwd()) + + @when('@1.5,1.6') + def extra_phase(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/hash-test2/package.py b/var/spack/repos/builtin.mock/packages/hash-test2/package.py index ec8a14a409..859eb86c95 100644 --- a/var/spack/repos/builtin.mock/packages/hash-test2/package.py +++ b/var/spack/repos/builtin.mock/packages/hash-test2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/hash-test3/package.py b/var/spack/repos/builtin.mock/packages/hash-test3/package.py new file mode 100644 index 0000000000..7c452c3ba1 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/hash-test3/package.py @@ -0,0 +1,42 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + +import os + + +class HashTest3(Package): + """Used to test package hashing + """ + + homepage = "http://www.hashtest3.org" + url = "http://www.hashtest1.org/downloads/hashtest3-1.1.tar.bz2" + + version('1.2', 'b' * 32) + version('1.3', 'c' * 32) + version('1.5', 'd' * 32) + version('1.6', 'e' * 32) + version('1.7', 'f' * 32) + + variant('variantx', default=False, description='Test variant X') + variant('varianty', default=False, description='Test variant Y') + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + pass + + @when('@:1.4') + def install(self, spec, prefix): + print("install 1") + os.listdir(os.getcwd()) + + @when('@1.5:') + def install(self, spec, prefix): + os.listdir(os.getcwd()) + + for _version_constraint in ['@1.5', '@1.6']: + @when(_version_constraint) + def extra_phase(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/hg-test/package.py b/var/spack/repos/builtin.mock/packages/hg-test/package.py index 62e0a3db0b..ede967ce0c 100644 --- a/var/spack/repos/builtin.mock/packages/hg-test/package.py +++ b/var/spack/repos/builtin.mock/packages/hg-test/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/hg-top-level/package.py b/var/spack/repos/builtin.mock/packages/hg-top-level/package.py index d503654721..6f402c801b 100644 --- a/var/spack/repos/builtin.mock/packages/hg-top-level/package.py +++ b/var/spack/repos/builtin.mock/packages/hg-top-level/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/hypre/package.py b/var/spack/repos/builtin.mock/packages/hypre/package.py index c0cf6487b3..27c641017a 100644 --- a/var/spack/repos/builtin.mock/packages/hypre/package.py +++ b/var/spack/repos/builtin.mock/packages/hypre/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py b/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py index e454b167d5..5a06f77dd3 100644 --- a/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py +++ b/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/libdwarf/package.py b/var/spack/repos/builtin.mock/packages/libdwarf/package.py index 37f0bd062c..737635a1a5 100644 --- a/var/spack/repos/builtin.mock/packages/libdwarf/package.py +++ b/var/spack/repos/builtin.mock/packages/libdwarf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/libelf/package.py b/var/spack/repos/builtin.mock/packages/libelf/package.py index dbb33e7a11..430ae53ab3 100644 --- a/var/spack/repos/builtin.mock/packages/libelf/package.py +++ b/var/spack/repos/builtin.mock/packages/libelf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/maintainers-1/package.py b/var/spack/repos/builtin.mock/packages/maintainers-1/package.py index 75917da005..7942ff3de7 100644 --- a/var/spack/repos/builtin.mock/packages/maintainers-1/package.py +++ b/var/spack/repos/builtin.mock/packages/maintainers-1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/maintainers-2/package.py b/var/spack/repos/builtin.mock/packages/maintainers-2/package.py index a198bde1e3..d16f9e30a6 100644 --- a/var/spack/repos/builtin.mock/packages/maintainers-2/package.py +++ b/var/spack/repos/builtin.mock/packages/maintainers-2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/missing-dependency/package.py b/var/spack/repos/builtin.mock/packages/missing-dependency/package.py new file mode 100644 index 0000000000..edad3f0b86 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/missing-dependency/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class MissingDependency(Package): + """Package with a dependency that does not exist.""" + + homepage = "http://www.example.com" + url = "http://www.example.com/missing-dependency-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + # intentionally missing to test possible_dependencies() + depends_on("this-is-a-missing-dependency") + + # this one is a "real" mock dependency + depends_on("a") diff --git a/var/spack/repos/builtin.mock/packages/mixedversions/package.py b/var/spack/repos/builtin.mock/packages/mixedversions/package.py index 82cb79d943..446278403b 100644 --- a/var/spack/repos/builtin.mock/packages/mixedversions/package.py +++ b/var/spack/repos/builtin.mock/packages/mixedversions/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/module-path-separator/package.py b/var/spack/repos/builtin.mock/packages/module-path-separator/package.py index 2a235e816f..bb65705d1c 100644 --- a/var/spack/repos/builtin.mock/packages/module-path-separator/package.py +++ b/var/spack/repos/builtin.mock/packages/module-path-separator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/mpich/package.py b/var/spack/repos/builtin.mock/packages/mpich/package.py index 6a3b1c90ca..c84a2cd30d 100644 --- a/var/spack/repos/builtin.mock/packages/mpich/package.py +++ b/var/spack/repos/builtin.mock/packages/mpich/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/mpich2/package.py b/var/spack/repos/builtin.mock/packages/mpich2/package.py index 19e8d3f8cc..8094c64acb 100644 --- a/var/spack/repos/builtin.mock/packages/mpich2/package.py +++ b/var/spack/repos/builtin.mock/packages/mpich2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/mpileaks/package.py b/var/spack/repos/builtin.mock/packages/mpileaks/package.py index ae80d16846..2e2e92d585 100644 --- a/var/spack/repos/builtin.mock/packages/mpileaks/package.py +++ b/var/spack/repos/builtin.mock/packages/mpileaks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py b/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py index 113582b66d..93babae83d 100644 --- a/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py +++ b/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/multimethod-base/package.py b/var/spack/repos/builtin.mock/packages/multimethod-base/package.py index 951fb6138d..142741f2d2 100644 --- a/var/spack/repos/builtin.mock/packages/multimethod-base/package.py +++ b/var/spack/repos/builtin.mock/packages/multimethod-base/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/multimethod-diamond-parent/package.py b/var/spack/repos/builtin.mock/packages/multimethod-diamond-parent/package.py index 1e91b6ea3f..cdde98165d 100644 --- a/var/spack/repos/builtin.mock/packages/multimethod-diamond-parent/package.py +++ b/var/spack/repos/builtin.mock/packages/multimethod-diamond-parent/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/multimethod-diamond/package.py b/var/spack/repos/builtin.mock/packages/multimethod-diamond/package.py index c7f51d9939..7f29e28411 100644 --- a/var/spack/repos/builtin.mock/packages/multimethod-diamond/package.py +++ b/var/spack/repos/builtin.mock/packages/multimethod-diamond/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/multimethod-inheritor/package.py b/var/spack/repos/builtin.mock/packages/multimethod-inheritor/package.py index 2ad77644d1..563e19dcb7 100644 --- a/var/spack/repos/builtin.mock/packages/multimethod-inheritor/package.py +++ b/var/spack/repos/builtin.mock/packages/multimethod-inheritor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/multimethod/package.py b/var/spack/repos/builtin.mock/packages/multimethod/package.py index 64067b5b22..2f0f869de0 100644 --- a/var/spack/repos/builtin.mock/packages/multimethod/package.py +++ b/var/spack/repos/builtin.mock/packages/multimethod/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/multimodule-inheritance/package.py b/var/spack/repos/builtin.mock/packages/multimodule-inheritance/package.py index 9690176a1c..8a3aeb0099 100644 --- a/var/spack/repos/builtin.mock/packages/multimodule-inheritance/package.py +++ b/var/spack/repos/builtin.mock/packages/multimodule-inheritance/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py b/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py index 3ae05c5110..3e3732aa84 100644 --- a/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py +++ b/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/netlib-blas/package.py b/var/spack/repos/builtin.mock/packages/netlib-blas/package.py index 5f8455ba4f..c4e8231d8f 100644 --- a/var/spack/repos/builtin.mock/packages/netlib-blas/package.py +++ b/var/spack/repos/builtin.mock/packages/netlib-blas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py b/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py index 46412d3764..d1a461d32c 100644 --- a/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/nosource-install/package.py b/var/spack/repos/builtin.mock/packages/nosource-install/package.py index 7ea8661d6e..74e95e75b0 100644 --- a/var/spack/repos/builtin.mock/packages/nosource-install/package.py +++ b/var/spack/repos/builtin.mock/packages/nosource-install/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/nosource/package.py b/var/spack/repos/builtin.mock/packages/nosource/package.py index 82e82267b0..cfc38fd5ff 100644 --- a/var/spack/repos/builtin.mock/packages/nosource/package.py +++ b/var/spack/repos/builtin.mock/packages/nosource/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/noversion-bundle/package.py b/var/spack/repos/builtin.mock/packages/noversion-bundle/package.py index de6400636d..57c26e1f25 100644 --- a/var/spack/repos/builtin.mock/packages/noversion-bundle/package.py +++ b/var/spack/repos/builtin.mock/packages/noversion-bundle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,5 +14,5 @@ class NoversionBundle(BundlePackage): """ homepage = "http://www.example.com" - + url = "http://www.example.com/a-1.0.tar.gz" depends_on('dependency-install') diff --git a/var/spack/repos/builtin.mock/packages/noversion/package.py b/var/spack/repos/builtin.mock/packages/noversion/package.py index 40889a6a11..e22519fcdf 100644 --- a/var/spack/repos/builtin.mock/packages/noversion/package.py +++ b/var/spack/repos/builtin.mock/packages/noversion/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py index e4756b727d..7bfea42eff 100644 --- a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py +++ b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/openblas/package.py b/var/spack/repos/builtin.mock/packages/openblas/package.py index 183dbcdb53..6947e3156f 100644 --- a/var/spack/repos/builtin.mock/packages/openblas/package.py +++ b/var/spack/repos/builtin.mock/packages/openblas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py index 5b7c61268b..585840a5b3 100644 --- a/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py +++ b/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py index 097f0aaf34..3529e9df5f 100644 --- a/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py +++ b/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py index bf57adeacf..363512c072 100644 --- a/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py +++ b/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/othervirtual/package.py b/var/spack/repos/builtin.mock/packages/othervirtual/package.py index bcf23e1a5b..d4cd1f4a2c 100644 --- a/var/spack/repos/builtin.mock/packages/othervirtual/package.py +++ b/var/spack/repos/builtin.mock/packages/othervirtual/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/override-context-templates/package.py b/var/spack/repos/builtin.mock/packages/override-context-templates/package.py index 246de8cc80..d67eabdeb8 100644 --- a/var/spack/repos/builtin.mock/packages/override-context-templates/package.py +++ b/var/spack/repos/builtin.mock/packages/override-context-templates/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/override-module-templates/package.py b/var/spack/repos/builtin.mock/packages/override-module-templates/package.py index f3cad009aa..90061399e8 100644 --- a/var/spack/repos/builtin.mock/packages/override-module-templates/package.py +++ b/var/spack/repos/builtin.mock/packages/override-module-templates/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py b/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py index f50888c173..aff2bf9722 100644 --- a/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py +++ b/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/patch-inheritance/package.py b/var/spack/repos/builtin.mock/packages/patch-inheritance/package.py index 6569af8a32..3f7486b878 100644 --- a/var/spack/repos/builtin.mock/packages/patch-inheritance/package.py +++ b/var/spack/repos/builtin.mock/packages/patch-inheritance/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py b/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py index 3c003d22f5..9d190c7658 100644 --- a/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py +++ b/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/patch/biz.patch b/var/spack/repos/builtin.mock/packages/patch/biz.patch new file mode 100644 index 0000000000..71a8a61460 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/patch/biz.patch @@ -0,0 +1 @@ +this patch is never applied, it is used to check spec semantics on when the concretizer chooses to include a patch diff --git a/var/spack/repos/builtin.mock/packages/patch/package.py b/var/spack/repos/builtin.mock/packages/patch/package.py index 37ea72fb1a..8219a4fbb6 100644 --- a/var/spack/repos/builtin.mock/packages/patch/package.py +++ b/var/spack/repos/builtin.mock/packages/patch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,11 +13,14 @@ class Patch(Package): url = "http://www.example.com/patch-1.0.tar.gz" version('1.0', '0123456789abcdef0123456789abcdef') + version('1.0.1') + version('1.0.2') version('2.0', '0123456789abcdef0123456789abcdef') patch('foo.patch') patch('bar.patch', when='@2:') patch('baz.patch') + patch('biz.patch', when='@1.0.1:1.0.2') def install(self, spec, prefix): pass diff --git a/var/spack/repos/builtin.mock/packages/patchelf/package.py b/var/spack/repos/builtin.mock/packages/patchelf/package.py index 14f6ae1bcd..0f72271921 100644 --- a/var/spack/repos/builtin.mock/packages/patchelf/package.py +++ b/var/spack/repos/builtin.mock/packages/patchelf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/perl-extension/package.py b/var/spack/repos/builtin.mock/packages/perl-extension/package.py index 18bd53e13d..af60caefd4 100644 --- a/var/spack/repos/builtin.mock/packages/perl-extension/package.py +++ b/var/spack/repos/builtin.mock/packages/perl-extension/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/perl/package.py b/var/spack/repos/builtin.mock/packages/perl/package.py index 9121ab1b7a..b9f75270bf 100644 --- a/var/spack/repos/builtin.mock/packages/perl/package.py +++ b/var/spack/repos/builtin.mock/packages/perl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/preferred-test/package.py b/var/spack/repos/builtin.mock/packages/preferred-test/package.py index 29da42242d..09e5aa034a 100644 --- a/var/spack/repos/builtin.mock/packages/preferred-test/package.py +++ b/var/spack/repos/builtin.mock/packages/preferred-test/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/printing-package/package.py b/var/spack/repos/builtin.mock/packages/printing-package/package.py index a4115ba99c..1d4d32d54d 100644 --- a/var/spack/repos/builtin.mock/packages/printing-package/package.py +++ b/var/spack/repos/builtin.mock/packages/printing-package/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/py-extension1/package.py b/var/spack/repos/builtin.mock/packages/py-extension1/package.py index 8bce48e9ce..d596440b78 100644 --- a/var/spack/repos/builtin.mock/packages/py-extension1/package.py +++ b/var/spack/repos/builtin.mock/packages/py-extension1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/py-extension2/package.py b/var/spack/repos/builtin.mock/packages/py-extension2/package.py index d60608d9ea..08e5d07f37 100644 --- a/var/spack/repos/builtin.mock/packages/py-extension2/package.py +++ b/var/spack/repos/builtin.mock/packages/py-extension2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/python/package.py b/var/spack/repos/builtin.mock/packages/python/package.py index f04cb8030f..b15a9fd38a 100644 --- a/var/spack/repos/builtin.mock/packages/python/package.py +++ b/var/spack/repos/builtin.mock/packages/python/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/raiser/package.py b/var/spack/repos/builtin.mock/packages/raiser/package.py index e8257887da..5337d8b127 100644 --- a/var/spack/repos/builtin.mock/packages/raiser/package.py +++ b/var/spack/repos/builtin.mock/packages/raiser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py b/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py index 3d23c94aec..a6f29f5ed5 100644 --- a/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py +++ b/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py b/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py index a3b788f1b4..640594f0ed 100644 --- a/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py +++ b/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/svn-test/package.py b/var/spack/repos/builtin.mock/packages/svn-test/package.py index 44c765f86a..c982bb0649 100644 --- a/var/spack/repos/builtin.mock/packages/svn-test/package.py +++ b/var/spack/repos/builtin.mock/packages/svn-test/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/svn-top-level/package.py b/var/spack/repos/builtin.mock/packages/svn-top-level/package.py index f82e304421..83588e97b3 100644 --- a/var/spack/repos/builtin.mock/packages/svn-top-level/package.py +++ b/var/spack/repos/builtin.mock/packages/svn-top-level/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py b/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py index 6322c52995..180eddcd94 100644 --- a/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py +++ b/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/url-list-test/package.py b/var/spack/repos/builtin.mock/packages/url-list-test/package.py index ff4b65af23..4a9bd1fc56 100644 --- a/var/spack/repos/builtin.mock/packages/url-list-test/package.py +++ b/var/spack/repos/builtin.mock/packages/url-list-test/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/url-only-override-with-gaps/package.py b/var/spack/repos/builtin.mock/packages/url-only-override-with-gaps/package.py index 971aabafc9..5ceaabdfd9 100644 --- a/var/spack/repos/builtin.mock/packages/url-only-override-with-gaps/package.py +++ b/var/spack/repos/builtin.mock/packages/url-only-override-with-gaps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/url-only-override/package.py b/var/spack/repos/builtin.mock/packages/url-only-override/package.py index ab1be9296e..fdc1584116 100644 --- a/var/spack/repos/builtin.mock/packages/url-only-override/package.py +++ b/var/spack/repos/builtin.mock/packages/url-only-override/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/url-test/package.py b/var/spack/repos/builtin.mock/packages/url-test/package.py index e736774863..6a7d2b9416 100644 --- a/var/spack/repos/builtin.mock/packages/url-test/package.py +++ b/var/spack/repos/builtin.mock/packages/url-test/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/url_override/package.py b/var/spack/repos/builtin.mock/packages/url_override/package.py index f921676305..52eaf47d48 100644 --- a/var/spack/repos/builtin.mock/packages/url_override/package.py +++ b/var/spack/repos/builtin.mock/packages/url_override/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/when-directives-false/package.py b/var/spack/repos/builtin.mock/packages/when-directives-false/package.py index bdb24cac79..105caeccdf 100644 --- a/var/spack/repos/builtin.mock/packages/when-directives-false/package.py +++ b/var/spack/repos/builtin.mock/packages/when-directives-false/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/when-directives-true/package.py b/var/spack/repos/builtin.mock/packages/when-directives-true/package.py index 69c90128b2..50dd5a00f4 100644 --- a/var/spack/repos/builtin.mock/packages/when-directives-true/package.py +++ b/var/spack/repos/builtin.mock/packages/when-directives-true/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin.mock/packages/zmpi/package.py b/var/spack/repos/builtin.mock/packages/zmpi/package.py index c29d14170e..f0060b319e 100644 --- a/var/spack/repos/builtin.mock/packages/zmpi/package.py +++ b/var/spack/repos/builtin.mock/packages/zmpi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/abinit/package.py b/var/spack/repos/builtin/packages/abinit/package.py index 98953214a7..6f07ffee81 100644 --- a/var/spack/repos/builtin/packages/abinit/package.py +++ b/var/spack/repos/builtin/packages/abinit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -71,7 +71,7 @@ class Abinit(AutotoolsPackage): # depends_on('elpa~openmp', when='+elpa+mpi~openmp') # depends_on('elpa+openmp', when='+elpa+mpi+openmp') - depends_on('fftw precision=float') + depends_on('fftw precision=float,double') depends_on('fftw~openmp', when='~openmp') depends_on('fftw+openmp', when='+openmp') diff --git a/var/spack/repos/builtin/packages/abseil-cpp/package.py b/var/spack/repos/builtin/packages/abseil-cpp/package.py new file mode 100644 index 0000000000..90fd6cbd87 --- /dev/null +++ b/var/spack/repos/builtin/packages/abseil-cpp/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class AbseilCpp(CMakePackage): + """Abseil Common Libraries (C++) """ + + homepage = "https://abseil.io/" + url = "https://github.com/abseil/abseil-cpp/archive/20180600.tar.gz" + + maintainers = ['jcftang'] + + version('20190808', sha256='8100085dada279bf3ee00cd064d43b5f55e5d913be0dfe2906f06f8f28d5b37e') + version('20181200', sha256='e2b53bfb685f5d4130b84c4f3050c81bf48c497614dc85d91dbd3ed9129bce6d') + version('20180600', sha256='794d483dd9a19c43dc1fbbe284ce8956eb7f2600ef350dac4c602f9b4eb26e90') + + def cmake_args(self): + args = ["-DBUILD_TESTING=OFF", "-DCMAKE_CXX_STANDARD=11"] + return args diff --git a/var/spack/repos/builtin/packages/abyss/package.py b/var/spack/repos/builtin/packages/abyss/package.py index 361d3e96c7..339441392d 100644 --- a/var/spack/repos/builtin/packages/abyss/package.py +++ b/var/spack/repos/builtin/packages/abyss/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/accfft/fix_narrowing_error.patch b/var/spack/repos/builtin/packages/accfft/fix_narrowing_error.patch new file mode 100644 index 0000000000..bdd48cbc1c --- /dev/null +++ b/var/spack/repos/builtin/packages/accfft/fix_narrowing_error.patch @@ -0,0 +1,11 @@ +--- spack-src/include/parUtils.txx.org 2019-11-27 16:41:07.438799437 +0900 ++++ spack-src/include/parUtils.txx 2019-11-27 16:54:51.654921619 +0900 +@@ -70,7 +70,7 @@ + } + omp_par::scan(&s_cnt[0],&s_dsp[0],np+1); + +- size_t range[2]={0,np}; ++ size_t range[2]={0,(unsigned long)np}; + for(size_t np_new=np; np_new>1; np_new/=kway){ + double tt=omp_get_wtime(); + if(kway>np_new) kway=np_new; diff --git a/var/spack/repos/builtin/packages/accfft/package.py b/var/spack/repos/builtin/packages/accfft/package.py index 8c200b76f9..7009695240 100644 --- a/var/spack/repos/builtin/packages/accfft/package.py +++ b/var/spack/repos/builtin/packages/accfft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,6 +24,9 @@ class Accfft(CMakePackage, CudaPackage): depends_on('parallel-netcdf', when='+pnetcdf') + # fix error [-Wc++11-narrowing] + patch('fix_narrowing_error.patch') + parallel = False def cmake_args(self): diff --git a/var/spack/repos/builtin/packages/ace/package.py b/var/spack/repos/builtin/packages/ace/package.py index 0c57bb6dbf..42250e3e6f 100644 --- a/var/spack/repos/builtin/packages/ace/package.py +++ b/var/spack/repos/builtin/packages/ace/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ack/package.py b/var/spack/repos/builtin/packages/ack/package.py index efbe029b32..1faf0f7a14 100644 --- a/var/spack/repos/builtin/packages/ack/package.py +++ b/var/spack/repos/builtin/packages/ack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,11 +25,13 @@ class Ack(Package): def install(self, spec, prefix): mkdirp(prefix.bin) - ack = 'ack-{0}-single-file'.format(self.version) + ack_source = 'ack-{0}-single-file'.format(self.version) + ack_installed = join_path(prefix.bin, "ack") + + # install source + install(ack_source, ack_installed) + set_executable(ack_installed) # rewrite the script's #! line to call the perl dependency shbang = '#!' + spec['perl'].command.path - filter_file(r'^#!/usr/bin/env perl', shbang, ack) - - install(ack, join_path(prefix.bin, "ack")) - set_executable(join_path(prefix.bin, "ack")) + filter_file(r'^#!/usr/bin/env perl', shbang, ack_installed) diff --git a/var/spack/repos/builtin/packages/activeharmony/package.py b/var/spack/repos/builtin/packages/activeharmony/package.py index f53ed791b6..179a5a68cc 100644 --- a/var/spack/repos/builtin/packages/activeharmony/package.py +++ b/var/spack/repos/builtin/packages/activeharmony/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/activemq/package.py b/var/spack/repos/builtin/packages/activemq/package.py new file mode 100644 index 0000000000..54cff4de32 --- /dev/null +++ b/var/spack/repos/builtin/packages/activemq/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Activemq(Package): + """ + Apache ActiveMQ is a high performance Apache 2.0 licensed Message Broker + and JMS 1.1 implementation. + """ + + homepage = "https://archive.apache.org/dist/activemq" + url = "https://archive.apache.org/dist/activemq/5.14.0/apache-activemq-5.14.0-bin.tar.gz" + + version('5.14.0', sha256='81c623465af277dd50a141a8d9308d6ec8e1b78d9019b845873dc12d117aa9a6') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/acts-core/package.py b/var/spack/repos/builtin/packages/acts-core/package.py index 30cba1eaa8..644397102a 100644 --- a/var/spack/repos/builtin/packages/acts-core/package.py +++ b/var/spack/repos/builtin/packages/acts-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,8 +31,17 @@ class ActsCore(CMakePackage): homepage = "http://acts.web.cern.ch/ACTS/" git = "https://gitlab.cern.ch/acts/acts-core.git" + maintainers = ['HadrienG2'] version('develop', branch='master') + version('0.15.0', commit='267c28f69c561e64369661a6235b03b5a610d6da') + version('0.14.0', commit='38d678fcb205b77d60326eae913fbb1b054acea1') + version('0.13.0', commit='b33f7270ddbbb33050b7ec60b4fa255dc2bfdc88') + version('0.12.1', commit='a8b3d36e7c6cb86487637589e0eff7bbe626054a') + version('0.12.0', commit='f9cda77299606d78c889fb1db2576c1971a271c4') + version('0.11.1', commit='c21196cd6c3ecc6da0f14d0a9ef227a274be584b') + version('0.11.0', commit='22bcea1f19adb0021ca61b843b95cfd2462dd31d') + version('0.10.5', commit='b6f7234ca8f18ee11e57709d019c14bf41cf9b19') version('0.10.4', commit='42cbc359c209f5cf386e620b5a497192c024655e') version('0.10.3', commit='a3bb86b79a65b3d2ceb962b60411fd0df4cf274c') version('0.10.2', commit='64cbf28c862d8b0f95232b00c0e8c38949d5015d') @@ -61,12 +70,13 @@ class ActsCore(CMakePackage): variant('json', default=False, description='Build the Json plugin') variant('tgeo', default=False, description='Build the TGeo plugin') - depends_on('cmake @3.9:', type='build') + depends_on('cmake @3.11:', type='build') depends_on('boost @1.62:1.69.99 +program_options +test', when='@:0.10.3') depends_on('boost @1.62: +program_options +test', when='@0.10.4:') depends_on('eigen @3.2.9:', type='build') + depends_on('nlohmann-json @3.2.0:', when='@0.14.0: +json') depends_on('root @6.10: cxxstd=14', when='+tgeo @:0.8.0') - depends_on('root @6.10:', when='+tgeo @0.8.1:') + depends_on('root @6.10: cxxstd=17', when='+tgeo @0.8.1:') depends_on('dd4hep @1.2:', when='+dd4hep') def cmake_args(self): @@ -83,7 +93,7 @@ class ActsCore(CMakePackage): cmake_variant("INTEGRATION_TESTS", "integration_tests"), cmake_variant("DIGITIZATION_PLUGIN", "digitization"), cmake_variant("DD4HEP_PLUGIN", "dd4hep"), - cmake_variant("IDENTIFICATION", "identification"), + cmake_variant("IDENTIFICATION_PLUGIN", "identification"), cmake_variant("JSON_PLUGIN", "json"), cmake_variant("TGEO_PLUGIN", "tgeo") ] @@ -92,4 +102,7 @@ class ActsCore(CMakePackage): cxxstd = spec['root'].variants['cxxstd'].value args.append("-DCMAKE_CXX_STANDARD={0}".format(cxxstd)) + if spec.satisfies('@0.14.0: +json'): + args.append("-DACTS_USE_BUNDLED_NLOHMANN_JSON=OFF") + return args diff --git a/var/spack/repos/builtin/packages/adept-utils/package.py b/var/spack/repos/builtin/packages/adept-utils/package.py index b5f03b3c9f..12cb357f9a 100644 --- a/var/spack/repos/builtin/packages/adept-utils/package.py +++ b/var/spack/repos/builtin/packages/adept-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/adf/package.py b/var/spack/repos/builtin/packages/adf/package.py new file mode 100644 index 0000000000..ca08794d10 --- /dev/null +++ b/var/spack/repos/builtin/packages/adf/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +class Adf(Package): + """Amsterdam Density Functional (ADF) is a program for first-principles + electronic structure calculations that makes use of density functional + theory.""" + + homepage = "https://www.scm.com/product/adf/" + version('2017.113', '666ef15d253b74c707dd14da35e7cf283ca20e21e24ed43cb953fb9d1f2f1e15') + + def url_for_version(self, version): + return "file://{0}/adf/adf{1}.pc64_linux.openmpi.bin.tgz".format( + os.getcwd(), version) + + # Licensing + license_required = True + license_files = ['license.txt'] + license_vars = ['SCMLICENSE'] + + def setup_run_environment(self, env): + env.set('ADFHOME', self.prefix) + env.set('ADFBIN', self.prefix.bin) + env.set('ADFRESOURCES', self.prefix.atomicdata) + env.set('SCMLICENSE', join_path(self.prefix, 'license.txt')) + env.set('SCM_TMPDIR', '/tmp') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/adiak/package.py b/var/spack/repos/builtin/packages/adiak/package.py index 774ef198c0..fc343c8d01 100644 --- a/var/spack/repos/builtin/packages/adiak/package.py +++ b/var/spack/repos/builtin/packages/adiak/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py index 4b8e417a11..6994963898 100644 --- a/var/spack/repos/builtin/packages/adios/package.py +++ b/var/spack/repos/builtin/packages/adios/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -84,7 +84,7 @@ class Adios(AutotoolsPackage): depends_on('c-blosc@1.12.0:', when='+blosc') # optional transports & file converters depends_on('hdf5@1.8:+hl+mpi', when='+hdf5') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('libevpath', when='staging=flexpath') depends_on('dataspaces+mpi', when='staging=dataspaces') diff --git a/var/spack/repos/builtin/packages/adios2/2.5-fix-clear_cache.patch b/var/spack/repos/builtin/packages/adios2/2.5-fix-clear_cache.patch new file mode 100644 index 0000000000..2a2e86cc32 --- /dev/null +++ b/var/spack/repos/builtin/packages/adios2/2.5-fix-clear_cache.patch @@ -0,0 +1,213 @@ +From 2f05a0b1def194001d1f6e0f9a07725c10b48301 Mon Sep 17 00:00:00 2001 +From: Greg Eisenhauer <eisen@cc.gatech.edu> +Date: Fri, 13 Dec 2019 10:00:15 -0500 +Subject: [PATCH] Merge branch 'upstream-dill' into DillUpstream + +* upstream-dill: + dill 2019-12-12 (dac6dfcc) +--- + thirdparty/dill/dill/CMakeLists.txt | 5 ++++- + thirdparty/dill/dill/LICENSE | 24 ++++++++++++++++++++++++ + thirdparty/dill/dill/arm6.c | 19 +++---------------- + thirdparty/dill/dill/arm6_rt.c | 19 +++---------------- + thirdparty/dill/dill/arm8.c | 19 +++---------------- + thirdparty/dill/dill/arm8_rt.c | 19 +++---------------- + thirdparty/dill/dill/config.h.cmake | 7 +++++-- + 7 files changed, 45 insertions(+), 67 deletions(-) + create mode 100644 thirdparty/dill/dill/LICENSE + +diff --git a/thirdparty/dill/dill/CMakeLists.txt b/thirdparty/dill/dill/CMakeLists.txt +index 0461556a..695db8c6 100644 +--- a/thirdparty/dill/dill/CMakeLists.txt ++++ b/thirdparty/dill/dill/CMakeLists.txt +@@ -1,6 +1,6 @@ + cmake_minimum_required(VERSION 3.0) + +-project(DILL VERSION 2.4.0 LANGUAGES C CXX) ++project(DILL VERSION 2.4.1 LANGUAGES C CXX) + + # Some boilerplate to setup nice output directories + include(GNUInstallDirs) +@@ -265,6 +265,9 @@ check_include_files(unistd.h HAVE_UNISTD_H) + check_include_files(stdarg.h STDC_HEADERS) + check_include_files(malloc.h HAVE_MALLOC_H) + check_include_files(memory.h HAVE_MEMORY_H) ++include(CheckSymbolExists) ++check_symbol_exists(__clear_cache "" CLEAR_CACHE_DEFINED) ++message(STATUS "Clear cache defined is ${CLEAR_CACHE_DEFINED}") + + set(NO_DISASSEMBLER TRUE) + if(DILL_ENABLE_DISASSEMBLY) +diff --git a/thirdparty/dill/dill/LICENSE b/thirdparty/dill/dill/LICENSE +new file mode 100644 +index 00000000..81b08341 +--- /dev/null ++++ b/thirdparty/dill/dill/LICENSE +@@ -0,0 +1,24 @@ ++Copyright (c) 2010, Georgia Tech Research Corporation ++All rights reserved. ++ ++Redistribution and use in source and binary forms, with or without ++modification, are permitted provided that the following conditions are met: ++ * Redistributions of source code must retain the above copyright ++ notice, this list of conditions and the following disclaimer. ++ * Redistributions in binary form must reproduce the above copyright ++ notice, this list of conditions and the following disclaimer in the ++ documentation and/or other materials provided with the distribution. ++ * Neither the name of the Georgia Tech Research Corporation nor the ++ names of its contributors may be used to endorse or promote products ++ derived from this software without specific prior written permission. ++ ++THIS SOFTWARE IS PROVIDED BY GEORGIA TECH RESEARCH CORPORATION ''AS IS'' AND ++ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ++WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE ++DISCLAIMED. IN NO EVENT SHALL GEORGIA TECH BE LIABLE FOR ANY DIRECT, INDIRECT, ++INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT ++LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, ++OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF ++LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE ++OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ++ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +diff --git a/thirdparty/dill/dill/arm6.c b/thirdparty/dill/dill/arm6.c +index f2be1725..da90507c 100644 +--- a/thirdparty/dill/dill/arm6.c ++++ b/thirdparty/dill/dill/arm6.c +@@ -1526,22 +1526,9 @@ arm6_call_link(dill_stream s) + } + + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm6_flush(void *base, void *limit) +diff --git a/thirdparty/dill/dill/arm6_rt.c b/thirdparty/dill/dill/arm6_rt.c +index 1f64b477..6b7e908e 100644 +--- a/thirdparty/dill/dill/arm6_rt.c ++++ b/thirdparty/dill/dill/arm6_rt.c +@@ -109,22 +109,9 @@ arm6_rt_call_link(char *code, call_t *t) + } + } + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm6_flush(void *base, void *limit) +diff --git a/thirdparty/dill/dill/arm8.c b/thirdparty/dill/dill/arm8.c +index fd5ed79f..d1894635 100644 +--- a/thirdparty/dill/dill/arm8.c ++++ b/thirdparty/dill/dill/arm8.c +@@ -1524,22 +1524,9 @@ arm8_call_link(dill_stream s) + } + + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm8_flush(void *base, void *limit) +diff --git a/thirdparty/dill/dill/arm8_rt.c b/thirdparty/dill/dill/arm8_rt.c +index bd0209cd..5cb107ed 100644 +--- a/thirdparty/dill/dill/arm8_rt.c ++++ b/thirdparty/dill/dill/arm8_rt.c +@@ -109,22 +109,9 @@ arm8_rt_call_link(char *code, call_t *t) + } + } + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm8_flush(void *base, void *limit) +diff --git a/thirdparty/dill/dill/config.h.cmake b/thirdparty/dill/dill/config.h.cmake +index a8519064..a9622f56 100644 +--- a/thirdparty/dill/dill/config.h.cmake ++++ b/thirdparty/dill/dill/config.h.cmake +@@ -16,10 +16,13 @@ + #cmakedefine HAVE_DIS_ASM_H + + /* Define to 1 if you have the <dlfcn.h> header file. */ +-#undef HAVE_DLFCN_H ++#cmakedefine HAVE_DLFCN_H + + /* Define to 1 if you have the <inttypes.h> header file. */ +-#undef HAVE_INTTYPES_H ++#cmakedefine HAVE_INTTYPES_H ++ ++/* Define to 1 if you have __clear_cache is defined */ ++#cmakedefine CLEAR_CACHE_DEFINED + + /* Define to 1 if you have the <malloc.h> header file. */ + #cmakedefine HAVE_MALLOC_H +-- +2.18.1 + diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py index e5e10db996..c9e32faec5 100644 --- a/var/spack/repos/builtin/packages/adios2/package.py +++ b/var/spack/repos/builtin/packages/adios2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -85,8 +85,8 @@ class Adios2(CMakePackage): # depends_on('flex', when='+sst') # optional in FFS, depends on BISON depends_on('mpi', when='+mpi') - depends_on('zeromq', when='+dataman') - depends_on('zeromq', when='@2.4: +ssc') + depends_on('libzmq', when='+dataman') + depends_on('libzmq', when='@2.4: +ssc') depends_on('dataspaces@1.8.0:', when='+dataspaces') depends_on('hdf5', when='+hdf5') @@ -109,6 +109,11 @@ class Adios2(CMakePackage): # See https://github.com/ornladios/ADIOS2/pull/1632 patch('cmake-update-findmpi.patch', when='@2.4.0') + # Fix the signature of the builtin clear_cache function in the + # third-party dill library. + # See https://github.com/ornladios/ADIOS2/pull/1899 + patch('2.5-fix-clear_cache.patch', when='@2.5.0') + def cmake_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/adlbx/package.py b/var/spack/repos/builtin/packages/adlbx/package.py index e4e7c178f9..dad534faaa 100644 --- a/var/spack/repos/builtin/packages/adlbx/package.py +++ b/var/spack/repos/builtin/packages/adlbx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class Adlbx(AutotoolsPackage): """ADLB/X: Master-worker library + work stealing and data dependencies""" homepage = 'http://swift-lang.org/Swift-T' - url = 'http://swift-lang.github.io/swift-t-downloads/spack/adlbx-0.0.0.tar.gz' + url = 'http://swift-lang.github.io/swift-t-downloads/spack/adlbx-0.9.2.tar.gz' git = "https://github.com/swift-lang/swift-t.git" version('master', branch='master') @@ -27,11 +27,11 @@ class Adlbx(AutotoolsPackage): depends_on('m4', type='build', when='@master') depends_on('mpi') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('CC', spec['mpi'].mpicc) - spack_env.set('CXX', spec['mpi'].mpicxx) - spack_env.set('CXXLD', spec['mpi'].mpicxx) + env.set('CC', spec['mpi'].mpicc) + env.set('CXX', spec['mpi'].mpicxx) + env.set('CXXLD', spec['mpi'].mpicxx) @property def configure_directory(self): diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py index cb83d4d68d..336f1833db 100644 --- a/var/spack/repos/builtin/packages/adol-c/package.py +++ b/var/spack/repos/builtin/packages/adol-c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/aegean/package.py b/var/spack/repos/builtin/packages/aegean/package.py index 9c5778b851..9198280e9a 100644 --- a/var/spack/repos/builtin/packages/aegean/package.py +++ b/var/spack/repos/builtin/packages/aegean/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/aida/package.py b/var/spack/repos/builtin/packages/aida/package.py index 349feb3629..592387b86b 100644 --- a/var/spack/repos/builtin/packages/aida/package.py +++ b/var/spack/repos/builtin/packages/aida/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/akantu/package.py b/var/spack/repos/builtin/packages/akantu/package.py new file mode 100644 index 0000000000..c58225261f --- /dev/null +++ b/var/spack/repos/builtin/packages/akantu/package.py @@ -0,0 +1,92 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Akantu(CMakePackage): + """ + Akantu means a little element in Kinyarwanda, a Bantu language. From now + on it is also an opensource object-oriented Finite Element library which + has the ambition to be generic and efficient. + + """ + homepage = "https://akantu.ch" + url = "https://gitlab.com/akantu/akantu/-/archive/v3.0.0/akantu-v3.0.0.tar.gz" + git = "https://gitlab.com/akantu/akantu.git" + + maintainers = ['nrichart'] + + version('master', branch='master') + version('3.0.0', sha256='7e8f64e25956eba44def1b2d891f6db8ba824e4a82ff0d51d6b585b60ab465db') + + variant('external_solvers', values=any_combination_of('mumps', 'petsc'), + description="Activates the implicit solver") + variant('mpi', default=True, + description="Activates parallel capabilities") + variant('python', default=False, + description="Activates python bindings") + + depends_on('boost@:1.66', when='@:3.0.99') + depends_on('boost') + depends_on('lapack') + depends_on('cmake@3.5.1:', type='build') + depends_on('python', when='+python', type=('build', 'run')) + depends_on('py-numpy', when='+python', type=('build', 'run')) + depends_on('py-scipy', when='+python', type=('build', 'run')) + depends_on('py-pybind11', when='@3.1:+python', type=('build', 'run')) + + depends_on('mumps', when='~mpi external_solvers=mumps') + depends_on('mumps+mpi', when='+mpi external_solvers=mumps') + depends_on('netlib-scalapack', when='+mpi external_solvers=mumps') + depends_on('petsc+double', when='~mpi external_solvers=petsc') + depends_on('petsc+double+mpi', when='+mpi external_solvers=petsc') + + depends_on('mpi', when='+mpi') + depends_on('scotch', when='+mpi') + + extends('python', when='+python') + + conflicts('gcc@:5.3.99') + conflicts('@:3.0.99 external_solvers=petsc') + conflicts('@:3.0.99 +python') + + def cmake_args(self): + spec = self.spec + + args = [ + '-DAKANTU_COHESIVE_ELEMENT:BOOL=ON', + '-DAKANTU_DAMAGE_NON_LOCAL:BOOL=ON', + '-DAKANTU_HEAT_TRANSFER:BOOL=ON', + '-DAKANTU_SOLID_MECHANICS:BOOL=ON', + '-DAKANTU_STRUCTURAL_MECHANICS:BOOL=OFF', + '-DAKANTU_PARALLEL:BOOL={0}'.format( + 'ON' if spec.satisfies('+mpi') else 'OFF'), + '-DAKANTU_PYTHON_INTERFACE:BOOL={0}'.format( + 'ON' if spec.satisfies('+python') else 'OFF'), + ] + + if spec.satisfies('@:3.0.99'): + args.extend(['-DCMAKE_CXX_FLAGS=-Wno-class-memaccess', + '-DAKANTU_TRACTION_AT_SPLIT_NODE_CONTACT:BOOL=OFF']) + else: + args.append('-DAKANTU_TRACTION_AT_SPLIT_NODE_CONTACT:BOOL=ON') + + solvers = [] + if spec.satisfies('external_solvers=mumps'): + solvers.append('Mumps') + args.append('-DMUMPS_DIR:PATH=${0}'.format(spec['mumps'].prefix)) + if spec.satisfies('external_solvers=petsc'): + solvers.append('PETSc') + + if len(solvers) > 0: + args.extend([ + '-DAKANTU_IMPLICIT_SOLVER:STRING={0}'.format( + '+'.join(solvers)), + '-DAKANTU_IMPLICIT:BOOL=ON']) + else: + args.append('-DAKANTU_IMPLICIT:BOOL=OFF') + + return args diff --git a/var/spack/repos/builtin/packages/alan/package.py b/var/spack/repos/builtin/packages/alan/package.py index aab36f4fbf..fcf0b69f92 100644 --- a/var/spack/repos/builtin/packages/alan/package.py +++ b/var/spack/repos/builtin/packages/alan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/albany/package.py b/var/spack/repos/builtin/packages/albany/package.py index 76207cfa69..c906d898f5 100644 --- a/var/spack/repos/builtin/packages/albany/package.py +++ b/var/spack/repos/builtin/packages/albany/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/albert/package.py b/var/spack/repos/builtin/packages/albert/package.py index 1d94483f4f..386220fa3a 100644 --- a/var/spack/repos/builtin/packages/albert/package.py +++ b/var/spack/repos/builtin/packages/albert/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/alglib/package.py b/var/spack/repos/builtin/packages/alglib/package.py index 30a1c0b2c4..82a1d0e3a3 100644 --- a/var/spack/repos/builtin/packages/alglib/package.py +++ b/var/spack/repos/builtin/packages/alglib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,9 +18,6 @@ class Alglib(MakefilePackage): version('3.11.0', sha256='34e391594aac89fb354bdaf58c42849489cd1199197398ba98bb69961f42bdb0') - def url_for_version(self, version): - return 'http://www.alglib.net/translator/re/alglib-{0}.cpp.gpl.tgz'.format(version.dotted) - build_directory = 'src' def edit(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/allpaths-lg/package.py b/var/spack/repos/builtin/packages/allpaths-lg/package.py index c8d580d08e..6ebca2eee6 100644 --- a/var/spack/repos/builtin/packages/allpaths-lg/package.py +++ b/var/spack/repos/builtin/packages/allpaths-lg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class AllpathsLg(AutotoolsPackage): small and large (mammalian size) genomes.""" homepage = "http://www.broadinstitute.org/software/allpaths-lg/blog/" - url = "ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz" + url = "ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/allpathslg-52488.tar.gz" version('52488', sha256='035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542') diff --git a/var/spack/repos/builtin/packages/alluxio/package.py b/var/spack/repos/builtin/packages/alluxio/package.py new file mode 100644 index 0000000000..d608af7a05 --- /dev/null +++ b/var/spack/repos/builtin/packages/alluxio/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Alluxio(Package): + """ + Alluxio (formerly known as Tachyon) is a virtual distributed storage + system. It bridges the gap between computation frameworks and storage + systems, enabling computation applications to connect to numerous + storage systems through a common interface. + """ + + homepage = "https://github.com/Alluxio/alluxio" + url = "https://github.com/Alluxio/alluxio/archive/v2.1.0.tar.gz" + + version('2.1.0', sha256='c8b5b7848488e0ac10b093eea02ef05fa822250669d184291cc51b2f8aac253e') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/alquimia/package.py b/var/spack/repos/builtin/packages/alquimia/package.py index 1484fc1fa5..89260a0cab 100644 --- a/var/spack/repos/builtin/packages/alquimia/package.py +++ b/var/spack/repos/builtin/packages/alquimia/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,6 +16,7 @@ class Alquimia(CMakePackage): maintainers = ['smolins', 'balay'] version('develop') + version('xsdk-0.5.0', commit='8397c3b00a09534c5473ff3ab21f0e32bb159380') version('xsdk-0.4.0', commit='2edad6733106142d014bb6e6a73c2b21d5e3cf2d') version('xsdk-0.3.0', tag='xsdk-0.3.0') version('xsdk-0.2.0', tag='xsdk-0.2.0') @@ -25,6 +26,7 @@ class Alquimia(CMakePackage): depends_on('mpi') depends_on('hdf5') + depends_on('pflotran@xsdk-0.5.0', when='@xsdk-0.5.0') depends_on('pflotran@xsdk-0.4.0', when='@xsdk-0.4.0') depends_on('pflotran@xsdk-0.3.0', when='@xsdk-0.3.0') depends_on('pflotran@xsdk-0.2.0', when='@xsdk-0.2.0') diff --git a/var/spack/repos/builtin/packages/alsa-lib/package.py b/var/spack/repos/builtin/packages/alsa-lib/package.py index b79bcd3d7c..e766a8cc16 100644 --- a/var/spack/repos/builtin/packages/alsa-lib/package.py +++ b/var/spack/repos/builtin/packages/alsa-lib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/aluminum/package.py b/var/spack/repos/builtin/packages/aluminum/package.py index cafb0595d9..535f4df5f2 100644 --- a/var/spack/repos/builtin/packages/aluminum/package.py +++ b/var/spack/repos/builtin/packages/aluminum/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,6 +19,9 @@ class Aluminum(CMakePackage): git = "https://github.com/LLNL/Aluminum.git" version('master', branch='master') + version('0.3.3', sha256='26e7f263f53c6c6ee0fe216e981a558dfdd7ec997d0dd2a24285a609a6c68f3b') + version('0.3.2', sha256='09b6d1bcc02ac54ba269b1123eee7be20f0104b93596956c014b794ba96b037f') + version('0.2.1-1', sha256='066b750e9d1134871709a3e2414b96b166e0e24773efc7d512df2f1d96ee8eef') version('0.2.1', sha256='3d5d15853cccc718f60df68205e56a2831de65be4d96e7f7e8497097e7905f89') version('0.2', sha256='fc8f06c6d8faab17a2aedd408d3fe924043bf857da1094d5553f35c4d2af893b') version('0.1', sha256='3880b736866e439dd94e6a61eeeb5bb2abccebbac82b82d52033bc6c94950bdb') diff --git a/var/spack/repos/builtin/packages/amber/package.py b/var/spack/repos/builtin/packages/amber/package.py index 94e3f23d1e..eae98b53bd 100644 --- a/var/spack/repos/builtin/packages/amber/package.py +++ b/var/spack/repos/builtin/packages/amber/package.py @@ -1,10 +1,11 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * import os +import shutil class Amber(Package, CudaPackage): @@ -17,63 +18,171 @@ class Amber(Package, CudaPackage): http://spack.readthedocs.io/en/latest/mirrors.html""" homepage = "http://ambermd.org/" - url = "file://{0}/Amber16.tar.bz2".format(os.getcwd()) + url = "file://{0}/Amber18.tar.bz2".format(os.getcwd()) + maintainers = ['hseara'] + version('18', sha256='2060897c0b11576082d523fb63a51ba701bc7519ff7be3d299d5ec56e8e6e277') version('16', sha256='3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d') - variant('mpi', description='Build MPI executables', default=True) + resources = [ + # [version amber, version ambertools , sha256sum] + ('18', '19', '0c86937904854b64e4831e047851f504ec45b42e593db4ded92c1bee5973e699'), + ('16', '16', '7b876afe566e9dd7eb6a5aa952a955649044360f15c1f5d4d91ba7f41f3105fa'), + ] + for ver, ambertools_ver, checksum in resources: + resource(when='@{0}'.format(ver), + name='AmberTools', + url='file://{0}/AmberTools{1}.tar.bz2'.format(os.getcwd(), + ambertools_ver), + sha256=checksum, + destination='', + placement='ambertools_tmpdir', + ) + + patches = [ + ('18', '1', '3cefac9a24ece99176d5d2d58fea2722de3e235be5138a128428b9260fe922ad'), + ('18', '2', '3a0707a9a59dcbffa765dcf87b68001450095c51b96ec39d21260ba548a2f66a'), + ('18', '3', '24c2e06f71ae553a408caa3f722254db2cbf1ca4db274542302184e3d6ca7015'), + ('18', '4', '51de613e8fda20cc92979265cf7179288df8c1af4202f02794ad7327fda2657b'), + ('18', '5', 'c70354bfa312603e4819efce11a242ddcc3830895453d9424f0c83f7ae98bc5b'), + ('18', '6', '3450433a8697b27e43172043be68d31515a7c7c00b2b248f84043dd70a2f59a8'), + ('18', '7', '10ba41422b7a3eb5b32bc6453231100544cf620c764ab8332c629a3b9fc749d4'), + ('18', '8', '73968dc0fd99bcbd5eae2223bd54f414879c062ac933948ba6b8b67383dc6a53'), + ('18', '9', 'e7d72fa31560f1e8ea572b8c73259d9fe512f56fbeb1b58ae014c43b9b5b6290'), + ('18', '10', '1bee419a3b0b686a729aa12515b0f96a9a8f43478ca2c01ea1661cc1698c6266'), + ('18', '11', '926557f0c137ea8dbf99a0487b25e131b12dfd39977d3e515f01f49187e6a09c'), + ('18', '12', '7e2645d539d257f7064808308048622818c9083dedfa4ac0a958cd15181231ac'), + ('18', '13', '95d2e33d0d05b8f9b6d8091d1c804271ec3a69e9aef792cc3b1ab8a2165eca3e'), + ('18', '14', 'a1adfb072f60ffcb67adb589df7c5578629441bee4ccb89ab635a6e8d7a35277'), + ('18', '15', '4deb3df329c05729561dcc7310e49059eaddc504c4210ad31fad11dc70f61742'), + ('18', '16', 'cf02f9b949127363bad1aa700ab662a3c7cf9ce0e2e4750e066d2204b9500a99'), + ('18', '17', '480300f949e0dd6402051810a9714adb388cf96e454a55346c76954cdd69413d'), + ('16', '1.txt', 'c7ef2303bb35131a48e2256c5a3c7b391efa73e2acf757d7e39760efb6320ed4'), + ('16', '2', 'a4db183f7c337a67f5d6b5015e3ae0af0d0edaa56894f0e9e3469c99708fed1c'), + ('16', '3', '5b279531c42445c6f58281dd94588460218d2258ec9013c8447f3e2b7b81bf02'), + ('16', '4', '035bddd63bc9d5fd6de26beab31887e5c14c3caa4958d2424d72f3c49832bd42'), + ('16', '5', '02d8a1fcb6baa466de4e3683afa48076394acd805f490fbbe50ab19040675136'), + ('16', '6', '69a3e64d75255d9179c98a2b3a63fe76d5be08c9fc41f27ac197663c97915113'), + ('16', '7', '0d674c907758e90a168345e6b35b7a0de79c2ead390ab372465a354fcab67d17'), + ('16', '8', 'd722c0db46af905a5bd13b60e3130c4ddfb0c9da86df0a33253e5f8d53068946'), + ('16', '9', 'b563e744fbc50c1240d23df369750879df2cec69fba933704b97a73a66d9c4f1'), + ('16', '10', '99affc65740080b7a1ab87c5c9119bf5be7cf47b2b2d8fc13407d35bd2ba6238'), + ('16', '11', '86b89dbcae80ef48720fd3c7da88cffbdabfd4021af5a827339b56a33ddae27a'), + ('16', '12', 'c8d61d1efbd44086f88d74ad9e07dfdc3737dc7053c7d2503131ba0918973a03'), + ('16', '13', '5ce28e6e0118a4780ad72fc096e617c874cde7d140e15f87451babb25aaf2d8f'), + ('16', '14', '93703e734e76da30a5e050189a66d5a4d6bec5885752503c4c798e2f44049080'), + ('16', '15', 'a156ec246cd06688043cefde24de0d715fd46b08f5c0235015c2c5c3c6e37488'), + ] + for ver, num, checksum in patches: + patch_url_str = 'https://ambermd.org/bugfixes/{0}.0/update.{1}' + patch(patch_url_str.format(ver, num), + sha256=checksum, level=0, when='@{0}'.format(ver)) + + variant('mpi', description='Build MPI executables', + default=True) + variant('openmp', description='Use OpenMP pragmas to parallelize', + default=False) + variant('x11', description='Build programs that require X11', + default=False) + variant('update', description='Update the sources prior compilation', + default=False) - resource( - name='AmberTools', - sha256='7b876afe566e9dd7eb6a5aa952a955649044360f15c1f5d4d91ba7f41f3105fa', - url='file://{0}/AmberTools16.tar.bz2'.format(os.getcwd()), - destination='.', - ) - - depends_on('mpi', when='+mpi') - depends_on('cuda@7.5.18', when='+cuda') - - depends_on('netcdf-fortran') - depends_on('python+tkinter@2.7:2.8', type=('build', 'run')) - depends_on('py-numpy', type=('build', 'run')) - depends_on('py-scipy', type=('build', 'run')) - depends_on('py-matplotlib@:2.9', type=('build', 'run')) depends_on('zlib') + depends_on('flex', type='build') + depends_on('bison', type='build') + depends_on('netcdf-fortran') + # Potential issues with openmpi 4 + # (http://archive.ambermd.org/201908/0105.html) + depends_on('mpi', when='+mpi') - def setup_environment(self, spack_env, run_env): - sp_dir = join_path(self.prefix, 'python2.7/site-packages') - - run_env.set('AMBERHOME', self.prefix) - run_env.prepend_path('PYTHONPATH', sp_dir) + # Cuda dependencies + depends_on('cuda@:10.1.243', when='@18:+cuda') + depends_on('cuda@7.5.18', when='@:16+cuda') + + # conflicts + conflicts('+x11', when='platform=cray', + msg='x11 amber applications not available for cray') + conflicts('+openmp', when='%clang', + msg='openmp optimizations not available for the clang compiler') + conflicts('+openmp', when='%pgi', + msg='openmp optimizations not available for the pgi compiler') + + def setup_build_environment(self, env): + amber_src = self.stage.source_path + env.set('AMBERHOME', amber_src) + # CUDA + if self.spec.satisfies('+cuda'): + env.set('CUDA_HOME', self.spec['cuda'].prefix) def install(self, spec, prefix): - # install AmberTools where it should be - install_tree('amber16', '.') - - base_args = [ - '-noX11', - '--no-updates', - '--skip-python', - '--with-netcdf', self.spec['netcdf-fortran'].prefix - ] - - configure_env = { - 'AMBERHOME': self.stage.source_path, - 'CUDA_HOME': self.spec['cuda'].prefix, - } - + # The resource command does not allow us to expand the package in the + # root stage folder as required, as it already contains files. Here we + # install AmberTools where it should be, which results in 3 copies of + # the ambertools (~9 GB). This has to be improved in the future. + install_tree('ambertools_tmpdir', '.') + shutil.rmtree(join_path(self.stage.source_path, 'ambertools_tmpdir')) + + # Select compiler style + if self.spec.satisfies('%cce'): + compiler = 'cray' + elif self.spec.satisfies('%gcc'): + compiler = 'gnu' + elif self.spec.satisfies('%intel'): + compiler = 'intel' + elif self.spec.satisfies('%pgi'): + compiler = 'pgi' + elif self.spec.satisfies('%clang'): + compiler = 'clang' + else: + raise InstallError('Unknown compiler, exiting!!!') + + # Base configuration conf = Executable('./configure') - - conf(*(base_args + ['gnu']), extra_env=configure_env) - make('install', extra_env=configure_env) - - if '+mpi' in spec: - conf(*(base_args + ['-mpi', 'gnu']), extra_env=configure_env) - make('install', extra_env=configure_env) - - if '+cuda' in spec: - conf(*(base_args + ['-cuda', 'gnu']), extra_env=configure_env) - make('install', extra_env=configure_env) + base_args = ['--skip-python', + '--with-netcdf', self.spec['netcdf-fortran'].prefix, + ] + if self.spec.satisfies('~x11'): + base_args += ['-noX11'] + + # Update the sources: Apply all upstream patches + if self.spec.satisfies('+update'): + update = Executable('./update_amber') + update(*(['--update'])) + else: + base_args += ['--no-updates'] + + # Single core + conf(*(base_args + [compiler])) + make('install') + + # CUDA + if self.spec.satisfies('+cuda'): + conf(*(base_args + ['-cuda', compiler])) + make('install') + + # MPI + if self.spec.satisfies('+mpi'): + conf(*(base_args + ['-mpi', compiler])) + make('install') + + # Openmp + if self.spec.satisfies('+openmp'): + make('clean') + conf(*(base_args + ['-openmp', compiler])) + make('openmp') + + # CUDA + MPI + if self.spec.satisfies('+cuda') and self.spec.satisfies('+mpi'): + make('clean') + conf(*(base_args + ['-cuda', '-mpi', compiler])) + make('install') # just install everything that was built install_tree('.', prefix) + + def setup_run_environment(self, env): + env.set('AMBER_PREFIX', self.prefix) + env.set('AMBERHOME', self.prefix) + # CUDA + if self.spec.satisfies('+cuda'): + env.prepend_path('LD_LIBRARY_PATH', self.spec['cuda'].prefix.lib) diff --git a/var/spack/repos/builtin/packages/amdblis/package.py b/var/spack/repos/builtin/packages/amdblis/package.py new file mode 100644 index 0000000000..5b216bebd7 --- /dev/null +++ b/var/spack/repos/builtin/packages/amdblis/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack.pkg.builtin.blis import BlisBase + + +class Amdblis(BlisBase): + """AMD Optimized BLIS. + + BLIS is a portable software framework for instantiating high-performance + BLAS-like dense linear algebra libraries. The framework was designed to + isolate essential kernels of computation that, when optimized, immediately + enable optimized implementations of most of its commonly used and + computationally intensive operations. + """ + + homepage = "https://developer.amd.com/amd-aocl/blas-library/" + url = "https://github.com/amd/blis/archive/2.1.tar.gz" + git = "https://github.com/amd/blis.git" + + version('2.1', sha256='3b1d611d46f0f13b3c0917e27012e0f789b23dbefdddcf877b20327552d72fb3') diff --git a/var/spack/repos/builtin/packages/amg/package.py b/var/spack/repos/builtin/packages/amg/package.py index e13c90acd9..c2817f161b 100644 --- a/var/spack/repos/builtin/packages/amg/package.py +++ b/var/spack/repos/builtin/packages/amg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/amg2013/package.py b/var/spack/repos/builtin/packages/amg2013/package.py index 5954bb615f..a63a6a4bac 100644 --- a/var/spack/repos/builtin/packages/amg2013/package.py +++ b/var/spack/repos/builtin/packages/amg2013/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/aml/package.py b/var/spack/repos/builtin/packages/aml/package.py index 41cd9085e5..922d24a36f 100644 --- a/var/spack/repos/builtin/packages/aml/package.py +++ b/var/spack/repos/builtin/packages/aml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,10 @@ class Aml(AutotoolsPackage): homepage = "https://xgitlab.cels.anl.gov/argo/aml" url = "https://www.mcs.anl.gov/research/projects/argo/downloads/aml-0.1.0.tar.gz" + git = "https://xgitlab.cels.anl.gov/argo/aml.git" version('0.1.0', sha256='cc89a8768693f1f11539378b21cdca9f0ce3fc5cb564f9b3e4154a051dcea69b') + version('develop', branch='staging') + version('master', branch='master') depends_on('numactl') diff --git a/var/spack/repos/builtin/packages/amp/package.py b/var/spack/repos/builtin/packages/amp/package.py index 5410db4849..62b9b2fee3 100644 --- a/var/spack/repos/builtin/packages/amp/package.py +++ b/var/spack/repos/builtin/packages/amp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -110,7 +110,7 @@ class Amp(CMakePackage): if '+netcdf' in spec: tpl_list = tpl_list + ";NETCDF" options.extend(['-DTPL_NETCDF_INSTALL_DIR=%s' % - spec['netcdf'].prefix, ]) + spec['netcdf-c'].prefix, ]) if '+hypre' in spec: tpl_list = tpl_list + ";HYPRE" options.extend(['-DTPL_HYPRE_INSTALL_DIR=%s' % diff --git a/var/spack/repos/builtin/packages/ampliconnoise/Fix-return-type.patch b/var/spack/repos/builtin/packages/ampliconnoise/Fix-return-type.patch new file mode 100644 index 0000000000..3af2072b2d --- /dev/null +++ b/var/spack/repos/builtin/packages/ampliconnoise/Fix-return-type.patch @@ -0,0 +1,63 @@ +diff -ur spack-src.org/FCluster/FCluster.c spack-src/FCluster/FCluster.c +--- spack-src.org/FCluster/FCluster.c 2013-08-01 23:37:40.000000000 +0900 ++++ spack-src/FCluster/FCluster.c 2019-11-15 16:24:19.912747987 +0900 +@@ -750,7 +750,7 @@ + return atResult;
+ }
+
+-int outputCluster(t_Params *ptParams, t_Node* tree, char **aszID, int nN)
++void outputCluster(t_Params *ptParams, t_Node* tree, char **aszID, int nN)
+ {
+ int i = 0, j = 0, k = 0, l = 0;
+ int nNodes = nN - 1;
+diff -ur spack-src.org/FCluster/FCluster.h spack-src/FCluster/FCluster.h +--- spack-src.org/FCluster/FCluster.h 2013-08-01 23:37:40.000000000 +0900 ++++ spack-src/FCluster/FCluster.h 2019-11-15 16:24:30.453873139 +0900 +@@ -71,7 +71,7 @@ +
+ void readDistanceMatrix(char ***paszID, char *szDistFile, float *** paafDist, int *pnN, t_Params *ptParams, float** pafW);
+
+-int outputCluster(t_Params *ptParams, t_Node* tree, char **aszID, int nN);
++void outputCluster(t_Params *ptParams, t_Node* tree, char **aszID, int nN);
+
+ void scaleDistances(float **aafDist, int nN);
+
+diff -ur spack-src.org/SplitClusterEven/SplitClusterEven.c spack-src/SplitClusterEven/SplitClusterEven.c +--- spack-src.org/SplitClusterEven/SplitClusterEven.c 2013-08-01 23:37:39.000000000 +0900 ++++ spack-src/SplitClusterEven/SplitClusterEven.c 2019-11-15 16:41:40.142569105 +0900 +@@ -366,7 +366,7 @@ + + } + +-double maxDepth(t_Node* ptTree, double* pdDepth) ++void maxDepth(t_Node* ptTree, double* pdDepth) + { + double dOldDepth = *pdDepth; + +@@ -378,7 +378,7 @@ + return; + } + +-double setDepth(t_Node* ptTree, double dDepth) ++void setDepth(t_Node* ptTree, double dDepth) + { + double dOldDepth = dDepth; + +diff -ur spack-src.org/SplitClusterEven/SplitClusterEven.h spack-src/SplitClusterEven/SplitClusterEven.h +--- spack-src.org/SplitClusterEven/SplitClusterEven.h 2013-08-01 23:37:39.000000000 +0900 ++++ spack-src/SplitClusterEven/SplitClusterEven.h 2019-11-15 16:42:17.936558096 +0900 +@@ -88,7 +88,7 @@ + + void treeSplit(t_Node* ptTree, double* pdDepth, double dSplit, t_Node **aptSplit,int* pnSplit); + +-double maxDepth(t_Node* ptTree, double* pdMaxDepth); ++void maxDepth(t_Node* ptTree, double* pdMaxDepth); + + void writeIndices(t_Node* ptTree, FILE* ofp); + +@@ -116,4 +116,4 @@ + + void treeSplitEven(t_Node* ptTree, int nSplit, t_Node **aptSplit,int* pnSplit); + +-double setDepth(t_Node* ptTree, double dDepth); ++void setDepth(t_Node* ptTree, double dDepth); diff --git a/var/spack/repos/builtin/packages/ampliconnoise/package.py b/var/spack/repos/builtin/packages/ampliconnoise/package.py index 381871bd69..20e1f8100c 100644 --- a/var/spack/repos/builtin/packages/ampliconnoise/package.py +++ b/var/spack/repos/builtin/packages/ampliconnoise/package.py @@ -1,9 +1,9 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * +import os.path class Ampliconnoise(MakefilePackage): @@ -18,12 +18,14 @@ class Ampliconnoise(MakefilePackage): depends_on('mpi@2:') depends_on('gsl') - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix.Scripts) - run_env.set('PYRO_LOOKUP_FILE', join_path(self.prefix, 'Data', - 'LookUp_E123.dat')) - run_env.set('SEQ_LOOKUP_FILE', join_path(self.prefix, 'Data', - 'Tran.dat')) + patch('Fix-return-type.patch') + + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix.Scripts) + env.set('PYRO_LOOKUP_FILE', os.path.join(self.prefix, 'Data', + 'LookUp_E123.dat')) + env.set('SEQ_LOOKUP_FILE', os.path.join(self.prefix, 'Data', + 'Tran.dat')) def install(self, spec, prefix): make('install') diff --git a/var/spack/repos/builtin/packages/amrex/package.py b/var/spack/repos/builtin/packages/amrex/package.py index 234584927b..9d55286168 100644 --- a/var/spack/repos/builtin/packages/amrex/package.py +++ b/var/spack/repos/builtin/packages/amrex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,11 +12,13 @@ class Amrex(CMakePackage): mesh refinement (AMR) applications.""" homepage = "https://amrex-codes.github.io/amrex/" + url = "https://github.com/AMReX-Codes/amrex/archive/20.01.tar.gz" git = "https://github.com/AMReX-Codes/amrex.git" maintainers = ['mic84', 'asalmgren'] version('develop', branch='development') + version('20.01', sha256='f7026d267ca5de79ec7e740264d54230f419776d40feae705e939be0b1d8e0d3') version('19.10', commit='52844b32b7da11e9733b9a7f4a782e51de7f5e1e') # tag:19.10 version('19.08', commit='bdd1146139e8727a513d451075f900c172eb81fd') # tag:19.08 version('18.10.1', commit='260b53169badaa760b91dfc60ea6b2ea3d9ccf06') # tag:18.10.1 @@ -79,4 +81,7 @@ class Amrex(CMakePackage): '-DENABLE_PARTICLES:BOOL=%s' % self.cmake_is_on('+particles'), '-DENABLE_SUNDIALS:BOOL=%s' % self.cmake_is_on('+sundials') ] + if self.spec.satisfies('%fj'): + args.append('-DCMAKE_Fortran_MODDIR_FLAG=-M') + return args diff --git a/var/spack/repos/builtin/packages/amrvis/package.py b/var/spack/repos/builtin/packages/amrvis/package.py index 9a21ba8eca..51c5787d4b 100644 --- a/var/spack/repos/builtin/packages/amrvis/package.py +++ b/var/spack/repos/builtin/packages/amrvis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -173,16 +173,16 @@ class Amrvis(MakefilePackage): with open('GNUmakefile', 'w') as file: file.writelines(contents) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # We don't want an AMREX_HOME the user may have set already - spack_env.unset('AMREX_HOME') + env.unset('AMREX_HOME') # Help force Amrvis to not pick up random system compilers if '+mpi' in self.spec: - spack_env.set('MPI_HOME', self.spec['mpi'].prefix) - spack_env.set('CC', self.spec['mpi'].mpicc) - spack_env.set('CXX', self.spec['mpi'].mpicxx) - spack_env.set('F77', self.spec['mpi'].mpif77) - spack_env.set('FC', self.spec['mpi'].mpifc) + env.set('MPI_HOME', self.spec['mpi'].prefix) + env.set('CC', self.spec['mpi'].mpicc) + env.set('CXX', self.spec['mpi'].mpicxx) + env.set('F77', self.spec['mpi'].mpif77) + env.set('FC', self.spec['mpi'].mpifc) def install(self, spec, prefix): # Install exe manually diff --git a/var/spack/repos/builtin/packages/andi/package.py b/var/spack/repos/builtin/packages/andi/package.py index c01c48f7f9..500c074add 100644 --- a/var/spack/repos/builtin/packages/andi/package.py +++ b/var/spack/repos/builtin/packages/andi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/angsd/package.py b/var/spack/repos/builtin/packages/angsd/package.py index 7959f2b20c..561fe97201 100644 --- a/var/spack/repos/builtin/packages/angsd/package.py +++ b/var/spack/repos/builtin/packages/angsd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,8 +22,8 @@ class Angsd(MakefilePackage): depends_on('htslib') conflicts('^htslib@1.6:', when='@0.919') - def setup_environment(self, spack_env, run_env): - run_env.set('R_LIBS', prefix.R) + def setup_run_environment(self, env): + env.set('R_LIBS', self.prefix.R) def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/ant/package.py b/var/spack/repos/builtin/packages/ant/package.py index 68c5047d1d..057a806b76 100644 --- a/var/spack/repos/builtin/packages/ant/package.py +++ b/var/spack/repos/builtin/packages/ant/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,13 @@ class Ant(Package): homepage = "http://ant.apache.org/" url = "https://archive.apache.org/dist/ant/source/apache-ant-1.9.7-src.tar.gz" + version('1.10.7', sha256='2f9c4ef094581663b41a7412324f65b854f17622e5b2da9fcb9541ca8737bd52') + version('1.10.6', sha256='c641721ae844196b28780e7999d2ae886085b89433438ab797d531413a924311') + version('1.10.5', sha256='5937cf11d74d75d6e8927402950b012e037e362f9f728262ce432ad289b9f6ca') + version('1.10.4', sha256='b0718c6c1b2b8d3bc77cd1e30ea183cd7741cfb52222a97c754e02b8e38d1948') + version('1.10.3', sha256='988b0cac947559f7347f314b9a3dae1af0dfdcc254de56d1469de005bf281c5a') + version('1.10.2', sha256='f3cf217b9befae2fef7198b51911e33a8809d98887cc971c8957596f459c6285') + version('1.10.1', sha256='68f7ced0aa15d1f9f672f23d67c86deaf728e9576936313cfbff4f7a0e6ce382') version('1.10.0', sha256='1f78036c38753880e16fb755516c8070187a78fe4b2e99b59eda5b81b58eccaf') version('1.9.9', sha256='d6a0c93777ab27db36212d77c5733ac80d17fe24e83f947df23a8e0ad4ac48cc') version('1.9.8', sha256='5f4daf56e66fc7a71de772920ca27c15eac80cf1fcf41f3b4f2d535724942681') diff --git a/var/spack/repos/builtin/packages/antlr/package.py b/var/spack/repos/builtin/packages/antlr/package.py index 0cb10751a9..359f2210dc 100644 --- a/var/spack/repos/builtin/packages/antlr/package.py +++ b/var/spack/repos/builtin/packages/antlr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ants/package.py b/var/spack/repos/builtin/packages/ants/package.py index 903be43a48..66d2571b8d 100644 --- a/var/spack/repos/builtin/packages/ants/package.py +++ b/var/spack/repos/builtin/packages/ants/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,5 +30,5 @@ class Ants(CMakePackage): make("install") install_tree('Scripts', prefix.bin) - def setup_environment(self, spack_env, run_env): - run_env.set('ANTSPATH', self.prefix.bin) + def setup_run_environment(self, env): + env.set('ANTSPATH', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/aoflagger/package.py b/var/spack/repos/builtin/packages/aoflagger/package.py index 76dc143196..9b7ae1abdb 100644 --- a/var/spack/repos/builtin/packages/aoflagger/package.py +++ b/var/spack/repos/builtin/packages/aoflagger/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/aom/package.py b/var/spack/repos/builtin/packages/aom/package.py index 9585f98624..84c027e272 100644 --- a/var/spack/repos/builtin/packages/aom/package.py +++ b/var/spack/repos/builtin/packages/aom/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ape/package.py b/var/spack/repos/builtin/packages/ape/package.py index 76633a1498..114185aaa4 100644 --- a/var/spack/repos/builtin/packages/ape/package.py +++ b/var/spack/repos/builtin/packages/ape/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/aperture-photometry/package.py b/var/spack/repos/builtin/packages/aperture-photometry/package.py index 274aa32e75..4eec8ad727 100644 --- a/var/spack/repos/builtin/packages/aperture-photometry/package.py +++ b/var/spack/repos/builtin/packages/aperture-photometry/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/apex/package.py b/var/spack/repos/builtin/packages/apex/package.py index 09c69e1dcb..edf8ef7fc2 100644 --- a/var/spack/repos/builtin/packages/apex/package.py +++ b/var/spack/repos/builtin/packages/apex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/apple-libunwind/package.py b/var/spack/repos/builtin/packages/apple-libunwind/package.py index a11797d687..0b7d8cc1cb 100644 --- a/var/spack/repos/builtin/packages/apple-libunwind/package.py +++ b/var/spack/repos/builtin/packages/apple-libunwind/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/applewmproto/package.py b/var/spack/repos/builtin/packages/applewmproto/package.py index 171ced2bf5..a9d52c7d59 100644 --- a/var/spack/repos/builtin/packages/applewmproto/package.py +++ b/var/spack/repos/builtin/packages/applewmproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/appres/package.py b/var/spack/repos/builtin/packages/appres/package.py index cb53cdf7d8..9369d5a7e5 100644 --- a/var/spack/repos/builtin/packages/appres/package.py +++ b/var/spack/repos/builtin/packages/appres/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py index 849cac0495..2d9354e817 100644 --- a/var/spack/repos/builtin/packages/apr-util/package.py +++ b/var/spack/repos/builtin/packages/apr-util/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/apr/package.py b/var/spack/repos/builtin/packages/apr/package.py index 97e615834b..cccf222a96 100644 --- a/var/spack/repos/builtin/packages/apr/package.py +++ b/var/spack/repos/builtin/packages/apr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/aragorn/package.py b/var/spack/repos/builtin/packages/aragorn/package.py index 1befdaf866..17927f7223 100644 --- a/var/spack/repos/builtin/packages/aragorn/package.py +++ b/var/spack/repos/builtin/packages/aragorn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/arborx/package.py b/var/spack/repos/builtin/packages/arborx/package.py index 45e368884e..2408dd1a99 100644 --- a/var/spack/repos/builtin/packages/arborx/package.py +++ b/var/spack/repos/builtin/packages/arborx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/archer/package.py b/var/spack/repos/builtin/packages/archer/package.py index 7437a3890d..95c3cc1bf8 100644 --- a/var/spack/repos/builtin/packages/archer/package.py +++ b/var/spack/repos/builtin/packages/archer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,15 +13,22 @@ class Archer(CMakePackage): homepage = "https://github.com/PRUNERS/ARCHER" url = "https://github.com/PRUNERS/archer/archive/v1.0.0.tar.gz" + version('2.0.0', sha256='3241cadb0078403368b69166b27f815e12c350486d4ceb3fb33147895b9ebde8') version('1.0.0', sha256='df814a475606b83c659932caa30a68bed1c62e713386b375c1b78eb8d60e0d15') depends_on('cmake@3.4.3:', type='build') - depends_on('llvm') + depends_on('llvm@:8.0.0') depends_on('ninja@1.5:', type='build') - depends_on('llvm-openmp-ompt') + depends_on('llvm-openmp-ompt@tr6_forwards') generator = 'Ninja' + def patch(self): + if self.spec.satisfies('^llvm@8.0.0:'): + filter_file(r'add_llvm_loadable_module\(LLVMArcher', + 'add_llvm_library(LLVMArcher MODULE', + 'lib/CMakeLists.txt') + def cmake_args(self): return [ '-DCMAKE_C_COMPILER=clang', diff --git a/var/spack/repos/builtin/packages/argobots/package.py b/var/spack/repos/builtin/packages/argobots/package.py index 80950bf3f1..11c8febea6 100644 --- a/var/spack/repos/builtin/packages/argobots/package.py +++ b/var/spack/repos/builtin/packages/argobots/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,18 +18,21 @@ class Argobots(AutotoolsPackage): homepage = "http://www.argobots.org/" url = "https://github.com/pmodels/argobots/releases/download/v1.0b1/argobots-1.0b1.tar.gz" git = "https://github.com/pmodels/argobots.git" + maintainers = ['shintaro-iwasaki'] - version("develop", branch="master") + version("master", branch="master") + version("1.0rc2", sha256="7496b8bd39930a548b01aa3b1fe8f8b582c272600ef6a05ddc4398cf21dc12a2") version("1.0rc1", sha256="2dc4487556dce602655a6535f501136f0edc3575708029c80b1af6dccd069ce7") version("1.0b1", sha256="480b85b0e8db288400088a57c2dc5639f556843b06b0492841920c38348a2a3e") version("1.0a1", sha256="bef93e06026ddeba8809474923176803e64d08e1425672cd7c5b424c797d5d9d") variant("valgrind", default=False, description="Enable Valgrind") + variant("debug", default=False, description="Compiled with debugging symbols") - depends_on("m4", type=("build"), when="@develop") - depends_on("autoconf", type=("build"), when="@develop") - depends_on("automake", type=("build"), when="@develop") - depends_on("libtool", type=("build"), when="@develop") + depends_on("m4", type=("build"), when="@master") + depends_on("autoconf", type=("build"), when="@master") + depends_on("automake", type=("build"), when="@master") + depends_on("libtool", type=("build"), when="@master") depends_on("valgrind", when="+valgrind") def configure_args(self): @@ -39,4 +42,9 @@ class Argobots(AutotoolsPackage): else: args.append('--disable-valgrind') + if '+debug' in self.spec: + args.append('--enable-debug=yes') + else: + args.append('--disable-debug') + return args diff --git a/var/spack/repos/builtin/packages/argp-standalone/package.py b/var/spack/repos/builtin/packages/argp-standalone/package.py index fe75693bd3..380bd4787b 100644 --- a/var/spack/repos/builtin/packages/argp-standalone/package.py +++ b/var/spack/repos/builtin/packages/argp-standalone/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/argtable/package.py b/var/spack/repos/builtin/packages/argtable/package.py index d78f5fcef1..fa39ee062b 100644 --- a/var/spack/repos/builtin/packages/argtable/package.py +++ b/var/spack/repos/builtin/packages/argtable/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/aria2/package.py b/var/spack/repos/builtin/packages/aria2/package.py index 7cb7e3cfae..db0fdfef27 100644 --- a/var/spack/repos/builtin/packages/aria2/package.py +++ b/var/spack/repos/builtin/packages/aria2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,5 +19,5 @@ class Aria2(AutotoolsPackage): depends_on('libssh2') depends_on('libgcrypt') depends_on('zlib') - depends_on('cares') + depends_on('c-ares') depends_on('sqlite') diff --git a/var/spack/repos/builtin/packages/arm-forge/package.py b/var/spack/repos/builtin/packages/arm-forge/package.py index 94f853fef6..551d910a82 100644 --- a/var/spack/repos/builtin/packages/arm-forge/package.py +++ b/var/spack/repos/builtin/packages/arm-forge/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,107 +19,107 @@ class ArmForge(Package): # versions (and checksums) based on the target platform shows up version( - "19.0.4-linux-rhel6-x86_64", + "19.0.4-Redhat-6.0-x86_64", sha256="0b0b6ed5c3d6833bad46d5ea84346cd46f0e4b3020c31f2fd4318b75ddaf01aa", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-6.0-x86_64.tar", ) version( - "19.0.4-linux-rhel7-x86_64", + "19.0.4-Redhat-7.0-x86_64", sha256="de3c669f7cb4daf274aae603294c416a953fb558e101eb03bcccf0ef4291e079", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-7.0-x86_64.tar", ) version( - "19.0.4-linux-sles11-x86_64", + "19.0.4-Suse-11-x86_64", sha256="24a2c7761c2163f128e4f4b60e963c53774196809ddfa880131c5dde5eb454c2", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-11-x86_64.tar", ) version( - "19.0.4-linux-sles12-x86_64", + "19.0.4-Suse-12-x86_64", sha256="6688192291fe9696922a34371d07ea66f89bff9b976fd99796e5f9a6651f86e6", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-12-x86_64.tar", ) version( - "19.0.4-linux-sles15-x86_64", + "19.0.4-Suse-15-x86_64", sha256="dea60d93a157ab6952fd6887f40123ab9d633d5589ffe7824d53fb269294cf35", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-15-x86_64.tar", ) version( - "19.0.4-linux-ubuntu16.04-x86_64", + "19.0.4-19.0.4-Ubuntu-16.04-x86_64", sha256="240741beff96f6a0b3976bc98d90863fe475366d5c093af9b96b877a230d479c", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Ubuntu-16.04-x86_64.tar", ) version( - "19.0.4-linux-ubuntu14.04-x86_64", + "19.0.4-Ubuntu-14.04-x86_64", sha256="135903906111b61045ddd3e98f1d8e8fd02b5b6ef554a68dfbe6760c76ec65a2", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Ubuntu-14.04-x86_64.tar", ) version( - "19.0.4-linux-rhel7-ppc64le", + "19.0.4-Redhat-7.2-ppc64le", sha256="73cb9f4005278e8dd2106a871dcbb53edb8855faeeda75c7abd7936f85fcce56", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-7.2-ppc64le.tar", ) version( - "19.0.4-linux-rhel7-aarch64", + "19.0.4-Redhat-7.4-aarch64", sha256="8d168e5665a158f65b72d7b996fd283f7f538efbff15648eff44cfb7371ecad7", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-7.4-aarch64.tar", ) version( - "19.0.4-linux-sles12-aarch64", + "19.0.4-Suse-12-aarch64", sha256="de3aa62c5b5d5181a7947dcd1dfa66df5d06fd482394044100147210c8182d75", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-12-aarch64.tar", ) version( - "19.0.4-linux-ubuntu16.04-aarch64", + "19.0.4-Ubuntu-16.04-aarch64", sha256="3910e320c635dd5c09af7f5696909c7c0ae25406910d2e592e522ed0233e0451", url="http://content.allinea.com/downloads/arm-forge-19.0.4-Ubuntu-16.04-aarch64.tar", ) version( - "19.0.3-linux-rhel6-x86_64", + "19.0.3-Redhat-6.0-x86_64", sha256="0ace88a1847d8f622f077cd38fa9dddf7f2d6dd6aad086be0e0a66e10fb8b64b", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-6.0-x86_64.tar", ) version( - "19.0.3-linux-rhel7-x86_64", + "19.0.3-Redhat-7.0-x86_64", sha256="35c7a9532aa19251343c37b8f5eb51ef04f7b6e8b42bea2bd932f4d83a1e8375", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-7.0-x86_64.tar", ) version( - "19.0.3-linux-sles11-x86_64", + "19.0.3-Suse-11-x86_64", sha256="48fe2b1b81a824909fedf5e02cd08d8a62033cce80440eca6efbea0ae8023e75", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Suse-11-x86_64.tar", ) version( - "19.0.3-linux-sles12-x86_64", + "19.0.3-Suse-12-x86_64", sha256="b4d0f91780dc43544ea946f5117a50ba18750fd50ef811cae5b6b6771b4ebb77", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Suse-12-x86_64.tar", ) version( - "19.0.3-linux-ubuntu16.04-x86_64", + "19.0.3-Ubuntu-16.04-x86_64", sha256="ed6726434a6d24d413ed6183756433d63438936dc671cb6a3567b407c8e233e1", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Ubuntu-16.04-x86_64.tar", ) version( - "19.0.3-linux-ubuntu14.04-x86_64", + "19.0.3-Ubuntu-14.04-x86_64", sha256="22350d068c4ef60d1aad330636d443f00269c0cc49bed4c05b80f93b9d9a9c66", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Ubuntu-14.04-x86_64.tar", ) version( - "19.0.3-linux-rhel7-ppc64le", + "19.0.3-Redhat-7.2-ppc64le", sha256="dc6ea53eead78f0d9ffd8fa74ffddb80e8bd3b4ab8a1edd6f8505ffbea9cea15", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-7.2-ppc64le.tar", ) version( - "19.0.3-linux-rhel7-aarch64", + "19.0.3-Redhat-7.4-aarch64", sha256="4e19d4200e2936d542bf2b9dc79c7f8b00ccfb37b9191dfc90ac0787680a8b0c", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-7.4-aarch64.tar", ) version( - "19.0.3-linux-sles12-aarch64", + "19.0.3-Suse-12-aarch64", sha256="9b27b678d0228b4e51fd517ef0acd1df65b780a3a0b226caa6b6f1b7dccf31e6", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Suse-12-aarch64.tar", ) version( - "19.0.3-linux-ubuntu16.04-aarch64", + "19.0.3-Ubuntu-16.04-aarch64", sha256="4470f7067d4a4e0369df8af28b6ca95f58fa0062bf8dffc49f0b7415112c0332", url="http://content.allinea.com/downloads/arm-forge-19.0.3-Ubuntu-16.04-aarch64.tar", ) diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py index de4c92c385..c4f5e94d15 100644 --- a/var/spack/repos/builtin/packages/armadillo/package.py +++ b/var/spack/repos/builtin/packages/armadillo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,8 +12,9 @@ class Armadillo(CMakePackage): ease of use.""" homepage = "http://arma.sourceforge.net/" - url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz" + url = "http://sourceforge.net/projects/arma/files/armadillo-8.100.1.tar.xz" + version('9.800.3', sha256='a481e1dc880b7cb352f8a28b67fe005dc1117d4341277f12999a2355d40d7599') version('8.100.1', sha256='54773f7d828bd3885c598f90122b530ded65d9b195c9034e082baea737cd138d') version('7.950.1', sha256='a32da32a0ea420b8397a53e4b40ed279c1a5fc791dd492a2ced81ffb14ad0d1b') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index d283403515..468a8947c2 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/arrow/package.py b/var/spack/repos/builtin/packages/arrow/package.py index c3ce7da229..8cc4a06766 100644 --- a/var/spack/repos/builtin/packages/arrow/package.py +++ b/var/spack/repos/builtin/packages/arrow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,9 @@ class Arrow(CMakePackage): homepage = "http://arrow.apache.org" url = "https://github.com/apache/arrow/archive/apache-arrow-0.9.0.tar.gz" + version('0.15.1', sha256='ab1c0d371a10b615eccfcead71bb79832245d788f4834cc6b278c03c3872d593') + version('0.15.0', sha256='d1072d8c4bf9166949f4b722a89350a88b7c8912f51642a5d52283448acdfd58') + version('0.14.1', sha256='69d9de9ec60a3080543b28a5334dbaf892ca34235b8bd8f8c1c01a33253926c1') version('0.12.1', sha256='aae68622edc3dcadaa16b2d25ae3f00290d5233100321993427b03bcf5b1dd3b') version('0.11.0', sha256='0ac629a7775d86108e403eb66d9f1a3d3bdd6b3a497a86228aa4e8143364b7cc') version('0.9.0', sha256='65f89a3910b6df02ac71e4d4283db9b02c5b3f1e627346c7b6a5982ae994af91') diff --git a/var/spack/repos/builtin/packages/asagi/package.py b/var/spack/repos/builtin/packages/asagi/package.py index f24c83a68d..37b16fbec3 100644 --- a/var/spack/repos/builtin/packages/asagi/package.py +++ b/var/spack/repos/builtin/packages/asagi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -46,8 +46,8 @@ class Asagi(CMakePackage): depends_on('mpi', when="+mpi") depends_on('mpi@3:', when="+mpi3") - depends_on('netcdf +mpi', when="+mpi") - depends_on('netcdf ~mpi', when="~mpi") + depends_on('netcdf-c +mpi', when="+mpi") + depends_on('netcdf-c ~mpi', when="~mpi") depends_on('numactl', when="+numa") conflicts('%gcc@5:', when='@:1.0.0') diff --git a/var/spack/repos/builtin/packages/ascent/package.py b/var/spack/repos/builtin/packages/ascent/package.py index d837e51010..242f17e8a2 100644 --- a/var/spack/repos/builtin/packages/ascent/package.py +++ b/var/spack/repos/builtin/packages/ascent/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,13 +28,14 @@ def cmake_cache_entry(name, value, vtype=None): return 'set({0} "{1}" CACHE {2} "")\n\n'.format(name, value, vtype) -class Ascent(Package): +class Ascent(Package, CudaPackage): """Ascent is an open source many-core capable lightweight in situ visualization and analysis infrastructure for multi-physics HPC simulations.""" homepage = "https://github.com/Alpine-DAV/ascent" git = "https://github.com/Alpine-DAV/ascent.git" + url = "https://github.com/Alpine-DAV/ascent/releases/download/v0.5.0/ascent-v0.5.0-src-with-blt.tar.gz" maintainers = ['cyrush'] @@ -42,6 +43,8 @@ class Ascent(Package): branch='develop', submodules=True) + version('0.5.0', sha256='2837b7371db3ac1bcc31a479d7cf0eb62a503cacadfa4187061502b3c4a89fa0') + ########################################################################### # package variants ########################################################################### @@ -50,6 +53,7 @@ class Ascent(Package): variant('test', default=True, description='Enable Ascent unit tests') variant("mpi", default=True, description="Build Ascent MPI Support") + variant("serial", default=True, description="build serial (non-mpi) libraries") # variants for language support variant("python", default=True, description="Build Ascent Python support") @@ -72,10 +76,15 @@ class Ascent(Package): # package dependencies ########################################################################### - depends_on("cmake@3.9.2:3.9.999", type='build') + # use cmake 3.14, newest that provides proper cuda support + # and we have seen errors with cuda in 3.15 + depends_on("cmake@3.14.1:3.14.99", type='build') depends_on("conduit~python", when="~python") depends_on("conduit+python", when="+python+shared") depends_on("conduit~shared~python", when="~shared") + depends_on("conduit~python~mpi", when="~python~mpi") + depends_on("conduit+python~mpi", when="+python+shared~mpi") + depends_on("conduit~shared~python~mpi", when="~shared~mpi") ####################### # Python @@ -85,6 +94,7 @@ class Ascent(Package): depends_on("python+shared", when="+python+shared") extends("python", when="+python+shared") depends_on("py-numpy", when="+python+shared", type=('build', 'run')) + depends_on("py-pip", when="+python+shared", type=('build', 'run')) ####################### # MPI @@ -96,22 +106,22 @@ class Ascent(Package): # TPLs for Runtime Features ############################# - depends_on("vtkh@develop", when="+vtkh") - depends_on("vtkh@develop~openmp", when="+vtkh~openmp") - depends_on("vtkh@develop+cuda+openmp", when="+vtkh+cuda+openmp") - depends_on("vtkh@develop+cuda~openmp", when="+vtkh+cuda~openmp") + depends_on("vtk-h@0.5.0", when="+vtkh") + depends_on("vtk-h@0.5.0~openmp", when="+vtkh~openmp") + depends_on("vtk-h@0.5.0+cuda+openmp", when="+vtkh+cuda+openmp") + depends_on("vtk-h@0.5.0+cuda~openmp", when="+vtkh+cuda~openmp") - depends_on("vtkh@develop~shared", when="~shared+vtkh") - depends_on("vtkh@develop~shared~openmp", when="~shared+vtkh~openmp") - depends_on("vtkh@develop~shared+cuda", when="~shared+vtkh+cuda") - depends_on("vtkh@develop~shared+cuda~openmp", when="~shared+vtkh+cuda~openmp") + depends_on("vtk-h@0.5.0~shared", when="~shared+vtkh") + depends_on("vtk-h@0.5.0~shared~openmp", when="~shared+vtkh~openmp") + depends_on("vtk-h@0.5.0~shared+cuda", when="~shared+vtkh+cuda") + depends_on("vtk-h@0.5.0~shared+cuda~openmp", when="~shared+vtkh+cuda~openmp") # mfem - depends_on("mfem+shared+mpi+conduit", when="+shared+mfem+mpi") - depends_on("mfem~shared+mpi+conduit", when="~shared+mfem+mpi") + depends_on("mfem+threadsafe+shared+mpi+conduit", when="+shared+mfem+mpi") + depends_on("mfem+threadsafe~shared+mpi+conduit", when="~shared+mfem+mpi") - depends_on("mfem+shared~mpi+conduit", when="+shared+mfem~mpi") - depends_on("mfem~shared~mpi+conduit", when="~shared+mfem~mpi") + depends_on("mfem+threadsafe+shared~mpi+conduit", when="+shared+mfem~mpi") + depends_on("mfem+threadsafe~shared~mpi+conduit", when="~shared+mfem~mpi") depends_on("adios", when="+adios") @@ -119,9 +129,10 @@ class Ascent(Package): # Documentation related ####################### depends_on("py-sphinx", when="+python+doc", type='build') + depends_on("py-sphinx-rtd-theme", when="+python+doc", type='build') - def setup_environment(self, spack_env, run_env): - spack_env.set('CTEST_OUTPUT_ON_FAILURE', '1') + def setup_build_environment(self, env): + env.set('CTEST_OUTPUT_ON_FAILURE', '1') def install(self, spec, prefix): """ @@ -178,8 +189,8 @@ class Ascent(Package): create=True): cmake_args = ["-DASCENT_DIR={0}".format(install_prefix), "-DCONDUIT_DIR={0}".format(spec['conduit'].prefix), - "-DVTKM_DIR={0}".format(spec['vtkm'].prefix), - "-DVTKH_DIR={0}".format(spec['vtkh'].prefix), + "-DVTKM_DIR={0}".format(spec['vtk-m'].prefix), + "-DVTKH_DIR={0}".format(spec['vtk-h'].prefix), example_src_dir] cmake(*cmake_args) make() @@ -227,7 +238,7 @@ class Ascent(Package): if self.compiler.fc: # even if this is set, it may not exist so do one more sanity check - f_compiler = which(env["SPACK_FC"]) + f_compiler = env["SPACK_FC"] ####################################################################### # By directly fetching the names of the actual compilers we appear @@ -283,7 +294,7 @@ class Ascent(Package): if "+fortran" in spec and f_compiler is not None: cfg.write(cmake_cache_entry("ENABLE_FORTRAN", "ON")) cfg.write(cmake_cache_entry("CMAKE_Fortran_COMPILER", - f_compiler.path)) + f_compiler)) else: cfg.write("# no fortran compiler found\n\n") cfg.write(cmake_cache_entry("ENABLE_FORTRAN", "OFF")) @@ -347,18 +358,36 @@ class Ascent(Package): cfg.write(cmake_cache_entry("ENABLE_DOCS", "OFF")) ####################### + # Serial + ####################### + + if "+serial" in spec: + cfg.write(cmake_cache_entry("ENABLE_SERIAL", "ON")) + else: + cfg.write(cmake_cache_entry("ENABLE_SERIAL", "OFF")) + + ####################### # MPI ####################### cfg.write("# MPI Support\n") if "+mpi" in spec: + mpicc_path = spec['mpi'].mpicc + mpicxx_path = spec['mpi'].mpicxx + mpifc_path = spec['mpi'].mpifc + # if we are using compiler wrappers on cray systems + # use those for mpi wrappers, b/c spec['mpi'].mpicxx + # etc make return the spack compiler wrappers + # which can trip up mpi detection in CMake 3.14 + if cpp_compiler == "CC": + mpicc_path = "cc" + mpicxx_path = "CC" + mpifc_path = "ftn" cfg.write(cmake_cache_entry("ENABLE_MPI", "ON")) - cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc)) - cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", - spec['mpi'].mpicxx)) - cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", - spec['mpi'].mpifc)) + cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path)) + cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path)) + cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path)) mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec') if os.path.isfile(mpiexe_bin): # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE @@ -396,10 +425,17 @@ class Ascent(Package): if "+vtkh" in spec: cfg.write("# vtk-m from spack\n") - cfg.write(cmake_cache_entry("VTKM_DIR", spec['vtkm'].prefix)) + cfg.write(cmake_cache_entry("VTKM_DIR", spec['vtk-m'].prefix)) cfg.write("# vtk-h from spack\n") - cfg.write(cmake_cache_entry("VTKH_DIR", spec['vtkh'].prefix)) + cfg.write(cmake_cache_entry("VTKH_DIR", spec['vtk-h'].prefix)) + + if "+cuda" in spec: + cfg.write(cmake_cache_entry("VTKm_ENABLE_CUDA", "ON")) + cfg.write(cmake_cache_entry("CMAKE_CUDA_HOST_COMPILER", + env["SPACK_CXX"])) + else: + cfg.write(cmake_cache_entry("VTKm_ENABLE_CUDA", "OFF")) else: cfg.write("# vtk-h not built by spack \n") diff --git a/var/spack/repos/builtin/packages/asciidoc/package.py b/var/spack/repos/builtin/packages/asciidoc/package.py index e8f71a0b3f..5571f85dba 100644 --- a/var/spack/repos/builtin/packages/asciidoc/package.py +++ b/var/spack/repos/builtin/packages/asciidoc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/asciidoctor/package.py b/var/spack/repos/builtin/packages/asciidoctor/package.py index 951d833f1a..c3cff43468 100644 --- a/var/spack/repos/builtin/packages/asciidoctor/package.py +++ b/var/spack/repos/builtin/packages/asciidoctor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/asdf-cxx/package.py b/var/spack/repos/builtin/packages/asdf-cxx/package.py new file mode 100644 index 0000000000..fadb49714e --- /dev/null +++ b/var/spack/repos/builtin/packages/asdf-cxx/package.py @@ -0,0 +1,47 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class AsdfCxx(CMakePackage): + """ASDF - Advanced Scientific Data Format, a C++ implementation""" + + homepage = "https://github.com/eschnett/asdf-cxx" + url = "https://github.com/eschnett/asdf-cxx/archive/version/1.0.0.tar.gz" + + maintainers = ['eschnett'] + + version('7.2.1', sha256='40864f4f27d3ce8acb5169b57211ce6ac3805f0a6de9c1dfd5f994f4a5beccda') + version('7.2.0', sha256='faded85d44288afb83f13634d2139adee07e06f7ea60960c6f2ef8d898c0aa09') + version('7.1.0', sha256='81fd8c7f91f8daf0f85a1486480ae9e736b9712e82ccb858271f7ee2c2b425f7') + version('7.0.0', sha256='a50718dfa68b86b0c3e280e6a9d0a4edb03d500ba70244bd38fa86bac1433979') + version('6.3.0', sha256='44a24cc490cf776106edcfded6006d63d28889dfe985cce3bd565d5151add9c8') + version('6.0.0', sha256='76ab0a893191a33a88a753d09a20135470f809c66173794fa3e37a2437ea3cde') + version('5.0.0', sha256='876c83bcc7514f2584dbf5462bd5b7de89b41301ec127451342079e703cd6a67') + version('4.0.1', sha256='c4597b8353b0e181d97c6702dae0cb69a558ae5b553945298757433615bb199b') + version('3.1.0', sha256='15de5156460ed581e1e755955e6a1b557758a6497d083c4873d143c05e720078') + version('3.0.0', sha256='a6d42f7d875eff2f1ff6af836a44e7a44fcc6be3409605d45f236e07d70c65db') + version('2.6.1', sha256='631426bd2784c2175b5a5035c12e91b0b0d36691f9972df427b41080ace43fc3') + version('2.5.1', sha256='d3c1f690716bd0883c4d429c9fa895ce41e6223bafa87624f9f1530c0d2e654c') + version('2.5.0', sha256='916e9021063c41eb7922ed69c958ea87757cdfcb7263d0d3fda31f0233dbbaaf') + version('2.4.1', sha256='a300bf11d4fd9923eb109c5f8e1067f2ef96f284ea43fafd871b469118d42597') + version('2.4.0', sha256='965360858bcacb6df4602fdff55924f7b9daf0750b27ac3f31781e23b54e8f93') + version('2.3.1', sha256='7c3ecf4fdafff5da57edb8b0c75b2e1f9c6bf42097c483025ff49f0a65094e22') + version('2.2.1', sha256='a34679d8690ff118bedd20652caebdb9c3fb5f628aca7ed2f535a026b28b3853') + version('2.1.1', sha256='f1a801b82facb2c0913ca3dce9c62970651e58fae8bc232f5079a1c4773ec6fa') + version('2.1.0', sha256='066c2c1033be41e10b874ceec1e87267fd792c40d46cbc768b05ba94cca234a1') + version('1.1.0', sha256='3e23b9cd16254f5adbf878145e320f56b4d3ad75de23d2c761eb7f04150926c5') + version('1.0.0', sha256='0b63594a1dec27cc85d25adbf900b6e936b5015f579b9b892b983151bec96775') + + variant('python', default=True, description="Enable Python support") + + depends_on('bzip2') + depends_on('openssl') + depends_on('py-numpy', type=('build', 'run'), when='+python') + depends_on('python', type=('build', 'run'), when='+python') + depends_on('swig', type='build', when='+python') + depends_on('yaml-cpp') + depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/aspa/fix_common_errors.patch b/var/spack/repos/builtin/packages/aspa/fix_common_errors.patch new file mode 100644 index 0000000000..093e95a3a5 --- /dev/null +++ b/var/spack/repos/builtin/packages/aspa/fix_common_errors.patch @@ -0,0 +1,59 @@ +diff -ur spack-src.org/src/mtl_headers/mtl/linalg_vec.h spack-src/src/mtl_headers/mtl/linalg_vec.h +--- spack-src.org/src/mtl_headers/mtl/linalg_vec.h 2019-12-25 13:38:14.191695748 +0900 ++++ spack-src/src/mtl_headers/mtl/linalg_vec.h 2019-12-25 13:39:08.887447770 +0900 +@@ -116,6 +116,7 @@ + typedef difference_type Vec_difference_type; + typedef iterator Vec_iterator; + typedef const_iterator Vec_const_iterator; ++ typedef value_type Vec_value_type; + + class IndexArray { + public: +diff -ur spack-src.org/src/utils/toolbox/database/HDFDatabase.cc spack-src/src/utils/toolbox/database/HDFDatabase.cc +--- spack-src.org/src/utils/toolbox/database/HDFDatabase.cc 2019-12-25 13:38:14.201696799 +0900 ++++ spack-src/src/utils/toolbox/database/HDFDatabase.cc 2019-12-25 14:50:42.627965265 +0900 +@@ -686,7 +686,7 @@ + herr_t errf; + if (nelements > 0) { + +- hsize_t dim[] = {nelements}; ++ hsize_t dim[] = {(unsigned long long)nelements}; + hid_t space = H5Screate_simple(1, dim, NULL); + #ifdef ASSERT_HDF5_RETURN_VALUES + assert( space >= 0 ); +@@ -1233,7 +1233,7 @@ + herr_t errf; + if (nelements > 0) { + +- hsize_t dim[] = {nelements}; ++ hsize_t dim[] = {(unsigned long long)nelements}; + hid_t space = H5Screate_simple(1, dim, NULL); + #ifdef ASSERT_HDF5_RETURN_VALUES + assert( space >= 0 ); +@@ -1478,7 +1478,7 @@ + herr_t errf; + if (nelements > 0) { + +- hsize_t dim[] = {nelements}; ++ hsize_t dim[] = {(unsigned long long)nelements}; + hid_t space = H5Screate_simple(1, dim, NULL); + #ifdef ASSERT_HDF5_RETURN_VALUES + assert( space >= 0 ); +@@ -1722,7 +1722,7 @@ + herr_t errf; + if (nelements > 0) { + +- hsize_t dim[] = {nelements}; ++ hsize_t dim[] = {(unsigned long long)nelements}; + hid_t space = H5Screate_simple(1, dim, NULL); + #ifdef ASSERT_HDF5_RETURN_VALUES + assert(space >= 0); +@@ -1998,7 +1998,7 @@ + assert( errf >= 0 ); + #endif + +- hsize_t dim[] = {nelements}; ++ hsize_t dim[] = {(unsigned long long)nelements}; + hid_t space = H5Screate_simple(1, dim, NULL); + #ifdef ASSERT_HDF5_RETURN_VALUES + assert( space >= 0 ); diff --git a/var/spack/repos/builtin/packages/aspa/package.py b/var/spack/repos/builtin/packages/aspa/package.py index e76da23af0..abd49f3896 100644 --- a/var/spack/repos/builtin/packages/aspa/package.py +++ b/var/spack/repos/builtin/packages/aspa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,6 +28,8 @@ class Aspa(MakefilePackage): depends_on('mpi', when='+mpi') depends_on('hdf5') + patch('fix_common_errors.patch') + @property def build_targets(self): targets = [ diff --git a/var/spack/repos/builtin/packages/aspcud/package.py b/var/spack/repos/builtin/packages/aspcud/package.py index b209e4c6cc..2521848f48 100644 --- a/var/spack/repos/builtin/packages/aspcud/package.py +++ b/var/spack/repos/builtin/packages/aspcud/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/aspect/package.py b/var/spack/repos/builtin/packages/aspect/package.py index 5c662d40db..e3e613d406 100644 --- a/var/spack/repos/builtin/packages/aspect/package.py +++ b/var/spack/repos/builtin/packages/aspect/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,12 +11,13 @@ class Aspect(CMakePackage): Earth's mantle and elsewhere.""" homepage = "https://aspect.geodynamics.org" - url = "https://github.com/geodynamics/aspect/releases/download/v2.0.0/aspect-2.0.0.tar.gz" + url = "https://github.com/geodynamics/aspect/releases/download/v2.1.0/aspect-2.1.0.tar.gz" git = "https://github.com/geodynamics/aspect.git" maintainers = ['tjhei'] version('develop', branch='master') + version('2.1.0', sha256='bd574d60ed9df1f4b98e68cd526a074d0527c0792763187c9851912327d861a3') version('2.0.1', sha256='0bf5600c42afce9d39c1d285b0654ecfdeb0f30e9f3421651c95f54ca01ac165') version('2.0.0', sha256='d485c07f54248e824bdfa35f3eec8971b65e8b7114552ffa2c771bc0dede8cc0') @@ -35,5 +36,5 @@ class Aspect(CMakePackage): ('ON' if '+fpe' in self.spec else 'OFF') ] - def setup_environment(self, spack_env, run_env): - run_env.set('Aspect_DIR', self.prefix) + def setup_run_environment(self, env): + env.set('Aspect_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/aspell/darwin.patch b/var/spack/repos/builtin/packages/aspell/fix_cpp.patch index 54ec257637..54ec257637 100644 --- a/var/spack/repos/builtin/packages/aspell/darwin.patch +++ b/var/spack/repos/builtin/packages/aspell/fix_cpp.patch diff --git a/var/spack/repos/builtin/packages/aspell/package.py b/var/spack/repos/builtin/packages/aspell/package.py index 84a3f0ec71..01f92ea39f 100644 --- a/var/spack/repos/builtin/packages/aspell/package.py +++ b/var/spack/repos/builtin/packages/aspell/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,16 @@ from spack import * # See also: AspellDictPackage -class Aspell(AutotoolsPackage): +class Aspell(AutotoolsPackage, GNUMirrorPackage): """GNU Aspell is a Free and Open Source spell checker designed to eventually replace Ispell.""" homepage = "http://aspell.net/" - url = "https://ftpmirror.gnu.org/aspell/aspell-0.60.6.1.tar.gz" + gnu_mirror_path = "aspell/aspell-0.60.6.1.tar.gz" - extendable = True # support activating dictionaries + extendable = True # support activating dictionaries version('0.60.6.1', sha256='f52583a83a63633701c5f71db3dc40aab87b7f76b29723aeb27941eff42df6e1') - patch('darwin.patch', when='platform=darwin') + patch('fix_cpp.patch') patch('issue-519.patch', when='@:0.60.6.1') diff --git a/var/spack/repos/builtin/packages/aspell6-de/package.py b/var/spack/repos/builtin/packages/aspell6-de/package.py index d73a80c5c7..2f3653985f 100644 --- a/var/spack/repos/builtin/packages/aspell6-de/package.py +++ b/var/spack/repos/builtin/packages/aspell6-de/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,10 +6,10 @@ from spack import * -class Aspell6De(AspellDictPackage): +class Aspell6De(AspellDictPackage, GNUMirrorPackage): """German (de) dictionary for aspell.""" homepage = "http://aspell.net/" - url = "https://ftpmirror.gnu.org/aspell/dict/de/aspell6-de-20030222-1.tar.bz2" + gnu_mirror_path = "aspell/dict/de/aspell6-de-20030222-1.tar.bz2" version('6-de-20030222-1', sha256='ba6c94e11bc2e0e6e43ce0f7822c5bba5ca5ac77129ef90c190b33632416e906') diff --git a/var/spack/repos/builtin/packages/aspell6-en/package.py b/var/spack/repos/builtin/packages/aspell6-en/package.py index 5464c81141..659e1dffe4 100644 --- a/var/spack/repos/builtin/packages/aspell6-en/package.py +++ b/var/spack/repos/builtin/packages/aspell6-en/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,10 +6,10 @@ from spack import * -class Aspell6En(AspellDictPackage): +class Aspell6En(AspellDictPackage, GNUMirrorPackage): """English (en) dictionary for aspell.""" homepage = "http://aspell.net/" - url = "https://ftpmirror.gnu.org/aspell/dict/en/aspell6-en-2017.01.22-0.tar.bz2" + gnu_mirror_path = "aspell/dict/en/aspell6-en-2017.01.22-0.tar.bz2" version('2017.01.22-0', sha256='93c73fae3eab5ea3ca6db3cea8770715a820f1b7d6ea2b932dd66a17f8fd55e1') diff --git a/var/spack/repos/builtin/packages/aspell6-es/package.py b/var/spack/repos/builtin/packages/aspell6-es/package.py index cf6892c80c..ab757e5e8e 100644 --- a/var/spack/repos/builtin/packages/aspell6-es/package.py +++ b/var/spack/repos/builtin/packages/aspell6-es/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,10 +6,10 @@ from spack import * -class Aspell6Es(AspellDictPackage): +class Aspell6Es(AspellDictPackage, GNUMirrorPackage): """Spanish (es) dictionary for aspell.""" homepage = "http://aspell.net/" - url = "https://ftpmirror.gnu.org/aspell/dict/es/aspell6-es-1.11-2.tar.bz2" + gnu_mirror_path = "aspell/dict/es/aspell6-es-1.11-2.tar.bz2" version('1.11-2', sha256='ad367fa1e7069c72eb7ae37e4d39c30a44d32a6aa73cedccbd0d06a69018afcc') diff --git a/var/spack/repos/builtin/packages/aspera-cli/package.py b/var/spack/repos/builtin/packages/aspera-cli/package.py index 00253a1973..f073fdcbb9 100644 --- a/var/spack/repos/builtin/packages/aspera-cli/package.py +++ b/var/spack/repos/builtin/packages/aspera-cli/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,8 +17,8 @@ class AsperaCli(Package): url='https://download.asperasoft.com/download/sw/cli/3.7.7/aspera-cli-3.7.7.608.927cce8-linux-64-release.sh', expand=False) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix.cli.bin) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix.cli.bin) def install(self, spec, prefix): runfile = glob(join_path(self.stage.source_path, 'aspera-cli*.sh'))[0] diff --git a/var/spack/repos/builtin/packages/assimp/package.py b/var/spack/repos/builtin/packages/assimp/package.py index 610086a0bb..9c9a937c8e 100644 --- a/var/spack/repos/builtin/packages/assimp/package.py +++ b/var/spack/repos/builtin/packages/assimp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/astra/package.py b/var/spack/repos/builtin/packages/astra/package.py index c51d069455..48b4a7fdc2 100644 --- a/var/spack/repos/builtin/packages/astra/package.py +++ b/var/spack/repos/builtin/packages/astra/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/astral/package.py b/var/spack/repos/builtin/packages/astral/package.py index f3a110a1bd..06cc6eb59e 100644 --- a/var/spack/repos/builtin/packages/astral/package.py +++ b/var/spack/repos/builtin/packages/astral/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -44,5 +44,5 @@ class Astral(Package): filter_file('astral.jar', join_path(prefix.tools, jar_file), script, **kwargs) - def setup_environment(self, spack_env, run_env): - run_env.set('ASTRAL_HOME', self.prefix.tools) + def setup_run_environment(self, env): + env.set('ASTRAL_HOME', self.prefix.tools) diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py index 2d086a5eb5..7b9fdf757e 100644 --- a/var/spack/repos/builtin/packages/astyle/package.py +++ b/var/spack/repos/builtin/packages/astyle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/at-spi2-atk/package.py b/var/spack/repos/builtin/packages/at-spi2-atk/package.py index 1e1fee8fe4..3b2fd04e05 100644 --- a/var/spack/repos/builtin/packages/at-spi2-atk/package.py +++ b/var/spack/repos/builtin/packages/at-spi2-atk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/at-spi2-core/package.py b/var/spack/repos/builtin/packages/at-spi2-core/package.py index 97d582b18d..11695fd4c5 100644 --- a/var/spack/repos/builtin/packages/at-spi2-core/package.py +++ b/var/spack/repos/builtin/packages/at-spi2-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -35,6 +35,6 @@ class AtSpi2Core(MesonPackage): url = 'http://ftp.gnome.org/pub/gnome/sources/at-spi2-core' return url + '/%s/at-spi2-core-%s.tar.xz' % (version.up_to(2), version) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # this avoids an "import site" error in the build - spack_env.unset('PYTHONHOME') + env.unset('PYTHONHOME') diff --git a/var/spack/repos/builtin/packages/athena/package.py b/var/spack/repos/builtin/packages/athena/package.py index 504bd5b767..3f587c2e1d 100644 --- a/var/spack/repos/builtin/packages/athena/package.py +++ b/var/spack/repos/builtin/packages/athena/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -146,23 +146,23 @@ class Athena(AutotoolsPackage): patch('missing-separator.patch') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('OPT', '-O3') + env.set('OPT', '-O3') if '+mpi' in spec: - spack_env.set('CC', spec['mpi'].mpicc) - spack_env.set('LDR', spec['mpi'].mpicc) - spack_env.set('MPILIB', spec['mpi'].libs.ld_flags) - spack_env.set('MPIINC', spec['mpi'].headers.include_flags) + env.set('CC', spec['mpi'].mpicc) + env.set('LDR', spec['mpi'].mpicc) + env.set('MPILIB', spec['mpi'].libs.ld_flags) + env.set('MPIINC', spec['mpi'].headers.include_flags) else: - spack_env.set('CC', spack_cc) - spack_env.set('LDR', spack_cc) + env.set('CC', spack_cc) + env.set('LDR', spack_cc) if '+fft' in spec: - spack_env.set('FFTWLIB', spec['fftw'].libs.ld_flags) - spack_env.set('FFTWINC', spec['fftw'].headers.include_flags) + env.set('FFTWLIB', spec['fftw'].libs.ld_flags) + env.set('FFTWINC', spec['fftw'].headers.include_flags) def configure_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/atk/package.py b/var/spack/repos/builtin/packages/atk/package.py index f3931e0ced..9bb7aeb296 100644 --- a/var/spack/repos/builtin/packages/atk/package.py +++ b/var/spack/repos/builtin/packages/atk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -35,11 +35,11 @@ class Atk(Package): url = 'http://ftp.gnome.org/pub/gnome/sources/atk' return url + '/%s/atk-%s.tar.xz' % (version.up_to(2), version) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path("XDG_DATA_DIRS", - self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", - self.prefix.share) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index da539def1c..4d56d0016d 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/atom-dft/package.py b/var/spack/repos/builtin/packages/atom-dft/package.py index 89e63234ee..81306354e9 100644 --- a/var/spack/repos/builtin/packages/atom-dft/package.py +++ b/var/spack/repos/builtin/packages/atom-dft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/atompaw/package.py b/var/spack/repos/builtin/packages/atompaw/package.py index b5f5898b0f..46b66a9382 100644 --- a/var/spack/repos/builtin/packages/atompaw/package.py +++ b/var/spack/repos/builtin/packages/atompaw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/atop/package.py b/var/spack/repos/builtin/packages/atop/package.py index f7c253b298..c06d27cbd7 100644 --- a/var/spack/repos/builtin/packages/atop/package.py +++ b/var/spack/repos/builtin/packages/atop/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,6 +11,10 @@ class Atop(Package): homepage = "http://www.atoptool.nl/index.php" url = "http://www.atoptool.nl/download/atop-2.2-3.tar.gz" + version('2.5.0', sha256='4b911057ce50463b6e8b3016c5963d48535c0cddeebc6eda817e292b22f93f33') + version('2.4.0', sha256='be1c010a77086b7d98376fce96514afcd73c3f20a8d1fe01520899ff69a73d69') + version('2.3.0', sha256='73e4725de0bafac8c63b032e8479e2305e3962afbe977ec1abd45f9e104eb264') + version('2.2.6', sha256='d0386840ee4df36e5d0ad55f144661b434d9ad35d94deadc0405b514485db615') version('2.2-3', sha256='c785b8a2355be28b3de6b58a8ea4c4fcab8fadeaa57a99afeb03c66fac8e055d') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/attr/package.py b/var/spack/repos/builtin/packages/attr/package.py index 99f6f776e3..a58dc75f4d 100644 --- a/var/spack/repos/builtin/packages/attr/package.py +++ b/var/spack/repos/builtin/packages/attr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index 18b30d29d4..f105674261 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ class Augustus(MakefilePackage): # Releases have moved to github version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2') - version('3.3.1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab', + version('3.3.1-tag1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab', url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz') version('3.3', sha256='b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee', url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz') @@ -34,6 +34,31 @@ class Augustus(MakefilePackage): depends_on('curl', when='@3.3.1:') def edit(self, spec, prefix): + # Set compile commands for each compiler and + # Fix for using 'boost' on Spack. (only after ver.3.3.1-tag1) + if self.version >= Version('3.3.1-tag1'): + with working_dir(join_path('auxprogs', 'utrrnaseq', 'Debug')): + filter_file('g++', spack_cxx, 'makefile', string=True) + filter_file('g++ -I/usr/include/boost', '{0} -I{1}' + .format(spack_cxx, + self.spec['boost'].prefix.include), + 'src/subdir.mk', string=True) + + # Set compile commands to all makefiles. + makefiles = [ + 'auxprogs/aln2wig/Makefile', + 'auxprogs/bam2hints/Makefile', + 'auxprogs/bam2wig/Makefile', + 'auxprogs/checkTargetSortedness/Makefile', + 'auxprogs/compileSpliceCands/Makefile', + 'auxprogs/homGeneMapping/src/Makefile', + 'auxprogs/joingenes/Makefile', + 'src/Makefile' + ] + for makefile in makefiles: + filter_file('gcc', spack_cc, makefile, string=True) + filter_file('g++', spack_cxx, makefile, string=True) + with working_dir(join_path('auxprogs', 'filterBam', 'src')): makefile = FileFilter('Makefile') makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = %s' % self.spec[ @@ -98,7 +123,7 @@ class Augustus(MakefilePackage): for file in files: filter_file(pattern, repl, *files, backup=False) - def setup_environment(self, spack_env, run_env): - run_env.set('AUGUSTUS_CONFIG_PATH', join_path( + def setup_run_environment(self, env): + env.set('AUGUSTUS_CONFIG_PATH', join_path( self.prefix, 'config')) - run_env.prepend_path('PATH', join_path(self.prefix, 'scripts')) + env.prepend_path('PATH', join_path(self.prefix, 'scripts')) diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py index 29a4a7cbbe..9e95af8a95 100644 --- a/var/spack/repos/builtin/packages/autoconf/package.py +++ b/var/spack/repos/builtin/packages/autoconf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,11 @@ from spack import * -class Autoconf(AutotoolsPackage): +class Autoconf(AutotoolsPackage, GNUMirrorPackage): """Autoconf -- system configuration part of autotools""" homepage = 'https://www.gnu.org/software/autoconf/' - url = 'https://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz' + gnu_mirror_path = 'autoconf/autoconf-2.69.tar.gz' version('2.69', sha256='954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969') version('2.62', sha256='83aa747e6443def0ebd1882509c53f5a2133f502ddefa21b3de141c433914bdd') diff --git a/var/spack/repos/builtin/packages/autodock-vina/package.py b/var/spack/repos/builtin/packages/autodock-vina/package.py index 2ce0555529..50330a433c 100644 --- a/var/spack/repos/builtin/packages/autodock-vina/package.py +++ b/var/spack/repos/builtin/packages/autodock-vina/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/autofact/package.py b/var/spack/repos/builtin/packages/autofact/package.py index a22af26671..e7650fd3ab 100644 --- a/var/spack/repos/builtin/packages/autofact/package.py +++ b/var/spack/repos/builtin/packages/autofact/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,9 +16,9 @@ class Autofact(Package): version('3_4', sha256='1465d263b19adb42f01f6e636ac40ef1c2e3dbd63461f977b89da9493fe9c6f4') depends_on('perl', type='run') - depends_on('perl-bio-perl', type='run') + depends_on('perl-bioperl', type='run') depends_on('perl-io-string', type='run') - depends_on('perl-lwp', type='run') + depends_on('perl-libwww-perl', type='run') depends_on('blast-legacy', type='run') def patch(self): @@ -31,6 +31,6 @@ class Autofact(Package): def install(self, spec, prefix): install_tree(self.stage.source_path, prefix) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix.scripts) - run_env.set('PATH2AUTOFACT', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix.scripts) + env.set('PATH2AUTOFACT', self.prefix) diff --git a/var/spack/repos/builtin/packages/autogen/package.py b/var/spack/repos/builtin/packages/autogen/package.py index de3e2e0dfd..e60d35ba1b 100644 --- a/var/spack/repos/builtin/packages/autogen/package.py +++ b/var/spack/repos/builtin/packages/autogen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,14 +6,14 @@ from spack import * -class Autogen(AutotoolsPackage): +class Autogen(AutotoolsPackage, GNUMirrorPackage): """AutoGen is a tool designed to simplify the creation and maintenance of programs that contain large amounts of repetitious text. It is especially valuable in programs that have several blocks of text that must be kept synchronized.""" homepage = "https://www.gnu.org/software/autogen/index.html" - url = "https://ftpmirror.gnu.org/autogen/rel5.18.12/autogen-5.18.12.tar.gz" + gnu_mirror_path = "autogen/rel5.18.12/autogen-5.18.12.tar.gz" list_url = "https://ftp.gnu.org/gnu/autogen" list_depth = 1 diff --git a/var/spack/repos/builtin/packages/automaded/package.py b/var/spack/repos/builtin/packages/automaded/package.py index 2ac1ab33cf..fe87369020 100644 --- a/var/spack/repos/builtin/packages/automaded/package.py +++ b/var/spack/repos/builtin/packages/automaded/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py index 4c460d8dde..aa5d16de5d 100644 --- a/var/spack/repos/builtin/packages/automake/package.py +++ b/var/spack/repos/builtin/packages/automake/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,11 @@ from spack import * -class Automake(AutotoolsPackage): +class Automake(AutotoolsPackage, GNUMirrorPackage): """Automake -- make file builder part of autotools""" homepage = 'http://www.gnu.org/software/automake/' - url = 'https://ftpmirror.gnu.org/automake/automake-1.15.tar.gz' + gnu_mirror_path = 'automake/automake-1.15.tar.gz' version('1.16.1', sha256='608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8') version('1.15.1', sha256='988e32527abe052307d21c8ca000aa238b914df363a617e38f4fb89f5abf6260') diff --git a/var/spack/repos/builtin/packages/avizo/package.py b/var/spack/repos/builtin/packages/avizo/package.py new file mode 100644 index 0000000000..283c2d5610 --- /dev/null +++ b/var/spack/repos/builtin/packages/avizo/package.py @@ -0,0 +1,52 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os +import tarfile + + +class Avizo(Package): + """Avizo is a 3D analysis software for scientific and industrial data. + Wherever three-dimensional imaging data sets need to be processed, in + materials science, geosciences or engineering applications, Avizo offers + abundant state-of-the-art image data processing, exploration and analysis + features within an intuitive workflow and easy-to-use graphical user + interface.""" + + homepage = "https://www.thermofisher.com/sa/en/home/industrial/electron-microscopy/electron-microscopy-instruments-workflow-solutions/3d-visualization-analysis-software.html" + version('9.7.0', '9c9b9e81957387f4218df0c5adbb80717e9ae80ab3ca6ff8da523f7f499dcc5b', + expand=False) + + def url_for_version(self, version): + return "file://{0}/Avizo-{1}-Linux64-gcc44.bin".format(os.getcwd(), + version.joined) + + # Licensing + license_required = True + license_comment = '#' + license_files = ['share/license/password.dat'] + license_vars = ['MCSLMD_LICENSE_FILE'] + + def setup_run_environment(self, env): + run_env.set('MCSLMD_LICENSE_FILE', join_path(self.prefix.share.license, + 'password.dat')) + + def install(self, spec, prefix): + ver = self.version.joined + sh = which('sh') + sh('Avizo-{0}-Linux64-gcc44.bin'.format(ver), '--noexec', '--keep') + + with working_dir('Avizo'): + avizo_tar = tarfile.open(name='Avizo-{0}-Linux64-gcc44.tar.bz2' + .format(self.version)) + avizo_tar.extractall() + + with working_dir('Avizo-{0}'.format(self.version)): + install_tree('bin', prefix.bin) + install_tree('lib', prefix.lib) + install_tree('data', prefix.data) + install_tree('share', prefix.share) + install_tree('python', prefix.python) diff --git a/var/spack/repos/builtin/packages/aws-parallelcluster/enum34.patch b/var/spack/repos/builtin/packages/aws-parallelcluster/enum34.patch new file mode 100644 index 0000000000..c96a5c2d41 --- /dev/null +++ b/var/spack/repos/builtin/packages/aws-parallelcluster/enum34.patch @@ -0,0 +1,17 @@ +diff -Naur a/setup.py b/setup.py +--- a/setup.py 2020-02-06 15:40:26.000000000 -0600 ++++ b/setup.py 2020-02-06 15:41:17.000000000 -0600 +@@ -27,10 +27,12 @@ + "future>=0.16.0,<=0.18.2", + "tabulate>=0.8.2,<=0.8.3", + "ipaddress>=1.0.22", +- "enum34>=1.1.6", + "PyYAML>=5.1.2", + ] + ++if sys.version_info < (3, 4): ++ REQUIRES.append("enum34>=1.1.6") ++ + if sys.version_info[0] == 2: + REQUIRES.append("configparser>=3.5.0,<=3.8.1") + diff --git a/var/spack/repos/builtin/packages/aws-parallelcluster/package.py b/var/spack/repos/builtin/packages/aws-parallelcluster/package.py new file mode 100644 index 0000000000..9a0bb4a9cc --- /dev/null +++ b/var/spack/repos/builtin/packages/aws-parallelcluster/package.py @@ -0,0 +1,49 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +class AwsParallelcluster(PythonPackage): + """AWS ParallelCluster is an AWS supported Open Source cluster management + tool to deploy and manage HPC clusters in the AWS cloud.""" + + homepage = "https://github.com/aws/aws-parallelcluster" + url = "https://pypi.io/packages/source/a/aws-parallelcluster/aws-parallelcluster-2.5.1.tar.gz" + + maintainers = [ + 'sean-smith', 'demartinofra', 'enrico-usai', 'lukeseawalker', 'rexcsn', + 'ddeidda', 'tilne' + ] + import_modules = [ + 'pcluster', 'awsbatch', 'pcluster.dcv', 'pcluster.configure', + 'pcluster.config', 'pcluster.networking' + ] + + version('2.5.1', sha256='4fd6e14583f8cf81f9e4aa1d6188e3708d3d14e6ae252de0a94caaf58be76303') + version('2.5.0', sha256='3b0209342ea0d9d8cc95505456103ad87c2d4e35771aa838765918194efd0ad3') + + depends_on('python@2.7:', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) + depends_on('py-boto3@1.10.15:', type=('build', 'run')) + depends_on('py-future@0.16.0:0.18.2', type=('build', 'run')) + depends_on('py-tabulate@0.8.2:0.8.3', type=('build', 'run')) + depends_on('py-ipaddress@1.0.22:', type=('build', 'run')) + depends_on('py-enum34@1.1.6:', when='^python@:3.3', type=('build', 'run')) + depends_on('py-pyyaml@5.1.2:', type=('build', 'run')) + depends_on('py-configparser@3.5.0:3.8.1', when='^python@:2', type=('build', 'run')) + + # https://github.com/aws/aws-parallelcluster/pull/1633 + patch('enum34.patch', when='@:2.5.1') + + @run_after('install') + @on_package_attributes(run_tests=True) + def install_test(self): + # Make sure executables work + for exe in ['awsbhosts', 'awsbkill', 'awsbout', 'awsbqueues', + 'awsbstat', 'awsbsub', 'pcluster']: + exe = Executable(os.path.join(self.prefix.bin, exe)) + exe('--help') diff --git a/var/spack/repos/builtin/packages/awscli/package.py b/var/spack/repos/builtin/packages/awscli/package.py index e502184382..fcdf4490f5 100644 --- a/var/spack/repos/builtin/packages/awscli/package.py +++ b/var/spack/repos/builtin/packages/awscli/package.py @@ -1,5 +1,5 @@ ############################################################################## -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,21 +12,21 @@ class Awscli(PythonPackage): Amazon Web Services""" homepage = "https://pypi.org/project/awscli/" - url = "https://pypi.io/packages/source/a/awscli/awscli-1.16.179.tar.gz" + url = "https://pypi.io/packages/source/a/awscli/awscli-1.16.308.tar.gz" + version('1.16.308', sha256='3632fb1db2538128509a7b5e89f2a2c4ea3426bec139944247bddc4d79bf7603') version('1.16.179', sha256='6a87114d1325358d000abe22b2103baae7b91f053ff245b9fde33cb0affb5e4f') depends_on('py-setuptools', type='build') - depends_on('py-docutils@0.10:', type=('build', 'run')) - depends_on('py-colorama@0.2.5:0.3.9', type=('build', 'run')) + depends_on('py-botocore@1.13.44', when='@1.16.308', type=('build', 'run')) + depends_on('py-botocore@1.12.169', when='@1.16.179', type=('build', 'run')) + depends_on('py-docutils@0.10:0.15', type=('build', 'run')) depends_on('py-rsa@3.1.2:3.5.0', type=('build', 'run')) - depends_on('py-pyyaml@3.10:3.13', type=('build', 'run'), - when='^python@2.6:2.6.99') - depends_on('py-pyyaml@3.10:5.1', type=('build', 'run'), - when='^python@2.7:') - depends_on('py-argparse@1.1:', when='^python@2.6:2.6.99', - type=('build', 'run')) depends_on('py-s3transfer@0.2.0:0.2.999', type=('build', 'run')) - depends_on('py-botocore@1.12.169', type=('build', 'run')) + depends_on('py-argparse@1.1:', when='^python@:2.6', type=('build', 'run')) + depends_on('py-pyyaml@3.10:3.13', when='^python@:2.6,3.0:3.3', type=('build', 'run')) + depends_on('py-pyyaml@3.10:5.2', when='^python@3.4:', type=('build', 'run')) + depends_on('py-colorama@0.2.5:0.3.9', when='^python@:2.6,3.0:3.3', type=('build', 'run')) + depends_on('py-colorama@0.2.5:0.4.1', when='^python@3.4:', type=('build', 'run')) depends_on('py-nose', type='test') depends_on('py-mock@1.3.0:', type='test') diff --git a/var/spack/repos/builtin/packages/axel/package.py b/var/spack/repos/builtin/packages/axel/package.py index 056803110a..14d50f95b5 100644 --- a/var/spack/repos/builtin/packages/axel/package.py +++ b/var/spack/repos/builtin/packages/axel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/axl/package.py b/var/spack/repos/builtin/packages/axl/package.py index a524ca0643..1725a2751c 100644 --- a/var/spack/repos/builtin/packages/axl/package.py +++ b/var/spack/repos/builtin/packages/axl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,7 +20,7 @@ class Axl(CMakePackage): """Asynchronous transfer library""" homepage = "https://github.com/ECP-VeloC/AXL" - url = "https://github.com/ECP-VeloC/AXL/archive/v0.1.0.zip" + url = "https://github.com/ECP-VeloC/AXL/archive/v0.1.1.zip" git = "https://github.com/ecp-veloc/axl.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/bam-readcount/package.py b/var/spack/repos/builtin/packages/bam-readcount/package.py new file mode 100644 index 0000000000..45476299eb --- /dev/null +++ b/var/spack/repos/builtin/packages/bam-readcount/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class BamReadcount(CMakePackage): + """Bam-readcount generates metrics at single nucleotide positions.""" + + homepage = "https://github.com/genome/bam-readcount" + url = "https://github.com/genome/bam-readcount/archive/v0.8.0.tar.gz" + + version('0.8.0', sha256='4f4dd558e3c6bfb24d6a57ec441568f7524be6639b24f13ea6f2bb350c7ea65f') diff --git a/var/spack/repos/builtin/packages/bamdst/package.py b/var/spack/repos/builtin/packages/bamdst/package.py index dc8440e868..9283d26d6a 100644 --- a/var/spack/repos/builtin/packages/bamdst/package.py +++ b/var/spack/repos/builtin/packages/bamdst/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bamtools/package.py b/var/spack/repos/builtin/packages/bamtools/package.py index 47e134daf8..cf68d9ef4a 100644 --- a/var/spack/repos/builtin/packages/bamtools/package.py +++ b/var/spack/repos/builtin/packages/bamtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bamutil/package.py b/var/spack/repos/builtin/packages/bamutil/package.py index 49bb4a96dd..0ea2d66eaf 100644 --- a/var/spack/repos/builtin/packages/bamutil/package.py +++ b/var/spack/repos/builtin/packages/bamutil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/barrnap/package.py b/var/spack/repos/builtin/packages/barrnap/package.py index e5bb5ac864..ce293fd228 100644 --- a/var/spack/repos/builtin/packages/barrnap/package.py +++ b/var/spack/repos/builtin/packages/barrnap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bash-completion/package.py b/var/spack/repos/builtin/packages/bash-completion/package.py index 1b16fa2a1d..d5f250ebc5 100644 --- a/var/spack/repos/builtin/packages/bash-completion/package.py +++ b/var/spack/repos/builtin/packages/bash-completion/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py index 906e98ee5d..2723b66790 100644 --- a/var/spack/repos/builtin/packages/bash/package.py +++ b/var/spack/repos/builtin/packages/bash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,11 @@ from spack import * -class Bash(AutotoolsPackage): +class Bash(AutotoolsPackage, GNUMirrorPackage): """The GNU Project's Bourne Again SHell.""" homepage = "https://www.gnu.org/software/bash/" - url = "https://ftpmirror.gnu.org/bash/bash-4.4.tar.gz" + gnu_mirror_path = "bash/bash-4.4.tar.gz" version('5.0', sha256='b4a80f2ac66170b2913efbfb9f2594f1f76c7b1afd11f799e22035d63077fb4d') version('4.4.12', sha256='57d8432be54541531a496fd4904fdc08c12542f43605a9202594fa5d5f9f2331') @@ -35,6 +35,7 @@ class Bash(AutotoolsPackage): ('5.0', '011', '2c4de332b91eaf797abbbd6c79709690b5cbd48b12e8dfe748096dbd7bf474ea'), ] + # TODO: patches below are not managed by the GNUMirrorPackage base class for ver, num, checksum in patches: ver = Version(ver) patch('https://ftpmirror.gnu.org/bash/bash-{0}-patches/bash{1}-{2}'.format(ver, ver.joined, num), diff --git a/var/spack/repos/builtin/packages/bats/package.py b/var/spack/repos/builtin/packages/bats/package.py index 279116bb30..531473a9e8 100644 --- a/var/spack/repos/builtin/packages/bats/package.py +++ b/var/spack/repos/builtin/packages/bats/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bazel/bazelconfiguration-0.3.patch b/var/spack/repos/builtin/packages/bazel/bazelconfiguration-0.3.patch new file mode 100644 index 0000000000..e6a974a98a --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/bazelconfiguration-0.3.patch @@ -0,0 +1,16 @@ +--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java ++++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java +@@ -150,6 +150,13 @@ + builder.put("PATH", null); + builder.put("LD_LIBRARY_PATH", null); + } ++ ++ Map<String, String> spackEnv = System.getenv(); ++ for (String envName : spackEnv.keySet()) { ++ if (envName.startsWith("SPACK_")) { ++ builder.put(envName, spackEnv.get(envName)); ++ } ++ } + } + + private static PathFragment determineShellExecutable(OS os, PathFragment fromOption) { diff --git a/var/spack/repos/builtin/packages/bazel/bazelruleclassprovider-0.14.patch b/var/spack/repos/builtin/packages/bazel/bazelruleclassprovider-0.14.patch new file mode 100644 index 0000000000..b0aebdf359 --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/bazelruleclassprovider-0.14.patch @@ -0,0 +1,16 @@ +--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java ++++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java +@@ -168,6 +168,13 @@ public class BazelRuleClassProvider { + env.put("PATH", null); + } + ++ Map<String, String> spackEnv = System.getenv(); ++ for (String envName : spackEnv.keySet()) { ++ if (envName.startsWith("SPACK_")) { ++ env.put(envName, spackEnv.get(envName)); ++ } ++ } ++ + // Shell environment variables specified via options take precedence over the + // ones inherited from the fragments. In the long run, these fragments will + // be replaced by appropriate default rc files anyway. diff --git a/var/spack/repos/builtin/packages/bazel/bazelruleclassprovider-0.25.patch b/var/spack/repos/builtin/packages/bazel/bazelruleclassprovider-0.25.patch new file mode 100644 index 0000000000..0d68cd98d9 --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/bazelruleclassprovider-0.25.patch @@ -0,0 +1,16 @@ +--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java ++++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java +@@ -181,6 +181,13 @@ public class BazelRuleClassProvider { + env.put("PATH", null); + } + ++ Map<String, String> spackEnv = System.getenv(); ++ for (String envName : spackEnv.keySet()) { ++ if (envName.startsWith("SPACK_")) { ++ env.put(envName, spackEnv.get(envName)); ++ } ++ } ++ + // Shell environment variables specified via options take precedence over the + // ones inherited from the fragments. In the long run, these fragments will + // be replaced by appropriate default rc files anyway. diff --git a/var/spack/repos/builtin/packages/bazel/cc_configure.patch b/var/spack/repos/builtin/packages/bazel/cc_configure-0.3.0.patch index 3e108c3b5e..79e12269a6 100644 --- a/var/spack/repos/builtin/packages/bazel/cc_configure.patch +++ b/var/spack/repos/builtin/packages/bazel/cc_configure-0.3.0.patch @@ -1,6 +1,6 @@ ---- bazel-0.3.1/tools/cpp/cc_configure.bzl 2016-10-13 14:00:32.118358387 +0200 -+++ bazel-0.3.1/tools/cpp/cc_configure.bzl 2016-10-13 13:52:45.342610147 +0200 -@@ -173,8 +173,23 @@ +--- a/tools/cpp/cc_configure.bzl ++++ b/tools/cpp/cc_configure.bzl +@@ -173,8 +173,19 @@ else: inc_dirs = result.stderr[index1 + 1:index2].strip() @@ -12,12 +12,8 @@ + ] + + env = repository_ctx.os.environ -+ if "SPACK_DEPENDENCIES" in env: -+ for dep in env["SPACK_DEPENDENCIES"].split(":"): -+ path = dep + "/include" -+ # path = repository_ctx.os.path.join(dep, "include") -+ # if not repository_ctx.os.path.exists(path): -+ # continue ++ if "SPACK_INCLUDE_DIRS" in env: ++ for path in env["SPACK_INCLUDE_DIRS"].split(":"): + default_inc_directories.append( + repository_ctx.path(_cxx_inc_convert(path)) + ) diff --git a/var/spack/repos/builtin/packages/bazel/cc_configure-0.5.0.patch b/var/spack/repos/builtin/packages/bazel/cc_configure-0.5.0.patch new file mode 100644 index 0000000000..470986bec6 --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/cc_configure-0.5.0.patch @@ -0,0 +1,24 @@ +--- a/tools/cpp/cc_configure.bzl ++++ b/tools/cpp/cc_configure.bzl +@@ -200,8 +200,19 @@ + else: + inc_dirs = result.stderr[index1 + 1:index2].strip() + +- return [_escape_string(repository_ctx.path(_cxx_inc_convert(p))) +- for p in inc_dirs.split("\n")] ++ default_inc_directories = [ ++ _escape_string(repository_ctx.path(_cxx_inc_convert(p))) ++ for p in inc_dirs.split("\n") ++ ] ++ ++ env = repository_ctx.os.environ ++ if "SPACK_INCLUDE_DIRS" in env: ++ for path in env["SPACK_INCLUDE_DIRS"].split(":"): ++ default_inc_directories.append( ++ repository_ctx.path(_cxx_inc_convert(path)) ++ ) ++ ++ return default_inc_directories + + + def _add_option_if_supported(repository_ctx, cc, option): diff --git a/var/spack/repos/builtin/packages/bazel/compile-0.13.patch b/var/spack/repos/builtin/packages/bazel/compile-0.13.patch new file mode 100644 index 0000000000..13c82e7631 --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/compile-0.13.patch @@ -0,0 +1,11 @@ +--- a/compile.sh ++++ b/compile.sh +@@ -92,7 +92,7 @@ + log "Building output/bazel" + # We set host and target platform directly since the defaults in @bazel_tools + # have not yet been generated. +-bazel_build "src:bazel${EXE_EXT}" \ ++CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \ + --host_platform=@bazel_tools//platforms:host_platform \ + --platforms=@bazel_tools//platforms:target_platform \ + || fail "Could not build Bazel" diff --git a/var/spack/repos/builtin/packages/bazel/compile-0.16.patch b/var/spack/repos/builtin/packages/bazel/compile-0.16.patch new file mode 100644 index 0000000000..f61f521a15 --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/compile-0.16.patch @@ -0,0 +1,11 @@ +--- a/compile.sh ++++ b/compile.sh +@@ -92,7 +92,7 @@ display "." + log "Building output/bazel" + # We set host and target platform directly since the defaults in @bazel_tools + # have not yet been generated. +-bazel_build "src:bazel_nojdk${EXE_EXT}" \ ++CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \ + --host_platform=@bazel_tools//platforms:host_platform \ + --platforms=@bazel_tools//platforms:target_platform \ + || fail "Could not build Bazel" diff --git a/var/spack/repos/builtin/packages/bazel/compile-0.21.patch b/var/spack/repos/builtin/packages/bazel/compile-0.21.patch new file mode 100644 index 0000000000..d666a0f055 --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/compile-0.21.patch @@ -0,0 +1,11 @@ +--- a/compile.sh ++++ b/compile.sh +@@ -92,7 +92,7 @@ display "." + log "Building output/bazel" + # We set host and target platform directly since the defaults in @bazel_tools + # have not yet been generated. +-bazel_build "src:bazel_nojdk${EXE_EXT}" \ ++CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \ + --action_env=PATH \ + --host_platform=@bazel_tools//platforms:host_platform \ + --platforms=@bazel_tools//platforms:target_platform \ diff --git a/var/spack/repos/builtin/packages/bazel/compile-0.29.patch b/var/spack/repos/builtin/packages/bazel/compile-0.29.patch new file mode 100644 index 0000000000..6cb2eb0b57 --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/compile-0.29.patch @@ -0,0 +1,11 @@ +--- a/compile.sh ++++ b/compile.sh +@@ -63,7 +63,7 @@ + log "Building output/bazel" + # We set host and target platform directly because we are building for the local + # host. +-bazel_build "src:bazel_nojdk${EXE_EXT}" \ ++CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \ + --action_env=PATH \ + --host_platform=@local_config_platform//:host \ + --platforms=@local_config_platform//:host \ diff --git a/var/spack/repos/builtin/packages/bazel/compile-0.3.patch b/var/spack/repos/builtin/packages/bazel/compile-0.3.patch new file mode 100644 index 0000000000..82db6efb6e --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/compile-0.3.patch @@ -0,0 +1,11 @@ +--- a/compile.sh ++++ b/compile.sh +@@ -99,7 +99,7 @@ + new_step 'Building Bazel with Bazel' + display "." + log "Building output/bazel" +- bazel_build "src:bazel${EXE_EXT}" ++ CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" + cp -f "bazel-bin/src/bazel${EXE_EXT}" "output/bazel${EXE_EXT}" + chmod 0755 "output/bazel${EXE_EXT}" + BAZEL="$(pwd)/output/bazel${EXE_EXT}" diff --git a/var/spack/repos/builtin/packages/bazel/compile-0.4.patch b/var/spack/repos/builtin/packages/bazel/compile-0.4.patch new file mode 100644 index 0000000000..80eab26a88 --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/compile-0.4.patch @@ -0,0 +1,11 @@ +--- a/compile.sh ++++ b/compile.sh +@@ -124,7 +124,7 @@ + new_step 'Building Bazel with Bazel' + display "." + log "Building output/bazel" +- bazel_build "src:bazel${EXE_EXT}" \ ++ CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \ + || fail "Could not build Bazel" + bazel_bin_path="$(get_bazel_bin_path)/src/bazel${EXE_EXT}" + [ -e "$bazel_bin_path" ] \ diff --git a/var/spack/repos/builtin/packages/bazel/compile-0.6.patch b/var/spack/repos/builtin/packages/bazel/compile-0.6.patch new file mode 100644 index 0000000000..64eb408e5d --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/compile-0.6.patch @@ -0,0 +1,11 @@ +--- a/compile.sh ++++ b/compile.sh +@@ -85,7 +85,7 @@ + log "Building output/bazel" + # We set host and target platform directly since the defaults in @bazel_tools + # have not yet been generated. +-bazel_build "src:bazel${EXE_EXT}" \ ++CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \ + --experimental_host_platform=//tools/platforms:host_platform \ + --experimental_platforms=//tools/platforms:target_platform \ + || fail "Could not build Bazel" diff --git a/var/spack/repos/builtin/packages/bazel/compile-0.9.patch b/var/spack/repos/builtin/packages/bazel/compile-0.9.patch new file mode 100644 index 0000000000..135de3a00f --- /dev/null +++ b/var/spack/repos/builtin/packages/bazel/compile-0.9.patch @@ -0,0 +1,11 @@ +--- a/compile.sh ++++ b/compile.sh +@@ -92,7 +92,7 @@ + log "Building output/bazel" + # We set host and target platform directly since the defaults in @bazel_tools + # have not yet been generated. +-bazel_build "src:bazel${EXE_EXT}" \ ++CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \ + --host_platform=//tools/platforms:host_platform \ + --platforms=//tools/platforms:target_platform \ + || fail "Could not build Bazel" diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.13.0.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.13.0.patch deleted file mode 100644 index 31b4cf1a8e..0000000000 --- a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.13.0.patch +++ /dev/null @@ -1,129 +0,0 @@ ---- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java.orig 2018-05-23 12:11:29.319402761 +0200 -+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java 2018-05-23 12:35:21.817904301 +0200 -@@ -150,6 +150,126 @@ - builder.put("PATH", null); - builder.put("LD_LIBRARY_PATH", null); - } -+ -+ String spack_prefix = System.getenv("SPACK_PREFIX"); -+ if (spack_prefix != null) { -+ builder.put("SPACK_PREFIX", spack_prefix); -+ } -+ -+ String spack_env_path = System.getenv("SPACK_ENV_PATH"); -+ if (spack_env_path != null) { -+ builder.put("SPACK_ENV_PATH", spack_env_path); -+ } -+ -+ String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID"); -+ if (spack_debug_log_id != null) { -+ builder.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id); -+ } -+ -+ String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR"); -+ if (spack_debug_log_dir != null) { -+ builder.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir); -+ } -+ -+ String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC"); -+ if (spack_compiler_spec != null) { -+ builder.put("SPACK_COMPILER_SPEC", spack_compiler_spec); -+ } -+ -+ String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG"); -+ if (spack_cc_rpath_arg != null) { -+ builder.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg); -+ } -+ -+ String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG"); -+ if (spack_cxx_rpath_arg != null) { -+ builder.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg); -+ } -+ -+ String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG"); -+ if (spack_f77_rpath_arg != null) { -+ builder.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg); -+ } -+ -+ String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG"); -+ if (spack_fc_rpath_arg != null) { -+ builder.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg); -+ } -+ -+ String spack_short_spec = System.getenv("SPACK_SHORT_SPEC"); -+ if (spack_short_spec != null) { -+ builder.put("SPACK_SHORT_SPEC", spack_short_spec); -+ } -+ -+ String spack_system_dirs = System.getenv("SPACK_SYSTEM_DIRS"); -+ if (spack_system_dirs != null) { -+ builder.put("SPACK_SYSTEM_DIRS", spack_system_dirs); -+ } -+ -+ String spack_cc = System.getenv("SPACK_CC"); -+ if (spack_cc != null) { -+ builder.put("SPACK_CC", spack_cc); -+ } -+ -+ String spack_cxx = System.getenv("SPACK_CXX"); -+ if (spack_cxx != null) { -+ builder.put("SPACK_CXX", spack_cxx); -+ } -+ -+ String spack_f77 = System.getenv("SPACK_F77"); -+ if (spack_f77 != null) { -+ builder.put("SPACK_F77", spack_f77); -+ } -+ -+ String spack_fc = System.getenv("SPACK_FC"); -+ if (spack_fc != null) { -+ builder.put("SPACK_FC", spack_fc); -+ } -+ -+ String spack_cflags = System.getenv("SPACK_CFLAGS"); -+ if (spack_cflags != null) { -+ builder.put("SPACK_CFLAGS", spack_cflags); -+ } -+ -+ String spack_cxxflags = System.getenv("SPACK_CXXFLAGS"); -+ if (spack_cxxflags != null) { -+ builder.put("SPACK_CXXFLAGS", spack_cxxflags); -+ } -+ -+ String spack_fcflags = System.getenv("SPACK_FCFLAGS"); -+ if (spack_fcflags != null) { -+ builder.put("SPACK_FCFLAGS", spack_fcflags); -+ } -+ -+ String spack_fflags = System.getenv("SPACK_FFLAGS"); -+ if (spack_fflags != null) { -+ builder.put("SPACK_FFLAGS", spack_fflags); -+ } -+ -+ String spack_ldflags = System.getenv("SPACK_LDFLAGS"); -+ if (spack_ldflags != null) { -+ builder.put("SPACK_LDFLAGS", spack_ldflags); -+ } -+ -+ String spack_ldlibs = System.getenv("SPACK_LDLIBS"); -+ if (spack_ldlibs != null) { -+ builder.put("SPACK_LDLIBS", spack_ldlibs); -+ } -+ -+ String spack_debug = System.getenv("SPACK_DEBUG"); -+ if (spack_debug != null) { -+ builder.put("SPACK_DEBUG", spack_debug); -+ } -+ -+ String spack_test_command = System.getenv("SPACK_TEST_COMMAND"); -+ if (spack_test_command != null) { -+ builder.put("SPACK_TEST_COMMAND", spack_test_command); -+ } -+ -+ String spack_dependencies = System.getenv("SPACK_DEPENDENCIES"); -+ if (spack_dependencies != null) { -+ builder.put("SPACK_DEPENDENCIES", spack_dependencies); -+ } - } - - private static PathFragment determineShellExecutable(OS os, PathFragment fromOption) { diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.17.2.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.17.2.patch deleted file mode 100644 index 89537387a6..0000000000 --- a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.17.2.patch +++ /dev/null @@ -1,131 +0,0 @@ -diff --git a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java -index 72c40ac..2e73530 100755 ---- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java -+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java -@@ -168,6 +168,126 @@ public class BazelRuleClassProvider { - env.put("PATH", null); - } - -+ String spack_prefix = System.getenv("SPACK_PREFIX"); -+ if (spack_prefix != null) { -+ env.put("SPACK_PREFIX", spack_prefix); -+ } -+ -+ String spack_env_path = System.getenv("SPACK_ENV_PATH"); -+ if (spack_env_path != null) { -+ env.put("SPACK_ENV_PATH", spack_env_path); -+ } -+ -+ String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID"); -+ if (spack_debug_log_id != null) { -+ env.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id); -+ } -+ -+ String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR"); -+ if (spack_debug_log_dir != null) { -+ env.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir); -+ } -+ -+ String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC"); -+ if (spack_compiler_spec != null) { -+ env.put("SPACK_COMPILER_SPEC", spack_compiler_spec); -+ } -+ -+ String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG"); -+ if (spack_cc_rpath_arg != null) { -+ env.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg); -+ } -+ -+ String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG"); -+ if (spack_cxx_rpath_arg != null) { -+ env.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg); -+ } -+ -+ String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG"); -+ if (spack_f77_rpath_arg != null) { -+ env.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg); -+ } -+ -+ String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG"); -+ if (spack_fc_rpath_arg != null) { -+ env.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg); -+ } -+ -+ String spack_short_spec = System.getenv("SPACK_SHORT_SPEC"); -+ if (spack_short_spec != null) { -+ env.put("SPACK_SHORT_SPEC", spack_short_spec); -+ } -+ -+ String spack_system_dirs = System.getenv("SPACK_SYSTEM_DIRS"); -+ if (spack_system_dirs != null) { -+ env.put("SPACK_SYSTEM_DIRS", spack_system_dirs); -+ } -+ -+ String spack_cc = System.getenv("SPACK_CC"); -+ if (spack_cc != null) { -+ env.put("SPACK_CC", spack_cc); -+ } -+ -+ String spack_cxx = System.getenv("SPACK_CXX"); -+ if (spack_cxx != null) { -+ env.put("SPACK_CXX", spack_cxx); -+ } -+ -+ String spack_f77 = System.getenv("SPACK_F77"); -+ if (spack_f77 != null) { -+ env.put("SPACK_F77", spack_f77); -+ } -+ -+ String spack_fc = System.getenv("SPACK_FC"); -+ if (spack_fc != null) { -+ env.put("SPACK_FC", spack_fc); -+ } -+ -+ String spack_cflags = System.getenv("SPACK_CFLAGS"); -+ if (spack_cflags != null) { -+ env.put("SPACK_CFLAGS", spack_cflags); -+ } -+ -+ String spack_cxxflags = System.getenv("SPACK_CXXFLAGS"); -+ if (spack_cxxflags != null) { -+ env.put("SPACK_CXXFLAGS", spack_cxxflags); -+ } -+ -+ String spack_fcflags = System.getenv("SPACK_FCFLAGS"); -+ if (spack_fcflags != null) { -+ env.put("SPACK_FCFLAGS", spack_fcflags); -+ } -+ -+ String spack_fflags = System.getenv("SPACK_FFLAGS"); -+ if (spack_fflags != null) { -+ env.put("SPACK_FFLAGS", spack_fflags); -+ } -+ -+ String spack_ldflags = System.getenv("SPACK_LDFLAGS"); -+ if (spack_ldflags != null) { -+ env.put("SPACK_LDFLAGS", spack_ldflags); -+ } -+ -+ String spack_ldlibs = System.getenv("SPACK_LDLIBS"); -+ if (spack_ldlibs != null) { -+ env.put("SPACK_LDLIBS", spack_ldlibs); -+ } -+ -+ String spack_debug = System.getenv("SPACK_DEBUG"); -+ if (spack_debug != null) { -+ env.put("SPACK_DEBUG", spack_debug); -+ } -+ -+ String spack_test_command = System.getenv("SPACK_TEST_COMMAND"); -+ if (spack_test_command != null) { -+ env.put("SPACK_TEST_COMMAND", spack_test_command); -+ } -+ -+ String spack_dependencies = System.getenv("SPACK_DEPENDENCIES"); -+ if (spack_dependencies != null) { -+ env.put("SPACK_DEPENDENCIES", spack_dependencies); -+ } -+ - // Shell environment variables specified via options take precedence over the - // ones inherited from the fragments. In the long run, these fragments will - // be replaced by appropriate default rc files anyway. diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.9.0.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.9.0.patch deleted file mode 100644 index 323748377f..0000000000 --- a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.9.0.patch +++ /dev/null @@ -1,126 +0,0 @@ -diff --git a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java.orig b/home/jtang/spack/var/spack/stage/bazel-0.9.0-xcsfcyrpdn3df755cwpk4sxtfwjdv4ub/spack-expanded-archive/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java -index f1a7a1f..32cd181 100755 ---- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java.orig -+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java -@@ -154,6 +154,121 @@ public class BazelConfiguration extends Fragment { - if (tmpdir != null) { - builder.put("TMPDIR", tmpdir); - } -+ -+ String spack_prefix = System.getenv("SPACK_PREFIX"); -+ if (spack_prefix != null) { -+ builder.put("SPACK_PREFIX", spack_prefix); -+ } -+ -+ String spack_env_path = System.getenv("SPACK_ENV_PATH"); -+ if (spack_env_path != null) { -+ builder.put("SPACK_ENV_PATH", spack_env_path); -+ } -+ -+ String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID"); -+ if (spack_debug_log_id != null) { -+ builder.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id); -+ } -+ -+ String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR"); -+ if (spack_debug_log_dir != null) { -+ builder.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir); -+ } -+ -+ String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC"); -+ if (spack_compiler_spec != null) { -+ builder.put("SPACK_COMPILER_SPEC", spack_compiler_spec); -+ } -+ -+ String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG"); -+ if (spack_cc_rpath_arg != null) { -+ builder.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg); -+ } -+ -+ String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG"); -+ if (spack_cxx_rpath_arg != null) { -+ builder.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg); -+ } -+ -+ String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG"); -+ if (spack_f77_rpath_arg != null) { -+ builder.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg); -+ } -+ -+ String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG"); -+ if (spack_fc_rpath_arg != null) { -+ builder.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg); -+ } -+ -+ String spack_short_spec = System.getenv("SPACK_SHORT_SPEC"); -+ if (spack_short_spec != null) { -+ builder.put("SPACK_SHORT_SPEC", spack_short_spec); -+ } -+ -+ String spack_cc = System.getenv("SPACK_CC"); -+ if (spack_cc != null) { -+ builder.put("SPACK_CC", spack_cc); -+ } -+ -+ String spack_cxx = System.getenv("SPACK_CXX"); -+ if (spack_cxx != null) { -+ builder.put("SPACK_CXX", spack_cxx); -+ } -+ -+ String spack_f77 = System.getenv("SPACK_F77"); -+ if (spack_f77 != null) { -+ builder.put("SPACK_F77", spack_f77); -+ } -+ -+ String spack_fc = System.getenv("SPACK_FC"); -+ if (spack_fc != null) { -+ builder.put("SPACK_FC", spack_fc); -+ } -+ -+ String spack_cflags = System.getenv("SPACK_CFLAGS"); -+ if (spack_cflags != null) { -+ builder.put("SPACK_CFLAGS", spack_cflags); -+ } -+ -+ String spack_cxxflags = System.getenv("SPACK_CXXFLAGS"); -+ if (spack_cxxflags != null) { -+ builder.put("SPACK_CXXFLAGS", spack_cxxflags); -+ } -+ -+ String spack_fcflags = System.getenv("SPACK_FCFLAGS"); -+ if (spack_fcflags != null) { -+ builder.put("SPACK_FCFLAGS", spack_fcflags); -+ } -+ -+ String spack_fflags = System.getenv("SPACK_FFLAGS"); -+ if (spack_fflags != null) { -+ builder.put("SPACK_FFLAGS", spack_fflags); -+ } -+ -+ String spack_ldflags = System.getenv("SPACK_LDFLAGS"); -+ if (spack_ldflags != null) { -+ builder.put("SPACK_LDFLAGS", spack_ldflags); -+ } -+ -+ String spack_ldlibs = System.getenv("SPACK_LDLIBS"); -+ if (spack_ldlibs != null) { -+ builder.put("SPACK_LDLIBS", spack_ldlibs); -+ } -+ -+ String spack_debug = System.getenv("SPACK_DEBUG"); -+ if (spack_debug != null) { -+ builder.put("SPACK_DEBUG", spack_debug); -+ } -+ -+ String spack_test_command = System.getenv("SPACK_TEST_COMMAND"); -+ if (spack_test_command != null) { -+ builder.put("SPACK_TEST_COMMAND", spack_test_command); -+ } -+ -+ String spack_dependencies = System.getenv("SPACK_DEPENDENCIES"); -+ if (spack_dependencies != null) { -+ builder.put("SPACK_DEPENDENCIES", spack_dependencies); -+ } - } - } - diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch deleted file mode 100644 index 14deccf950..0000000000 --- a/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch +++ /dev/null @@ -1,124 +0,0 @@ -diff -pu bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java ---- bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java 2016-09-14 11:56:01.565756979 +0200 -+++ bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java 2016-09-14 12:04:13.292839801 +0200 -@@ -92,5 +92,120 @@ public class BazelConfiguration extends - if (tmpdir != null) { - builder.put("TMPDIR", tmpdir); - } -+ -+ String spack_prefix = System.getenv("SPACK_PREFIX"); -+ if (spack_prefix != null) { -+ builder.put("SPACK_PREFIX", spack_prefix); -+ } -+ -+ String spack_env_path = System.getenv("SPACK_ENV_PATH"); -+ if (spack_env_path != null) { -+ builder.put("SPACK_ENV_PATH", spack_env_path); -+ } -+ -+ String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID"); -+ if (spack_debug_log_id != null) { -+ builder.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id); -+ } -+ -+ String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR"); -+ if (spack_debug_log_dir != null) { -+ builder.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir); -+ } -+ -+ String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC"); -+ if (spack_compiler_spec != null) { -+ builder.put("SPACK_COMPILER_SPEC", spack_compiler_spec); -+ } -+ -+ String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG"); -+ if (spack_cc_rpath_arg != null) { -+ builder.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg); -+ } -+ -+ String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG"); -+ if (spack_cxx_rpath_arg != null) { -+ builder.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg); -+ } -+ -+ String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG"); -+ if (spack_f77_rpath_arg != null) { -+ builder.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg); -+ } -+ -+ String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG"); -+ if (spack_fc_rpath_arg != null) { -+ builder.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg); -+ } -+ -+ String spack_short_spec = System.getenv("SPACK_SHORT_SPEC"); -+ if (spack_short_spec != null) { -+ builder.put("SPACK_SHORT_SPEC", spack_short_spec); -+ } -+ -+ String spack_cc = System.getenv("SPACK_CC"); -+ if (spack_cc != null) { -+ builder.put("SPACK_CC", spack_cc); -+ } -+ -+ String spack_cxx = System.getenv("SPACK_CXX"); -+ if (spack_cxx != null) { -+ builder.put("SPACK_CXX", spack_cxx); -+ } -+ -+ String spack_f77 = System.getenv("SPACK_F77"); -+ if (spack_f77 != null) { -+ builder.put("SPACK_F77", spack_f77); -+ } -+ -+ String spack_fc = System.getenv("SPACK_FC"); -+ if (spack_fc != null) { -+ builder.put("SPACK_FC", spack_fc); -+ } -+ -+ String spack_cflags = System.getenv("SPACK_CFLAGS"); -+ if (spack_cflags != null) { -+ builder.put("SPACK_CFLAGS", spack_cflags); -+ } -+ -+ String spack_cxxflags = System.getenv("SPACK_CXXFLAGS"); -+ if (spack_cxxflags != null) { -+ builder.put("SPACK_CXXFLAGS", spack_cxxflags); -+ } -+ -+ String spack_fcflags = System.getenv("SPACK_FCFLAGS"); -+ if (spack_fcflags != null) { -+ builder.put("SPACK_FCFLAGS", spack_fcflags); -+ } -+ -+ String spack_fflags = System.getenv("SPACK_FFLAGS"); -+ if (spack_fflags != null) { -+ builder.put("SPACK_FFLAGS", spack_fflags); -+ } -+ -+ String spack_ldflags = System.getenv("SPACK_LDFLAGS"); -+ if (spack_ldflags != null) { -+ builder.put("SPACK_LDFLAGS", spack_ldflags); -+ } -+ -+ String spack_ldlibs = System.getenv("SPACK_LDLIBS"); -+ if (spack_ldlibs != null) { -+ builder.put("SPACK_LDLIBS", spack_ldlibs); -+ } -+ -+ String spack_debug = System.getenv("SPACK_DEBUG"); -+ if (spack_debug != null) { -+ builder.put("SPACK_DEBUG", spack_debug); -+ } -+ -+ String spack_test_command = System.getenv("SPACK_TEST_COMMAND"); -+ if (spack_test_command != null) { -+ builder.put("SPACK_TEST_COMMAND", spack_test_command); -+ } -+ -+ String spack_dependencies = System.getenv("SPACK_DEPENDENCIES"); -+ if (spack_dependencies != null) { -+ builder.put("SPACK_DEPENDENCIES", spack_dependencies); -+ } - } - } diff --git a/var/spack/repos/builtin/packages/bazel/link.patch b/var/spack/repos/builtin/packages/bazel/link.patch deleted file mode 100644 index 5c8824b87d..0000000000 --- a/var/spack/repos/builtin/packages/bazel/link.patch +++ /dev/null @@ -1,138 +0,0 @@ ---- bazel-0.3.1/src/main/java/com/google/devtools/build/lib/rules/cpp/CppLinkAction.java 2016-07-29 10:22:16.000000000 +0200 -+++ bazel-0.3.1/src/main/java/com/google/devtools/build/lib/rules/cpp/CppLinkAction.java 2016-10-13 15:21:35.036617890 +0200 -@@ -214,6 +214,135 @@ - .getParentDirectory() - .getPathString()); - } -+ -+ String path = System.getenv("PATH"); -+ result.put("PATH", path == null ? "/bin:/usr/bin" : path); -+ -+ String ldLibraryPath = System.getenv("LD_LIBRARY_PATH"); -+ if (ldLibraryPath != null) { -+ result.put("LD_LIBRARY_PATH", ldLibraryPath); -+ } -+ -+ String tmpdir = System.getenv("TMPDIR"); -+ if (tmpdir != null) { -+ result.put("TMPDIR", tmpdir); -+ } -+ -+ String spack_prefix = System.getenv("SPACK_PREFIX"); -+ if (spack_prefix != null) { -+ result.put("SPACK_PREFIX", spack_prefix); -+ } -+ -+ String spack_env_path = System.getenv("SPACK_ENV_PATH"); -+ if (spack_env_path != null) { -+ result.put("SPACK_ENV_PATH", spack_env_path); -+ } -+ -+ String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID"); -+ if (spack_debug_log_id != null) { -+ result.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id); -+ } -+ -+ String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR"); -+ if (spack_debug_log_dir != null) { -+ result.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir); -+ } -+ -+ String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC"); -+ if (spack_compiler_spec != null) { -+ result.put("SPACK_COMPILER_SPEC", spack_compiler_spec); -+ } -+ -+ String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG"); -+ if (spack_cc_rpath_arg != null) { -+ result.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg); -+ } -+ -+ String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG"); -+ if (spack_cxx_rpath_arg != null) { -+ result.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg); -+ } -+ -+ String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG"); -+ if (spack_f77_rpath_arg != null) { -+ result.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg); -+ } -+ -+ String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG"); -+ if (spack_fc_rpath_arg != null) { -+ result.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg); -+ } -+ -+ String spack_short_spec = System.getenv("SPACK_SHORT_SPEC"); -+ if (spack_short_spec != null) { -+ result.put("SPACK_SHORT_SPEC", spack_short_spec); -+ } -+ -+ String spack_cc = System.getenv("SPACK_CC"); -+ if (spack_cc != null) { -+ result.put("SPACK_CC", spack_cc); -+ } -+ -+ String spack_cxx = System.getenv("SPACK_CXX"); -+ if (spack_cxx != null) { -+ result.put("SPACK_CXX", spack_cxx); -+ } -+ -+ String spack_f77 = System.getenv("SPACK_F77"); -+ if (spack_f77 != null) { -+ result.put("SPACK_F77", spack_f77); -+ } -+ -+ String spack_fc = System.getenv("SPACK_FC"); -+ if (spack_fc != null) { -+ result.put("SPACK_FC", spack_fc); -+ } -+ -+ String spack_cflags = System.getenv("SPACK_CFLAGS"); -+ if (spack_cflags != null) { -+ result.put("SPACK_CFLAGS", spack_cflags); -+ } -+ -+ String spack_cxxflags = System.getenv("SPACK_CXXFLAGS"); -+ if (spack_cxxflags != null) { -+ result.put("SPACK_CXXFLAGS", spack_cxxflags); -+ } -+ -+ String spack_fcflags = System.getenv("SPACK_FCFLAGS"); -+ if (spack_fcflags != null) { -+ result.put("SPACK_FCFLAGS", spack_fcflags); -+ } -+ -+ String spack_fflags = System.getenv("SPACK_FFLAGS"); -+ if (spack_fflags != null) { -+ result.put("SPACK_FFLAGS", spack_fflags); -+ } -+ -+ String spack_ldflags = System.getenv("SPACK_LDFLAGS"); -+ if (spack_ldflags != null) { -+ result.put("SPACK_LDFLAGS", spack_ldflags); -+ } -+ -+ String spack_ldlibs = System.getenv("SPACK_LDLIBS"); -+ if (spack_ldlibs != null) { -+ result.put("SPACK_LDLIBS", spack_ldlibs); -+ } -+ -+ String spack_debug = System.getenv("SPACK_DEBUG"); -+ if (spack_debug != null) { -+ result.put("SPACK_DEBUG", spack_debug); -+ } -+ -+ String spack_test_command = System.getenv("SPACK_TEST_COMMAND"); -+ if (spack_test_command != null) { -+ result.put("SPACK_TEST_COMMAND", spack_test_command); -+ } -+ -+ String spack_dependencies = System.getenv("SPACK_DEPENDENCIES"); -+ if (spack_dependencies != null) { -+ result.put("SPACK_DEPENDENCIES", spack_dependencies); -+ } -+ - return result.build(); - } - diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py index ef5e26edde..655c915178 100644 --- a/var/spack/repos/builtin/packages/bazel/package.py +++ b/var/spack/repos/builtin/packages/bazel/package.py @@ -1,95 +1,175 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import inspect - from spack import * -from multiprocessing import cpu_count -from spack.util.environment import env_flag -from spack.build_environment import SPACK_NO_PARALLEL_MAKE class Bazel(Package): - """Bazel is Google's own build tool""" - - homepage = "https://www.bazel.io" - url = "https://github.com/bazelbuild/bazel/releases/download/0.11.1/bazel-0.11.1-dist.zip" - + """Bazel is an open-source build and test tool similar to Make, Maven, and + Gradle. It uses a human-readable, high-level build language. Bazel supports + projects in multiple languages and builds outputs for multiple platforms. + Bazel supports large codebases across multiple repositories, and large + numbers of users.""" + + homepage = "https://bazel.build/" + url = "https://github.com/bazelbuild/bazel/releases/download/1.2.0/bazel-1.2.0-dist.zip" + + maintainers = ['adamjstewart'] + + version('1.2.1', sha256='255da49d0f012bc4f2c1d6d3ccdbe578e22fe97b8d124e1629a486fe2a09d3e1') + version('1.2.0', sha256='9cb46b0a18b9166730307a0e82bf4c02281a1cc6da0fb11239e6fe4147bdee6e') + version('1.1.0', sha256='4b66a8c93af7832ed32e7236cf454a05f3aa06d25a8576fc3f83114f142f95ab') + version('1.0.1', sha256='f4d2dfad011ff03a5fae41b9b02cd96cd7297c1205d496603d66516934fbcfee') + version('1.0.0', sha256='c61daf0b69dd95205c695b2f9022d296d052c727062cfd396d54ffb2154f8cac') + version('0.29.1', sha256='872a52cff208676e1169b3e1cae71b1fe572c4109cbd66eab107d8607c378de5') + version('0.29.0', sha256='01cb6f2e808bd016cf0e217e12373c9efb808123e58b37885be8364458d3a40a') + version('0.28.1', sha256='2cea463d611f5255d2f3d41c8de5dcc0961adccb39cf0ac036f07070ba720314') + version('0.28.0', sha256='26ad8cdadd413b8432cf46d9fc3801e8db85d9922f85dd8a7f5a92fec876557f') + version('0.27.2', sha256='5e1bf2b48e54eb7e518430667d29aef53695d6dd7c718665a52131ab27aadab2') + version('0.27.1', sha256='8051d77da4ec338acd91770f853e4c25f4407115ed86fd35a6de25921673e779') + version('0.27.0', sha256='c3080d3b959ac08502ad5c84a51608c291accb1481baad88a628bbf79b30c67a') + version('0.26.1', sha256='c0e94f8f818759f3f67af798c38683520c540f469cb41aea8f5e5a0e43f11600') + version('0.26.0', sha256='d26dadf62959255d58e523da3448a6222af768fe1224e321b120c1d5bbe4b4f2') + version('0.25.3', sha256='23eafd3e439bc71baba9c592b52cb742dabc8640a13b9da1751fec090a2dda99') + version('0.25.2', sha256='7456032199852c043e6c5b3e4c71dd8089c1158f72ec554e6ec1c77007f0ab51') + version('0.25.1', sha256='a52bb31aeb1f821e649d25ef48023cfb54a12887aff875c6349ebcac36c2f056') + version('0.25.0', sha256='f624fe9ca8d51de192655369ac538c420afb7cde16e1ad052554b582fff09287') + version('0.24.1', sha256='56ea1b199003ad832813621744178e42b39e6206d34fbae342562c287da0cd54') + version('0.24.0', sha256='621d2a97899a88850a913eabf9285778331a309fd4658b225b1377f80060fa85') + version('0.23.2', sha256='293a5a7d851e0618eeb5e6958d94a11d45b6a00f2ba9376de61ac2bd5f917439') + version('0.23.1', sha256='dd47199f92452bf67b2c5d60ad4b7143554eaf2c6196ab6e8713449d81a0491d') + version('0.23.0', sha256='2daf9c2c6498836ed4ebae7706abb809748b1350cacd35b9f89452f31ac0acc1') + version('0.22.0', sha256='6860a226c8123770b122189636fb0c156c6e5c9027b5b245ac3b2315b7b55641') + version('0.21.0', sha256='6ccb831e683179e0cfb351cb11ea297b4db48f9eab987601c038aa0f83037db4') + version('0.20.0', sha256='1945afa84fd8858b0a3c68c09915a4bc81065c61df2591387b2985e2297d30bd') + version('0.19.2', sha256='11234cce4f6bdc62c3ac688f41c7b5c178eecb6f7e2c4ba0bcf00ba8565b1d19') + version('0.19.1', sha256='c9405f7b8c79ebc81f9f0e49bb656df4a0da246771d010c2cdd6bb30e2500ac0') + version('0.19.0', sha256='ee6135c5c47306c8421d43ad83aabc4f219cb065376ee37797f2c8ba9a615315') + version('0.18.1', sha256='baed9f28c317000a4ec1ad2571b3939356d22746ca945ac2109148d7abb860d4') + version('0.18.0', sha256='d0e86d2f7881ec8742a9823a986017452d2da0dfe4e989111da787cb89257155') version('0.17.2', sha256='b6e87acfa0a405bb8b3417c58477b66d5bc27dc0d31ba6fa12bc255b9278d33b') + version('0.17.1', sha256='23e4281c3628cbd746da3f51330109bbf69780bd64461b63b386efae37203f20') version('0.16.1', sha256='09c66b94356c82c52f212af52a81ac28eb06de1313755a2f23eeef84d167b36c') + version('0.16.0', sha256='c730593916ef0ba62f3d113cc3a268e45f7e8039daf7b767c8641b6999bd49b1') + version('0.15.2', sha256='bf53ec73be3a6d412d85ef612cec6e9c85db45da42001fab0cf1dad44cfc03f1') + version('0.15.1', sha256='c62b351fa4c1ba5aeb34d0a137176f8e8f1d89a32f548a10e96c11df176ffc6c') version('0.15.0', sha256='c3b716e6625e6b8c323350c95cd3ae0f56aeb00458dddd10544d5bead8a7b602') version('0.14.1', sha256='d49cdcd82618ae7a7a190e6f0a80d9bf85c1a66b732f994f37732dc14ffb0025') + version('0.14.0', sha256='259627de8b9d415cc80904523facf3d50e6e8e68448ab968eb1c9cb8ca1ef843') + version('0.13.1', sha256='b0269e75b40d87ff87886e5f3432cbf88f70c96f907ab588e6c21b2922d72db0') version('0.13.0', sha256='82e9035084660b9c683187618a29aa896f8b05b5f16ae4be42a80b5e5b6a7690') version('0.12.0', sha256='3b3e7dc76d145046fdc78db7cac9a82bc8939d3b291e53a7ce85315feb827754') version('0.11.1', sha256='e8d762bcc01566fa50952c8028e95cfbe7545a39b8ceb3a0d0d6df33b25b333f') version('0.11.0', sha256='abfeccc94728cb46be8dbb3507a23ccffbacef9fbda96a977ef4ea8d6ab0d384') version('0.10.1', sha256='708248f6d92f2f4d6342006c520f22dffa2f8adb0a9dc06a058e3effe7fee667') version('0.10.0', sha256='47e0798caaac4df499bce5fe554a914abd884a855a27085a4473de1d737d9548') - version('0.9.0', sha256='efb28fed4ffcfaee653e0657f6500fc4cbac61e32104f4208da385676e76312a') - version('0.4.5', sha256='2b737be42678900470ae9e48c975ac5b2296d9ae23c007bf118350dbe7c0552b') - version('0.4.4', sha256='d52a21dda271ae645711ce99c70cf44c5d3a809138e656bbff00998827548ebb') - - depends_on('java@8:', type=('build', 'link', 'run')) - depends_on('zip') - - patch('fix_env_handling.patch', when='@:0.4.5') - patch('fix_env_handling-0.9.0.patch', when='@0.9.0:0.12.0') - patch('fix_env_handling-0.13.0.patch', when='@0.13.0:0.13.999') - patch('fix_env_handling-0.17.2.patch', when='@0.14.0:') - patch('link.patch') - patch('cc_configure.patch', when='@:0.4.5') - patch('unix_cc_configure.patch', when='@0.9.0') - patch('unix_cc_configure-0.10.0.patch', when='@0.10.0:0.14.999') - patch('unix_cc_configure-0.17.2.patch', when='@0.15.0:') + version('0.9.0', sha256='efb28fed4ffcfaee653e0657f6500fc4cbac61e32104f4208da385676e76312a') + version('0.8.1', sha256='dfd0761e0b7e36c1d74c928ad986500c905be5ebcfbc29914d574af1db7218cf') + version('0.8.0', sha256='aa840321d056abd3c6be10c4a1e98a64f9f73fff9aa89c468dae8c003974a078') + version('0.7.0', sha256='a084a9c5d843e2343bf3f319154a48abe3d35d52feb0ad45dec427a1c4ffc416') + version('0.6.1', sha256='dada1f60a512789747011184b2767d2b44136ef3b036d86947f1896d200d2ba7') + version('0.6.0', sha256='a0e53728a9541ef87934831f3d05f2ccfdc3b8aeffe3e037be2b92b12400598e') + version('0.5.4', sha256='2157b05309614d6af0e4bbc6065987aede590822634a0522161f3af5d647abc9') + version('0.5.3', sha256='76b5c5880a0b15f5b91f7d626c5bc3b76ce7e5d21456963c117ab711bf1c5333') + version('0.5.2', sha256='2418c619bdd44257a170b85b9d2ecb75def29e751b725e27186468ada2e009ea') + version('0.5.1', sha256='85e6a18b111afeea2e475fe991db2a441ec3824211d659bee7b0012c36be9a40') + version('0.5.0', sha256='ebba7330a8715e96a6d6dc0aa085125d529d0740d788f0544c6169d892e4f861') + version('0.4.5', sha256='2b737be42678900470ae9e48c975ac5b2296d9ae23c007bf118350dbe7c0552b') + version('0.4.4', sha256='d52a21dda271ae645711ce99c70cf44c5d3a809138e656bbff00998827548ebb') + version('0.4.3', sha256='cbd2ab580181c17317cf18b2bf825bcded2d97cab01cd5b5fe4f4d520b64f90f') + version('0.4.2', sha256='8e6f41252abadcdb2cc7a07f910ec4b45fb12c46f0a578672c6a186c7efcdb36') + version('0.4.1', sha256='008c648d3c46ece063ae8b5008480d8ae6d359d35967356685d1c09da07e1064') + version('0.4.0', sha256='6474714eee72ba2d4e271ed00ce8c05d67a9d15327bc03962b821b2af2c5ca36') + version('0.3.2', sha256='ca5caf7b2b48c7639f45d815b32e76d69650f3199eb8caa541d402722e3f6c10') + version('0.3.1', sha256='218d0e28b4d1ee34585f2ac6b18d169c81404d93958815e73e60cc0368efcbb7') + version('0.3.0', sha256='357fd8bdf86034b93902616f0844bd52e9304cccca22971ab7007588bf9d5fb3') + + # https://docs.bazel.build/versions/master/install-compile-source.html#bootstrap-bazel + # Until https://github.com/spack/spack/issues/14058 is fixed, use jdk to build bazel + # Strict dependency on java@8 as per + # https://docs.bazel.build/versions/master/install-compile-source.html#bootstrap-unix-prereq + depends_on('jdk@1.8.0:1.8.999', type=('build', 'run')) + depends_on('python', type=('build', 'run')) + + # Pass Spack environment variables to the build + patch('bazelruleclassprovider-0.25.patch', when='@0.25:') + patch('bazelruleclassprovider-0.14.patch', when='@0.14:0.24') + patch('bazelconfiguration-0.3.patch', when='@:0.13') + + # Inject include paths + patch('unix_cc_configure-0.15.patch', when='@0.15:') + patch('unix_cc_configure-0.10.patch', when='@0.10:0.14') + patch('unix_cc_configure-0.5.3.patch', when='@0.5.3:0.9') + patch('cc_configure-0.5.0.patch', when='@0.5.0:0.5.2') + patch('cc_configure-0.3.0.patch', when='@:0.4') + + # Set CC and CXX + patch('compile-0.29.patch', when='@0.29:') + patch('compile-0.21.patch', when='@0.21:0.28') + patch('compile-0.16.patch', when='@0.16:0.20') + patch('compile-0.13.patch', when='@0.13:0.15') + patch('compile-0.9.patch', when='@0.9:0.12') + patch('compile-0.6.patch', when='@0.6:0.8') + patch('compile-0.4.patch', when='@0.4:0.5') + patch('compile-0.3.patch', when='@:0.3') + + phases = ['bootstrap', 'install'] def url_for_version(self, version): if version >= Version('0.4.1'): - return 'https://github.com/bazelbuild/bazel/releases/download/{0}/bazel-{0}-dist.zip'.format(version) + url = 'https://github.com/bazelbuild/bazel/releases/download/{0}/bazel-{0}-dist.zip' else: - return 'https://github.com/bazelbuild/bazel/archive/{0}.tar.gz'.format(version) + url = 'https://github.com/bazelbuild/bazel/archive/{0}.tar.gz' - def install(self, spec, prefix): + return url.format(version) + + def setup_build_environment(self, env): + env.set('EXTRA_BAZEL_ARGS', + # Spack's logs don't handle colored output well + '--color=no --host_javabase=@local_jdk//:jdk') + + def bootstrap(self, spec, prefix): bash = which('bash') - bash('-c', './compile.sh') + bash('./compile.sh') + + def install(self, spec, prefix): mkdir(prefix.bin) install('output/bazel', prefix.bin) + @run_after('install') + @on_package_attributes(run_tests=True) + def test(self): + # https://github.com/Homebrew/homebrew-core/blob/master/Formula/bazel.rb + + # Bazel does not work properly on NFS, switch to /tmp + with working_dir('/tmp/spack/bazel/spack-test', create=True): + touch('WORKSPACE') + + with open('ProjectRunner.java', 'w') as f: + f.write("""\ +public class ProjectRunner { + public static void main(String args[]) { + System.out.println("Hi!"); + } +}""") + + with open('BUILD', 'w') as f: + f.write("""\ +java_binary( + name = "bazel-test", + srcs = glob(["*.java"]), + main_class = "ProjectRunner", +)""") + + # Spack's logs don't handle colored output well + bazel = Executable(self.prefix.bin.bazel) + bazel('--output_user_root=/tmp/spack/bazel/spack-test', + 'build', '--color=no', '//:bazel-test') + + exe = Executable('bazel-bin/bazel-test') + assert exe(output=str) == 'Hi!\n' + def setup_dependent_package(self, module, dependent_spec): - class BazelExecutable(Executable): - """Special callable executable object for bazel so the user can - specify parallel or not on a per-invocation basis. Using - 'parallel' as a kwarg will override whatever the package's - global setting is, so you can either default to true or false - and override particular calls. - - Note that if the SPACK_NO_PARALLEL_MAKE env var is set it - overrides everything. - """ - - def __init__(self, name, command, jobs): - super(BazelExecutable, self).__init__(name) - self.bazel_command = command - self.jobs = jobs - - def __call__(self, *args, **kwargs): - disable = env_flag(SPACK_NO_PARALLEL_MAKE) - parallel = ((not disable) and kwargs.get('parallel', - self.jobs > 1)) - - jobs = "--jobs=1" - if parallel: - jobs = "--jobs=%d" % self.jobs - - args = (self.bazel_command,) + (jobs,) + args - - return super(BazelExecutable, self).__call__(*args, **kwargs) - - jobs = cpu_count() - dependent_module = inspect.getmodule(dependent_spec.package) - if not dependent_spec.package.parallel: - jobs = 1 - elif dependent_module.make_jobs: - jobs = dependent_module.make_jobs - module.bazel = BazelExecutable('bazel', 'build', jobs) + module.bazel = Executable('bazel') diff --git a/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.10.0.patch b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.10.patch index e375283fed..bdd24e1152 100644 --- a/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.10.0.patch +++ b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.10.patch @@ -1,6 +1,4 @@ -diff --git a/tools/cpp/unix_cc_configure.bzl.orig b/tools/cpp/unix_cc_configure.bzl -index f67b9b5..cc952e0 100755 ---- a/tools/cpp/unix_cc_configure.bzl.orig +--- a/tools/cpp/unix_cc_configure.bzl +++ b/tools/cpp/unix_cc_configure.bzl @@ -147,9 +147,18 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, additional_flags = []): else: @@ -12,14 +10,13 @@ index f67b9b5..cc952e0 100755 + _prepare_include_path(repository_ctx, _cxx_inc_convert(p)) + for p in inc_dirs.split("\n") + ] - ++ + env = repository_ctx.os.environ -+ if "SPACK_DEPENDENCIES" in env: -+ for dep in env["SPACK_DEPENDENCIES"].split(":"): -+ path = dep + "/include" ++ if "SPACK_INCLUDE_DIRS" in env: ++ for path in env["SPACK_INCLUDE_DIRS"].split(":"): + default_inc_directories.append(path) + + return default_inc_directories + def _is_option_supported(repository_ctx, cc, option): - """Checks that `option` is supported by the C compiler. Doesn't %-escape the option.""" diff --git a/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.17.2.patch b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.15.patch index d1a502a49a..74fd8bfb79 100644 --- a/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.17.2.patch +++ b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.15.patch @@ -1,8 +1,6 @@ -diff --git a/tools/cpp/unix_cc_configure.bzl b/tools/cpp/unix_cc_configure.bzl -index 361931b..a79129b 100755 --- a/tools/cpp/unix_cc_configure.bzl +++ b/tools/cpp/unix_cc_configure.bzl -@@ -145,11 +145,19 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, lang_flag, additional_fl +@@ -145,11 +145,18 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, lang_flag, additional_fl else: inc_dirs = result.stderr[index1 + 1:index2].strip() @@ -13,9 +11,8 @@ index 361931b..a79129b 100755 ] + env = repository_ctx.os.environ -+ if "SPACK_DEPENDENCIES" in env: -+ for dep in env["SPACK_DEPENDENCIES"].split(":"): -+ path = dep + "/include" ++ if "SPACK_INCLUDE_DIRS" in env: ++ for path in env["SPACK_INCLUDE_DIRS"].split(":"): + default_inc_directories.append(path) + + return default_inc_directories diff --git a/var/spack/repos/builtin/packages/bazel/unix_cc_configure.patch b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.5.3.patch index 3f14bc2fc0..79b583ba84 100644 --- a/var/spack/repos/builtin/packages/bazel/unix_cc_configure.patch +++ b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.5.3.patch @@ -1,10 +1,6 @@ -diff --git a/spack-expanded-archive/tools/cpp/unix_cc_configure.bzl.orig b/spack-expanded-archive/tools/cpp/unix_cc_configure.bzl -old mode 100644 -new mode 100755 -index aa46f55..ae3c689 ---- spack-expanded-archive/tools/cpp/unix_cc_configure.bzl -+++ spack-expanded-archive/tools/cpp/unix_cc_configure.bzl -@@ -117,9 +117,23 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc): +--- a/tools/cpp/unix_cc_configure.bzl ++++ b/tools/cpp/unix_cc_configure.bzl +@@ -117,9 +117,19 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc): else: inc_dirs = result.stderr[index1 + 1:index2].strip() @@ -16,12 +12,8 @@ index aa46f55..ae3c689 + ] + env = repository_ctx.os.environ -+ if "SPACK_DEPENDENCIES" in env: -+ for dep in env["SPACK_DEPENDENCIES"].split(":"): -+ path = dep + "/include" -+ # path = repository_ctx.os.path.join(dep, "include") -+ # if not repository_ctx.os.path.exists(path): -+ # continue ++ if "SPACK_INCLUDE_DIRS" in env: ++ for path in env["SPACK_INCLUDE_DIRS"].split(":"): + default_inc_directories.append( + repository_ctx.path(_cxx_inc_convert(path)) + ) diff --git a/var/spack/repos/builtin/packages/bbcp/package.py b/var/spack/repos/builtin/packages/bbcp/package.py index 6c9446e5ad..70c453825f 100644 --- a/var/spack/repos/builtin/packages/bbcp/package.py +++ b/var/spack/repos/builtin/packages/bbcp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bbmap/package.py b/var/spack/repos/builtin/packages/bbmap/package.py index 47197d1c17..a9f51c614f 100644 --- a/var/spack/repos/builtin/packages/bbmap/package.py +++ b/var/spack/repos/builtin/packages/bbmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,6 +20,6 @@ class Bbmap(Package): def install(self, spec, prefix): install_tree('.', prefix.bin) - def setup_environment(self, spack_env, run_env): - run_env.set('BBMAP_CONFIG', self.prefix.bin.config) - run_env.set('BBMAP_RESOURCES', self.prefix.bin.resources) + def setup_run_environment(self, env): + env.set('BBMAP_CONFIG', self.prefix.bin.config) + env.set('BBMAP_RESOURCES', self.prefix.bin.resources) diff --git a/var/spack/repos/builtin/packages/bc/package.py b/var/spack/repos/builtin/packages/bc/package.py index 99dc0b1d99..b78bf8878c 100644 --- a/var/spack/repos/builtin/packages/bc/package.py +++ b/var/spack/repos/builtin/packages/bc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,13 +6,13 @@ from spack import * -class Bc(AutotoolsPackage): +class Bc(AutotoolsPackage, GNUMirrorPackage): """bc is an arbitrary precision numeric processing language. Syntax is similar to C, but differs in many substantial areas. It supports interactive execution of statements.""" homepage = "https://www.gnu.org/software/bc" - url = "https://ftpmirror.gnu.org/bc/bc-1.07.tar.gz" + gnu_mirror_path = "bc/bc-1.07.tar.gz" version('1.07', sha256='55cf1fc33a728d7c3d386cc7b0cb556eb5bacf8e0cb5a3fcca7f109fc61205ad') diff --git a/var/spack/repos/builtin/packages/bcftools/fix_mk.patch b/var/spack/repos/builtin/packages/bcftools/fix_mk.patch new file mode 100644 index 0000000000..0625138ac8 --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/fix_mk.patch @@ -0,0 +1,16 @@ +diff -ru a/plugins/fixploidy.mk b/plugins/fixploidy.mk +--- a/plugins/fixploidy.mk 2014-10-09 04:01:22.000000000 -0500 ++++ b/plugins/fixploidy.mk 2020-01-13 21:55:28.926309796 -0600 +@@ -1,2 +1,2 @@ +-plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so +- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts ++plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c ++ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< $(HTSLIB) +diff -ru a/plugins/vcf2sex.mk b/plugins/vcf2sex.mk +--- a/plugins/vcf2sex.mk 2014-10-09 04:01:22.000000000 -0500 ++++ b/plugins/vcf2sex.mk 2020-01-13 21:55:55.056277406 -0600 +@@ -1,2 +1,2 @@ +-plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so +- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts ++plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c ++ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< $(HTSLIB) diff --git a/var/spack/repos/builtin/packages/bcftools/guess-ploidy.py_2to3.patch b/var/spack/repos/builtin/packages/bcftools/guess-ploidy.py_2to3.patch new file mode 100644 index 0000000000..68918a547e --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/guess-ploidy.py_2to3.patch @@ -0,0 +1,13 @@ +--- a/misc/guess-ploidy.py 2017-04-07 04:52:44.000000000 -0500 ++++ b/misc/guess-ploidy.py 2020-01-14 10:59:49.738128654 -0600 +@@ -33,8 +33,8 @@ + csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE) + + if len(sys.argv) != 3: +- print >> sys.stderr, 'About: Plot output of "bcftools +guess-ploidy -v"' +- print >> sys.stderr, 'Usage: guess-ploidy.py <guess-ploidy.out> <image-prefix>' ++ print('About: Plot output of "bcftools +guess-ploidy -v"', file=sys.stderr) ++ print('Usage: guess-ploidy.py <guess-ploidy.out> <image-prefix>', file=sys.stderr) + sys.exit() + + prefix = sys.argv[2] diff --git a/var/spack/repos/builtin/packages/bcftools/makefile_12.patch b/var/spack/repos/builtin/packages/bcftools/makefile_12.patch new file mode 100644 index 0000000000..1083a0dce9 --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/makefile_12.patch @@ -0,0 +1,109 @@ +--- a/Makefile 2015-02-03 10:27:19.000000000 -0600 ++++ b/Makefile 2020-01-13 21:22:54.554904229 -0600 +@@ -30,10 +30,11 @@ + + # Adjust $(HTSDIR) to point to your top-level htslib directory + HTSDIR = htslib-1.2.1 +-include $(HTSDIR)/htslib.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip +-TABIX = $(HTSDIR)/tabix ++#include $(HTSDIR)/htslib.mk ++HTSINC = $(HTSDIR)/include ++HTSLIB = -L$(HTSDIR)/lib -lhts ++BGZIP = $(HTSDIR)/bin/bgzip ++TABIX = $(HTSDIR)/bin/tabix + + CC = gcc + CFLAGS = -g -Wall -Wc++-compat -O2 +@@ -44,7 +45,7 @@ + vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \ + vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \ + ccall.o em.o prob1.o kmin.o # the original samtools calling +-INCLUDES = -I. -I$(HTSDIR) ++INCLUDES = -I. -I$(HTSINC) + + # The polysomy command is not compiled by default because it brings dependency + # on libgsl. The command can be compiled wth `make USE_GPL=1`. See the INSTALL +@@ -52,7 +53,7 @@ + ifdef USE_GPL + CFLAGS += -DUSE_GPL + OBJS += polysomy.o +- LDLIBS = -lgsl -lcblas ++ LDLIBS = -lgsl -lgslcblas + endif + + prefix = /usr/local +@@ -102,8 +103,8 @@ + PLUGINS = $(PLUGINC:.c=.so) + PLUGINM = $(PLUGINC:.c=.mk) + +-%.so: %.c version.h version.c $(HTSDIR)/libhts.so +- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts ++%.so: %.c version.h version.c ++ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< $(HTSLIB) + + -include $(PLUGINM) + +@@ -116,20 +117,20 @@ + tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h) + filter_h = filter.h $(htslib_vcf_h) + prob1_h = prob1.h $(htslib_vcf_h) $(call_h) +-roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kstring.h $(HTSINC)/htslib/kseq.h $(bcftools_h) + cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) + + main.o: main.c $(htslib_hts_h) version.h $(bcftools_h) +-vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) +-vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) +-vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h) +-vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) ++vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) ++vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSINC)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h) ++vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) + vcfconvert.o: vcfconvert.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h) + vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h + vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) + vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h) + vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) +-vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSDIR)/htslib/khash.h ++vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSINC)/htslib/khash.h + vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(bcftools_h) rbuf.h + vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) + vcfroh.o: vcfroh.c $(roh_h) +@@ -137,20 +138,20 @@ + vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) + vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h) + vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) +-reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) + tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h) +-ccall.o: ccall.c $(HTSDIR)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h) ++ccall.o: ccall.c $(HTSINC)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h) + convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h) + tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h) + em.o: em.c $(htslib_vcf_h) kmin.h $(call_h) +-filter.o: filter.c $(HTSDIR)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) ++filter.o: filter.c $(HTSINC)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) + gvcf.o: gvcf.c $(call_h) + kmin.o: kmin.c kmin.h +-mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h) ++mcall.o: mcall.c $(HTSINC)/htslib/kfunc.h $(call_h) + prob1.o: prob1.c $(prob1_h) + vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h + polysomy.o: polysomy.c $(htslib_hts_h) +-consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h ++consensus.o: consensus.c $(htslib_hts_h) $(HTSINC)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSINC)/htslib/regidx.h + version.o: version.h version.c + + test/test-rbuf.o: test/test-rbuf.c rbuf.h +@@ -158,7 +159,7 @@ + test/test-rbuf: test/test-rbuf.o + $(CC) $(CFLAGS) -o $@ -lm -ldl $< + +-bcftools: $(HTSLIB) $(OBJS) ++bcftools: $(OBJS) + $(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS) + + doc/bcftools.1: doc/bcftools.txt diff --git a/var/spack/repos/builtin/packages/bcftools/makefile_13.patch b/var/spack/repos/builtin/packages/bcftools/makefile_13.patch new file mode 100644 index 0000000000..5be31ed2ca --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/makefile_13.patch @@ -0,0 +1,102 @@ +--- a/Makefile 2016-10-02 21:23:39.289320362 -0500 ++++ b/Makefile 2016-10-02 21:30:41.163562704 -0500 +@@ -30,10 +30,11 @@ + + # Adjust $(HTSDIR) to point to your top-level htslib directory + HTSDIR = htslib-1.3.1 +-include $(HTSDIR)/htslib.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip +-TABIX = $(HTSDIR)/tabix ++#include $(HTSDIR)/htslib.mk ++HTSINC = $(HTSDIR)/include ++HTSLIB = -L$(HTSDIR)/lib -lhts ++BGZIP = $(HTSDIR)/bin/bgzip ++TABIX = $(HTSDIR)/bin/tabix + + CC = gcc + CPPFLAGS = +@@ -48,7 +49,7 @@ + vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \ + ccall.o em.o prob1.o kmin.o # the original samtools calling + +-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\" ++EXTRA_CPPFLAGS = -I. -I$(HTSINC) -DPLUGINPATH=\"$(pluginpath)\" + GSL_LIBS = + + # The polysomy command is not compiled by default because it brings dependency +@@ -57,7 +58,7 @@ + ifdef USE_GPL + EXTRA_CPPFLAGS += -DUSE_GPL + OBJS += polysomy.o peakfit.o +- GSL_LIBS = -lgsl -lcblas ++ GSL_LIBS = -lgsl -lgslcblas + endif + + prefix = /usr/local +@@ -136,20 +137,20 @@ + filter_h = filter.h $(htslib_vcf_h) + ploidy_h = ploidy.h $(htslib_regidx_h) + prob1_h = prob1.h $(htslib_vcf_h) $(call_h) +-roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kstring.h $(HTSINC)/htslib/kseq.h $(bcftools_h) + cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) + + main.o: main.c $(htslib_hts_h) version.h $(bcftools_h) +-vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) +-vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) +-vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/khash_str2int.h $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) +-vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(htslib_bgzf_h) $(htslib_tbx_h) $(bcftools_h) ++vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) ++vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) ++vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSINC)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/khash_str2int.h $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) ++vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(htslib_bgzf_h) $(htslib_tbx_h) $(bcftools_h) + vcfconvert.o: vcfconvert.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h) + vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h + vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) + vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h) + vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) +-vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSDIR)/htslib/khash.h ++vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSINC)/htslib/khash.h + vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(bcftools_h) rbuf.h + vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) + vcfroh.o: vcfroh.c $(roh_h) +@@ -157,22 +158,22 @@ + vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) + vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h) + vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) +-reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) + tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h) +-ccall.o: ccall.c $(HTSDIR)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h) ++ccall.o: ccall.c $(HTSINC)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h) + convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h) + tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h) + em.o: em.c $(htslib_vcf_h) kmin.h $(call_h) +-filter.o: filter.c $(HTSDIR)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) ++filter.o: filter.c $(HTSINC)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) + gvcf.o: gvcf.c $(call_h) + kmin.o: kmin.c kmin.h +-mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h) ++mcall.o: mcall.c $(HTSINC)/htslib/kfunc.h $(call_h) + prob1.o: prob1.c $(prob1_h) + vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h +-ploidy.o: ploidy.c $(htslib_regidx_h) $(HTSDIR)/htslib/khash_str2int.h $(HTSDIR)/htslib/kseq.h $(htslib_hts_h) $(bcftools_h) $(ploidy_h) ++ploidy.o: ploidy.c $(htslib_regidx_h) $(HTSINC)/htslib/khash_str2int.h $(HTSINC)/htslib/kseq.h $(htslib_hts_h) $(bcftools_h) $(ploidy_h) + polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h +-peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h +-consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h ++peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSINC)/htslib/kstring.h ++consensus.o: consensus.c $(htslib_hts_h) $(HTSINC)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSINC)/htslib/regidx.h + version.o: version.h version.c + + test/test-rbuf.o: test/test-rbuf.c rbuf.h +@@ -180,7 +181,7 @@ + test/test-rbuf: test/test-rbuf.o + $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS) + +-bcftools: $(HTSLIB) $(OBJS) ++bcftools: $(OBJS) + $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) + + doc/bcftools.1: doc/bcftools.txt diff --git a/var/spack/repos/builtin/packages/bcftools/makefile_14.patch b/var/spack/repos/builtin/packages/bcftools/makefile_14.patch new file mode 100644 index 0000000000..fe780cf8f7 --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/makefile_14.patch @@ -0,0 +1,64 @@ +--- a/Makefile 2017-03-13 09:55:48.000000000 -0500 ++++ b/Makefile 2020-01-13 17:42:49.359554802 -0600 +@@ -30,13 +30,14 @@ + + # Adjust $(HTSDIR) to point to your top-level htslib directory + HTSDIR = htslib-1.4 +-include $(HTSDIR)/htslib.mk +-include $(HTSDIR)/htslib_static.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip +-TABIX = $(HTSDIR)/tabix +-HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) +-HTSLIB_LIBS = $(HTSLIB_static_LIBS) ++#include $(HTSDIR)/htslib.mk ++#include $(HTSDIR)/htslib_static.mk ++HTSINC = $(HTSDIR)/include ++HTSLIB = -L$(HTSDIR)/lib -lhts ++BGZIP = $(HTSDIR)/bin/bgzip ++TABIX = $(HTSDIR)/bin/tabix ++#HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) ++#HTSLIB_LIBS = $(HTSLIB_static_LIBS) + + CC = gcc + CPPFLAGS = +@@ -51,7 +52,7 @@ + endif + + # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally +-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) ++ALL_CPPFLAGS = -I. -I$(HTSINC) + ALL_LDFLAGS = $(DYNAMIC_FLAGS) $(HTSLIB_LDFLAGS) $(LDFLAGS) + ALL_LIBS = -lm -lz -ldl $(LIBS) + +@@ -64,7 +65,7 @@ + mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \ + ccall.o em.o prob1.o kmin.o # the original samtools calling + +-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\" ++EXTRA_CPPFLAGS = -I. -I$(HTSINC) -DPLUGINPATH=\"$(pluginpath)\" + GSL_LIBS = + + # The polysomy command is not compiled by default because it brings dependency +@@ -73,7 +74,7 @@ + ifdef USE_GPL + EXTRA_CPPFLAGS += -DUSE_GPL + OBJS += polysomy.o peakfit.o +- GSL_LIBS = -lgsl -lcblas ++ GSL_LIBS = -lgsl -lgslcblas + endif + + prefix = /usr/local +@@ -208,10 +209,10 @@ + + test/test-regidx.o: test/test-regidx.c regidx.h + +-test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB) ++test/test-regidx: test/test-regidx.o regidx.o + $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS) + +-bcftools: $(HTSLIB) $(OBJS) ++bcftools: $(OBJS) + $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS) + + doc/bcftools.1: doc/bcftools.txt diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py index cfdea1a3c9..28f431e346 100644 --- a/var/spack/repos/builtin/packages/bcftools/package.py +++ b/var/spack/repos/builtin/packages/bcftools/package.py @@ -1,9 +1,10 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import glob class Bcftools(AutotoolsPackage): @@ -15,6 +16,7 @@ class Bcftools(AutotoolsPackage): homepage = "http://samtools.github.io/bcftools/" url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2" + version('1.10.2', sha256='f57301869d0055ce3b8e26d8ad880c0c1989bf25eaec8ea5db99b60e31354e2c') version('1.9', sha256='6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8') version('1.8', sha256='4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced') version('1.7', sha256='dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1') @@ -23,8 +25,22 @@ class Bcftools(AutotoolsPackage): version('1.3.1', sha256='12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924') version('1.2', sha256='53c628339020dd45334a007c9cefdaf1cba3f1032492ec813b116379fa684fd6') - depends_on('libzip', when='@1.8:') + variant('libgsl', + default=False, + description='build options that require the GNU scientific ' + 'library') + variant('perl-filters', + default=False, + description='build in support for PERL scripts in -i/-e ' + 'filtering expressions, for versions >= 1.8.') + + depends_on('gsl', when='+libgsl') + depends_on('py-matplotlib', when='@1.6:', type='run') + depends_on('perl', when='@1.8:~perl-filters', type='run') + depends_on('perl', when='@1.8:+perl-filters', type=('build', 'run')) + + depends_on('htslib@1.10.2', when='@1.10.2') depends_on('htslib@1.9', when='@1.9') depends_on('htslib@1.8', when='@1.8') depends_on('htslib@1.7', when='@1.7') @@ -33,8 +49,59 @@ class Bcftools(AutotoolsPackage): depends_on('htslib@1.3.1', when='@1.3.1') depends_on('htslib@1.2', when='@1.2') + patch('makefile_12.patch', when='@1.2') + patch('fix_mk.patch', when='@1.2') + patch('makefile_13.patch', when='@1.3') + patch('makefile_14.patch', when='@1.4') + patch('guess-ploidy.py_2to3.patch', when='@1.6:1.9') + + @when('@1.5:') def configure_args(self): args = [] + args.append('--with-htslib={0}'.format(self.spec['htslib'].prefix)) + args.extend(self.enable_or_disable('libgsl')) + + if self.spec.satisfies('@1.8:'): + args.extend(self.enable_or_disable('perl-filters')) return args + + @when('@1.2:1.4') + def set_make_options(self): + options = [] + + options.append('prefix={0}'.format(self.prefix)) + options.append('HTSDIR={0}'.format(self.spec['htslib'].prefix)) + + if '+libgsl' in self.spec: + options.append('USE_GPL=1') + + return options + + @when('@1.2:1.4') + def autoreconf(self, spec, prefix): + touch('configure') + + @when('@1.2:1.4') + def configure(self, spec, prefix): + pass + + @when('@1.2:1.4') + def build(self, spec, prefix): + make_options = self.set_make_options() + make(*make_options) + + @when('@1.2:1.4') + def install(self, spec, prefix): + make_options = self.set_make_options() + make('install', *make_options) + + if spec.satisfies('@1.2'): + mkdirp(self.prefix.libexec.bcftools) + for files in glob.glob('plugins/*.so'): + install(files, self.prefix.libexec.bcftools) + + @when('@1.2') + def setup_run_environment(self, env): + env.set('BCFTOOLS_PLUGINS', self.prefix.libexec.bcftools) diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/package.py b/var/spack/repos/builtin/packages/bcl2fastq2/package.py index 009386b85a..5f2062859d 100644 --- a/var/spack/repos/builtin/packages/bcl2fastq2/package.py +++ b/var/spack/repos/builtin/packages/bcl2fastq2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bdftopcf/package.py b/var/spack/repos/builtin/packages/bdftopcf/package.py index 38576dbed3..78ff26c2d9 100644 --- a/var/spack/repos/builtin/packages/bdftopcf/package.py +++ b/var/spack/repos/builtin/packages/bdftopcf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bdw-gc/package.py b/var/spack/repos/builtin/packages/bdw-gc/package.py index 5d5f882bab..40a5aca8cf 100644 --- a/var/spack/repos/builtin/packages/bdw-gc/package.py +++ b/var/spack/repos/builtin/packages/bdw-gc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/beagle/beagle.sh b/var/spack/repos/builtin/packages/beagle/beagle.sh new file mode 100644 index 0000000000..58093103f3 --- /dev/null +++ b/var/spack/repos/builtin/packages/beagle/beagle.sh @@ -0,0 +1,4 @@ +#!/bin/sh +# convenience wrapper for the jar file +java $JAVA_ARGS $JAVA_OPTS -jar beagle.jar "$@" + diff --git a/var/spack/repos/builtin/packages/beagle/package.py b/var/spack/repos/builtin/packages/beagle/package.py new file mode 100644 index 0000000000..cbe12a83aa --- /dev/null +++ b/var/spack/repos/builtin/packages/beagle/package.py @@ -0,0 +1,43 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os.path + + +class Beagle(Package): + """Beagle is a software package for phasing genotypes and for imputing + ungenotyped markers.""" + + homepage = "http://faculty.washington.edu/browning/beagle/beagle.html" + + version('5.1', sha256='994f926a4ec0eac665631f37c4a961d3f75c966c71841079275364013c90996c', + expand=False, url='http://faculty.washington.edu/browning/beagle/beagle.25Nov19.28d.jar') + version('5.0', sha256='8390fe18b53786b676b67dddae6d1c086d6225e518f6a82047f4138196b48621', + expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.12Jul19.0df.jar') + version('4.1', sha256='6c94610b278fc108c3e80b1134226911be1fc92b7d378ba648ac3eb97c5a3207', + expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.27Jan18.7e1.jar') + + depends_on('java@8', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + jar_file = os.path.basename(self.stage.archive_file) + install(jar_file, prefix.bin) + + # Set up a helper script to call java on the jar file, + # explicitly codes the path for java and the jar file. + script_sh = join_path(os.path.dirname(__file__), "beagle.sh") + script = prefix.bin.beagle + install(script_sh, script) + set_executable(script) + + # Munge the helper script to explicitly point to java and the + # jar file. + java = self.spec['java'].prefix.bin.java + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + filter_file('^java', java, script, **kwargs) + filter_file('beagle.jar', join_path(prefix.bin, jar_file), + script, **kwargs) diff --git a/var/spack/repos/builtin/packages/bear/package.py b/var/spack/repos/builtin/packages/bear/package.py index 85210b0af8..df43e55736 100644 --- a/var/spack/repos/builtin/packages/bear/package.py +++ b/var/spack/repos/builtin/packages/bear/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/beast-tracer/package.py b/var/spack/repos/builtin/packages/beast-tracer/package.py index 024ad75537..e7e4a344d7 100644 --- a/var/spack/repos/builtin/packages/beast-tracer/package.py +++ b/var/spack/repos/builtin/packages/beast-tracer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/beast1/package.py b/var/spack/repos/builtin/packages/beast1/package.py index 2361dd95c0..cee34e4814 100644 --- a/var/spack/repos/builtin/packages/beast1/package.py +++ b/var/spack/repos/builtin/packages/beast1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,8 +24,9 @@ class Beast1(Package): base = 'https://github.com/beast-dev/beast-mcmc/releases/download' return '{0}/v{1}/BEASTv{1}.tgz'.format(base, ver.dotted) - def setup_environment(self, spack_env, run_env): - run_env.set('BEAST1', self.prefix) + def setup_run_environment(self, env): + env.set('BEAST1', self.prefix) + env.set('BEAST_LIB', self.prefix.lib) def install(self, spec, prefix): install_tree('bin', prefix.bin) diff --git a/var/spack/repos/builtin/packages/beast2/package.py b/var/spack/repos/builtin/packages/beast2/package.py index 299fbba849..f7ff1b0e72 100644 --- a/var/spack/repos/builtin/packages/beast2/package.py +++ b/var/spack/repos/builtin/packages/beast2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,8 +22,8 @@ class Beast2(Package): depends_on('java') - def setup_environment(self, spack_env, run_env): - run_env.set('BEAST', self.prefix) + def setup_run_environment(self, env): + env.set('BEAST', self.prefix) def install(self, spec, prefix): install_tree('bin', prefix.bin) diff --git a/var/spack/repos/builtin/packages/bedops/package.py b/var/spack/repos/builtin/packages/bedops/package.py index 02f85d9b82..a8a6e7a607 100644 --- a/var/spack/repos/builtin/packages/bedops/package.py +++ b/var/spack/repos/builtin/packages/bedops/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bedtools2/package.py b/var/spack/repos/builtin/packages/bedtools2/package.py index 80c1359719..69260dd6e6 100644 --- a/var/spack/repos/builtin/packages/bedtools2/package.py +++ b/var/spack/repos/builtin/packages/bedtools2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/beforelight/package.py b/var/spack/repos/builtin/packages/beforelight/package.py index 512b77373c..b4646eafc0 100644 --- a/var/spack/repos/builtin/packages/beforelight/package.py +++ b/var/spack/repos/builtin/packages/beforelight/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/benchmark/package.py b/var/spack/repos/builtin/packages/benchmark/package.py index 07bd2790f0..c02a9e8b5f 100644 --- a/var/spack/repos/builtin/packages/benchmark/package.py +++ b/var/spack/repos/builtin/packages/benchmark/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/berkeley-db/package.py b/var/spack/repos/builtin/packages/berkeley-db/package.py index 244f7ddaa1..fc2fe3c4a9 100644 --- a/var/spack/repos/builtin/packages/berkeley-db/package.py +++ b/var/spack/repos/builtin/packages/berkeley-db/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,17 +12,23 @@ class BerkeleyDb(AutotoolsPackage): homepage = "http://www.oracle.com/technetwork/database/database-technologies/berkeleydb/overview/index.html" url = "http://download.oracle.com/berkeley-db/db-5.3.28.tar.gz" - version('5.3.28', sha256='e0a992d740709892e81f9d93f06daf305cf73fb81b545afe72478043172c3628') - version('6.0.35', sha256='24421affa8ae436fe427ae4f5f2d1634da83d3d55a5ad6354a98eeedb825de55') - version('6.1.29', sha256='b3c18180e4160d97dd197ba1d37c19f6ea2ec91d31bbfaf8972d99ba097af17d') version('6.2.32', sha256='a9c5e2b004a5777aa03510cfe5cd766a4a3b777713406b02809c17c8e0e7a8fb') + version('6.1.29', sha256='b3c18180e4160d97dd197ba1d37c19f6ea2ec91d31bbfaf8972d99ba097af17d') + version('6.0.35', sha256='24421affa8ae436fe427ae4f5f2d1634da83d3d55a5ad6354a98eeedb825de55') + version('5.3.28', sha256='e0a992d740709892e81f9d93f06daf305cf73fb81b545afe72478043172c3628') configure_directory = 'dist' build_directory = 'spack-build' - def url_for_version(self, version): - # newer version need oracle login, so get them from gentoo mirror - return 'http://distfiles.gentoo.org/distfiles/db-{0}.tar.gz'.format(version) +# TODO: Gentoo's website removed the BerkeleyDB archives. +# Please update the function bellow with a valid mirror. +# Right now this package will fetch from the Oracle website, +# and versions 5.3.28 and 6.0.35 will fail to download. +# +# def url_for_version(self, version): +# # newer version need oracle login, so get them from gentoo mirror +# url_fmt = 'http://distfiles.gentoo.org/distfiles/db-{0}.tar.gz' +# return url_fmt.format(version) def configure_args(self): return ['--disable-static', '--enable-cxx', '--enable-stl'] diff --git a/var/spack/repos/builtin/packages/bertini/package.py b/var/spack/repos/builtin/packages/bertini/package.py index 41d31097bd..aba08990c6 100644 --- a/var/spack/repos/builtin/packages/bertini/package.py +++ b/var/spack/repos/builtin/packages/bertini/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bib2xhtml/package.py b/var/spack/repos/builtin/packages/bib2xhtml/package.py index 3d75b7ebc9..057b202ca2 100644 --- a/var/spack/repos/builtin/packages/bib2xhtml/package.py +++ b/var/spack/repos/builtin/packages/bib2xhtml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bigreqsproto/package.py b/var/spack/repos/builtin/packages/bigreqsproto/package.py index ef6eecfd81..1e4a1fc1bd 100644 --- a/var/spack/repos/builtin/packages/bigreqsproto/package.py +++ b/var/spack/repos/builtin/packages/bigreqsproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bind9/package.py b/var/spack/repos/builtin/packages/bind9/package.py new file mode 100644 index 0000000000..7c31821e6c --- /dev/null +++ b/var/spack/repos/builtin/packages/bind9/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Bind9(AutotoolsPackage): + """ + BIND 9 has evolved to be a very flexible, full-featured DNS system. + """ + + homepage = "https://github.com/isc-projects/bind9" + url = "https://github.com/isc-projects/bind9/archive/v9_14_6.tar.gz" + + version('9_14_6', sha256='98be7a7b6d614b519f6c8d6ec7a8a39759ae9604d87228d9dc7c034471e5433e') + + def configure_args(self): + args = ["--without-python", "--disable-linux-caps"] + return args diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index 9f42882f03..ad5f7fb5ef 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,14 @@ from spack import * import glob -class Binutils(AutotoolsPackage): +class Binutils(AutotoolsPackage, GNUMirrorPackage): """GNU binutils, which contain the linker, assembler, objdump and others""" homepage = "http://www.gnu.org/software/binutils/" - url = "https://ftpmirror.gnu.org/binutils/binutils-2.28.tar.bz2" + gnu_mirror_path = "binutils/binutils-2.28.tar.bz2" - version('2.32', sha256='de38b15c902eb2725eac6af21183a5f34ea4634cb0bcef19612b50e5ed31072d') + version('2.33.1', sha256='0cb4843da15a65a953907c96bad658283f3c4419d6bcc56bf2789db16306adb2') + version('2.32', sha256='de38b15c902eb2725eac6af21183a5f34ea4634cb0bcef19612b50e5ed31072d') version('2.31.1', sha256='ffcc382695bf947da6135e7436b8ed52d991cf270db897190f19d6f9838564d0') version('2.29.1', sha256='1509dff41369fb70aed23682351b663b56db894034773e6dbf7d5d6071fc55cc') version('2.28', sha256='6297433ee120b11b4b0a1c8f3512d7d73501753142ab9e2daa13c5a3edd32a72') diff --git a/var/spack/repos/builtin/packages/bioawk/package.py b/var/spack/repos/builtin/packages/bioawk/package.py index c01be2d8d5..d7317d4293 100644 --- a/var/spack/repos/builtin/packages/bioawk/package.py +++ b/var/spack/repos/builtin/packages/bioawk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/biobloom/package.py b/var/spack/repos/builtin/packages/biobloom/package.py index 2d15e6a46e..c9d1ac687f 100644 --- a/var/spack/repos/builtin/packages/biobloom/package.py +++ b/var/spack/repos/builtin/packages/biobloom/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/biopieces/package.py b/var/spack/repos/builtin/packages/biopieces/package.py index 2091f8508f..6e94f3855d 100644 --- a/var/spack/repos/builtin/packages/biopieces/package.py +++ b/var/spack/repos/builtin/packages/biopieces/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,21 +21,21 @@ class Biopieces(Package): depends_on('perl-module-build', type=('build', 'run')) depends_on('perl-bit-vector', type=('build', 'run')) depends_on('perl-svg', type=('build', 'run')) - depends_on('perl-term-readkey', type=('build', 'run')) + depends_on('perl-termreadkey', type=('build', 'run')) depends_on('perl-time-hires', type=('build', 'run')) depends_on('perl-dbi', type=('build', 'run')) depends_on('perl-xml-parser', type=('build', 'run')) depends_on('perl-carp-clan', type=('build', 'run')) depends_on('perl-class-inspector', type=('build', 'run')) depends_on('perl-html-parser', type=('build', 'run')) - depends_on('perl-lwp', type=('build', 'run')) + depends_on('perl-libwww-perl', type=('build', 'run')) depends_on('perl-soap-lite', type=('build', 'run')) depends_on('perl-uri', type=('build', 'run')) depends_on('perl-inline', type=('build', 'run')) depends_on('perl-inline-c', type=('build', 'run')) depends_on('perl-parse-recdescent', type=('build', 'run')) - depends_on('perl-version', type=('build', 'run')) - depends_on('perl-dbfile', type=('build', 'run')) + depends_on('perl-perl-version', type=('build', 'run')) + depends_on('perl-db-file', type=('build', 'run')) depends_on('perl-dbd-mysql', type=('build', 'run')) depends_on('ruby@1.9:') @@ -61,10 +61,10 @@ class Biopieces(Package): def install(self, spec, prefix): install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # Note: user will need to set environment variables on their own, # dependent on where they will want data to be located: # BP_DATA - Contains genomic data etc. # BP_TMP - Required temporary directory # BP_LOG - Required log directory - run_env.prepend_path('BP_DIR', prefix) + env.prepend_path('BP_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/bismark/package.py b/var/spack/repos/builtin/packages/bismark/package.py index 057ccd1dad..cb71eed678 100644 --- a/var/spack/repos/builtin/packages/bismark/package.py +++ b/var/spack/repos/builtin/packages/bismark/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index 167171c54c..7738b38a8f 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,13 +8,13 @@ from spack.operating_systems.mac_os import macos_version import sys -class Bison(AutotoolsPackage): +class Bison(AutotoolsPackage, GNUMirrorPackage): """Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" homepage = "https://www.gnu.org/software/bison/" - url = "https://ftpmirror.gnu.org/bison/bison-3.4.2.tar.gz" + gnu_mirror_path = "bison/bison-3.4.2.tar.gz" version('3.4.2', sha256='ff3922af377d514eca302a6662d470e857bd1a591e96a2050500df5a9d59facf') version('3.0.5', sha256='cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566') @@ -31,6 +31,9 @@ class Bison(AutotoolsPackage): patch('pgi.patch', when='@3.0.4') + conflicts('%intel@:14', when='@3.4.2:', + msg="Intel 14 has immature C11 support") + if sys.platform == 'darwin' and macos_version() >= Version('10.13'): patch('secure_snprintf.patch', level=0, when='@3.0.4') diff --git a/var/spack/repos/builtin/packages/bitmap/package.py b/var/spack/repos/builtin/packages/bitmap/package.py index af6b2582f9..c8937e1520 100644 --- a/var/spack/repos/builtin/packages/bitmap/package.py +++ b/var/spack/repos/builtin/packages/bitmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/blasr-libcpp/package.py b/var/spack/repos/builtin/packages/blasr-libcpp/package.py index 40693d9e89..ab2491feb7 100644 --- a/var/spack/repos/builtin/packages/blasr-libcpp/package.py +++ b/var/spack/repos/builtin/packages/blasr-libcpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -45,10 +45,7 @@ class BlasrLibcpp(Package): install_tree('hdf', prefix.hdf) install_tree('pbdata', prefix.pbdata) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path('LD_LIBRARY_PATH', - self.spec.prefix.hdf) - spack_env.prepend_path('LD_LIBRARY_PATH', - self.spec.prefix.alignment) - spack_env.prepend_path('LD_LIBRARY_PATH', - self.spec.prefix.pbdata) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path('LD_LIBRARY_PATH', self.spec.prefix.hdf) + env.prepend_path('LD_LIBRARY_PATH', self.spec.prefix.alignment) + env.prepend_path('LD_LIBRARY_PATH', self.spec.prefix.pbdata) diff --git a/var/spack/repos/builtin/packages/blasr/package.py b/var/spack/repos/builtin/packages/blasr/package.py index a25f1486da..5c6afdba3a 100644 --- a/var/spack/repos/builtin/packages/blasr/package.py +++ b/var/spack/repos/builtin/packages/blasr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,19 +26,19 @@ class Blasr(Package): phases = ['configure', 'build', 'install'] - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.spec.prefix.utils) - spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix) - spack_env.prepend_path('CPATH', self.spec[ - 'blasr-libcpp'].prefix.pbdata) - spack_env.prepend_path('CPATH', self.spec[ - 'blasr-libcpp'].prefix.alignment) - spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.hdf) + def setup_build_environment(self, env): + env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix) + env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.pbdata) + env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.alignment) + env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.hdf) # hdf has +mpi by default, so handle that possibility if ('+mpi' in self.spec['hdf5']): - spack_env.set('CC', self.spec['mpi'].mpicc) - spack_env.set('CXX', self.spec['mpi'].mpicxx) + env.set('CC', self.spec['mpi'].mpicc) + env.set('CXX', self.spec['mpi'].mpicxx) + + def setup_run_environment(self, env): + env.prepend_path('PATH', self.spec.prefix.utils) def configure(self, spec, prefix): configure_args = [ diff --git a/var/spack/repos/builtin/packages/blast-legacy/package.py b/var/spack/repos/builtin/packages/blast-legacy/package.py index 9bd9d48637..faf5a155af 100644 --- a/var/spack/repos/builtin/packages/blast-legacy/package.py +++ b/var/spack/repos/builtin/packages/blast-legacy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/blast-plus/package.py b/var/spack/repos/builtin/packages/blast-plus/package.py index 71ba17eb4a..febe4fc159 100644 --- a/var/spack/repos/builtin/packages/blast-plus/package.py +++ b/var/spack/repos/builtin/packages/blast-plus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/blast2go/package.py b/var/spack/repos/builtin/packages/blast2go/package.py index e8abcddf0a..d272065474 100644 --- a/var/spack/repos/builtin/packages/blast2go/package.py +++ b/var/spack/repos/builtin/packages/blast2go/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/blat/package.py b/var/spack/repos/builtin/packages/blat/package.py index 7b2f5de649..34c9f0da6b 100644 --- a/var/spack/repos/builtin/packages/blat/package.py +++ b/var/spack/repos/builtin/packages/blat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,8 +17,8 @@ class Blat(Package): depends_on('libpng') - def setup_environment(self, spack_env, run_env): - spack_env.set('MACHTYPE', 'x86_64') + def setup_build_environment(self, env): + env.set('MACHTYPE', 'x86_64') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/blaze/package.py b/var/spack/repos/builtin/packages/blaze/package.py index 531449a320..8801b9b1d6 100644 --- a/var/spack/repos/builtin/packages/blaze/package.py +++ b/var/spack/repos/builtin/packages/blaze/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/blis/package.py b/var/spack/repos/builtin/packages/blis/package.py index 45f81689d8..ea7ca8ff42 100644 --- a/var/spack/repos/builtin/packages/blis/package.py +++ b/var/spack/repos/builtin/packages/blis/package.py @@ -1,40 +1,18 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * - # Although this looks like an Autotools package, it's not one. Refer to: # https://github.com/flame/blis/issues/17 # https://github.com/flame/blis/issues/195 # https://github.com/flame/blis/issues/197 -class Blis(Package): - """BLIS is a portable software framework for instantiating high-performance - BLAS-like dense linear algebra libraries. The framework was designed to - isolate essential kernels of computation that, when optimized, immediately - enable optimized implementations of most of its commonly used and - computationally intensive operations. BLIS is written in ISO C99 and - available under a new/modified/3-clause BSD license. While BLIS exports a - new BLAS-like API, it also includes a BLAS compatibility layer which gives - application developers access to BLIS implementations via traditional BLAS - routine calls. An object-based API unique to BLIS is also available.""" - - homepage = "https://github.com/flame/blis" - url = "https://github.com/flame/blis/archive/0.4.0.tar.gz" - git = "https://github.com/flame/blis.git" - - version('master', branch='master') - version('0.6.0', sha256='ad5765cc3f492d0c663f494850dafc4d72f901c332eb442f404814ff2995e5a9') - version('0.5.0', sha256='1a004d69c139e8a0448c6a6007863af3a8c3551b8d9b8b73fe08e8009f165fa8') - version('0.4.0', sha256='9c7efd75365a833614c01b5adfba93210f869d92e7649e0b5d9edc93fc20ea76') - version('0.3.2', sha256='b87e42c73a06107d647a890cbf12855925777dc7124b0c7698b90c5effa7f58f') - version('0.3.1', sha256='957f28d47c5cf71ffc62ce8cc1277e17e44d305b1c2fa8506b0b55617a9f28e4') - version('0.3.0', sha256='d34d17df7bdc2be8771fe0b7f867109fd10437ac91e2a29000a4a23164c7f0da') - version('0.2.2', sha256='4a7ecb56034fb20e9d1d8b16e2ef587abbc3d30cb728e70629ca7e795a7998e8') - +class BlisBase(Package): + """Base class for building BLIS, shared with the AMD optimized version + of the library in the 'amdblis' package. + """ depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) variant( @@ -73,10 +51,6 @@ class Blis(Package): provides('blas', when="+blas") provides('blas', when="+cblas") - # Problems with permissions on installed libraries: - # https://github.com/flame/blis/issues/343 - patch('Makefile_0.6.0.patch', when='@0.4.0:0.6.0') - phases = ['configure', 'build', 'install'] def configure(self, spec, prefix): @@ -127,3 +101,36 @@ class Blis(Package): # The shared library is not installed correctly on Darwin; fix this if self.spec.satisfies('platform=darwin'): fix_darwin_install_name(self.prefix.lib) + + +class Blis(BlisBase): + """BLIS is a portable software framework for instantiating high-performance + BLAS-like dense linear algebra libraries. + + The framework was designed to isolate essential kernels of computation + that, when optimized, immediately enable optimized implementations of + most of its commonly used and computationally intensive operations. BLIS + is written in ISO C99 and available under a new/modified/3-clause BSD + license. While BLIS exports a new BLAS-like API, it also includes a + BLAS compatibility layer which gives application developers access to + BLIS implementations via traditional BLAS routine calls. + An object-based API unique to BLIS is also available. + """ + + homepage = "https://github.com/flame/blis" + url = "https://github.com/flame/blis/archive/0.4.0.tar.gz" + git = "https://github.com/flame/blis.git" + + version('master', branch='master') + version('0.6.1', sha256='76b22f29b7789cf117c0873d2a6b2a6d61f903869168148f2e7306353c105c37') + version('0.6.0', sha256='ad5765cc3f492d0c663f494850dafc4d72f901c332eb442f404814ff2995e5a9') + version('0.5.0', sha256='1a004d69c139e8a0448c6a6007863af3a8c3551b8d9b8b73fe08e8009f165fa8') + version('0.4.0', sha256='9c7efd75365a833614c01b5adfba93210f869d92e7649e0b5d9edc93fc20ea76') + version('0.3.2', sha256='b87e42c73a06107d647a890cbf12855925777dc7124b0c7698b90c5effa7f58f') + version('0.3.1', sha256='957f28d47c5cf71ffc62ce8cc1277e17e44d305b1c2fa8506b0b55617a9f28e4') + version('0.3.0', sha256='d34d17df7bdc2be8771fe0b7f867109fd10437ac91e2a29000a4a23164c7f0da') + version('0.2.2', sha256='4a7ecb56034fb20e9d1d8b16e2ef587abbc3d30cb728e70629ca7e795a7998e8') + + # Problems with permissions on installed libraries: + # https://github.com/flame/blis/issues/343 + patch('Makefile_0.6.0.patch', when='@0.4.0:0.6.0') diff --git a/var/spack/repos/builtin/packages/bliss/package.py b/var/spack/repos/builtin/packages/bliss/package.py index 3134aa9293..7878f16cb0 100644 --- a/var/spack/repos/builtin/packages/bliss/package.py +++ b/var/spack/repos/builtin/packages/bliss/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/blitz/package.py b/var/spack/repos/builtin/packages/blitz/package.py index 005de899c4..4a823b3e20 100644 --- a/var/spack/repos/builtin/packages/blitz/package.py +++ b/var/spack/repos/builtin/packages/blitz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/blktrace/package.py b/var/spack/repos/builtin/packages/blktrace/package.py new file mode 100644 index 0000000000..d088439139 --- /dev/null +++ b/var/spack/repos/builtin/packages/blktrace/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Blktrace(MakefilePackage): + """ + blktrace is a block layer IO tracing mechanism which provides detailed + information about request queue operations up to user space. There are + three major components: a kernel component, a utility to record the i/o + trace information for the kernel to user space, and utilities to analyse + and view the trace information. + """ + + homepage = "https://brick.kernel.dk" + url = "https://brick.kernel.dk/snaps/blktrace-1.2.0.tar.gz" + + version('1.2.0', sha256='d14029bc096026dacb206bf115c912dcdb795320b5aba6dff3e46d7f94c5242d') + version('1.1.0', sha256='dc1e5da64b8fef454ec24aa4fcc760112b4ea7c973e2485961aa5668b3a8ce1d') + version('1.0.5', sha256='783b4c8743498de74b3492725815d31f3842828baf8710c53bc4e7e82cee387c') + version('1.0.4', sha256='c1b53e2382f7309e822d48fef187cf44e84bb44df52a0a9786d447d127af75cf') + version('1.0.3', sha256='78c6825212fe6700039fab77d53bc02e6b324e712caea718fff190e4e034cfa8') + version('1.0.2', sha256='15f01e2a952919ba3c7b90f8bd891d1a98c454626501094030df632666786343') + + depends_on('libaio') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/bmake/package.py b/var/spack/repos/builtin/packages/bmake/package.py index bce12a1440..8d103513f5 100644 --- a/var/spack/repos/builtin/packages/bmake/package.py +++ b/var/spack/repos/builtin/packages/bmake/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bmi/package.py b/var/spack/repos/builtin/packages/bmi/package.py index a41619182a..ad2cb53cac 100644 --- a/var/spack/repos/builtin/packages/bmi/package.py +++ b/var/spack/repos/builtin/packages/bmi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bml/package.py b/var/spack/repos/builtin/packages/bml/package.py index 95bf6e1b25..9cc70e14f5 100644 --- a/var/spack/repos/builtin/packages/bml/package.py +++ b/var/spack/repos/builtin/packages/bml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bohrium/package.py b/var/spack/repos/builtin/packages/bohrium/package.py index eb3f644d00..1fb05be2a0 100644 --- a/var/spack/repos/builtin/packages/bohrium/package.py +++ b/var/spack/repos/builtin/packages/bohrium/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -201,11 +201,11 @@ class Bohrium(CMakePackage, CudaPackage): # # Environment setup # - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # Bohrium needs an extra include dir apart from # the self.prefix.include dir - run_env.prepend_path("CPATH", self.prefix.include.bohrium) - run_env.set("BH_CONFIG", self.config_file) + env.prepend_path("CPATH", self.prefix.include.bohrium) + env.set("BH_CONFIG", self.config_file) # # Quick tests diff --git a/var/spack/repos/builtin/packages/bolt/package.py b/var/spack/repos/builtin/packages/bolt/package.py index 981dfae611..d0750e615d 100644 --- a/var/spack/repos/builtin/packages/bolt/package.py +++ b/var/spack/repos/builtin/packages/bolt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,8 +20,10 @@ class Bolt(CMakePackage): homepage = "http://www.bolt-omp.org/" url = "https://github.com/pmodels/bolt/releases/download/v1.0b1/bolt-1.0b1.tar.gz" git = "https://github.com/pmodels/bolt.git" + maintainers = ['shintaro-iwasaki'] version("master", branch="master") + version("1.0rc3", sha256="beec522d26e74f0a562762ea5ae7805486a17b40013090ea1472f0c34c3379c8") version("1.0rc2", sha256="662ab0bb9583e8d733e8af62a97b41828e8bfe4bd65902f1195b986901775a45") version("1.0rc1", sha256="c08cde0695b9d1252ab152425be96eb29c70d764e3083e276c013804883a15a4") version("1.0b1", sha256="fedba46ad2f8835dd1cec1a9a52bcc9d8923071dc40045d0360517d09cd1a57d") diff --git a/var/spack/repos/builtin/packages/bookleaf-cpp/package.py b/var/spack/repos/builtin/packages/bookleaf-cpp/package.py index 0dcbc7646e..1fec8cbc6d 100644 --- a/var/spack/repos/builtin/packages/bookleaf-cpp/package.py +++ b/var/spack/repos/builtin/packages/bookleaf-cpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index 094a96954c..884aaa40b6 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,8 +22,11 @@ class Boost(Package): git = "https://github.com/boostorg/boost.git" list_url = "http://sourceforge.net/projects/boost/files/boost/" list_depth = 1 + maintainers = ['hainest'] version('develop', branch='develop', submodules=True) + version('1.72.0', sha256='59c9b274bc451cf91a9ba1dd2c7fdcaf5d60b1b3aa83f2c9fa143417cc660722') + version('1.71.0', sha256='d73a8da01e8bf8c7eda40b4c84915071a8c8a0df4a6734537ddde4a8580524ee') version('1.70.0', sha256='430ae8354789de4fd19ee52f3b1f739e1fba576f0aded0897c3c2bc00fb38778') version('1.69.0', sha256='8f32d4617390d1c2d16f26a27ab60d97807b35440d45891fa340fc2648b04406') version('1.68.0', sha256='7f6130bc3cf65f56a618888ce9d5ea704fa10b462be126ad053e80e553d6d8b7') @@ -205,7 +208,7 @@ class Boost(Package): # Add option to C/C++ compile commands in clang-linux.jam patch('clang-linux_add_option.patch', when='@1.56.0:1.63.0') - patch('clang-linux_add_option2.patch', when='@:1.55.0') + patch('clang-linux_add_option2.patch', when='@1.47.0:1.55.0') def url_for_version(self, version): if version >= Version('1.63.0'): @@ -216,9 +219,6 @@ class Boost(Package): return url.format(version.dotted, version.underscored) def determine_toolset(self, spec): - if spec.satisfies("platform=darwin"): - return 'darwin' - toolsets = {'g++': 'gcc', 'icpc': 'intel', 'clang++': 'clang', @@ -367,6 +367,12 @@ class Boost(Package): cxxflags.append('-stdlib=libc++') options.extend(['toolset=clang', 'linkflags="-stdlib=libc++"']) + elif spec.satisfies('%xl') or spec.satisfies('%xl_r'): + # see also: https://lists.boost.org/boost-users/2019/09/89953.php + # the cxxstd setting via spack is not sufficient to drive the + # change into boost compilation + if spec.variants['cxxstd'].value == '11': + cxxflags.append('-std=c++11') if cxxflags: options.append('cxxflags="{0}"'.format(' '.join(cxxflags))) diff --git a/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py b/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py index a193fba98b..93ae4a8322 100644 --- a/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py +++ b/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bowtie/package.py b/var/spack/repos/builtin/packages/bowtie/package.py index 0454e68e50..ce7f8b03a0 100644 --- a/var/spack/repos/builtin/packages/bowtie/package.py +++ b/var/spack/repos/builtin/packages/bowtie/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py index ec54582d03..9989f37c02 100644 --- a/var/spack/repos/builtin/packages/bowtie2/package.py +++ b/var/spack/repos/builtin/packages/bowtie2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/boxlib/package.py b/var/spack/repos/builtin/packages/boxlib/package.py index 032faad56d..def583de9f 100644 --- a/var/spack/repos/builtin/packages/boxlib/package.py +++ b/var/spack/repos/builtin/packages/boxlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py index 86326ccc1b..02eb02681b 100644 --- a/var/spack/repos/builtin/packages/bpp-core/package.py +++ b/var/spack/repos/builtin/packages/bpp-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bpp-phyl/package.py b/var/spack/repos/builtin/packages/bpp-phyl/package.py index e2b8f0588a..a0b73d804d 100644 --- a/var/spack/repos/builtin/packages/bpp-phyl/package.py +++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bpp-seq/package.py b/var/spack/repos/builtin/packages/bpp-seq/package.py index 74ca003851..57141e3afb 100644 --- a/var/spack/repos/builtin/packages/bpp-seq/package.py +++ b/var/spack/repos/builtin/packages/bpp-seq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bpp-suite/clarify_isinf.patch b/var/spack/repos/builtin/packages/bpp-suite/clarify_isinf.patch new file mode 100644 index 0000000000..ad92f08da7 --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-suite/clarify_isinf.patch @@ -0,0 +1,90 @@ +diff -ur spack-src.org/bppSuite/bppAncestor.cpp spack-src/bppSuite/bppAncestor.cpp +--- spack-src.org/bppSuite/bppAncestor.cpp 2019-11-18 15:59:34.786164416 +0900 ++++ spack-src/bppSuite/bppAncestor.cpp 2019-11-18 16:26:25.385749490 +0900 +@@ -237,7 +237,7 @@ + delete tree; + + double logL = tl->getValue(); +- if (isinf(logL)) ++ if (std::isinf(logL)) + { + // This may be due to null branch lengths, leading to null likelihood! + ApplicationTools::displayWarning("!!! Warning!!! Likelihood is zero."); +@@ -251,7 +251,7 @@ + tl->matchParametersValues(pl); + logL = tl->getValue(); + } +- if (isinf(logL)) ++ if (std::isinf(logL)) + { + ApplicationTools::displayError("!!! Unexpected likelihood == 0."); + ApplicationTools::displayError("!!! Looking at each site:"); +diff -ur spack-src.org/bppSuite/bppML.cpp spack-src/bppSuite/bppML.cpp +--- spack-src.org/bppSuite/bppML.cpp 2019-11-18 15:59:34.786164416 +0900 ++++ spack-src/bppSuite/bppML.cpp 2019-11-18 16:29:09.373021202 +0900 +@@ -425,7 +425,7 @@ + + //Check initial likelihood: + double logL = tl->getValue(); +- if (isinf(logL)) ++ if (std::isinf(logL)) + { + // This may be due to null branch lengths, leading to null likelihood! + ApplicationTools::displayWarning("!!! Warning!!! Initial likelihood is zero."); +@@ -440,7 +440,7 @@ + logL = tl->getValue(); + } + ApplicationTools::displayResult("Initial log likelihood", TextTools::toString(-logL, 15)); +- if (isinf(logL)) ++ if (std::isinf(logL)) + { + ApplicationTools::displayError("!!! Unexpected initial likelihood == 0."); + if (codonAlphabet) +@@ -448,7 +448,7 @@ + bool f = false; + size_t s; + for (size_t i = 0; i < sites->getNumberOfSites(); i++) { +- if (isinf(tl->getLogLikelihoodForASite(i))) { ++ if (std::isinf(tl->getLogLikelihoodForASite(i))) { + const Site& site = sites->getSite(i); + s = site.size(); + for (size_t j = 0; j < s; j++) { +@@ -477,7 +477,7 @@ + } else { + ApplicationTools::displayBooleanResult("Saturated site removal enabled", true); + for (size_t i = sites->getNumberOfSites(); i > 0; --i) { +- if (isinf(tl->getLogLikelihoodForASite(i - 1))) { ++ if (std::isinf(tl->getLogLikelihoodForASite(i - 1))) { + ApplicationTools::displayResult("Ignore saturated site", sites->getSite(i - 1).getPosition()); + sites->deleteSite(i - 1); + } +@@ -486,7 +486,7 @@ + tl->setData(*sites); + tl->initialize(); + logL = tl->getValue(); +- if (isinf(logL)) { ++ if (std::isinf(logL)) { + throw Exception("Likelihood is still 0 after saturated sites are removed! Looks like a bug..."); + } + ApplicationTools::displayResult("Initial log likelihood", TextTools::toString(-logL, 15)); +diff -ur spack-src.org/bppSuite/bppMixedLikelihoods.cpp spack-src/bppSuite/bppMixedLikelihoods.cpp +--- spack-src.org/bppSuite/bppMixedLikelihoods.cpp 2019-11-18 15:59:34.786164416 +0900 ++++ spack-src/bppSuite/bppMixedLikelihoods.cpp 2019-11-18 16:26:48.338168188 +0900 +@@ -220,7 +220,7 @@ + tl->initialize(); + + double logL = tl->getValue(); +- if (isinf(logL)) ++ if (std::isinf(logL)) + { + // This may be due to null branch lengths, leading to null likelihood! + ApplicationTools::displayWarning("!!! Warning!!! Likelihood is zero."); +@@ -235,7 +235,7 @@ + tl->matchParametersValues(pl); + logL = tl->getValue(); + } +- if (isinf(logL)) ++ if (std::isinf(logL)) + { + ApplicationTools::displayError("!!! Unexpected likelihood == 0."); + ApplicationTools::displayError("!!! Looking at each site:"); diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py index 542a5cf73e..889a25de49 100644 --- a/var/spack/repos/builtin/packages/bpp-suite/package.py +++ b/var/spack/repos/builtin/packages/bpp-suite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,3 +20,7 @@ class BppSuite(CMakePackage): depends_on('bpp-core') depends_on('bpp-seq') depends_on('bpp-phyl') + + # Clarify isinf's namespace, because Fujitsu compiler can't + # resolve ambiguous of 'isinf' function. + patch('clarify_isinf.patch', when='%fj') diff --git a/var/spack/repos/builtin/packages/bracken/package.py b/var/spack/repos/builtin/packages/bracken/package.py index 3584690937..bc250f8b1e 100644 --- a/var/spack/repos/builtin/packages/bracken/package.py +++ b/var/spack/repos/builtin/packages/bracken/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/braker/package.py b/var/spack/repos/builtin/packages/braker/package.py index f9db018c1d..7bada09715 100644 --- a/var/spack/repos/builtin/packages/braker/package.py +++ b/var/spack/repos/builtin/packages/braker/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -62,5 +62,5 @@ class Braker(Package): for file in files: filter_file(pattern, repl, *files, backup=False) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PERL5LIB', prefix.lib) + def setup_run_environment(self, env): + env.prepend_path('PERL5LIB', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/branson/package.py b/var/spack/repos/builtin/packages/branson/package.py index 8104ad4085..ffa9df0a84 100644 --- a/var/spack/repos/builtin/packages/branson/package.py +++ b/var/spack/repos/builtin/packages/branson/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py index 3ad2cdfc01..0852d763c2 100644 --- a/var/spack/repos/builtin/packages/breakdancer/package.py +++ b/var/spack/repos/builtin/packages/breakdancer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -32,7 +32,7 @@ class Breakdancer(CMakePackage): depends_on('perl-statistics-descriptive', type='run') depends_on('perl-math-cdf', type='run') - depends_on('perl-gd-graph', type='run') + depends_on('perl-gdgraph', type='run') depends_on('perl-gdgraph-histogram', type='run') depends_on('perl-list-moreutils', type='run') depends_on('perl-exporter-tiny', type='run') @@ -41,9 +41,9 @@ class Breakdancer(CMakePackage): parallel = False - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # get the perl tools in the path - run_env.prepend_path('PATH', self.prefix.lib) + env.prepend_path('PATH', self.prefix.lib) def edit(self, spec, prefix): # perl tools end up in a silly lib subdirectory, fixing that diff --git a/var/spack/repos/builtin/packages/bref3/bref.sh b/var/spack/repos/builtin/packages/bref3/bref.sh new file mode 100644 index 0000000000..5a182fe01c --- /dev/null +++ b/var/spack/repos/builtin/packages/bref3/bref.sh @@ -0,0 +1,4 @@ +#!/bin/sh +# convenience wrapper for the jar file +java $JAVA_ARGS $JAVA_OPTS -jar bref.jar "$@" + diff --git a/var/spack/repos/builtin/packages/bref3/package.py b/var/spack/repos/builtin/packages/bref3/package.py new file mode 100644 index 0000000000..521f2f1043 --- /dev/null +++ b/var/spack/repos/builtin/packages/bref3/package.py @@ -0,0 +1,46 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os.path + + +class Bref3(Package): + """Bref3: Converts from VCF format to bref3 format.""" + + homepage = "http://faculty.washington.edu/browning/beagle/beagle.html" + + version('2019-11-25', sha256='969c0881050c4a48d19be9ea64bf49fa68c1403b69f9f739bbfd865dda639b2d', + expand=False, url='http://faculty.washington.edu/browning/beagle/bref3.25Nov19.28d.jar') + version('2019-07-12', sha256='8a9c3b6c38e36ef4c05a61108f083005fd985026c67d75a8173088f88816a202', + expand=False, url='https://faculty.washington.edu/browning/beagle/bref3.12Jul19.0df.jar') + version('2018-01-27', sha256='4d32f0b6d536c88d5332d961309466c8c3dd9572907a3755450d26d7ba841083', + expand=False, url='https://faculty.washington.edu/browning/beagle/bref.27Jan18.7e1.jar') + depends_on('java@8', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + jar_file = os.path.basename(self.stage.archive_file) + install(jar_file, prefix.bin) + + # Set up a helper script to call java on the jar file, + # explicitly codes the path for java and the jar file. + + if self.version >= Version('2019'): + script = prefix.bin.bref3 + else: + script = prefix.bin.bref + + script_sh = join_path(os.path.dirname(__file__), "bref.sh") + install(script_sh, script) + set_executable(script) + + # Munge the helper script to explicitly point to java and the + # jar file. + java = self.spec['java'].prefix.bin.java + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + filter_file('^java', java, script, **kwargs) + filter_file('bref.jar', join_path(prefix.bin, jar_file), + script, **kwargs) diff --git a/var/spack/repos/builtin/packages/breseq/package.py b/var/spack/repos/builtin/packages/breseq/package.py index 82893663d9..4efb1207fe 100644 --- a/var/spack/repos/builtin/packages/breseq/package.py +++ b/var/spack/repos/builtin/packages/breseq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,8 +30,6 @@ class Breseq(AutotoolsPackage): conflicts('%gcc@:4.8') conflicts('%clang@:3.3') - def setup_environment(self, spack_env, run_env): - spack_env.set('LDFLAGS', - "-L{0}".format(self.spec['zlib'].prefix.lib)) - spack_env.set('CFLAGS', - "-I{0}".format(self.spec['zlib'].prefix.include)) + def setup_build_environment(self, env): + env.set('LDFLAGS', "-L{0}".format(self.spec['zlib'].prefix.lib)) + env.set('CFLAGS', "-I{0}".format(self.spec['zlib'].prefix.include)) diff --git a/var/spack/repos/builtin/packages/bridger/package.py b/var/spack/repos/builtin/packages/bridger/package.py index 4071046478..04e44faf87 100644 --- a/var/spack/repos/builtin/packages/bridger/package.py +++ b/var/spack/repos/builtin/packages/bridger/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/brigand/package.py b/var/spack/repos/builtin/packages/brigand/package.py index 54c3b52a47..1de0f09cf1 100644 --- a/var/spack/repos/builtin/packages/brigand/package.py +++ b/var/spack/repos/builtin/packages/brigand/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/brotli/package.py b/var/spack/repos/builtin/packages/brotli/package.py index e11c681029..f5f2e478ac 100644 --- a/var/spack/repos/builtin/packages/brotli/package.py +++ b/var/spack/repos/builtin/packages/brotli/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bsseeker2/package.py b/var/spack/repos/builtin/packages/bsseeker2/package.py index 73fd8ca24b..6b909156d1 100644 --- a/var/spack/repos/builtin/packages/bsseeker2/package.py +++ b/var/spack/repos/builtin/packages/bsseeker2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,7 @@ class Bsseeker2(Package): url = "https://github.com/BSSeeker/BSseeker2/archive/BSseeker2-v2.1.8.tar.gz" version('2.1.8', sha256='34ebedce36a0fca9e22405d4c2c20bc978439d4a34d1d543657fbc53ff847934') - version('2.1.5', sha256='ac90fb4ad8853ee920f1ffea2b1a8cfffcdb1508ff34be0091d5a9c90ac8c74a', + version('2.1.7', sha256='ac90fb4ad8853ee920f1ffea2b1a8cfffcdb1508ff34be0091d5a9c90ac8c74a', url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.7.tar.gz') version('2.1.2', sha256='08055dd314f85a9b74c259c2cb894ea2affdab2c7a120af3589c649e1900c5c6', url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.2.tar.gz') diff --git a/var/spack/repos/builtin/packages/bucky/package.py b/var/spack/repos/builtin/packages/bucky/package.py index c88fd91b61..859fabde34 100644 --- a/var/spack/repos/builtin/packages/bucky/package.py +++ b/var/spack/repos/builtin/packages/bucky/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bumpversion/package.py b/var/spack/repos/builtin/packages/bumpversion/package.py index 1f8d3d519d..ac7e839153 100644 --- a/var/spack/repos/builtin/packages/bumpversion/package.py +++ b/var/spack/repos/builtin/packages/bumpversion/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/busco/package.py b/var/spack/repos/builtin/packages/busco/package.py index c23ad62fb3..fec0761deb 100644 --- a/var/spack/repos/builtin/packages/busco/package.py +++ b/var/spack/repos/builtin/packages/busco/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/busybox/package.py b/var/spack/repos/builtin/packages/busybox/package.py new file mode 100644 index 0000000000..8b8d11c534 --- /dev/null +++ b/var/spack/repos/builtin/packages/busybox/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Busybox(MakefilePackage): + """BusyBox combines tiny versions of many common UNIX utilities into + a single small executable. It provides replacements for most of + the utilities you usually find in GNU fileutils, shellutils, etc""" + + homepage = "https://busybox.net" + url = "https://busybox.net/downloads/busybox-1.31.0.tar.bz2" + + version('1.31.1', sha256='d0f940a72f648943c1f2211e0e3117387c31d765137d92bd8284a3fb9752a998') + version('1.31.0', sha256='0e4925392fd9f3743cc517e031b68b012b24a63b0cf6c1ff03cce7bb3846cc99') + version('1.30.1', sha256='3d1d04a4dbd34048f4794815a5c48ebb9eb53c5277e09ffffc060323b95dfbdc') + version('1.30.0', sha256='9553da068c0a30b1b8b72479908c1ba58672e2be7b535363a88de5e0f7bc04ce') + + def build(self, spec, prefix): + make('defconfig') + make() + + def install(self, spec, prefix): + make('install') + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/butter/package.py b/var/spack/repos/builtin/packages/butter/package.py index c7d2c02ef0..b06126e339 100644 --- a/var/spack/repos/builtin/packages/butter/package.py +++ b/var/spack/repos/builtin/packages/butter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/butterflypack/package.py b/var/spack/repos/builtin/packages/butterflypack/package.py index fee827e064..bb5f7b3c91 100644 --- a/var/spack/repos/builtin/packages/butterflypack/package.py +++ b/var/spack/repos/builtin/packages/butterflypack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,13 +22,14 @@ class Butterflypack(CMakePackage): homepage = "https://github.com/liuyangzhuan/ButterflyPACK" git = "https://github.com/liuyangzhuan/ButterflyPACK.git" - url = "https://github.com/liuyangzhuan/ButterflyPACK/archive/v1.0.3.tar.gz" + url = "https://github.com/liuyangzhuan/ButterflyPACK/archive/v1.1.0.tar.gz" maintainers = ['liuyangzhuan'] version('master', branch='master') - version('1.0.0', sha256='86c5eb09a18522367d63ce2bacf67ca1c9813ef351a1443baaab3c53f0d77232') - version('1.0.1', sha256='e8ada37466a19f49e13456b150700d4c3afaad2ddbe3678f4e933f9d556a24a5') + version('1.1.0', sha256='0e6fd0f9e27b3ee8a273dc52f4d24b8737e7279dc26d461ef5658b317215f1dc') version('1.0.3', sha256='acf9bc98dd7fea31ab73756b68b3333228b53ab0e85400a8250fcc749a1a6656') + version('1.0.1', sha256='e8ada37466a19f49e13456b150700d4c3afaad2ddbe3678f4e933f9d556a24a5') + version('1.0.0', sha256='86c5eb09a18522367d63ce2bacf67ca1c9813ef351a1443baaab3c53f0d77232') variant('shared', default=True, description='Build shared libraries') diff --git a/var/spack/repos/builtin/packages/bwa/package.py b/var/spack/repos/builtin/packages/bwa/package.py index 6e0864f2b6..8447f7848f 100644 --- a/var/spack/repos/builtin/packages/bwa/package.py +++ b/var/spack/repos/builtin/packages/bwa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bwtool/package.py b/var/spack/repos/builtin/packages/bwtool/package.py index 9fe48971a9..8bdaa4b3ec 100644 --- a/var/spack/repos/builtin/packages/bwtool/package.py +++ b/var/spack/repos/builtin/packages/bwtool/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/byobu/package.py b/var/spack/repos/builtin/packages/byobu/package.py index 672a0e61ad..918ec59513 100644 --- a/var/spack/repos/builtin/packages/byobu/package.py +++ b/var/spack/repos/builtin/packages/byobu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py index 83b5fabf0f..57d7046f93 100644 --- a/var/spack/repos/builtin/packages/bzip2/package.py +++ b/var/spack/repos/builtin/packages/bzip2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cares/package.py b/var/spack/repos/builtin/packages/c-ares/package.py index f3b35ee610..878ffc663e 100644 --- a/var/spack/repos/builtin/packages/cares/package.py +++ b/var/spack/repos/builtin/packages/c-ares/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,14 +6,15 @@ from spack import * -class Cares(CMakePackage): +class CAres(CMakePackage): """c-ares: A C library for asynchronous DNS requests""" homepage = "https://c-ares.haxx.se" - url = "https://github.com/c-ares/c-ares/archive/cares-1_13_0.tar.gz" + url = "https://github.com/c-ares/c-ares/archive/cares-1_15_0.tar.gz" git = "https://github.com/c-ares/c-ares.git" - version('develop', branch='master') + version('master', branch='master') + version('1.15.0', sha256='7deb7872cbd876c29036d5f37e30c4cbc3cc068d59d8b749ef85bb0736649f04') version('1.13.0', sha256='7c48c57706a38691041920e705d2a04426ad9c68d40edd600685323f214b2d57') def url_for_version(self, version): diff --git a/var/spack/repos/builtin/packages/c-blosc/package.py b/var/spack/repos/builtin/packages/c-blosc/package.py index da22f4ff17..8e11cb0956 100644 --- a/var/spack/repos/builtin/packages/c-blosc/package.py +++ b/var/spack/repos/builtin/packages/c-blosc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/c-blosc2/package.py b/var/spack/repos/builtin/packages/c-blosc2/package.py index d9bcdde290..98b4326f06 100644 --- a/var/spack/repos/builtin/packages/c-blosc2/package.py +++ b/var/spack/repos/builtin/packages/c-blosc2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,6 @@ class CBlosc2(CMakePackage): other bells and whistles""" homepage = "http://www.blosc.org" - url = "https://github.com/Blosc/c-blosc2/archive/v2.0.0-beta.1.tar.gz" git = "https://github.com/Blosc/c-blosc2.git" maintainers = ['ax3l'] @@ -32,12 +31,11 @@ class CBlosc2(CMakePackage): description='support for ZSTD') depends_on('cmake@2.8.10:', type='build') - # TODO https://github.com/inikep/lizard/issues/21 - # depends_on('lizard') - depends_on('lz4') - depends_on('snappy') - depends_on('zlib') - depends_on('zstd') + depends_on('lizard', when='+lizard') + depends_on('lz4', when='+lz4') + depends_on('snappy', when='+snappy') + depends_on('zlib', when='+zlib') + depends_on('zstd', when='+zstd') def cmake_args(self): spec = self.spec @@ -53,8 +51,7 @@ class CBlosc2(CMakePackage): 'ON' if '~zlib' in spec else 'OFF'), '-DDEACTIVATE_ZSTD={0}'.format( 'ON' if '~zstd' in spec else 'OFF'), - # TODO https://github.com/inikep/lizard/issues/21 - '-DPREFER_EXTERNAL_LIZARD=OFF', + '-DPREFER_EXTERNAL_LIZARD=ON', '-DPREFER_EXTERNAL_LZ4=ON', # snappy is supported via external install only '-DPREFER_EXTERNAL_ZLIB=ON', diff --git a/var/spack/repos/builtin/packages/c-lime/package.py b/var/spack/repos/builtin/packages/c-lime/package.py index c8550e7ded..525861a161 100644 --- a/var/spack/repos/builtin/packages/c-lime/package.py +++ b/var/spack/repos/builtin/packages/c-lime/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cabana/package.py b/var/spack/repos/builtin/packages/cabana/package.py index 44221e827a..0efff53f92 100644 --- a/var/spack/repos/builtin/packages/cabana/package.py +++ b/var/spack/repos/builtin/packages/cabana/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/caffe/package.py b/var/spack/repos/builtin/packages/caffe/package.py index 1484d2bded..e07f545f73 100644 --- a/var/spack/repos/builtin/packages/caffe/package.py +++ b/var/spack/repos/builtin/packages/caffe/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cairo/fontconfig.patch b/var/spack/repos/builtin/packages/cairo/fontconfig.patch new file mode 100644 index 0000000000..dc550abda5 --- /dev/null +++ b/var/spack/repos/builtin/packages/cairo/fontconfig.patch @@ -0,0 +1,36 @@ +diff --git a/test/Makefile.am b/test/Makefile.am +index e3c42ea88..7b5568d85 100644 +--- a/test/Makefile.am ++++ b/test/Makefile.am +@@ -158,8 +158,10 @@ ps-features \ + svg-clip \ + svg-surface \ + toy-font-face \ +-font-variations \ + user-data ++#if CAIRO_HAS_FT_FONT ++NOLOG_TESTS += font-variations ++#endif + + # A target to summarise the failures + check-summary: +diff --git a/test/Makefile.sources b/test/Makefile.sources +index c47131faf..8568f7cf8 100644 +--- a/test/Makefile.sources ++++ b/test/Makefile.sources +@@ -144,7 +144,6 @@ test_sources = \ + font-face-get-type.c \ + font-matrix-translation.c \ + font-options.c \ +- font-variations.c \ + glyph-cache-pressure.c \ + get-and-set.c \ + get-clip.c \ +@@ -399,6 +398,7 @@ pthread_test_sources = \ + + ft_font_test_sources = \ + bitmap-font.c \ ++ font-variations.c \ + ft-font-create-for-ft-face.c \ + ft-show-glyphs-positioning.c \ + ft-show-glyphs-table.c \ diff --git a/var/spack/repos/builtin/packages/cairo/package.py b/var/spack/repos/builtin/packages/cairo/package.py index c752122e50..829bb0866b 100644 --- a/var/spack/repos/builtin/packages/cairo/package.py +++ b/var/spack/repos/builtin/packages/cairo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,18 +21,39 @@ class Cairo(AutotoolsPackage): variant('X', default=False, description="Build with X11 support") variant('pdf', default=False, description="Enable cairo's PDF surface backend feature") variant('gobject', default=False, description="Enable cairo's gobject functions feature") + variant('ft', default=False, description="Enable cairo's FreeType font backend feature") + variant('fc', default=False, description="Enable cairo's Fontconfig font backend feature") + variant('png', default=False, description="Enable cairo's PNG functions feature") + variant('svg', default=False, description="Enable cairo's SVN functions feature") depends_on('libx11', when='+X') depends_on('libxext', when='+X') depends_on('libxrender', when='+X') depends_on('libxcb', when='+X') depends_on('python', when='+X', type='build') - depends_on('libpng') + depends_on('libpng', when='+png') + depends_on('librsvg', when='+svg') depends_on('glib') depends_on('pixman') - depends_on('freetype') + depends_on('automake', type='build') + depends_on('autoconf', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('freetype', when='+ft') depends_on('pkgconfig', type='build') - depends_on('fontconfig@2.10.91:') # Require newer version of fontconfig. + depends_on('fontconfig@2.10.91:', when='+fc') # Require newer version of fontconfig. + + conflicts('+png', when='platform=darwin') + conflicts('+svg', when='platform=darwin') + + # patch from https://gitlab.freedesktop.org/cairo/cairo/issues/346 + patch('fontconfig.patch', when='@1.16.0') + + def setup_build_environment(self, env): + env.set('NOCONFIGURE', "1") + + def autoreconf(self, spec, prefix): + which('sh')('./autogen.sh') def configure_args(self): args = [ @@ -47,5 +68,7 @@ class Cairo(AutotoolsPackage): args.extend(self.enable_or_disable('pdf')) args.extend(self.enable_or_disable('gobject')) + args.extend(self.enable_or_disable('ft')) + args.extend(self.enable_or_disable('fc')) return args diff --git a/var/spack/repos/builtin/packages/cairomm/package.py b/var/spack/repos/builtin/packages/cairomm/package.py index 2443d1536c..39424e7c7e 100644 --- a/var/spack/repos/builtin/packages/cairomm/package.py +++ b/var/spack/repos/builtin/packages/cairomm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py index 9d45640eb1..6169a7ee78 100644 --- a/var/spack/repos/builtin/packages/caliper/package.py +++ b/var/spack/repos/builtin/packages/caliper/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,16 +10,17 @@ import sys class Caliper(CMakePackage): """Caliper is a program instrumentation and performance measurement - framework. It provides data collection mechanisms and a source-code - annotation API for a variety of performance engineering use cases, - e.g., performance profiling, tracing, monitoring, and - auto-tuning. + framework. It is designed as a performance analysis toolbox in a + library, allowing one to bake performance analysis capabilities + directly into applications and activate them at runtime. """ homepage = "https://github.com/LLNL/Caliper" git = "https://github.com/LLNL/Caliper.git" version('master') + version('2.2.0', tag='v2.2.0') + version('2.1.1', tag='v2.1.1') version('2.0.1', tag='v2.0.1') version('1.9.1', tag='v1.9.1') version('1.9.0', tag='v1.9.0') @@ -29,6 +30,8 @@ class Caliper(CMakePackage): is_linux = sys.platform.startswith('linux') variant('shared', default=True, description='Build shared libraries') + variant('adiak', default=True, + description='Enable Adiak support') variant('mpi', default=True, description='Enable MPI wrappers') variant('dyninst', default=False, @@ -49,6 +52,8 @@ class Caliper(CMakePackage): variant('sosflow', default=False, description='Enable SOSflow support') + depends_on('adiak@0.1:', when='@2.2: +adiak') + depends_on('gotcha@1.0.2:1.0.99', when='+gotcha') depends_on('dyninst@9.3.0:9.99', when='@:1.99 +dyninst') @@ -67,7 +72,8 @@ class Caliper(CMakePackage): depends_on('python', type='build') # sosflow support not yet in 2.0 - conflicts('+sosflow', '@2.0.0:2.0.99') + conflicts('+sosflow', '@2.0.0:2.2.99') + conflicts('+adiak', '@:2.1.99') def cmake_args(self): spec = self.spec @@ -76,6 +82,7 @@ class Caliper(CMakePackage): '-DBUILD_TESTING=Off', '-DBUILD_DOCS=Off', '-DBUILD_SHARED_LIBS=%s' % ('On' if '+shared' in spec else 'Off'), + '-DWITH_ADIAK=%s' % ('On' if '+adiak' in spec else 'Off'), '-DWITH_DYNINST=%s' % ('On' if '+dyninst' in spec else 'Off'), '-DWITH_CALLPATH=%s' % ('On' if '+callpath' in spec else 'Off'), '-DWITH_GOTCHA=%s' % ('On' if '+gotcha' in spec else 'Off'), diff --git a/var/spack/repos/builtin/packages/callpath/package.py b/var/spack/repos/builtin/packages/callpath/package.py index fe3b9d18a0..300f55e8d5 100644 --- a/var/spack/repos/builtin/packages/callpath/package.py +++ b/var/spack/repos/builtin/packages/callpath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/camellia/package.py b/var/spack/repos/builtin/packages/camellia/package.py index af82f0c501..ba443a80af 100644 --- a/var/spack/repos/builtin/packages/camellia/package.py +++ b/var/spack/repos/builtin/packages/camellia/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/camx/package.py b/var/spack/repos/builtin/packages/camx/package.py index 1dc38d41a6..b65ffeaf38 100644 --- a/var/spack/repos/builtin/packages/camx/package.py +++ b/var/spack/repos/builtin/packages/camx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/candle-benchmarks/package.py b/var/spack/repos/builtin/packages/candle-benchmarks/package.py index fb8401108d..d88e605c22 100644 --- a/var/spack/repos/builtin/packages/candle-benchmarks/package.py +++ b/var/spack/repos/builtin/packages/candle-benchmarks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class CandleBenchmarks(Package): """ECP-CANDLE Benchmarks""" homepage = "https://github.com/ECP-CANDLE/Benchmarks" - url = "https://github.com/ECP-CANDLE/Benchmarks/archive/v1.0.tar.gz" + url = "https://github.com/ECP-CANDLE/Benchmarks/archive/v0.1.tar.gz" tags = ['proxy-app', 'ecp-proxy-app'] diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py index fd66cef27c..4e2728fad8 100644 --- a/var/spack/repos/builtin/packages/cantera/package.py +++ b/var/spack/repos/builtin/packages/cantera/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,10 +27,10 @@ class Cantera(SConsPackage): # Required dependencies depends_on('fmt@3.0.0:3.0.2', when='@2.3.0:') - depends_on('googletest', when='@2.3.0:') + depends_on('googletest+gmock', when='@2.3.0:') depends_on('eigen', when='@2.3.0:') depends_on('boost') - depends_on('sundials', when='+sundials') # must be compiled with -fPIC + depends_on('sundials@:3.1.2', when='+sundials') # must be compiled with -fPIC depends_on('blas') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/canu/package.py b/var/spack/repos/builtin/packages/canu/package.py index 01d7ad8ff1..2ab5cd0084 100644 --- a/var/spack/repos/builtin/packages/canu/package.py +++ b/var/spack/repos/builtin/packages/canu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cap3/package.py b/var/spack/repos/builtin/packages/cap3/package.py index 99da025c68..45feee4ef0 100644 --- a/var/spack/repos/builtin/packages/cap3/package.py +++ b/var/spack/repos/builtin/packages/cap3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/capnproto/package.py b/var/spack/repos/builtin/packages/capnproto/package.py new file mode 100644 index 0000000000..2533e8aabe --- /dev/null +++ b/var/spack/repos/builtin/packages/capnproto/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Capnproto(AutotoolsPackage): + """Cap'n Proto is an insanely fast data interchange + format and capability-based RPC system. + """ + + homepage = "https://capnproto.org/" + url = "https://capnproto.org/capnproto-c++-0.7.0.tar.gz" + git = "https://github.com/capnproto/capnproto" + + version('0.7.0', sha256='c9a4c0bd88123064d483ab46ecee777f14d933359e23bff6fb4f4dbd28b4cd41') + + def configure_args(self): + return ['--without-openssl'] diff --git a/var/spack/repos/builtin/packages/capstone/package.py b/var/spack/repos/builtin/packages/capstone/package.py index 02220ec2b9..59769e1c17 100644 --- a/var/spack/repos/builtin/packages/capstone/package.py +++ b/var/spack/repos/builtin/packages/capstone/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cardioid/package.py b/var/spack/repos/builtin/packages/cardioid/package.py index 54d9b2e54f..73e980be24 100644 --- a/var/spack/repos/builtin/packages/cardioid/package.py +++ b/var/spack/repos/builtin/packages/cardioid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/casacore/package.py b/var/spack/repos/builtin/packages/casacore/package.py index 816a5fbca2..24bb8defb4 100644 --- a/var/spack/repos/builtin/packages/casacore/package.py +++ b/var/spack/repos/builtin/packages/casacore/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,26 +12,41 @@ class Casacore(CMakePackage): homepage = "https://github.com/casacore/casacore" url = "https://github.com/casacore/casacore/archive/v2.4.1.tar.gz" + maintainers = ['mpokorny'] + + version('3.2.0', sha256='ae5d3786cb6dfdd7ebc5eecc0c724ff02bbf6929720bc23be43a027978e79a5f') + version('3.1.2', sha256='ac94f4246412eb45d503f1019cabe2bb04e3861e1f3254b832d9b1164ea5f281') + version('3.1.1', sha256='85d2b17d856592fb206b17e0a344a29330650a4269c80b87f8abb3eaf3dadad4') + version('3.1.0', sha256='a6adf2d77ad0d6f32995b1e297fd88d31ded9c3e0bb8f28966d7b35a969f7897') + version('3.0.0', sha256='6f0e68fd77b5c96299f7583a03a53a90980ec347bff9dfb4c0abb0e2933e6bcb') version('2.4.1', sha256='58eccc875053b2c6fe44fe53b6463030ef169597ec29926936f18d27b5087d63') variant('openmp', default=False, description='Build OpenMP support') variant('shared', default=True, description='Build shared libraries') - variant('sofa', default=False, description='Build SOFA support') + # see note below about the reason for disabling the "sofa" variant + # variant('sofa', default=False, description='Build SOFA support') variant('fftw', default=False, description='Build FFTW3 support') variant('hdf5', default=False, description='Build HDF5 support') variant('python', default=False, description='Build python support') - variant('ncurses', default=False, description='Build ncurses support') depends_on('flex', type='build') depends_on('bison', type='build') depends_on('blas') depends_on('lapack') depends_on('cfitsio@3.181:') - depends_on('wcslib@4.20:') + depends_on('wcslib@4.20:+cfitsio') depends_on('fftw~mpi@3.0.0:', when='+fftw') - depends_on('sofa-c', when='+sofa') + # SOFA dependency suffers the same problem in CMakeLists.txt as readline; + # however, as SOFA is far less likely to be present on most systems, and as + # it's an unneeded dependency except for testing, for now we leave out the + # option for a dependency on SOFA. + # depends_on('sofa-c', when='+sofa') depends_on('hdf5', when='+hdf5') - depends_on('ncurses', when='+ncurses') + # Force dependency on readline. Although the presence of readline is tested + # in CMakeLists.txt, and casacore can be built without it, there's no way + # to control that dependency at build time; since many systems come with + # readline, it's better to explicitly depend on it here always. + depends_on('readline') depends_on('python@2.6:', when='+python') depends_on('boost+python', when='+python') depends_on('py-numpy', when='+python') diff --git a/var/spack/repos/builtin/packages/cask/package.py b/var/spack/repos/builtin/packages/cask/package.py index 28afef887f..ed115ca3e6 100644 --- a/var/spack/repos/builtin/packages/cask/package.py +++ b/var/spack/repos/builtin/packages/cask/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/casper/package.py b/var/spack/repos/builtin/packages/casper/package.py index 088a0b49b1..a15365ccaa 100644 --- a/var/spack/repos/builtin/packages/casper/package.py +++ b/var/spack/repos/builtin/packages/casper/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,5 +25,5 @@ class Casper(MakefilePackage): def install(self, spec, prefix): install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.spec.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/cassandra/package.py b/var/spack/repos/builtin/packages/cassandra/package.py new file mode 100644 index 0000000000..fab6d9c9c4 --- /dev/null +++ b/var/spack/repos/builtin/packages/cassandra/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Cassandra(Package): + """ + Apache Cassandra is a highly-scalable partitioned row store. Rows are + organized into tables with a required primary key. + """ + + homepage = "https://github.com/apache/cassandra" + url = "https://github.com/apache/cassandra/archive/cassandra-4.0-alpha2.tar.gz" + + version('4.0-alpha2', sha256='6a8e99d8bc51efd500981c85c6aa547387b2fdbedecd692308f4632dbc1de3ba') + version('4.0-alpha1', sha256='2fdf5e3d6c03a29d24a09cd52bb17575e5faccdc4c75a07edd63a9bf4f740105') + version('3.11.5', sha256='0ee3da12a2be86d7e03203fcc56c3589ddb38347b9cd031495a2b7fcf639fea6', preferred=True) + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/catalyst/package.py b/var/spack/repos/builtin/packages/catalyst/package.py index a37574a888..c00aca23e9 100644 --- a/var/spack/repos/builtin/packages/catalyst/package.py +++ b/var/spack/repos/builtin/packages/catalyst/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -148,7 +148,7 @@ class Catalyst(CMakePackage): tty.msg("Already generated %s in %s" % (self.name, self.stage.source_path)) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # paraview 5.5 and later # - cmake under lib/cmake/paraview-5.5 # - libs under lib @@ -160,18 +160,18 @@ class Catalyst(CMakePackage): if self.spec.version <= Version('5.4.1'): lib_dir = join_path(lib_dir, paraview_subdir) - run_env.set('ParaView_DIR', self.prefix) - run_env.prepend_path('LIBRARY_PATH', lib_dir) - run_env.prepend_path('LD_LIBRARY_PATH', lib_dir) + env.set('ParaView_DIR', self.prefix) + env.prepend_path('LIBRARY_PATH', lib_dir) + env.prepend_path('LD_LIBRARY_PATH', lib_dir) if '+python' in self.spec or '+python3' in self.spec: python_version = self.spec['python'].version.up_to(2) - run_env.prepend_path('PYTHONPATH', join_path(lib_dir, - 'python{0}'.format(python_version), - 'site-packages')) + env.prepend_path('PYTHONPATH', join_path(lib_dir, + 'python{0}'.format(python_version), + 'site-packages')) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('ParaView_DIR', self.prefix) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('ParaView_DIR', self.prefix) @property def root_cmakelists_dir(self): diff --git a/var/spack/repos/builtin/packages/catch/package.py b/var/spack/repos/builtin/packages/catch2/package.py index a9d8cb412b..367c93a282 100644 --- a/var/spack/repos/builtin/packages/catch/package.py +++ b/var/spack/repos/builtin/packages/catch2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,12 @@ from spack import * -class Catch(CMakePackage): - """Catch tests""" +class Catch2(CMakePackage): + """Catch2 is a multi-paradigm test framework for C++, which also + supports Objective-C (and maybe C).""" homepage = "https://github.com/catchorg/Catch2" - url = "https://github.com/catchorg/Catch2/archive/v1.3.0.tar.gz" + url = "https://github.com/catchorg/Catch2/archive/v2.9.1.tar.gz" variant('single_header', default=True, description='Install a single header only.') diff --git a/var/spack/repos/builtin/packages/cbench/package.py b/var/spack/repos/builtin/packages/cbench/package.py index 8c00aeeadd..ceeec3b468 100644 --- a/var/spack/repos/builtin/packages/cbench/package.py +++ b/var/spack/repos/builtin/packages/cbench/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,27 +31,27 @@ class Cbench(MakefilePackage): conflicts('%xl') conflicts('%xl_r') - def setup_environment(self, build_env, run_env): + def setup_build_environment(self, env): # The location of the Cbench source tree - build_env.set('CBENCHOME', self.stage.source_path) + env.set('CBENCHOME', self.stage.source_path) # The location that will contain all of your tests and their results - build_env.set('CBENCHTEST', self.prefix) + env.set('CBENCHTEST', self.prefix) # The location of the system MPI tree - build_env.set('MPIHOME', self.spec['mpi'].prefix) + env.set('MPIHOME', self.spec['mpi'].prefix) # Pick the compiler collection/chain you want to compile with. # Examples include: intel, gcc, pgi. - build_env.set('COMPILERCOLLECTION', self.compiler.name) + env.set('COMPILERCOLLECTION', self.compiler.name) # Linking flags for BLAS/LAPACK and FFTW - build_env.set('BLASLIB', self.spec['blas'].libs.ld_flags) - build_env.set('LAPACKLIB', self.spec['lapack'].libs.ld_flags) - build_env.set('FFTWLIB', self.spec['fftw'].libs.ld_flags) + env.set('BLASLIB', self.spec['blas'].libs.ld_flags) + env.set('LAPACKLIB', self.spec['lapack'].libs.ld_flags) + env.set('FFTWLIB', self.spec['fftw'].libs.ld_flags) # The number of make jobs (commands) to run simultaneously - build_env.set('JOBS', str(make_jobs)) + env.set('JOBS', str(make_jobs)) @run_before('build') @on_package_attributes(run_tests=True) diff --git a/var/spack/repos/builtin/packages/cblas/package.py b/var/spack/repos/builtin/packages/cblas/package.py index 7ade542e2f..92ea521b94 100644 --- a/var/spack/repos/builtin/packages/cblas/package.py +++ b/var/spack/repos/builtin/packages/cblas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py index 58d699b7da..1ae389d801 100644 --- a/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py +++ b/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -52,19 +52,22 @@ class CbtfArgonavisGui(QMakePackage): parallel = False - def setup_environment(self, spack_env, run_env): - """Set up the compile and runtime environments for a package.""" - spack_env.set('BOOSTROOT', self.spec['boost'].prefix) - spack_env.set('CBTF_ROOT', self.spec['cbtf'].prefix) - spack_env.set('CBTF_KRELL_ROOT', self.spec['cbtf-krell'].prefix) - spack_env.set('CBTF_ARGONAVIS_ROOT', - self.spec['cbtf-argonavis'].prefix) - spack_env.set('OSS_CBTF_ROOT', self.spec['openspeedshop-utils'].prefix) - spack_env.set('GRAPHVIZ_ROOT', self.spec['graphviz'].prefix) - spack_env.set('QTGRAPHLIB_ROOT', self.spec['qtgraph'].prefix) - spack_env.set('KRELL_ROOT_MRNET', self.spec['mrnet'].prefix) - spack_env.set('KRELL_ROOT_XERCES', self.spec['xerces-c'].prefix) - spack_env.set('INSTALL_ROOT', self.spec.prefix) + def setup_build_environment(self, env): + """Set up the build environment for this package.""" + env.set('BOOSTROOT', self.spec['boost'].prefix) + env.set('CBTF_ROOT', self.spec['cbtf'].prefix) + env.set('CBTF_KRELL_ROOT', self.spec['cbtf-krell'].prefix) + env.set('CBTF_ARGONAVIS_ROOT', + self.spec['cbtf-argonavis'].prefix) + env.set('OSS_CBTF_ROOT', self.spec['openspeedshop-utils'].prefix) + env.set('GRAPHVIZ_ROOT', self.spec['graphviz'].prefix) + env.set('QTGRAPHLIB_ROOT', self.spec['qtgraph'].prefix) + env.set('KRELL_ROOT_MRNET', self.spec['mrnet'].prefix) + env.set('KRELL_ROOT_XERCES', self.spec['xerces-c'].prefix) + env.set('INSTALL_ROOT', self.spec.prefix) + + def setup_run_environment(self, env): + """Set up the runtime environment for this package.""" # The implementor of qtgraph has set up the library and include # paths in a non-conventional way. We reflect that here. @@ -74,14 +77,14 @@ class CbtfArgonavisGui(QMakePackage): else: qtgraph_lib_dir = self.spec['qtgraph'].prefix.lib - run_env.prepend_path( + env.prepend_path( 'LD_LIBRARY_PATH', join_path( qtgraph_lib_dir, '{0}'.format(self.spec['qt'].version.up_to(3)))) # The openspeedshop libraries are needed to actually load the # performance information into the GUI. - run_env.prepend_path( + env.prepend_path( 'LD_LIBRARY_PATH', self.spec['openspeedshop-utils'].prefix.lib64) def qmake_args(self): diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py index 93fcfe204f..45fa4e09d3 100644 --- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py +++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -41,38 +41,38 @@ class CbtfArgonavis(CMakePackage): depends_on("boost@1.66.0:1.69.0") # For MRNet - depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti') - depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop~cti') - depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti') - depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999~cti') + depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti', type=('build', 'link', 'run')) + depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop~cti', type=('build', 'link', 'run')) + depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti', type=('build', 'link', 'run')) + depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999~cti', type=('build', 'link', 'run')) # For CBTF - depends_on("cbtf@develop", when='@develop') - depends_on("cbtf@1.9.1.0:9999", when='@1.9.1.0:9999') + depends_on("cbtf@develop", when='@develop', type=('build', 'link', 'run')) + depends_on("cbtf@1.9.1.0:9999", when='@1.9.1.0:9999', type=('build', 'link', 'run')) # For CBTF with cti - depends_on("cbtf@develop+cti", when='@develop+cti') - depends_on("cbtf@1.9.1.0:9999+cti", when='@1.9.1.0:9999+cti') + depends_on("cbtf@develop+cti", when='@develop+cti', type=('build', 'link', 'run')) + depends_on("cbtf@1.9.1.0:9999+cti", when='@1.9.1.0:9999+cti', type=('build', 'link', 'run')) # For CBTF with runtime - depends_on("cbtf@develop+runtime", when='@develop+runtime') - depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime') + depends_on("cbtf@develop+runtime", when='@develop+runtime', type=('build', 'link', 'run')) + depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime', type=('build', 'link', 'run')) # For libmonitor - depends_on("libmonitor@2013.02.18+krellpatch") + depends_on("libmonitor@2013.02.18+krellpatch", type=('build', 'link', 'run')) # For PAPI - depends_on("papi@5.4.1:") + depends_on("papi@5.4.1:", type=('build', 'link', 'run')) # For CBTF-KRELL - depends_on("cbtf-krell@develop", when='@develop') - depends_on("cbtf-krell@1.9.1.0:9999", when='@1.9.1.0:9999') + depends_on("cbtf-krell@develop", when='@develop', type=('build', 'link', 'run')) + depends_on("cbtf-krell@1.9.1.0:9999", when='@1.9.1.0:9999', type=('build', 'link', 'run')) - depends_on('cbtf-krell@develop+cti', when='@develop+cti') - depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@1.9.1.0:9999+cti') + depends_on('cbtf-krell@develop+cti', when='@develop+cti', type=('build', 'link', 'run')) + depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@1.9.1.0:9999+cti', type=('build', 'link', 'run')) - depends_on('cbtf-krell@develop+runtime', when='@develop+runtime') - depends_on('cbtf-krell@1.9.1.0:9999+runtime', when='@1.9.1.0:9999+runtime') + depends_on('cbtf-krell@develop+runtime', when='@develop+runtime', type=('build', 'link', 'run')) + depends_on('cbtf-krell@1.9.1.0:9999+runtime', when='@1.9.1.0:9999+runtime', type=('build', 'link', 'run')) # For CUDA depends_on("cuda") @@ -105,12 +105,16 @@ class CbtfArgonavis(CMakePackage): return cmake_args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set up the compile and runtime environments for a package.""" - run_env.prepend_path( + env.prepend_path( 'LD_LIBRARY_PATH', self.spec['cuda'].prefix + '/extras/CUPTI/lib64') - spack_env.prepend_path( + + def setup_build_environment(self, env): + """Set up the compile and runtime environments for a package.""" + + env.prepend_path( 'LD_LIBRARY_PATH', self.spec['cuda'].prefix + '/extras/CUPTI/lib64') diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py index 194367060c..fb43c22f5c 100644 --- a/var/spack/repos/builtin/packages/cbtf-krell/package.py +++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -50,6 +50,12 @@ class CbtfKrell(CMakePackage): # Dependencies for cbtf-krell depends_on("cmake@3.0.2:", type='build') + # For rpcgen + depends_on("rpcsvc-proto", type='build') + + # For rpc + depends_on("libtirpc", type='link') + # For binutils depends_on("binutils") @@ -83,21 +89,21 @@ class CbtfKrell(CMakePackage): depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime', type=('build', 'link', 'run')) # for services and collectors - depends_on("libmonitor@2013.02.18+krellpatch") + depends_on("libmonitor@2013.02.18+krellpatch", type=('build', 'link', 'run')) depends_on("libunwind", when='@develop') depends_on("libunwind@1.2.1", when='@1.9.1.0:9999') - depends_on("papi@5.4.1:") + depends_on("papi@5.4.1:", type=('build', 'link', 'run')) depends_on("llvm-openmp-ompt@tr6_forwards+standalone") # MPI Installations depends_on("openmpi", when='+openmpi') - depends_on("mpich", when='+mpich') - depends_on("mpich2", when='+mpich2') - depends_on("mvapich2", when='+mvapich2') - depends_on("mvapich", when='+mvapich') + depends_on("mpich@:1", when='+mpich') + depends_on("mpich@2:", when='+mpich2') + depends_on("mvapich2@2:", when='+mvapich2') + depends_on("mvapich2@:1", when='+mvapich') depends_on("mpt", when='+mpt') depends_on("python", when='@develop', type=('build', 'run')) @@ -229,15 +235,15 @@ class CbtfKrell(CMakePackage): return cmake_args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set up the compile and runtime environments for a package.""" # Environment settings for cbtf-krell, bin is automatically # added to the path in the module file - run_env.prepend_path('PATH', self.prefix.sbin) + env.prepend_path('PATH', self.prefix.sbin) - run_env.set('XPLAT_RSH', 'ssh') - run_env.set('MRNET_COMM_PATH', self.prefix.sbin.cbtf_mrnet_commnode) + env.set('XPLAT_RSH', 'ssh') + env.set('MRNET_COMM_PATH', self.prefix.sbin.cbtf_mrnet_commnode) # Set CBTF_MPI_IMPLEMENTATON to the appropriate mpi implementation # This is needed by CBTF tools to deploy the correct @@ -246,19 +252,23 @@ class CbtfKrell(CMakePackage): # manually if multiple mpi's are specified in the build if self.spec.satisfies('+mpich'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mpich") + env.set('CBTF_MPI_IMPLEMENTATION', "mpich") if self.spec.satisfies('+mvapich'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich") + env.set('CBTF_MPI_IMPLEMENTATION', "mvapich") if self.spec.satisfies('+mvapich2'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2") + env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2") if self.spec.satisfies('+mpt'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mpt") + env.set('CBTF_MPI_IMPLEMENTATION', "mpt") if self.spec.satisfies('+openmpi'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "openmpi") + env.set('CBTF_MPI_IMPLEMENTATION', "openmpi") + + env.set('CBTF_MRNET_BACKEND_PATH', + self.prefix.sbin.cbtf_libcbtf_mrnet_backend) - run_env.set('CBTF_MRNET_BACKEND_PATH', - self.prefix.sbin.cbtf_libcbtf_mrnet_backend) + env.prepend_path('PATH', self.spec['libmonitor'].prefix.bin) + env.prepend_path('PATH', self.spec['papi'].prefix.bin) + env.prepend_path('PATH', self.spec['mrnet'].prefix.bin) diff --git a/var/spack/repos/builtin/packages/cbtf-lanl/package.py b/var/spack/repos/builtin/packages/cbtf-lanl/package.py index 41eabbe0d8..719ddc45ff 100644 --- a/var/spack/repos/builtin/packages/cbtf-lanl/package.py +++ b/var/spack/repos/builtin/packages/cbtf-lanl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cbtf/package.py b/var/spack/repos/builtin/packages/cbtf/package.py index eabf029d18..eca4263858 100644 --- a/var/spack/repos/builtin/packages/cbtf/package.py +++ b/var/spack/repos/builtin/packages/cbtf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -34,6 +34,12 @@ class Cbtf(CMakePackage): depends_on("cmake@3.0.2:", type='build') + # for rpcgen + depends_on("rpcsvc-proto", type='build') + + # for rpc + depends_on("libtirpc", type='link') + depends_on("boost@1.66.0:1.69.0") # For MRNet diff --git a/var/spack/repos/builtin/packages/ccache/package.py b/var/spack/repos/builtin/packages/ccache/package.py index ef6a0d79b6..1060c89f42 100644 --- a/var/spack/repos/builtin/packages/ccache/package.py +++ b/var/spack/repos/builtin/packages/ccache/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ccfits/package.py b/var/spack/repos/builtin/packages/ccfits/package.py index 1e90dac5df..a4eb088a75 100644 --- a/var/spack/repos/builtin/packages/ccfits/package.py +++ b/var/spack/repos/builtin/packages/ccfits/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ccs-qcd/package.py b/var/spack/repos/builtin/packages/ccs-qcd/package.py index 97068918e2..d1e5c9abd8 100644 --- a/var/spack/repos/builtin/packages/ccs-qcd/package.py +++ b/var/spack/repos/builtin/packages/ccs-qcd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cctools/cctools_6.1.1.python.patch b/var/spack/repos/builtin/packages/cctools/cctools_6.1.1.python.patch new file mode 100755 index 0000000000..726e216e59 --- /dev/null +++ b/var/spack/repos/builtin/packages/cctools/cctools_6.1.1.python.patch @@ -0,0 +1,11 @@ +--- spack-src.org/umbrella/src/Makefile 2017-05-30 20:49:30.000000000 +0900 ++++ spack-src/umbrella/src/Makefile 2019-11-20 17:23:42.101854924 +0900 +@@ -16,7 +16,7 @@ + + umbrella_helper.html: umbrella.py + # pydoc2/pydoc creates a html file, umbrella.html. +- if which pydoc2; then pydoc2 -w umbrella; elif which pydoc; then pydoc -w umbrella; fi ++ if which pydoc; then pydoc -w umbrella; elif which pydoc2; then pydoc2 -w umbrella; fi + if [ -f umbrella.html ]; then mv umbrella.html umbrella_helper.html; fi + + clean: diff --git a/var/spack/repos/builtin/packages/cctools/cctools_7.0.18.python.patch b/var/spack/repos/builtin/packages/cctools/cctools_7.0.18.python.patch new file mode 100755 index 0000000000..1c8dfc428e --- /dev/null +++ b/var/spack/repos/builtin/packages/cctools/cctools_7.0.18.python.patch @@ -0,0 +1,116 @@ +--- spack-src.org/configure 2019-11-25 14:33:33.991883993 +0900 ++++ spack-src/configure 2019-11-25 14:47:11.591066274 +0900 +@@ -973,18 +973,46 @@ + fi + fi + ++PYDOC="" + python=0 #to be set to the python path + if [ $config_python_path != no ] + then + if [ -n "$PYTHON" ] && check_file ${PYTHON} + then + python=${PYTHON} ++ python_dir=`dirname ${PYTHON}` ++ python_cmd=`basename ${PYTHON}` ++ pydoc_cmd=`echo $python_cmd | sed s/python/pydoc/` ++ pydoc2_cmd=`echo $python_cmd | sed s/python/pydoc2/` ++ pydoc=${python_dir}/${pydoc_cmd} ++ pydoc2=${python_dir}/${pydoc2_cmd} ++ if check_file $pydoc ++ then ++ PYDOC=$pydoc ++ elif check_file $pydoc2 ++ then ++ PYDOC=$pydoc2 ++ fi + elif check_file ${python_path}/bin/python2 + then + python=${python_path}/bin/python2 ++ if check_file ${python_path}/bin/pydoc ++ then ++ PYDOC=${python_path}/bin/pydoc ++ elif check_file ${python_path}/bin/pydoc2 ++ then ++ PYDOC=${python_path}/bin/pydoc2 ++ fi + elif check_file ${python_path}/bin/python + then + python=${python_path}/bin/python ++ if check_file ${python_path}/bin/pydoc ++ then ++ PYDOC=${python_path}/bin/pydoc ++ elif check_file ${python_path}/bin/pydoc2 ++ then ++ PYDOC=${python_path}/bin/pydoc2 ++ fi + else + python=0 + fi +@@ -1056,7 +1084,7 @@ + fi + fi + +-if [ $python_dev = no ] ++if [ "$python_dev" = no ] + then + if [ $config_python_path = yes ] + then +@@ -1073,12 +1101,48 @@ + if [ -n "$PYTHON3" ] && check_file ${PYTHON3} + then + python3=${PYTHON3} ++ if [ "$PYDOC" = "" ] ++ then ++ python_dir=`dirname ${PYTHON3}` ++ python_cmd=`basename ${PYTHON3}` ++ pydoc_cmd=`echo $python_cmd | sed s/python/pydoc/` ++ pydoc3_cmd=`echo $python_cmd | sed s/python/pydoc3/` ++ pydoc=${python_dir}/${pydoc_cmd} ++ pydoc3=${python_dir}/${pydoc3_cmd} ++ if check_file $pydoc ++ then ++ PYDOC=$pydoc ++ elif heck_file $pydoc3 ++ then ++ PYDOC=$pydoc3 ++ fi ++ fi + elif check_file ${python3_path}/bin/python3 + then + python3=${python3_path}/bin/python3 ++ if [ "$PYDOC" = "" ] ++ then ++ if check_file ${python3_path}/bin/pydoc ++ then ++ PYDOC=${python3_path}/bin/pydoc ++ elif check_file ${python3_path}/bin/pydoc3 ++ then ++ PYDOC=${python3_path}/bin/pydoc3 ++ fi ++ fi + elif check_file ${python3_path}/bin/python + then + python3=${python3_path}/bin/python ++ if [ "$PYDOC" = "" ] ++ then ++ if check_file ${python3_path}/bin/pydoc ++ then ++ PYDOC=${python3_path}/bin/pydoc ++ elif check_file ${python3_path}/bin/pydoc3 ++ then ++ PYDOC=${python3_path}/bin/pydoc3 ++ fi ++ fi + else + python3=0 + fi +@@ -1630,7 +1694,7 @@ + CCTOOLS_PYTHON3_2TO3=${python3_2to3} + CCTOOLS_PYTHON3_PATH=\$(CCTOOLS_INSTALL_DIR)/lib/python\$(CCTOOLS_PYTHON3_VERSION)/site-packages + +-CCTOOLS_PYDOC=$(which pydoc 2> /dev/null || which pydoc2 2> /dev/null || which pydoc3 > /dev/null) ++CCTOOLS_PYDOC=${PYDOC} + + CCTOOLS_SGE_PARAMETERS=$(echo ${sge_parameters} | sed -e 's/\$/\\\$\$/g') + diff --git a/var/spack/repos/builtin/packages/cctools/package.py b/var/spack/repos/builtin/packages/cctools/package.py index fb546fc628..481e4a47f1 100644 --- a/var/spack/repos/builtin/packages/cctools/package.py +++ b/var/spack/repos/builtin/packages/cctools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,12 +20,15 @@ class Cctools(AutotoolsPackage): depends_on('openssl') depends_on('perl+shared', type=('build', 'run')) - depends_on('python@:3', type=('build', 'run')) + depends_on('python@:2.9', when='@6.1.1', type=('build', 'run')) + depends_on('python', type=('build', 'run')) depends_on('readline') depends_on('swig') # depends_on('xrootd') depends_on('zlib') patch('arm.patch', when='target=aarch64:') + patch('cctools_7.0.18.python.patch', when='@7.0.18') + patch('cctools_6.1.1.python.patch', when='@6.1.1') # Generally SYS_foo is defined to __NR_foo (sys/syscall.h) which # is then defined to a syscall number (asm/unistd_64.h). Certain @@ -41,10 +44,21 @@ class Cctools(AutotoolsPackage): def configure_args(self): args = [] + # For python + if self.spec.satisfies('^python@3:'): + args.append('--with-python-path=no') + args.append( + '--with-python3-path={0}'.format(self.spec['python'].prefix) + ) + else: + args.append('--with-python3-path=no') + args.append( + '--with-python-path={0}'.format(self.spec['python'].prefix) + ) # disable these bits - for p in ['mysql', 'python3', 'xrootd']: + for p in ['mysql', 'xrootd']: args.append('--with-{0}-path=no'.format(p)) # point these bits at the Spack installations - for p in ['openssl', 'perl', 'python', 'readline', 'swig', 'zlib']: + for p in ['openssl', 'perl', 'readline', 'swig', 'zlib']: args.append('--with-{0}-path={1}'.format(p, self.spec[p].prefix)) return args diff --git a/var/spack/repos/builtin/packages/cdbfasta/package.py b/var/spack/repos/builtin/packages/cdbfasta/package.py index 4d6beabcb5..812dd7a7db 100644 --- a/var/spack/repos/builtin/packages/cdbfasta/package.py +++ b/var/spack/repos/builtin/packages/cdbfasta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cdd/package.py b/var/spack/repos/builtin/packages/cdd/package.py index b2d11c0bce..2487b8bb77 100644 --- a/var/spack/repos/builtin/packages/cdd/package.py +++ b/var/spack/repos/builtin/packages/cdd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cddlib/package.py b/var/spack/repos/builtin/packages/cddlib/package.py index 60d352c0ba..199d283ab7 100644 --- a/var/spack/repos/builtin/packages/cddlib/package.py +++ b/var/spack/repos/builtin/packages/cddlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cdecimal/package.py b/var/spack/repos/builtin/packages/cdecimal/package.py index 38abf47476..882af3bb21 100644 --- a/var/spack/repos/builtin/packages/cdecimal/package.py +++ b/var/spack/repos/builtin/packages/cdecimal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cdhit/package.py b/var/spack/repos/builtin/packages/cdhit/package.py index a2ba8c72bb..a58b959942 100644 --- a/var/spack/repos/builtin/packages/cdhit/package.py +++ b/var/spack/repos/builtin/packages/cdhit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,5 +31,5 @@ class Cdhit(MakefilePackage): make_args.append('zlib=no') make(*make_args) - def setup_environment(self, spack_env, run_env): - spack_env.set('PREFIX', prefix.bin) + def setup_build_environment(self, env): + env.set('PREFIX', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py index 7711128186..4cb06132ac 100644 --- a/var/spack/repos/builtin/packages/cdo/package.py +++ b/var/spack/repos/builtin/packages/cdo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,7 @@ class Cdo(AutotoolsPackage): maintainers = ['skosukhin'] + version('1.9.8', sha256='f2660ac6f8bf3fa071cf2a3a196b3ec75ad007deb3a782455e80f28680c5252a', url='https://code.mpimet.mpg.de/attachments/download/20286/cdo-1.9.8.tar.gz') version('1.9.7.1', sha256='3771952e065bcf935d43e492707370ed2a0ecb59a06bea24f9ab69d77943962c', url='https://code.mpimet.mpg.de/attachments/download/20124/cdo-1.9.7.1.tar.gz') version('1.9.6', sha256='b31474c94548d21393758caa33f35cf7f423d5dfc84562ad80a2bdcb725b5585', url='https://code.mpimet.mpg.de/attachments/download/19299/cdo-1.9.6.tar.gz') @@ -51,7 +52,7 @@ class Cdo(AutotoolsPackage): depends_on('pkgconfig', type='build') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') # In this case CDO does not depend on hdf5 directly but we need the backend # of netcdf to be thread safe. depends_on('hdf5+threadsafe', when='+netcdf') @@ -63,7 +64,7 @@ class Cdo(AutotoolsPackage): depends_on('hdf5+threadsafe', when='+hdf5') - depends_on('udunits2', when='+udunits2') + depends_on('udunits', when='+udunits2') depends_on('libxml2', when='+libxml2') depends_on('proj@:5', when='+proj') depends_on('curl', when='+curl') @@ -79,7 +80,9 @@ class Cdo(AutotoolsPackage): msg='GCC 9 changed OpenMP data sharing behavior') def configure_args(self): - config_args = self.with_or_without('netcdf', activation_value='prefix') + config_args = self.with_or_without( + 'netcdf', + activation_value=lambda x: self.spec['netcdf-c'].prefix) if self.spec.variants['grib2'].value == 'eccodes': config_args.append('--with-eccodes=' + @@ -108,8 +111,9 @@ class Cdo(AutotoolsPackage): config_args += self.with_or_without('hdf5', activation_value='prefix') - config_args += self.with_or_without('udunits2', - activation_value='prefix') + config_args += self.with_or_without( + 'udunits2', + activation_value=lambda x: self.spec['udunits'].prefix) config_args += self.with_or_without('libxml2', activation_value='prefix') diff --git a/var/spack/repos/builtin/packages/ceed/README.md b/var/spack/repos/builtin/packages/ceed/README.md deleted file mode 100644 index 74bcae1d17..0000000000 --- a/var/spack/repos/builtin/packages/ceed/README.md +++ /dev/null @@ -1,3 +0,0 @@ -This is a bundle for the CEED software suite. - -See https://ceed.exascaleproject.org for details. diff --git a/var/spack/repos/builtin/packages/ceed/package.py b/var/spack/repos/builtin/packages/ceed/package.py index 4d598c03db..3b47deb25b 100644 --- a/var/spack/repos/builtin/packages/ceed/package.py +++ b/var/spack/repos/builtin/packages/ceed/package.py @@ -1,13 +1,12 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * -import os -class Ceed(Package): +class Ceed(BundlePackage): """Ceed is a collection of benchmarks, miniapps, software libraries and APIs for efficient high-order finite element and spectral element discretizations for exascale applications developed in the Department of @@ -17,11 +16,7 @@ class Ceed(Package): homepage = "https://ceed.exascaleproject.org" - url = 'file://' + os.path.dirname(__file__) + '/README.md' - sha256 = '418c4b6b6a098648e25befdc28cdf9c351ecea9deaa660c0d9a674f8c6917122' - - version('2.0.0', sha256, expand=False) - version('1.0.0', sha256, expand=False) + version('2.0') variant('cuda', default=False, description='Build MAGMA; enable CUDA support in libCEED and OCCA') @@ -139,7 +134,3 @@ class Ceed(Package): # If using gcc version <= 4.8 build suite-sparse version <= 5.1.0 depends_on('suite-sparse@:5.1.0', when='@1.0.0%gcc@:4.8+mfem+petsc') - - # Dummy install - def install(self, spec, prefix): - install('README.md', prefix) diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py index 0d0735f713..ddab891654 100644 --- a/var/spack/repos/builtin/packages/cereal/package.py +++ b/var/spack/repos/builtin/packages/cereal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ceres-solver/package.py b/var/spack/repos/builtin/packages/ceres-solver/package.py index fa081154f7..599c180121 100644 --- a/var/spack/repos/builtin/packages/ceres-solver/package.py +++ b/var/spack/repos/builtin/packages/ceres-solver/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cfitsio/package.py b/var/spack/repos/builtin/packages/cfitsio/package.py index b41261c18b..dfac754190 100644 --- a/var/spack/repos/builtin/packages/cfitsio/package.py +++ b/var/spack/repos/builtin/packages/cfitsio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py index 2252655c85..9adef8140c 100644 --- a/var/spack/repos/builtin/packages/cgal/package.py +++ b/var/spack/repos/builtin/packages/cgal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cgdb/package.py b/var/spack/repos/builtin/packages/cgdb/package.py index 6eadbf547a..269561b070 100644 --- a/var/spack/repos/builtin/packages/cgdb/package.py +++ b/var/spack/repos/builtin/packages/cgdb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cgm/package.py b/var/spack/repos/builtin/packages/cgm/package.py index d572e1b73f..295b85a7ba 100644 --- a/var/spack/repos/builtin/packages/cgm/package.py +++ b/var/spack/repos/builtin/packages/cgm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cgns/package.py b/var/spack/repos/builtin/packages/cgns/package.py index 9836d5fa44..4e8a112634 100644 --- a/var/spack/repos/builtin/packages/cgns/package.py +++ b/var/spack/repos/builtin/packages/cgns/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/channelflow/package.py b/var/spack/repos/builtin/packages/channelflow/package.py index 4a22819678..12e70b4332 100644 --- a/var/spack/repos/builtin/packages/channelflow/package.py +++ b/var/spack/repos/builtin/packages/channelflow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,13 +12,9 @@ class Channelflow(CMakePackage): """ homepage = 'https://github.com/epfl-ecps/channelflow' - url = 'https://github.com/epfl-ecps/channelflow.git' + git = 'https://github.com/epfl-ecps/channelflow.git' - version( - 'develop', - git='https://github.com/epfl-ecps/channelflow.git', - branch='master' - ) + version('master', branch='master') variant('shared', default=True, description='Build shared libs') variant('mpi', default=True, description='Enable MPI parallelism') @@ -38,8 +34,8 @@ class Channelflow(CMakePackage): # Support for different I/O formats depends_on('hdf5+cxx', when='+hdf5') - depends_on('netcdf', when='netcdf=serial') - depends_on('netcdf+mpi', when='netcdf=parallel') + depends_on('netcdf-c', when='netcdf=serial') + depends_on('netcdf-c+mpi', when='netcdf=parallel') # Python bindings depends_on('boost+python', when='+python') @@ -73,7 +69,7 @@ class Channelflow(CMakePackage): } args.append('-DWITH_NETCDF:STRING={0}'.format( - netcdf_str[spec.variants['netcdf'].value] + netcdf_str[spec.variants['netcdf-c'].value] )) # Set an MPI compiler for parallel builds diff --git a/var/spack/repos/builtin/packages/chapel/package.py b/var/spack/repos/builtin/packages/chapel/package.py index 689222fd8c..142fb60a8b 100644 --- a/var/spack/repos/builtin/packages/chapel/package.py +++ b/var/spack/repos/builtin/packages/chapel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/charliecloud/package.py b/var/spack/repos/builtin/packages/charliecloud/package.py index 4183d923b7..9329455d84 100644 --- a/var/spack/repos/builtin/packages/charliecloud/package.py +++ b/var/spack/repos/builtin/packages/charliecloud/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Charliecloud(MakefilePackage): +class Charliecloud(AutotoolsPackage): """Lightweight user-defined software stacks for HPC.""" homepage = "https://hpc.github.io/charliecloud" @@ -14,18 +14,7 @@ class Charliecloud(MakefilePackage): git = "https://github.com/hpc/charliecloud.git" version('master', branch='master') - version('0.11', sha256='942d3c7a74c978fd7420cb2b255e618f4f0acaafb6025160bc3a4deeb687ef3c') - version('0.10', sha256='5cf00b170e7568750ca0b828c43c0857c39674860b480d757057450d69f1a21e') - version('0.9.10', sha256='44e821b62f9c447749d3ed0d2b2e44d374153058814704a5543e83f42db2a45a') - version('0.9.9', sha256='2624c5a0b19a01c9bca0acf873ceeaec401b9185a23e9108fadbcee0b9d74736') - version('0.9.8', sha256='903bcce05b19501b5524ef57a929d2f4c6ddeacb0e8443fcb2fe6963e2f29229') - version('0.9.7', sha256='ec80a4b9bef3a2161a783e11d99cc58e09a32dfbc8a6234c8f7ce7fa76e2f62d') - version('0.9.6', sha256='50e20d5e2a3710cd06e7c999db22495b07ef0fb15ffbc0af3bccac5387f0fddb') - version('0.9.3', sha256='f1bf032377b8845bc9a93b8a4fad6386161e35900223c0acc61d1f3aa3a87bc7') - version('0.9.2', sha256='8d0e4804d412beef720a66f886a0a78bce42f3269e880ebf11f602581f8047d4') - version('0.9.1', sha256='8e69150a271285da71ece7a09b48251ef6593f72207c5126741d9976aa737d95') - version('0.9.0', sha256='7e74cb16e31fd9d502198f7509bab14d1049ec68ba90b15e277e76f805db9458') - version('0.2.4', sha256='b9a8ff54b9d296e30b2cf5d64a7e732ad09e14b989645aaa5eee8a1dc7ee34e5') + version('0.13', sha256='5740bff6e410ca99484c1bdf3dbe834c0f753c846d55c19d6162967a3e2718e0') depends_on('python@3.4:', type=('build', 'run')) @@ -44,13 +33,14 @@ class Charliecloud(MakefilePackage): # bash automated testing harness (bats) depends_on('bats@0.4.0', type='test') - def url_for_version(self, version): - if version >= Version('0.9.8'): - url = "https://github.com/hpc/charliecloud/releases/download/v{0}/charliecloud-{0}.tar.gz" - else: - url = "https://github.com/hpc/charliecloud/archive/v{0}.tar.gz" - return url.format(version) + def configure_args(self): - @property - def install_targets(self): - return ['install', 'PREFIX=%s' % self.prefix] + args = [] + + if '+docs' not in self.spec: + args.append('--disable-html') + + if '+builder' not in self.spec: + args.append('--disable-ch-grow') + + return args diff --git a/var/spack/repos/builtin/packages/charmpp/package.py b/var/spack/repos/builtin/packages/charmpp/package.py index c667ff28ef..9f8629be8e 100644 --- a/var/spack/repos/builtin/packages/charmpp/package.py +++ b/var/spack/repos/builtin/packages/charmpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -82,17 +82,17 @@ class Charmpp(Package): provides('mpi@2', when='@6.7.1: build-target=AMPI backend={0}'.format(b)) provides('mpi@2', when='@6.7.1: build-target=LIBS backend={0}'.format(b)) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('MPICC', join_path(self.prefix.bin, 'ampicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'ampicxx')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'ampif77')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'ampif90')) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('MPICC', self.prefix.bin.ampicc) + env.set('MPICXX', self.prefix.bin.ampicxx) + env.set('MPIF77', self.prefix.bin.ampif77) + env.set('MPIF90', self.prefix.bin.ampif90) def setup_dependent_package(self, module, dependent_spec): - self.spec.mpicc = join_path(self.prefix.bin, 'ampicc') - self.spec.mpicxx = join_path(self.prefix.bin, 'ampicxx') - self.spec.mpifc = join_path(self.prefix.bin, 'ampif90') - self.spec.mpif77 = join_path(self.prefix.bin, 'ampif77') + self.spec.mpicc = self.prefix.bin.ampicc + self.spec.mpicxx = self.prefix.bin.ampicxx + self.spec.mpifc = self.prefix.bin.ampif90 + self.spec.mpif77 = self.prefix.bin.ampif77 depends_on("mpi", when="backend=mpi") depends_on("papi", when="+papi") @@ -238,6 +238,14 @@ class Charmpp(Package): pass shutil.rmtree(join_path(prefix, "tmp")) + # A broken 'doc' link in the prefix can break the build. + # Remove it and replace it if it is broken. + try: + os.stat(prefix.doc) + except OSError: + os.remove(prefix.doc) + mkdirp(prefix.doc) + @run_after('install') @on_package_attributes(run_tests=True) def check_build(self): diff --git a/var/spack/repos/builtin/packages/chatterbug/package.py b/var/spack/repos/builtin/packages/chatterbug/package.py index 277e89ff57..7bee6bd4cb 100644 --- a/var/spack/repos/builtin/packages/chatterbug/package.py +++ b/var/spack/repos/builtin/packages/chatterbug/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/check/package.py b/var/spack/repos/builtin/packages/check/package.py index ed7e933bc8..93121f2cd3 100644 --- a/var/spack/repos/builtin/packages/check/package.py +++ b/var/spack/repos/builtin/packages/check/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,8 @@ class Check(AutotoolsPackage): logging format.""" homepage = "https://libcheck.github.io/check/index.html" - url = "https://downloads.sourceforge.net/project/check/check/0.10.0/check-0.10.0.tar.gz" + url = "https://github.com/libcheck/check/releases/download/0.12.0/check-0.12.0.tar.gz" + version('0.12.0', sha256='464201098bee00e90f5c4bdfa94a5d3ead8d641f9025b560a27755a83b824234') + version('0.11.0', sha256='24f7a48aae6b74755bcbe964ce8bc7240f6ced2141f8d9cf480bc3b3de0d5616') version('0.10.0', sha256='f5f50766aa6f8fe5a2df752666ca01a950add45079aa06416b83765b1cf71052') diff --git a/var/spack/repos/builtin/packages/chgcentre/package.py b/var/spack/repos/builtin/packages/chgcentre/package.py new file mode 100644 index 0000000000..7d93b296a0 --- /dev/null +++ b/var/spack/repos/builtin/packages/chgcentre/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Chgcentre(CMakePackage): + """The chgcentre tool can be used + to change the phase centre of a measurement set.""" + + homepage = "https://sourceforge.net/p/wsclean/wiki/chgcentre/" + url = "https://downloads.sourceforge.net/project/wsclean/chgcentre-1.6/chgcentre-1.6.tar.bz2" + + version('1.6', sha256='5b14f9f56b900072c42dab2a8217cd399fb1bb50aae20f9e3b6ff30ec5b12008') + + depends_on('casacore') + depends_on('gsl') diff --git a/var/spack/repos/builtin/packages/chill/package.py b/var/spack/repos/builtin/packages/chill/package.py index 998f9500f2..d33ab4a959 100644 --- a/var/spack/repos/builtin/packages/chill/package.py +++ b/var/spack/repos/builtin/packages/chill/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -35,22 +35,27 @@ class Chill(AutotoolsPackage): bash = which('bash') bash('./bootstrap') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): rose_home = self.spec['rose'].prefix boost_home = self.spec['boost'].prefix iegen_home = self.spec['iegenlib'].prefix - spack_env.append_path('LD_LIBRARY_PATH', rose_home.lib) - spack_env.append_path('LD_LIBRARY_PATH', boost_home.lib) - spack_env.append_path('LD_LIBRARY_PATH', iegen_home.lib) + env.set('ROSEHOME', rose_home) + env.set('BOOSTHOME', boost_home) + env.set('IEGENHOME', iegen_home) - run_env.append_path('LD_LIBRARY_PATH', rose_home.lib) - run_env.append_path('LD_LIBRARY_PATH', boost_home.lib) - run_env.append_path('LD_LIBRARY_PATH', iegen_home.lib) + env.append_path('LD_LIBRARY_PATH', rose_home.lib) + env.append_path('LD_LIBRARY_PATH', boost_home.lib) + env.append_path('LD_LIBRARY_PATH', iegen_home.lib) - spack_env.set('ROSEHOME', rose_home) - spack_env.set('BOOSTHOME', boost_home) - spack_env.set('IEGENHOME', iegen_home) + def setup_run_environment(self, env): + rose_home = self.spec['rose'].prefix + boost_home = self.spec['boost'].prefix + iegen_home = self.spec['iegenlib'].prefix + + env.append_path('LD_LIBRARY_PATH', rose_home.lib) + env.append_path('LD_LIBRARY_PATH', boost_home.lib) + env.append_path('LD_LIBRARY_PATH', iegen_home.lib) def configure_args(self): args = ['--with-rose={0}'.format(self.spec['rose'].prefix), diff --git a/var/spack/repos/builtin/packages/chlorop/package.py b/var/spack/repos/builtin/packages/chlorop/package.py index 13e3af34bb..a7bcb696f1 100644 --- a/var/spack/repos/builtin/packages/chlorop/package.py +++ b/var/spack/repos/builtin/packages/chlorop/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -29,5 +29,5 @@ class Chlorop(Package): os.rename('chlorop', 'bin/chlorop') install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): - run_env.set('CHLOROP', self.prefix) + def setup_run_environment(self, env): + env.set('CHLOROP', self.prefix) diff --git a/var/spack/repos/builtin/packages/chombo/package.py b/var/spack/repos/builtin/packages/chombo/package.py index e3cf622e3c..bfe37bcfeb 100644 --- a/var/spack/repos/builtin/packages/chombo/package.py +++ b/var/spack/repos/builtin/packages/chombo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/chrpath/package.py b/var/spack/repos/builtin/packages/chrpath/package.py index 68e0cb054b..0cfbc2a7fc 100644 --- a/var/spack/repos/builtin/packages/chrpath/package.py +++ b/var/spack/repos/builtin/packages/chrpath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cinch/package.py b/var/spack/repos/builtin/packages/cinch/package.py index caba1e469f..65281b8455 100644 --- a/var/spack/repos/builtin/packages/cinch/package.py +++ b/var/spack/repos/builtin/packages/cinch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,6 +23,6 @@ class Cinch(Package): # (CMake) Header Only library so just copy install_tree(self.stage.source_path, prefix) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path('CMAKE_PREFIX_PATH', self.prefix) - spack_env.set('CINCH_SOURCE_DIR', self.prefix) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path('CMAKE_PREFIX_PATH', self.prefix) + env.set('CINCH_SOURCE_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/circos/package.py b/var/spack/repos/builtin/packages/circos/package.py index 7a7b90445c..9a4cb997d1 100644 --- a/var/spack/repos/builtin/packages/circos/package.py +++ b/var/spack/repos/builtin/packages/circos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cistem/package.py b/var/spack/repos/builtin/packages/cistem/package.py index 4fdde6c1b4..b12d35934f 100644 --- a/var/spack/repos/builtin/packages/cistem/package.py +++ b/var/spack/repos/builtin/packages/cistem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/citcoms/package.py b/var/spack/repos/builtin/packages/citcoms/package.py index d7d9d13b58..2529e544f6 100644 --- a/var/spack/repos/builtin/packages/citcoms/package.py +++ b/var/spack/repos/builtin/packages/citcoms/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -36,9 +36,9 @@ class Citcoms(AutotoolsPackage): conflicts('+pyre', when='@3.3:', msg='Pyre support was removed from 3.3+') conflicts('+exchanger', when='@3.3:', msg='Exchanger support was removed from 3.3+') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if '+ggrd' in self.spec: - spack_env.set('HC_HOME', self.spec['hc'].prefix) + env.set('HC_HOME', self.spec['hc'].prefix) def configure_args(self): args = ['CC={0}'.format(self.spec['mpi'].mpicc)] diff --git a/var/spack/repos/builtin/packages/cityhash/package.py b/var/spack/repos/builtin/packages/cityhash/package.py index 17a31d6c8b..ebe96e58e2 100644 --- a/var/spack/repos/builtin/packages/cityhash/package.py +++ b/var/spack/repos/builtin/packages/cityhash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/clamav/package.py b/var/spack/repos/builtin/packages/clamav/package.py index 28542c115d..567fd38555 100644 --- a/var/spack/repos/builtin/packages/clamav/package.py +++ b/var/spack/repos/builtin/packages/clamav/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/clamr/package.py b/var/spack/repos/builtin/packages/clamr/package.py index 6f939322b3..ea72bbb1e2 100644 --- a/var/spack/repos/builtin/packages/clamr/package.py +++ b/var/spack/repos/builtin/packages/clamr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/clapack/package.py b/var/spack/repos/builtin/packages/clapack/package.py index 758d0df5ef..6796bf97ff 100644 --- a/var/spack/repos/builtin/packages/clapack/package.py +++ b/var/spack/repos/builtin/packages/clapack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/clara/package.py b/var/spack/repos/builtin/packages/clara/package.py new file mode 100644 index 0000000000..f60b885a7b --- /dev/null +++ b/var/spack/repos/builtin/packages/clara/package.py @@ -0,0 +1,39 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Clara(CMakePackage): + """A simple to use, composable, command line parser for C++ 11 + and beyond.""" + + homepage = "https://github.com/catchorg/Clara" + url = "https://github.com/catchorg/Clara/archive/v1.1.5.tar.gz" + + maintainers = ['bvanessen'] + + variant('single_header', default=True, + description='Install a single header only.') + + version('1.1.5', sha256='767dc1718e53678cbea00977adcd0a8a195802a505aec3c537664cf25a173142') + version('1.1.4', sha256='ed3f9cc32e4ea6075c26caff63ee14a87e43dee1f3010c02bd041b9a0c86f72d') + version('1.1.3', sha256='a8132befb6b32bf447a74f7e758ac0b63e7bab86974aeb55ee2fd1cd77385f9e') + version('1.1.2', sha256='87c8e9440cc339c2a7b7efa0313070ff0081eca7780f098f6aff624ffa640c16') + version('1.1.1', sha256='10915a49a94d371f05af360d40e9cc9615ab86f200d261edf196a8ddd7efa7f8') + version('1.1.0', sha256='29ca29d843150aabad702356f79009f5b30dda05ac9674a064362b7edcba5477') + + @when('+single_header') + def cmake(self, spec, prefix): + pass + + @when('+single_header') + def build(self, spec, prefix): + pass + + @when('+single_header') + def install(self, spec, prefix): + mkdirp(prefix.include) + install_tree('single_include', prefix.include) diff --git a/var/spack/repos/builtin/packages/claw/package.py b/var/spack/repos/builtin/packages/claw/package.py index f0790340a2..b15f5324e7 100644 --- a/var/spack/repos/builtin/packages/claw/package.py +++ b/var/spack/repos/builtin/packages/claw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cleaveland4/package.py b/var/spack/repos/builtin/packages/cleaveland4/package.py index ba4eb32c32..d9d845bfdc 100644 --- a/var/spack/repos/builtin/packages/cleaveland4/package.py +++ b/var/spack/repos/builtin/packages/cleaveland4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cleverleaf/package.py b/var/spack/repos/builtin/packages/cleverleaf/package.py index 5bd8b5cb10..afb4b25ce2 100644 --- a/var/spack/repos/builtin/packages/cleverleaf/package.py +++ b/var/spack/repos/builtin/packages/cleverleaf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/clfft/package.py b/var/spack/repos/builtin/packages/clfft/package.py index 2dd4e790fe..8fc1a2895a 100644 --- a/var/spack/repos/builtin/packages/clfft/package.py +++ b/var/spack/repos/builtin/packages/clfft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/clhep/package.py b/var/spack/repos/builtin/packages/clhep/package.py index 9e73e35bef..5f1294e480 100644 --- a/var/spack/repos/builtin/packages/clhep/package.py +++ b/var/spack/repos/builtin/packages/clhep/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/clingo/package.py b/var/spack/repos/builtin/packages/clingo/package.py index 3a22186866..8f1b64af60 100644 --- a/var/spack/repos/builtin/packages/clingo/package.py +++ b/var/spack/repos/builtin/packages/clingo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,6 +19,8 @@ class Clingo(CMakePackage): homepage = "https://potassco.org/clingo/" url = "https://github.com/potassco/clingo/archive/v5.2.2.tar.gz" + version('5.4.0', sha256='e2de331ee0a6d254193aab5995338a621372517adcf91568092be8ac511c18f3') + version('5.3.0', sha256='b0d406d2809352caef7fccf69e8864d55e81ee84f4888b0744894977f703f976') version('5.2.2', sha256='da1ef8142e75c5a6f23c9403b90d4f40b9f862969ba71e2aaee9a257d058bfcf') depends_on('doxygen', type=('build')) diff --git a/var/spack/repos/builtin/packages/cln/package.py b/var/spack/repos/builtin/packages/cln/package.py index 0ead23d3f2..e6374ecaf5 100644 --- a/var/spack/repos/builtin/packages/cln/package.py +++ b/var/spack/repos/builtin/packages/cln/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,6 +16,8 @@ class Cln(AutotoolsPackage): homepage = "https://www.ginac.de/CLN/" git = "git://www.ginac.de/cln.git" + version('1.3.6', commit='d4ba1cc869be2c647c4ab48ac571b1fc9c2021a9') + version('1.3.5', commit='b221c033c082b462455502b7e63702a9c466aede') version('1.3.4', commit='9b86a7fc69feb1b288469982001af565f73057eb') version('1.3.3', commit='1c9bd61ff0b89b0bf8030e44cb398e8f75112222') version('1.3.2', commit='00817f7b60a961b860f6d305ac82dd51b70d6ba6') diff --git a/var/spack/repos/builtin/packages/cloc/package.py b/var/spack/repos/builtin/packages/cloc/package.py index 7a6ca7fe42..aa4f237c71 100644 --- a/var/spack/repos/builtin/packages/cloc/package.py +++ b/var/spack/repos/builtin/packages/cloc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cloog/package.py b/var/spack/repos/builtin/packages/cloog/package.py index 70bd67c370..cc62b11e27 100644 --- a/var/spack/repos/builtin/packages/cloog/package.py +++ b/var/spack/repos/builtin/packages/cloog/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cloverleaf/package.py b/var/spack/repos/builtin/packages/cloverleaf/package.py index 6d81f1c9c5..a3d4bd02b0 100644 --- a/var/spack/repos/builtin/packages/cloverleaf/package.py +++ b/var/spack/repos/builtin/packages/cloverleaf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ class Cloverleaf(MakefilePackage): """ homepage = "http://uk-mac.github.io/CloverLeaf" - url = "http://mantevo.org/downloads/releaseTarballs/miniapps/CloverLeaf/CloverLeaf-1.1.tar.gz" + url = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/CloverLeaf-1.1.tar.gz" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/cloverleaf3d/package.py b/var/spack/repos/builtin/packages/cloverleaf3d/package.py index 59aba4a001..17638b54e5 100644 --- a/var/spack/repos/builtin/packages/cloverleaf3d/package.py +++ b/var/spack/repos/builtin/packages/cloverleaf3d/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,7 +17,7 @@ class Cloverleaf3d(MakefilePackage): """ homepage = "http://uk-mac.github.io/CloverLeaf3D/" - url = "http://mantevo.org/downloads/releaseTarballs/miniapps/CloverLeaf3D/CloverLeaf3D-1.0.tar.gz" + url = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/CloverLeaf3D-1.0.tar.gz" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/clp/package.py b/var/spack/repos/builtin/packages/clp/package.py index 5362ce7a84..5dd217d41d 100644 --- a/var/spack/repos/builtin/packages/clp/package.py +++ b/var/spack/repos/builtin/packages/clp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/clustalo/package.py b/var/spack/repos/builtin/packages/clustal-omega/package.py index 59b7606e6c..d966eb65d2 100644 --- a/var/spack/repos/builtin/packages/clustalo/package.py +++ b/var/spack/repos/builtin/packages/clustal-omega/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Clustalo(AutotoolsPackage): +class ClustalOmega(AutotoolsPackage): """Clustal Omega: the last alignment program you'll ever need.""" homepage = "http://www.clustal.org/omega/" diff --git a/var/spack/repos/builtin/packages/clustalw/package.py b/var/spack/repos/builtin/packages/clustalw/package.py index d279adc4a0..42aca319d4 100644 --- a/var/spack/repos/builtin/packages/clustalw/package.py +++ b/var/spack/repos/builtin/packages/clustalw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cmake/fix-xlf-ninja-mr-4075.patch b/var/spack/repos/builtin/packages/cmake/fix-xlf-ninja-mr-4075.patch new file mode 100644 index 0000000000..584e33850e --- /dev/null +++ b/var/spack/repos/builtin/packages/cmake/fix-xlf-ninja-mr-4075.patch @@ -0,0 +1,145 @@ +From 19f267c75e84b72c4de42570be0c4222bb93aaff Mon Sep 17 00:00:00 2001 +From: Brad King <brad.king@kitware.com> +Date: Thu, 21 Nov 2019 14:38:35 -0500 +Subject: [PATCH] XL: Add support for Ninja and XL Fortran + +The Ninja generator's support for Fortran requires that source files +be preprocessed explicitly first. However, the `xlf` compiler does +not have a simple `-E` option or equivalent to do preprocessing. +The only documented way to get preprocessed output is to use `-d` +to leave it behind, but only at an inflexible location. + +Instead, create our own `cpp` wrapper script and substitute it for the +real preprocessor using `-tF -B ...`. Teach the wrapper to map the +`cpp` output to the location we need and then invoke the real `cpp` +underneath. + +Fixes: #19450 +--- + Help/release/dev/xlf-ninja.rst | 5 ++++ + Modules/CMakeDetermineCompilerId.cmake | 10 +++++++ + Modules/CMakeDetermineFortranCompiler.cmake | 5 ++++ + Modules/CMakeFortranCompiler.cmake.in | 1 + + Modules/Compiler/XL-Fortran.cmake | 4 +++ + Modules/Compiler/XL-Fortran/cpp | 29 +++++++++++++++++++++ + 6 files changed, 54 insertions(+) + create mode 100644 Help/release/dev/xlf-ninja.rst + create mode 100755 Modules/Compiler/XL-Fortran/cpp + +diff --git a/Help/release/dev/xlf-ninja.rst b/Help/release/dev/xlf-ninja.rst +new file mode 100644 +index 0000000000..916e713008 +--- /dev/null ++++ b/Help/release/dev/xlf-ninja.rst +@@ -0,0 +1,5 @@ ++xlf-ninja ++--------- ++ ++* The IBM XL Fortran compiler is now supported by the :generator:`Ninja` ++ generator. +diff --git a/Modules/CMakeDetermineCompilerId.cmake b/Modules/CMakeDetermineCompilerId.cmake +index f7ef755aeb..0b3664c5de 100644 +--- a/Modules/CMakeDetermineCompilerId.cmake ++++ b/Modules/CMakeDetermineCompilerId.cmake +@@ -182,6 +182,10 @@ function(CMAKE_DETERMINE_COMPILER_ID lang flagvar src) + message(STATUS "The ${lang} compiler identification is unknown") + endif() + ++ if(lang STREQUAL "Fortran" AND CMAKE_${lang}_COMPILER_ID STREQUAL "XL") ++ set(CMAKE_${lang}_XL_CPP "${CMAKE_${lang}_COMPILER_ID_CPP}" PARENT_SCOPE) ++ endif() ++ + set(CMAKE_${lang}_COMPILER_ID "${CMAKE_${lang}_COMPILER_ID}" PARENT_SCOPE) + set(CMAKE_${lang}_PLATFORM_ID "${CMAKE_${lang}_PLATFORM_ID}" PARENT_SCOPE) + set(CMAKE_${lang}_COMPILER_ARCHITECTURE_ID "${CMAKE_${lang}_COMPILER_ARCHITECTURE_ID}" PARENT_SCOPE) +@@ -542,6 +546,12 @@ Id flags: ${testflags} ${CMAKE_${lang}_COMPILER_ID_FLAGS_ALWAYS} + ERROR_VARIABLE CMAKE_${lang}_COMPILER_ID_OUTPUT + RESULT_VARIABLE CMAKE_${lang}_COMPILER_ID_RESULT + ) ++ if("${CMAKE_${lang}_COMPILER_ID_OUTPUT}" MATCHES "exec: [^\n]*\\((/[^,\n]*/cpp),CMakeFortranCompilerId.F") ++ set(_cpp "${CMAKE_MATCH_1}") ++ if(EXISTS "${_cpp}") ++ set(CMAKE_${lang}_COMPILER_ID_CPP "${_cpp}" PARENT_SCOPE) ++ endif() ++ endif() + endif() + + # Check the result of compilation. +diff --git a/Modules/CMakeDetermineFortranCompiler.cmake b/Modules/CMakeDetermineFortranCompiler.cmake +index 5ddd64fae8..e8505417d6 100644 +--- a/Modules/CMakeDetermineFortranCompiler.cmake ++++ b/Modules/CMakeDetermineFortranCompiler.cmake +@@ -271,6 +271,11 @@ include(CMakeFindBinUtils) + include(Compiler/${CMAKE_Fortran_COMPILER_ID}-FindBinUtils OPTIONAL) + unset(_CMAKE_PROCESSING_LANGUAGE) + ++if(CMAKE_Fortran_XL_CPP) ++ set(_SET_CMAKE_Fortran_XL_CPP ++ "set(CMAKE_Fortran_XL_CPP \"${CMAKE_Fortran_XL_CPP}\")") ++endif() ++ + if(CMAKE_Fortran_COMPILER_ARCHITECTURE_ID) + set(_SET_CMAKE_Fortran_COMPILER_ARCHITECTURE_ID + "set(CMAKE_Fortran_COMPILER_ARCHITECTURE_ID ${CMAKE_Fortran_COMPILER_ARCHITECTURE_ID})") +diff --git a/Modules/CMakeFortranCompiler.cmake.in b/Modules/CMakeFortranCompiler.cmake.in +index ae7b73ac4a..34f44aa542 100644 +--- a/Modules/CMakeFortranCompiler.cmake.in ++++ b/Modules/CMakeFortranCompiler.cmake.in +@@ -6,6 +6,7 @@ set(CMAKE_Fortran_COMPILER_WRAPPER "@CMAKE_Fortran_COMPILER_WRAPPER@") + set(CMAKE_Fortran_PLATFORM_ID "@CMAKE_Fortran_PLATFORM_ID@") + set(CMAKE_Fortran_SIMULATE_ID "@CMAKE_Fortran_SIMULATE_ID@") + set(CMAKE_Fortran_SIMULATE_VERSION "@CMAKE_Fortran_SIMULATE_VERSION@") ++@_SET_CMAKE_Fortran_XL_CPP@ + @_SET_CMAKE_Fortran_COMPILER_ARCHITECTURE_ID@ + @SET_MSVC_Fortran_ARCHITECTURE_ID@ + set(CMAKE_AR "@CMAKE_AR@") +diff --git a/Modules/Compiler/XL-Fortran.cmake b/Modules/Compiler/XL-Fortran.cmake +index c4fb09712a..1683dff4f0 100644 +--- a/Modules/Compiler/XL-Fortran.cmake ++++ b/Modules/Compiler/XL-Fortran.cmake +@@ -18,3 +18,7 @@ string(APPEND CMAKE_Fortran_FLAGS_INIT " -qthreaded -qhalt=e") + # xlf: 1501-214 (W) command option E reserved for future use - ignored + set(CMAKE_Fortran_CREATE_PREPROCESSED_SOURCE) + set(CMAKE_Fortran_CREATE_ASSEMBLY_SOURCE) ++ ++set(CMAKE_Fortran_PREPROCESS_SOURCE ++ "<CMAKE_Fortran_COMPILER> <DEFINES> <INCLUDES> <FLAGS> -qpreprocess -qnoobject -qsuppress=1517-020 -tF -B \"${CMAKE_CURRENT_LIST_DIR}/XL-Fortran/\" -WF,--cpp,\"${CMAKE_Fortran_XL_CPP}\",--out,<PREPROCESSED_SOURCE> <SOURCE>" ++ ) +diff --git a/Modules/Compiler/XL-Fortran/cpp b/Modules/Compiler/XL-Fortran/cpp +new file mode 100755 +index 0000000000..1fd62c26a0 +--- /dev/null ++++ b/Modules/Compiler/XL-Fortran/cpp +@@ -0,0 +1,29 @@ ++#!/usr/bin/env bash ++ ++# Source file. ++src="$(printf %q "$1")" ++shift ++ ++# Output file the compiler expects. ++out="$(printf %q "$1")" ++shift ++ ++# Create the file the compiler expects. It will check syntax. ++>"$out" ++ ++cpp='cpp' ++opts='' ++while test "$#" != 0; do ++ case "$1" in ++ # Extract the option for the path to cpp. ++ --cpp) shift; cpp="$(printf %q "$1")" ;; ++ # Extract the option for our own output file. ++ --out) shift; out="$(printf %q "$1")" ;; ++ # Collect the rest of the command line. ++ *) opts="$opts $(printf %q "$1")" ;; ++ esac ++ shift ++done ++ ++# Execute the real preprocessor tool. ++eval "exec $cpp $src $out $opts" +-- +2.24.1 + diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index ac74bea71a..4f6e30874b 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,20 +10,24 @@ class Cmake(Package): """A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" homepage = 'https://www.cmake.org' - url = 'https://github.com/Kitware/CMake/releases/download/v3.15.4/cmake-3.15.4.tar.gz' + url = 'https://github.com/Kitware/CMake/releases/download/v3.15.5/cmake-3.15.5.tar.gz' maintainers = ['chuckatkins'] - version('3.15.4', sha256='8a211589ea21374e49b25fc1fc170e2d5c7462b795f1b29c84dd0e984301ed7a') - version('3.15.3', sha256='13958243a01365b05652fa01b21d40fa834f70a9e30efa69c02604e64f58b8f5') - version('3.15.2', sha256='539088cb29a68e6d6a8fba5c00951e5e5b1a92c68fa38a83e1ed2f355933f768') - version('3.15.1', sha256='18dec548d8f8b04d53c60f9cedcebaa6762f8425339d1e2c889c383d3ccdd7f7') - version('3.15.0', sha256='0678d74a45832cacaea053d85a5685f3ed8352475e6ddf9fcb742ffca00199b5') - version('3.14.5', sha256='505ae49ebe3c63c595fa5f814975d8b72848447ee13b6613b0f8b96ebda18c06') - version('3.14.4', sha256='00b4dc9b0066079d10f16eed32ec592963a44e7967371d2f5077fd1670ff36d9') - version('3.14.3', sha256='215d0b64e81307182b29b63e562edf30b3875b834efdad09b3fcb5a7d2f4b632') - version('3.14.2', sha256='a3cbf562b99270c0ff192f692139e98c605f292bfdbc04d70da0309a5358e71e') - version('3.14.1', sha256='7321be640406338fc12590609c42b0fae7ea12980855c1be363d25dcd76bb25f') - version('3.14.0', sha256='aa76ba67b3c2af1946701f847073f4652af5cbd9f141f221c97af99127e75502') + version('3.16.2', sha256='8c09786ec60ca2be354c29829072c38113de9184f29928eb9da8446a5f2ce6a9') + version('3.16.1', sha256='a275b3168fa8626eca4465da7bb159ff07c8c6cb0fb7179be59e12cbdfa725fd') + version('3.16.0', sha256='6da56556c63cab6e9a3e1656e8763ed4a841ac9859fefb63cbe79472e67e8c5f') + version('3.15.5', sha256='fbdd7cef15c0ced06bb13024bfda0ecc0dedbcaaaa6b8a5d368c75255243beb4') + version('3.15.4', sha256='8a211589ea21374e49b25fc1fc170e2d5c7462b795f1b29c84dd0e984301ed7a') + version('3.15.3', sha256='13958243a01365b05652fa01b21d40fa834f70a9e30efa69c02604e64f58b8f5') + version('3.15.2', sha256='539088cb29a68e6d6a8fba5c00951e5e5b1a92c68fa38a83e1ed2f355933f768') + version('3.15.1', sha256='18dec548d8f8b04d53c60f9cedcebaa6762f8425339d1e2c889c383d3ccdd7f7') + version('3.15.0', sha256='0678d74a45832cacaea053d85a5685f3ed8352475e6ddf9fcb742ffca00199b5') + version('3.14.5', sha256='505ae49ebe3c63c595fa5f814975d8b72848447ee13b6613b0f8b96ebda18c06') + version('3.14.4', sha256='00b4dc9b0066079d10f16eed32ec592963a44e7967371d2f5077fd1670ff36d9') + version('3.14.3', sha256='215d0b64e81307182b29b63e562edf30b3875b834efdad09b3fcb5a7d2f4b632') + version('3.14.2', sha256='a3cbf562b99270c0ff192f692139e98c605f292bfdbc04d70da0309a5358e71e') + version('3.14.1', sha256='7321be640406338fc12590609c42b0fae7ea12980855c1be363d25dcd76bb25f') + version('3.14.0', sha256='aa76ba67b3c2af1946701f847073f4652af5cbd9f141f221c97af99127e75502') version('3.13.4', sha256='fdd928fee35f472920071d1c7f1a6a2b72c9b25e04f7a37b409349aef3f20e9b') version('3.13.3', sha256='665f905036b1f731a2a16f83fb298b1fb9d0f98c382625d023097151ad016b25') version('3.13.2', sha256='c925e7d2c5ba511a69f43543ed7b4182a7d446c274c7480d0e42cd933076ae25') @@ -71,6 +75,10 @@ class Cmake(Package): # See https://gitlab.kitware.com/cmake/cmake/merge_requests/2873 patch('cmake-macos-add-coreservices.patch', when='@3.11.0:3.13.3') + # Fix builds with XLF + Ninja generator + # https://gitlab.kitware.com/cmake/cmake/merge_requests/4075 + patch('fix-xlf-ninja-mr-4075.patch', sha256="42d8b2163a2f37a745800ec13a96c08a3a20d5e67af51031e51f63313d0dedd1", when="@3.15.5") + # We default ownlibs to true because it greatly speeds up the CMake # build, and CMake is built frequently. Also, CMake is almost always # a build dependency, and its libs will not interfere with others in @@ -93,7 +101,8 @@ class Cmake(Package): depends_on('zlib', when='~ownlibs') depends_on('bzip2', when='~ownlibs') depends_on('xz', when='~ownlibs') - depends_on('libarchive', when='~ownlibs') + depends_on('libarchive@3.1.0:', when='~ownlibs') + depends_on('libarchive@3.3.3:', when='@3.15.0:~ownlibs') depends_on('libuv@1.0.0:1.10.99', when='@3.7.0:3.10.3~ownlibs') depends_on('libuv@1.10.0:1.10.99', when='@3.11.0:3.11.99~ownlibs') depends_on('libuv@1.10.0:', when='@3.12.0:~ownlibs') @@ -116,6 +125,8 @@ class Cmake(Package): # https://gitlab.kitware.com/cmake/cmake/issues/18166 conflicts('%intel', when='@3.11.0:3.11.4') + conflicts('%intel@:14', when='@3.14:', + msg="Intel 14 has immature C++11 support") phases = ['bootstrap', 'build', 'install'] @@ -158,8 +169,15 @@ class Cmake(Package): args.append('--sphinx-html') args.append('--sphinx-man') + # Now for CMake arguments to pass after the initial bootstrap + args.append('--') + + # Make sure to create an optimized release build + args.append('-DCMAKE_BUILD_TYPE=Release') + + # When building our own private copy of curl then we need to properly + # enable / disable oepnssl if '+ownlibs' in spec: - args.append('--') args.append('-DCMAKE_USE_OPENSSL=%s' % str('+openssl' in spec)) return args diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py index eedc77f312..4fd6324375 100644 --- a/var/spack/repos/builtin/packages/cmocka/package.py +++ b/var/spack/repos/builtin/packages/cmocka/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cmor/package.py b/var/spack/repos/builtin/packages/cmor/package.py index 31460e1645..5cbfa69613 100644 --- a/var/spack/repos/builtin/packages/cmor/package.py +++ b/var/spack/repos/builtin/packages/cmor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,8 +24,8 @@ class Cmor(AutotoolsPackage): variant('python', default=False, description='Enable PYTHON support') depends_on('uuid') - depends_on('netcdf') - depends_on('udunits2') + depends_on('netcdf-c') + depends_on('udunits') depends_on('hdf5@:1.8.19') extends('python', when='+python') diff --git a/var/spack/repos/builtin/packages/cnmem/package.py b/var/spack/repos/builtin/packages/cnmem/package.py index 1007a074c2..9e6ebd4d86 100644 --- a/var/spack/repos/builtin/packages/cnmem/package.py +++ b/var/spack/repos/builtin/packages/cnmem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cnpy/package.py b/var/spack/repos/builtin/packages/cnpy/package.py index c9602ac168..c80db33b57 100644 --- a/var/spack/repos/builtin/packages/cnpy/package.py +++ b/var/spack/repos/builtin/packages/cnpy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cntk/package.py b/var/spack/repos/builtin/packages/cntk/package.py index 3f7ede7eaf..098341402e 100644 --- a/var/spack/repos/builtin/packages/cntk/package.py +++ b/var/spack/repos/builtin/packages/cntk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cntk1bitsgd/package.py b/var/spack/repos/builtin/packages/cntk1bitsgd/package.py index b92769b3fc..efaa6e1af3 100644 --- a/var/spack/repos/builtin/packages/cntk1bitsgd/package.py +++ b/var/spack/repos/builtin/packages/cntk1bitsgd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cnvnator/package.py b/var/spack/repos/builtin/packages/cnvnator/package.py index 7ac9e01d78..8160f21e02 100644 --- a/var/spack/repos/builtin/packages/cnvnator/package.py +++ b/var/spack/repos/builtin/packages/cnvnator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/codar-cheetah/package.py b/var/spack/repos/builtin/packages/codar-cheetah/package.py index a7a8dca46a..5a8975a048 100644 --- a/var/spack/repos/builtin/packages/codar-cheetah/package.py +++ b/var/spack/repos/builtin/packages/codar-cheetah/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,20 +6,18 @@ from spack import * -class CodarCheetah(Package): +class CodarCheetah(PythonPackage): """CODAR Cheetah: The CODAR Experiment Harness for Exascale science applications. """ + maintainers = ['kshitij-v-mehta'] + homepage = "https://github.com/CODARcode/cheetah" url = "https://github.com/CODARcode/cheetah/archive/v0.1.tar.gz" git = "https://github.com/CODARcode/cheetah.git" - version('develop', branch='master') - version('0.1', sha256='281564f8ae57a70ce28457616fde26247ea4efb29e55c7bf89a782a259a1a028') - - depends_on('python@3:', type=('build', 'run')) - depends_on('savanna') + version('develop', branch='dev') + version('0.5', sha256='f37a554741eff4bb8407a68f799dd042dfc4df525e84896cad70fccbd6aca6ee') - def install(self, spec, prefix): - install_tree('.', prefix) + depends_on('python@3.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/codes/package.py b/var/spack/repos/builtin/packages/codes/package.py index 70207194d2..23ea42cf8c 100644 --- a/var/spack/repos/builtin/packages/codes/package.py +++ b/var/spack/repos/builtin/packages/codes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/coevp/package.py b/var/spack/repos/builtin/packages/coevp/package.py index dd9ddf1331..2438da1d69 100644 --- a/var/spack/repos/builtin/packages/coevp/package.py +++ b/var/spack/repos/builtin/packages/coevp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cohmm/package.py b/var/spack/repos/builtin/packages/cohmm/package.py index be133b7877..80b53e39c8 100644 --- a/var/spack/repos/builtin/packages/cohmm/package.py +++ b/var/spack/repos/builtin/packages/cohmm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/coinhsl/package.py b/var/spack/repos/builtin/packages/coinhsl/package.py index e251306b9b..bfd4830a26 100644 --- a/var/spack/repos/builtin/packages/coinhsl/package.py +++ b/var/spack/repos/builtin/packages/coinhsl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/colm/package.py b/var/spack/repos/builtin/packages/colm/package.py index 6e2eed2de8..e455c3a8f7 100644 --- a/var/spack/repos/builtin/packages/colm/package.py +++ b/var/spack/repos/builtin/packages/colm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/colordiff/package.py b/var/spack/repos/builtin/packages/colordiff/package.py index eb59fcf472..7c7073cadc 100644 --- a/var/spack/repos/builtin/packages/colordiff/package.py +++ b/var/spack/repos/builtin/packages/colordiff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/comd/package.py b/var/spack/repos/builtin/packages/comd/package.py index 1f42ca1cbf..8f2446c2a9 100644 --- a/var/spack/repos/builtin/packages/comd/package.py +++ b/var/spack/repos/builtin/packages/comd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/commons-lang/package.py b/var/spack/repos/builtin/packages/commons-lang/package.py index daf88df975..a324565093 100644 --- a/var/spack/repos/builtin/packages/commons-lang/package.py +++ b/var/spack/repos/builtin/packages/commons-lang/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/commons-lang3/package.py b/var/spack/repos/builtin/packages/commons-lang3/package.py index 4309e40620..d9aca99e35 100644 --- a/var/spack/repos/builtin/packages/commons-lang3/package.py +++ b/var/spack/repos/builtin/packages/commons-lang3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/commons-logging/package.py b/var/spack/repos/builtin/packages/commons-logging/package.py index b5b7a8189b..3ca20d2d5e 100644 --- a/var/spack/repos/builtin/packages/commons-logging/package.py +++ b/var/spack/repos/builtin/packages/commons-logging/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/compiz/package.py b/var/spack/repos/builtin/packages/compiz/package.py index 36bd995dae..b78dcd410f 100644 --- a/var/spack/repos/builtin/packages/compiz/package.py +++ b/var/spack/repos/builtin/packages/compiz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/compositeproto/package.py b/var/spack/repos/builtin/packages/compositeproto/package.py index 96286eaa96..eb8b8fc078 100644 --- a/var/spack/repos/builtin/packages/compositeproto/package.py +++ b/var/spack/repos/builtin/packages/compositeproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py index af1cc70c85..eecc15d798 100644 --- a/var/spack/repos/builtin/packages/conduit/package.py +++ b/var/spack/repos/builtin/packages/conduit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -38,6 +38,8 @@ class Conduit(Package): git = "https://github.com/LLNL/conduit.git" version('master', branch='master', submodules=True, preferred=True) + version('0.5.1', sha256='68a3696d1ec6d3a4402b44a464d723e6529ec41016f9b44c053676affe516d44') + version('0.5.0', sha256='7efac668763d02bd0a2c0c1b134d9f5ee27e99008183905bb0512e5502b8b4fe') version('0.4.0', sha256='c228e6f0ce5a9c0ffb98e0b3d886f2758ace1a4b40d00f3f118542c0747c1f52') version('0.3.1', sha256='7b358ca03bb179876291d4a55d6a1c944b7407a80a588795b9e47940b1990521') version('0.3.0', sha256='52e9cf5720560e5f7492876c39ef2ea20ae73187338361d2744bdf67567da155') @@ -66,6 +68,9 @@ class Conduit(Package): variant("silo", default=False, description="Build Conduit Silo support") variant("adios", default=False, description="Build Conduit ADIOS support") + # zfp compression + variant("zfp", default=False, description="Build Conduit ZFP support") + # variants for dev-tools (docs, etc) variant("doc", default=False, description="Build Conduit's documentation") # doxygen support is wip, since doxygen has several dependencies @@ -85,15 +90,17 @@ class Conduit(Package): ####################### # Python ####################### - # we need a shared version of python b/c linking with static python lib - # causes duplicate state issues when running compiled python modules. - depends_on("python+shared", when="+python") + depends_on("python", when="+python") extends("python", when="+python") depends_on("py-numpy", when="+python", type=('build', 'run')) ####################### # I/O Packages ####################### + + ############### + # HDF5 + ############### # TODO: cxx variant is disabled due to build issue Cyrus # experienced on BGQ. When on, the static build tries # to link against shared libs. @@ -105,16 +112,27 @@ class Conduit(Package): depends_on("hdf5~cxx~mpi~fortran", when="+hdf5~hdf5_compat+shared") depends_on("hdf5~shared~cxx~mpi~fortran", when="+hdf5~hdf5_compat~shared") + ############### + # Silo + ############### # we are not using silo's fortran features depends_on("silo~fortran", when="+silo+shared") depends_on("silo~shared~fortran", when="+silo~shared") + ############### + # ADIOS + ############### depends_on("adios+mpi~hdf5+shared", when="+adios+mpi+shared") depends_on("adios+mpi~hdf5~shared~blosc", when="+adios+mpi~shared") depends_on("adios~mpi~hdf5+shared", when="+adios~mpi+shared") depends_on("adios~mpi~hdf5~shared~blosc", when="+adios~mpi~shared") ####################### + # ZFP + ####################### + depends_on("zfp", when="+zfp") + + ####################### # MPI ####################### depends_on("mpi", when="+mpi") @@ -123,10 +141,14 @@ class Conduit(Package): # Documentation related ####################### depends_on("py-sphinx", when="+python+doc", type='build') + depends_on("py-sphinx-rtd-theme", when="+python+doc", type='build') depends_on("doxygen", when="+doc+doxygen") - def setup_environment(self, spack_env, run_env): - spack_env.set('CTEST_OUTPUT_ON_FAILURE', '1') + # build phases used by this package + phases = ["configure", "build", "install"] + + def setup_build_environment(self, env): + env.set('CTEST_OUTPUT_ON_FAILURE', '1') def url_for_version(self, version): """ @@ -145,9 +167,9 @@ class Conduit(Package): return "https://github.com/LLNL/conduit/releases/download/v{0}/conduit-v{1}-src-with-blt.tar.gz".format(v, v) return url - def install(self, spec, prefix): + def configure(self, spec, prefix): """ - Build and install Conduit. + Configure Conduit. """ with working_dir('spack-build', create=True): py_site_pkgs_dir = None @@ -157,6 +179,9 @@ class Conduit(Package): host_cfg_fname = self.create_host_config(spec, prefix, py_site_pkgs_dir) + # save this filename for + # other package recipe steps to access + self.host_cfg_fname = host_cfg_fname cmake_args = [] # if we have a static build, we need to avoid any of # spack's default cmake settings related to rpaths @@ -170,17 +195,31 @@ class Conduit(Package): cmake_args.extend(["-C", host_cfg_fname, "../src"]) print("Configuring Conduit...") cmake(*cmake_args) + + def build(self, spec, prefix): + """ + Build Conduit. + """ + with working_dir('spack-build'): print("Building Conduit...") make() - # run unit tests if requested - if "+test" in spec and self.run_tests: - print("Running Conduit Unit Tests...") - make("test") - print("Installing Conduit...") + + @run_after('build') + @on_package_attributes(run_tests=True) + def test(self): + with working_dir('spack-build'): + print("Running Conduit Unit Tests...") + make("test") + + def install(self, spec, prefix): + """ + Install Conduit. + """ + with working_dir('spack-build'): make("install") # install copy of host config for provenance print("Installing Conduit CMake Host Config File...") - install(host_cfg_fname, prefix) + install(self.host_cfg_fname, prefix) @run_after('install') @on_package_attributes(run_tests=True) @@ -203,7 +242,7 @@ class Conduit(Package): example_src_dir] cmake(*cmake_args) make() - example = Executable('./example') + example = Executable('./conduit_example') example() print("Checking using-with-make example...") example_src_dir = join_path(install_prefix, @@ -216,7 +255,7 @@ class Conduit(Package): for example_file in example_files: shutil.copy(example_file, ".") make("CONDUIT_DIR={0}".format(install_prefix)) - example = Executable('./example') + example = Executable('./conduit_example') example() def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): @@ -330,7 +369,7 @@ class Conduit(Package): cfg.write("# Python Support\n") - if "+python" in spec and "+shared" in spec: + if "+python" in spec: cfg.write("# Enable python module builds\n") cfg.write(cmake_cache_entry("ENABLE_PYTHON", "ON")) cfg.write("# python from spack \n") @@ -366,12 +405,21 @@ class Conduit(Package): cfg.write("# MPI Support\n") if "+mpi" in spec: + mpicc_path = spec['mpi'].mpicc + mpicxx_path = spec['mpi'].mpicxx + mpifc_path = spec['mpi'].mpifc + # if we are using compiler wrappers on cray systems + # use those for mpi wrappers, b/c spec['mpi'].mpicxx + # etc make return the spack compiler wrappers + # which can trip up mpi detection in CMake 3.14 + if cpp_compiler == "CC": + mpicc_path = "cc" + mpicxx_path = "CC" + mpifc_path = "ftn" cfg.write(cmake_cache_entry("ENABLE_MPI", "ON")) - cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc)) - cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", - spec['mpi'].mpicxx)) - cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", - spec['mpi'].mpifc)) + cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path)) + cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path)) + cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path)) mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec') if os.path.isfile(mpiexe_bin): # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE @@ -385,6 +433,15 @@ class Conduit(Package): else: cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF")) + ####################### + # ZFP + ####################### + cfg.write("# zfp from spack \n") + if "+zfp" in spec: + cfg.write(cmake_cache_entry("ZFP_DIR", spec['zfp'].prefix)) + else: + cfg.write("# zfp not built by spack \n") + ####################################################################### # I/O Packages ####################################################################### diff --git a/var/spack/repos/builtin/packages/connect-proxy/package.py b/var/spack/repos/builtin/packages/connect-proxy/package.py index fdd303fba7..e4fde75b9e 100644 --- a/var/spack/repos/builtin/packages/connect-proxy/package.py +++ b/var/spack/repos/builtin/packages/connect-proxy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/constype/package.py b/var/spack/repos/builtin/packages/constype/package.py index 2587cb236f..98d2ea6f38 100644 --- a/var/spack/repos/builtin/packages/constype/package.py +++ b/var/spack/repos/builtin/packages/constype/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/converge/package.py b/var/spack/repos/builtin/packages/converge/package.py index 3b990ebd6a..639b799ee7 100644 --- a/var/spack/repos/builtin/packages/converge/package.py +++ b/var/spack/repos/builtin/packages/converge/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -215,7 +215,7 @@ class Converge(Package): if not os.path.exists('make_surface'): os.symlink(make_surface, 'make_surface') - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # CONVERGE searches for a valid license file in: # $CONVERGE_ROOT/license/license.lic - run_env.set('CONVERGE_ROOT', self.prefix) + env.set('CONVERGE_ROOT', self.prefix) diff --git a/var/spack/repos/builtin/packages/coreutils/package.py b/var/spack/repos/builtin/packages/coreutils/package.py index ff5239900c..4aa938a434 100644 --- a/var/spack/repos/builtin/packages/coreutils/package.py +++ b/var/spack/repos/builtin/packages/coreutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,15 +6,17 @@ from spack import * -class Coreutils(AutotoolsPackage): +class Coreutils(AutotoolsPackage, GNUMirrorPackage): """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. """ homepage = "http://www.gnu.org/software/coreutils/" - url = "https://ftpmirror.gnu.org/coreutils/coreutils-8.26.tar.xz" + gnu_mirror_path = "coreutils/coreutils-8.26.tar.xz" + version('8.31', sha256='ff7a9c918edce6b4f4b2725e3f9b37b0c4d193531cac49a48b56c4d0d3a9e9fd') + version('8.30', sha256='e831b3a86091496cdba720411f9748de81507798f6130adeaef872d206e1b057') version('8.29', sha256='92d0fa1c311cacefa89853bdb53c62f4110cdfda3820346b59cbd098f40f955e') version('8.26', sha256='155e94d748f8e2bc327c66e0cbebdb8d6ab265d2f37c3c928f7bf6c3beba9a8e') version('8.23', sha256='ec43ca5bcfc62242accb46b7f121f6b684ee21ecd7d075059bf650ff9e37b82d') diff --git a/var/spack/repos/builtin/packages/corset/package.py b/var/spack/repos/builtin/packages/corset/package.py index afc74f6ca4..c429b1dca4 100644 --- a/var/spack/repos/builtin/packages/corset/package.py +++ b/var/spack/repos/builtin/packages/corset/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cosbench/package.py b/var/spack/repos/builtin/packages/cosbench/package.py new file mode 100644 index 0000000000..2e3fd5997a --- /dev/null +++ b/var/spack/repos/builtin/packages/cosbench/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Cosbench(Package): + """ + COSBench is a benchmarking tool to measure the performance of + Cloud Object Storage services. Object storage is an emerging + technology that is different from traditional file systems + (e.g., NFS) or block device systems (e.g., iSCSI). Amazon S3 + and Openstack* swift are well-known object storage solutions + """ + + homepage = "https://github.com/intel-cloud/cosbench" + url = "https://github.com/intel-cloud/cosbench/releases/download/v0.4.2/0.4.2.zip" + + version('0.4.2', sha256='9e82518d4fac3c23cfac47c8a571d4a61bf8e5f11286606c79a0f923e983dc61') + version('0.4.1.0', sha256='a044cd232b3cc376802aa6a4a697988ec690a8b1d70040641710066acd322c5a') + version('0.4.0.1', sha256='384e4de218a9a61040f45cf9aa0a555e88ff25fb2b5cd11c540627cd604b4961') + + depends_on('java@6:', type='run') + depends_on('curl@7.22.0:', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/cosmomc/package.py b/var/spack/repos/builtin/packages/cosmomc/package.py index a4a4a4a4b9..60374e6fbe 100644 --- a/var/spack/repos/builtin/packages/cosmomc/package.py +++ b/var/spack/repos/builtin/packages/cosmomc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cosp2/package.py b/var/spack/repos/builtin/packages/cosp2/package.py index 7c35668067..36f64a1a38 100644 --- a/var/spack/repos/builtin/packages/cosp2/package.py +++ b/var/spack/repos/builtin/packages/cosp2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cotter/package.py b/var/spack/repos/builtin/packages/cotter/package.py index dfa0395288..3614f68ef5 100644 --- a/var/spack/repos/builtin/packages/cotter/package.py +++ b/var/spack/repos/builtin/packages/cotter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cowsay/package.py b/var/spack/repos/builtin/packages/cowsay/package.py index e09b0eeace..05f818a9f3 100644 --- a/var/spack/repos/builtin/packages/cowsay/package.py +++ b/var/spack/repos/builtin/packages/cowsay/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py index 36b94926da..e551e790a7 100644 --- a/var/spack/repos/builtin/packages/cp2k/package.py +++ b/var/spack/repos/builtin/packages/cp2k/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -50,7 +50,7 @@ class Cp2k(MakefilePackage, CudaPackage): variant('cuda_arch', description='CUDA architecture', default='none', - values=('none', '35', '37', '60'), + values=('none', '35', '37', '60', '70'), multi=False) variant('cuda_arch_35_k20x', default=False, description=('CP2K (resp. DBCSR) has specific parameter sets for' @@ -121,8 +121,6 @@ class Cp2k(MakefilePackage, CudaPackage): # a consistent/compat. combination is pulled in to the dependency graph. depends_on('sirius+fortran+vdwxc+shared+openmp', when='+sirius+openmp') depends_on('sirius+fortran+vdwxc+shared~openmp', when='+sirius~openmp') - # to get JSON-based UPF format support used in combination with SIRIUS - depends_on('json-fortran', when='+sirius') # the bundled libcusmm uses numpy in the parameter prediction (v7+) depends_on('py-numpy', when='@7:+cuda', type='build') @@ -370,10 +368,6 @@ class Cp2k(MakefilePackage, CudaPackage): fcflags += ['-I{0}'.format(os.path.join(sirius.prefix, 'fortran'))] libs += list(sirius.libs) - cppflags.append('-D__JSON') - fcflags += ['$(shell pkg-config --cflags json-fortran)'] - libs += ['$(shell pkg-config --libs json-fortran)'] - if self.spec.satisfies('+cuda'): cppflags += ['-D__ACC'] libs += ['-lcudart', '-lnvrtc', '-lcuda'] @@ -394,6 +388,7 @@ class Cp2k(MakefilePackage, CudaPackage): '35': 'K40', '37': 'K80', '60': 'P100', + '70': 'V100', }[cuda_arch] if (cuda_arch == '35' @@ -442,6 +437,7 @@ class Cp2k(MakefilePackage, CudaPackage): mkf.write('CC = {0.compiler.cc}\n'.format(self)) if '%intel' in self.spec: + intel_bin_dir = ancestor(self.compiler.cc) # CPP is a commented command in Intel arch of CP2K # This is the hack through which cp2k developers avoid doing : # @@ -449,7 +445,7 @@ class Cp2k(MakefilePackage, CudaPackage): # # and use `-fpp` instead mkf.write('CPP = # {0.compiler.cc} -P\n\n'.format(self)) - mkf.write('AR = xiar -r\n\n') + mkf.write('AR = {0}/xiar -r\n\n'.format(intel_bin_dir)) else: mkf.write('CPP = # {0.compiler.cc} -E\n\n'.format(self)) mkf.write('AR = ar -r\n\n') diff --git a/var/spack/repos/builtin/packages/cppad/package.py b/var/spack/repos/builtin/packages/cppad/package.py index de6b4a5c23..28b1e4faee 100644 --- a/var/spack/repos/builtin/packages/cppad/package.py +++ b/var/spack/repos/builtin/packages/cppad/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cppcheck/package.py b/var/spack/repos/builtin/packages/cppcheck/package.py index d7405825c9..fc943e9517 100644 --- a/var/spack/repos/builtin/packages/cppcheck/package.py +++ b/var/spack/repos/builtin/packages/cppcheck/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cppgsl/package.py b/var/spack/repos/builtin/packages/cppgsl/package.py index fe9c222c78..4f4c68841f 100644 --- a/var/spack/repos/builtin/packages/cppgsl/package.py +++ b/var/spack/repos/builtin/packages/cppgsl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cpprestsdk/package.py b/var/spack/repos/builtin/packages/cpprestsdk/package.py index a4f4a73817..51acc882b6 100644 --- a/var/spack/repos/builtin/packages/cpprestsdk/package.py +++ b/var/spack/repos/builtin/packages/cpprestsdk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cppunit/package.py b/var/spack/repos/builtin/packages/cppunit/package.py index b85f06218a..ac6c22340f 100644 --- a/var/spack/repos/builtin/packages/cppunit/package.py +++ b/var/spack/repos/builtin/packages/cppunit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,8 +21,8 @@ class Cppunit(AutotoolsPackage): multi=False, description='Use the specified C++ standard when building.') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): cxxstd = self.spec.variants['cxxstd'].value cxxstdflag = '' if cxxstd == 'default' else \ getattr(self.compiler, 'cxx{0}_flag'.format(cxxstd)) - spack_env.append_flags('CXXFLAGS', cxxstdflag) + env.append_flags('CXXFLAGS', cxxstdflag) diff --git a/var/spack/repos/builtin/packages/cppzmq/package.py b/var/spack/repos/builtin/packages/cppzmq/package.py index 0adaebf9c3..9b5129752a 100644 --- a/var/spack/repos/builtin/packages/cppzmq/package.py +++ b/var/spack/repos/builtin/packages/cppzmq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,5 +18,5 @@ class Cppzmq(CMakePackage): version('4.2.2', sha256='3ef50070ac5877c06c6bb25091028465020e181bbfd08f110294ed6bc419737d') depends_on('cmake@3.0.0:', type='build') - depends_on('zeromq@4.2.5', when='@4.3.0') - depends_on('zeromq@4.2.2', when='@4.2.2') + depends_on('libzmq@4.2.5', when='@4.3.0') + depends_on('libzmq@4.2.2', when='@4.2.2') diff --git a/var/spack/repos/builtin/packages/cpu-features/package.py b/var/spack/repos/builtin/packages/cpu-features/package.py index f94155f027..9ee4d483ee 100644 --- a/var/spack/repos/builtin/packages/cpu-features/package.py +++ b/var/spack/repos/builtin/packages/cpu-features/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cpuinfo/package.py b/var/spack/repos/builtin/packages/cpuinfo/package.py index 1a41d039d5..ba341f822a 100644 --- a/var/spack/repos/builtin/packages/cpuinfo/package.py +++ b/var/spack/repos/builtin/packages/cpuinfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cquery/package.py b/var/spack/repos/builtin/packages/cquery/package.py index 40edd13ce2..76e05d086f 100644 --- a/var/spack/repos/builtin/packages/cquery/package.py +++ b/var/spack/repos/builtin/packages/cquery/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,10 +11,10 @@ class Cquery(CMakePackage): """ homepage = "https://github.com/cquery-project/cquery" - url = "https://github.com/cquery-project/cquery/archive/v20180718.tar.gz" + git = "https://github.com/cquery-project/cquery.git" - version('v20180823', commit='70c755b2e390d3edfb594a84a7531beb26b2bc07', - submodules=True, git='https://github.com/cquery-project/cquery') + version('2018-08-23', commit='70c755b2e390d3edfb594a84a7531beb26b2bc07', + submodules=True) depends_on('llvm') diff --git a/var/spack/repos/builtin/packages/cram/package.py b/var/spack/repos/builtin/packages/cram/package.py index e3ea8d16b9..c294f5af36 100644 --- a/var/spack/repos/builtin/packages/cram/package.py +++ b/var/spack/repos/builtin/packages/cram/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cray-libsci/package.py b/var/spack/repos/builtin/packages/cray-libsci/package.py new file mode 100755 index 0000000000..c0313a1e39 --- /dev/null +++ b/var/spack/repos/builtin/packages/cray-libsci/package.py @@ -0,0 +1,43 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from llnl.util.filesystem import LibraryList +from spack import * +import os + + +class CrayLibsci(Package): + """The Cray Scientific Libraries package, LibSci, is a collection of + numerical routines optimized for best performance on Cray systems.""" + + homepage = "http://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/" + url = "http://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/" + + version("18.11.1.2") + version("16.11.1") + version("16.09.1") + version('16.07.1') + version("16.06.1") + version("16.03.1") + + provides("blas") + provides("lapack") + provides("scalapack") + + # NOTE: Cray compiler wrappers already include linking for the following + @property + def blas_libs(self): + return LibraryList(os.path.join(self.prefix.lib, 'libsci.so')) + + @property + def lapack_libs(self): + return self.blas_libs + + @property + def scalapack_libs(self): + return self.blas_libs + + def install(self, spec, prefix): + raise NoBuildError(spec) diff --git a/var/spack/repos/builtin/packages/cromwell-womtool/package.py b/var/spack/repos/builtin/packages/cromwell-womtool/package.py index 4256e8ffc8..f40ce13c4f 100644 --- a/var/spack/repos/builtin/packages/cromwell-womtool/package.py +++ b/var/spack/repos/builtin/packages/cromwell-womtool/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cromwell/package.py b/var/spack/repos/builtin/packages/cromwell/package.py index cb1562cc20..21e1d9c779 100644 --- a/var/spack/repos/builtin/packages/cromwell/package.py +++ b/var/spack/repos/builtin/packages/cromwell/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index f4b5370136..a96e358d2a 100644 --- a/var/spack/repos/builtin/packages/cryptopp/package.py +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cryptsetup/package.py b/var/spack/repos/builtin/packages/cryptsetup/package.py index 1ff2c98c66..10519100ee 100644 --- a/var/spack/repos/builtin/packages/cryptsetup/package.py +++ b/var/spack/repos/builtin/packages/cryptsetup/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -47,7 +47,10 @@ class Cryptsetup(AutotoolsPackage): ] return args - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Prepend the sbin directory to PATH.""" - spack_env.prepend_path('PATH', self.prefix.sbin) - run_env.prepend_path('PATH', self.prefix.sbin) + env.prepend_path('PATH', self.prefix.sbin) + + def setup_dependent_run_environment(self, env, dependent_spec): + """Prepend the sbin directory to PATH.""" + env.prepend_path('PATH', self.prefix.sbin) diff --git a/var/spack/repos/builtin/packages/cscope/package.py b/var/spack/repos/builtin/packages/cscope/package.py index 061bd80586..f0cc8f9fc5 100644 --- a/var/spack/repos/builtin/packages/cscope/package.py +++ b/var/spack/repos/builtin/packages/cscope/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/csdp/package.py b/var/spack/repos/builtin/packages/csdp/package.py index 81574dc0c0..ef35d6551c 100644 --- a/var/spack/repos/builtin/packages/csdp/package.py +++ b/var/spack/repos/builtin/packages/csdp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ctffind/package.py b/var/spack/repos/builtin/packages/ctffind/package.py index 03ec76b6c0..b20ce75ad7 100644 --- a/var/spack/repos/builtin/packages/ctffind/package.py +++ b/var/spack/repos/builtin/packages/ctffind/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cub/package.py b/var/spack/repos/builtin/packages/cub/package.py index 9076ac78b1..2e3480df8f 100644 --- a/var/spack/repos/builtin/packages/cub/package.py +++ b/var/spack/repos/builtin/packages/cub/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class Cub(Package): and other utilities for CUDA kernel programming.""" homepage = "https://nvlabs.github.com/cub" - url = "https://github.com/NVlabs/cub/archive/1.6.4.zip" + url = "https://github.com/NVlabs/cub/archive/1.7.1.zip" version('1.7.1', sha256='50b8777b83093fdfdab429a61fccdbfbbb991b3bbc08385118e5ad58e8f62e1d') diff --git a/var/spack/repos/builtin/packages/cube/package.py b/var/spack/repos/builtin/packages/cube/package.py index 89297a86bf..d3bdd36617 100644 --- a/var/spack/repos/builtin/packages/cube/package.py +++ b/var/spack/repos/builtin/packages/cube/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cubelib/package.py b/var/spack/repos/builtin/packages/cubelib/package.py index 0d229a54c4..42b756648d 100644 --- a/var/spack/repos/builtin/packages/cubelib/package.py +++ b/var/spack/repos/builtin/packages/cubelib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cubew/package.py b/var/spack/repos/builtin/packages/cubew/package.py index dd03295226..d761f102f3 100644 --- a/var/spack/repos/builtin/packages/cubew/package.py +++ b/var/spack/repos/builtin/packages/cubew/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cuda-memtest/package.py b/var/spack/repos/builtin/packages/cuda-memtest/package.py index 000cb5552a..5cd6940659 100644 --- a/var/spack/repos/builtin/packages/cuda-memtest/package.py +++ b/var/spack/repos/builtin/packages/cuda-memtest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py index f388bf4c73..df71f62608 100644 --- a/var/spack/repos/builtin/packages/cuda/package.py +++ b/var/spack/repos/builtin/packages/cuda/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,6 +7,42 @@ from spack import * from glob import glob from llnl.util.filesystem import LibraryList import os +import platform + +# FIXME Remove hack for polymorphic versions +# This package uses a ugly hack to be able to dispatch, given the same +# version, to different binary packages based on the platform that is +# running spack. See #13827 for context. +# If you need to add a new version, please be aware that: +# - versions in the following dict are automatically added to the package +# - version tuple must be in the form (checksum, url) +# - checksum must be sha256 +# - package key must be in the form '{os}-{arch}' where 'os' is in the +# format returned by platform.system() and 'arch' by platform.machine() + +_versions = { + '10.2.89': { + 'Linux-x86_64': ('560d07fdcf4a46717f2242948cd4f92c5f9b6fc7eae10dd996614da913d5ca11', 'http://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda_10.2.89_440.33.01_linux.run'), + 'Linux-ppc64le': ('5227774fcb8b10bd2d8714f0a716a75d7a2df240a9f2a49beb76710b1c0fc619', 'http://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda_10.2.89_440.33.01_linux_ppc64le.run')}, + '10.1.243': { + 'Linux-x86_64': ('e7c22dc21278eb1b82f34a60ad7640b41ad3943d929bebda3008b72536855d31', 'https://developer.download.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda_10.1.243_418.87.00_linux.run')}, + '10.0.130': { + 'Linux-x86_64': ('92351f0e4346694d0fcb4ea1539856c9eb82060c25654463bfd8574ec35ee39a', 'https://developer.nvidia.com/compute/cuda/10.0/Prod/local_installers/cuda_10.0.130_410.48_linux')}, + '9.2.88': { + 'Linux-x86_64': ('8d02cc2a82f35b456d447df463148ac4cc823891be8820948109ad6186f2667c', 'https://developer.nvidia.com/compute/cuda/9.2/Prod/local_installers/cuda_9.2.88_396.26_linux')}, + '9.1.85': { + 'Linux-x86_64': ('8496c72b16fee61889f9281449b5d633d0b358b46579175c275d85c9205fe953', 'https://developer.nvidia.com/compute/cuda/9.1/Prod/local_installers/cuda_9.1.85_387.26_linux')}, + '9.0.176': { + 'Linux-x86_64': ('96863423feaa50b5c1c5e1b9ec537ef7ba77576a3986652351ae43e66bcd080c', 'https://developer.nvidia.com/compute/cuda/9.0/Prod/local_installers/cuda_9.0.176_384.81_linux-run')}, + '8.0.61': { + 'Linux-x86_64': ('9ceca9c2397f841024e03410bfd6eabfd72b384256fbed1c1e4834b5b0ce9dc4', 'https://developer.nvidia.com/compute/cuda/8.0/Prod2/local_installers/cuda_8.0.61_375.26_linux-run')}, + '8.0.44': { + 'Linux-x86_64': ('64dc4ab867261a0d690735c46d7cc9fc60d989da0d69dc04d1714e409cacbdf0', 'https://developer.nvidia.com/compute/cuda/8.0/prod/local_installers/cuda_8.0.44_linux-run')}, + '7.5.18': { + 'Linux-x86_64': ('08411d536741075131a1858a68615b8b73c51988e616e83b835e4632eea75eec', 'http://developer.download.nvidia.com/compute/cuda/7.5/Prod/local_installers/cuda_7.5.18_linux.run')}, + '6.5.14': { + 'Linux-x86_64': ('f3e527f34f317314fe8fcd8c85f10560729069298c0f73105ba89225db69da48', 'http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run')}, +} class Cuda(Package): @@ -20,26 +56,11 @@ class Cuda(Package): homepage = "https://developer.nvidia.com/cuda-zone" - version('10.1.243', - sha256='e7c22dc21278eb1b82f34a60ad7640b41ad3943d929bebda3008b72536855d31', - expand=False, - url="https://developer.download.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda_10.1.243_418.87.00_linux.run") - version('10.0.130', sha256='92351f0e4346694d0fcb4ea1539856c9eb82060c25654463bfd8574ec35ee39a', expand=False, - url="https://developer.nvidia.com/compute/cuda/10.0/Prod/local_installers/cuda_10.0.130_410.48_linux") - version('9.2.88', sha256='8d02cc2a82f35b456d447df463148ac4cc823891be8820948109ad6186f2667c', expand=False, - url="https://developer.nvidia.com/compute/cuda/9.2/Prod/local_installers/cuda_9.2.88_396.26_linux") - version('9.1.85', sha256='8496c72b16fee61889f9281449b5d633d0b358b46579175c275d85c9205fe953', expand=False, - url="https://developer.nvidia.com/compute/cuda/9.1/Prod/local_installers/cuda_9.1.85_387.26_linux") - version('9.0.176', sha256='96863423feaa50b5c1c5e1b9ec537ef7ba77576a3986652351ae43e66bcd080c', expand=False, - url="https://developer.nvidia.com/compute/cuda/9.0/Prod/local_installers/cuda_9.0.176_384.81_linux-run") - version('8.0.61', sha256='9ceca9c2397f841024e03410bfd6eabfd72b384256fbed1c1e4834b5b0ce9dc4', expand=False, - url="https://developer.nvidia.com/compute/cuda/8.0/Prod2/local_installers/cuda_8.0.61_375.26_linux-run") - version('8.0.44', sha256='64dc4ab867261a0d690735c46d7cc9fc60d989da0d69dc04d1714e409cacbdf0', expand=False, - url="https://developer.nvidia.com/compute/cuda/8.0/prod/local_installers/cuda_8.0.44_linux-run") - version('7.5.18', sha256='08411d536741075131a1858a68615b8b73c51988e616e83b835e4632eea75eec', expand=False, - url="http://developer.download.nvidia.com/compute/cuda/7.5/Prod/local_installers/cuda_7.5.18_linux.run") - version('6.5.14', sha256='f3e527f34f317314fe8fcd8c85f10560729069298c0f73105ba89225db69da48', expand=False, - url="http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run") + for ver, packages in _versions.items(): + key = "{0}-{1}".format(platform.system(), platform.machine()) + pkg = packages.get(key) + if pkg: + version(ver, sha256=pkg[0], url=pkg[1], expand=False) # macOS Mojave drops NVIDIA graphics card support -- official NVIDIA # drivers do not exist for Mojave. See @@ -52,8 +73,8 @@ class Cuda(Package): # Mojave support -- only macOS High Sierra 10.13 is supported. conflicts('arch=darwin-mojave-x86_64') - def setup_environment(self, spack_env, run_env): - run_env.set('CUDA_HOME', self.prefix) + def setup_run_environment(self, env): + env.set('CUDA_HOME', self.prefix) def install(self, spec, prefix): runfile = glob(join_path(self.stage.source_path, 'cuda*_linux*'))[0] diff --git a/var/spack/repos/builtin/packages/cudnn/package.py b/var/spack/repos/builtin/packages/cudnn/package.py index b56aacab4f..4491af18a8 100644 --- a/var/spack/repos/builtin/packages/cudnn/package.py +++ b/var/spack/repos/builtin/packages/cudnn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,35 +13,182 @@ class Cudnn(Package): homepage = "https://developer.nvidia.com/cudnn" - version('7.5.1-10.1-x86_64', sha256='2c833f43c9147d9a25a20947a4c5a5f5c33b2443240fd767f63b330c482e68e0', - url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.1/cudnn-10.1-linux-x64-v7.5.1.10.tgz') - version('7.5.1-10.1-ppc64le', sha256='a9e23bc83c970daec20874ccd1d8d80b648adf15440ecd0164818b330b1e2663', - url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.1/cudnn-10.1-linux-ppc64le-v7.5.1.10.tgz') - version('7.5.1-10.0-x86_64', sha256='c0a4ec438920aa581dd567117b9c316745b4a451ac739b1e04939a3d8b229985', - url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.1/cudnn-10.0-linux-x64-v7.5.1.10.tgz') - version('7.5.1-10.0-ppc64le', sha256='d9205718da5fbab85433476f9ff61fcf4b889d216d6eea26753bbc24d115dd70', - url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.1/cudnn-10.0-linux-ppc64le-v7.5.1.10.tgz') - version('7.5.0-10.1-x86_64', sha256='c31697d6b71afe62838ad2e57da3c3c9419c4e9f5635d14b683ebe63f904fbc8', - url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.0/cudnn-10.1-linux-x64-v7.5.0.56.tgz') - version('7.5.0-10.1-ppc64le', sha256='15415eb714ab86ab6c7531f2cac6474b5dafd989479b062776c670b190e43638', - url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.0/cudnn-10.1-linux-ppc64le-v7.5.0.56.tgz') - version('7.5.0-10.0-x86_64', sha256='701097882cb745d4683bb7ff6c33b8a35c7c81be31bac78f05bad130e7e0b781', - url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.0/cudnn-10.0-linux-x64-v7.5.0.56.tgz') - version('7.5.0-10.0-ppc64le', sha256='f0c1cbd9de553c8e2a3893915bd5fff57b30e368ef4c964d783b6a877869e93a', - url='https://developer.download.nvidia.com/compute/redist/cudnn/v7.5.0/cudnn-10.0-linux-ppc64le-v7.5.0.56.tgz') - version('7.3.0', sha256='403f9043ff2c7b2c5967454872275d07bca11fd41dfc7b21995eadcad6dbe49b', - url='http://developer.download.nvidia.com/compute/redist/cudnn/v7.3.0/cudnn-9.0-linux-x64-v7.3.0.29.tgz') - version('7.2.1', sha256='cf007437b9ac6250ec63b89c25f248d2597fdd01369c80146567f78e75ce4e37', - url='http://developer.download.nvidia.com/compute/redist/cudnn/v7.2.1/cudnn-9.0-linux-x64-v7.2.1.38.tgz') - version('6.0', sha256='9b09110af48c9a4d7b6344eb4b3e344daa84987ed6177d5c44319732f3bb7f9c', - url='http://developer.download.nvidia.com/compute/redist/cudnn/v6.0/cudnn-8.0-linux-x64-v6.0.tgz') - version('5.1', sha256='c10719b36f2dd6e9ddc63e3189affaa1a94d7d027e63b71c3f64d449ab0645ce', - url='http://developer.download.nvidia.com/compute/redist/cudnn/v5.1/cudnn-8.0-linux-x64-v5.1.tgz') - - depends_on('cuda@8:', when='@5.1:@7') - depends_on('cuda@9:', when='@7.2:@7.4') - depends_on('cuda@10:', when='@7.5.0-10.0-ppc64le,7.5.0-10.0-x86_64,7.5.1-10.0-ppc64le,7.5.1-10.0-x86_64') - depends_on('cuda@10.1:', when='@7.5.0-10.1-ppc64le,7.5.0-10.1-x86_64,7.5.1-10.1-ppc64le,7.5.1-10.1-x86_64') + # Latest versions available at: + # https://developer.nvidia.com/rdp/cudnn-download + # Archived versions available at: + # https://developer.nvidia.com/rdp/cudnn-archive + # Note that download links don't work from command line, + # need to use modified URLs like in url_for_version. + + maintainers = ['adamjstewart'] + + # cuDNN 7.6.5 + version('7.6.5.32-10.2-linux-x64', + sha256='600267f2caaed2fd58eb214ba669d8ea35f396a7d19b94822e6b36f9f7088c20', + preferred=True) + version('7.6.5.32-10.1-linux-x64', + sha256='7eaec8039a2c30ab0bc758d303588767693def6bf49b22485a2c00bf2e136cb3') + version('7.6.5.32-10.1-osx-x64', + sha256='8ecce28a5ed388a2b9b2d239e08d7c550f53b79288e6d9e5eb4c152bfc711aff') + version('7.6.5.32-10.1-linux-ppc64le', + sha256='97b2faf73eedfc128f2f5762784d21467a95b2d5ba719825419c058f427cbf56') + + version('7.6.5.32-10.0-linux-x64', + sha256='28355e395f0b2b93ac2c83b61360b35ba6cd0377e44e78be197b6b61b4b492ba') + version('7.6.5.32-10.0-osx-x64', + sha256='6fa0b819374da49102e285ecf7fcb8879df4d0b3cc430cc8b781cdeb41009b47') + version('7.6.5.32-10.0-linux-ppc64le', + sha256='b1717f4570083bbfc6b8b59f280bae4e4197cc1cb50e9d873c05adf670084c5b') + + version('7.6.5.32-9.2-linux-x64', + sha256='a2a2c7a8ba7b16d323b651766ee37dcfdbc2b50d920f73f8fde85005424960e4') + version('7.6.5.32-9.2-linux-ppc64le', + sha256='a11f44f9a827b7e69f527a9d260f1637694ff7c1674a3e46bd9ec054a08f9a76') + + version('7.6.5.32-9.0-linux-x64', + sha256='bd0a4c0090d5b02feec3f195738968690cc2470b9bc6026e6fe8ff245cd261c8') + + # cuDNN 7.6.4 + version('7.6.4.38-10.1-linux-x64', + sha256='32091d115c0373027418620a09ebec3658a6bc467d011de7cdd0eb07d644b099') + version('7.6.4.38-10.1-osx-x64', + sha256='bfced062c3689ced2c1fb49c7d5052e6bc3da6974c1eb707e4dcf8cd209d4236') + version('7.6.4.38-10.1-linux-ppc64le', + sha256='f3615fea50986a4dfd05d7a0cf83396dfdceefa9c209e8bf9691e20a48e420ce') + + version('7.6.4.38-10.0-linux-x64', + sha256='417bb5daf51377037eb2f5c87649000ca1b9cec0acb16cfe07cb1d3e9a961dbf') + version('7.6.4.38-10.0-osx-x64', + sha256='af01ab841caec25087776a6b8fc7782883da12e590e24825ad1031f9ae0ed4b1') + version('7.6.4.38-10.0-linux-ppc64le', + sha256='c1725ad6bd7d7741e080a1e6da4b62eac027a94ac55c606cce261e3f829400bb') + + version('7.6.4.38-9.2-linux-x64', + sha256='c79156531e641289b6a6952888b9637059ef30defd43c3cf82acf38d67f60a27') + version('7.6.4.38-9.2-linux-ppc64le', + sha256='98d8aae2dcd851558397a9a30b73242f257e1556be17c83650e63a0685969884') + + version('7.6.4.38-9.0-linux-x64', + sha256='8db78c3623c192d4f03f3087b41c32cb0baac95e13408b5d9dabe626cb4aab5d') + + # cuDNN 7.6.3 + version('7.6.3.30-10.1-linux-x64', + sha256='352557346d8111e2f954c494be1a90207103d316b8777c33e62b3a7f7b708961') + version('7.6.3.30-10.1-linux-ppc64le', + sha256='f274735a8fc31923d3623b1c3d2b1d0d35bb176687077c6a4d4353c6b900d8ee') + + # cuDNN 7.5.1 + version('7.5.1.10-10.1-linux-x64', + sha256='2c833f43c9147d9a25a20947a4c5a5f5c33b2443240fd767f63b330c482e68e0') + version('7.5.1.10-10.1-linux-ppc64le', + sha256='a9e23bc83c970daec20874ccd1d8d80b648adf15440ecd0164818b330b1e2663') + + version('7.5.1.10-10.0-linux-x64', + sha256='c0a4ec438920aa581dd567117b9c316745b4a451ac739b1e04939a3d8b229985') + version('7.5.1.10-10.0-linux-ppc64le', + sha256='d9205718da5fbab85433476f9ff61fcf4b889d216d6eea26753bbc24d115dd70') + + # cuDNN 7.5.0 + version('7.5.0.56-10.1-linux-x64', + sha256='c31697d6b71afe62838ad2e57da3c3c9419c4e9f5635d14b683ebe63f904fbc8') + version('7.5.0.56-10.1-linux-ppc64le', + sha256='15415eb714ab86ab6c7531f2cac6474b5dafd989479b062776c670b190e43638') + + version('7.5.0.56-10.0-linux-x64', + sha256='701097882cb745d4683bb7ff6c33b8a35c7c81be31bac78f05bad130e7e0b781') + version('7.5.0.56-10.0-linux-ppc64le', + sha256='f0c1cbd9de553c8e2a3893915bd5fff57b30e368ef4c964d783b6a877869e93a') + + # cuDNN 7.3.0 + version('7.3.0.29-9.0-linux-x64', + sha256='403f9043ff2c7b2c5967454872275d07bca11fd41dfc7b21995eadcad6dbe49b') + + # cuDNN 7.2.1 + version('7.2.1.38-9.0-linux-x64', + sha256='cf007437b9ac6250ec63b89c25f248d2597fdd01369c80146567f78e75ce4e37') + + # cuDNN 7.1.3 + version('7.1.3-9.1-linux-x64', + sha256='dd616d3794167ceb923d706bf73e8d6acdda770751492b921ee6827cdf190228') + version('7.1.3-9.1-linux-ppc64le', + sha256='e3b4837f711b98a52faacc872a68b332c833917ef3cf87c0108f1d01af9b2931') + + # cuDNN 6.0 + version('6.0-8.0-linux-x64', + sha256='9b09110af48c9a4d7b6344eb4b3e344daa84987ed6177d5c44319732f3bb7f9c') + + # cuDNN 5.1 + version('5.1-8.0-linux-x64', + sha256='c10719b36f2dd6e9ddc63e3189affaa1a94d7d027e63b71c3f64d449ab0645ce') + + # CUDA 10.2 + depends_on('cuda@10.2.0:10.2.999', when='@7.6.5.32-10.2-linux-x64') + + # CUDA 10.1 + depends_on('cuda@10.1.0:10.1.999', when='@7.6.5.32-10.1-osx-x64') + depends_on('cuda@10.1.0:10.1.999', when='@7.6.5.32-10.1-linux-x64') + depends_on('cuda@10.1.0:10.1.999', when='@7.6.5.32-10.1-linux-ppc64le') + depends_on('cuda@10.1.0:10.1.999', when='@7.6.4.38-10.1-osx-x64') + depends_on('cuda@10.1.0:10.1.999', when='@7.6.4.38-10.1-linux-x64') + depends_on('cuda@10.1.0:10.1.999', when='@7.6.4.38-10.1-linux-ppc64le') + depends_on('cuda@10.1.0:10.1.999', when='@7.6.3.30-10.1-linux-x64') + depends_on('cuda@10.1.0:10.1.999', when='@7.6.3.30-10.1-linux-ppc64le') + depends_on('cuda@10.1.0:10.1.999', when='@7.5.0.56-10.1-linux-x64') + depends_on('cuda@10.1.0:10.1.999', when='@7.5.0.56-10.1-linux-ppc64le') + + # CUDA 10.0 + depends_on('cuda@10.0.0:10.0.999', when='@7.6.5.32-10.0-osx-x64') + depends_on('cuda@10.0.0:10.0.999', when='@7.6.5.32-10.0-linux-x64') + depends_on('cuda@10.0.0:10.0.999', when='@7.6.5.32-10.0-linux-ppc64le') + depends_on('cuda@10.0.0:10.0.999', when='@7.6.4.38-10.0-osx-x64') + depends_on('cuda@10.0.0:10.0.999', when='@7.6.4.38-10.0-linux-x64') + depends_on('cuda@10.0.0:10.0.999', when='@7.6.4.38-10.0-linux-ppc64le') + depends_on('cuda@10.0.0:10.0.999', when='@7.5.1.10-10.0-linux-x64') + depends_on('cuda@10.0.0:10.0.999', when='@7.5.1.10-10.0-linux-ppc64le') + depends_on('cuda@10.0.0:10.0.999', when='@7.5.0.56-10.0-linux-x64') + depends_on('cuda@10.0.0:10.0.999', when='@7.5.0.56-10.0-linux-ppc64le') + + # CUDA 9.2 + depends_on('cuda@9.2.0:9.2.999', when='@7.6.5.32-9.2-linux-x64') + depends_on('cuda@9.2.0:9.2.999', when='@7.6.5.32-9.2-linux-ppc64le') + depends_on('cuda@9.2.0:9.2.999', when='@7.6.4.38-9.2-linux-x64') + depends_on('cuda@9.2.0:9.2.999', when='@7.6.4.38-9.2-linux-ppc64le') + + # CUDA 9.1 + depends_on('cuda@9.1.0:9.1.999', when='@7.1.3-9.1-linux-x64') + depends_on('cuda@9.1.0:9.1.999', when='@7.1.3-9.1-linux-ppc64le') + + # CUDA 9.0 + depends_on('cuda@9.0.0:9.0.999', when='@7.6.5.32-9.0-linux-x64') + depends_on('cuda@9.0.0:9.0.999', when='@7.6.4.38-9.0-linux-x64') + depends_on('cuda@9.0.0:9.0.999', when='@7.3.0.29-9.0-linux-x64') + depends_on('cuda@9.0.0:9.0.999', when='@7.2.1.38-9.0-linux-x64') + + # CUDA 8.0 + depends_on('cuda@8.0.0:8.0.999', when='@6.0-8.0-linux-x64') + depends_on('cuda@8.0.0:8.0.999', when='@5.1-8.0-linux-x64') + + def url_for_version(self, version): + url = 'https://developer.download.nvidia.com/compute/redist/cudnn/v{0}/cudnn-{1}-v{2}.tgz' + + if version >= Version('7.2'): + directory = version[:3] + ver = version[:4] + cuda = version[4:] + elif version >= Version('7.1'): + directory = version[:3] + ver = version[:2] + cuda = version[3:] + elif version >= Version('7.0'): + directory = version[:3] + ver = version[0] + cuda = version[3:] + else: + directory = version[:2] + ver = version[:2] + cuda = version[2:] + + return url.format(directory, cuda, ver) def install(self, spec, prefix): install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/cufflinks/package.py b/var/spack/repos/builtin/packages/cufflinks/package.py index 10576680c9..93e8cb9075 100644 --- a/var/spack/repos/builtin/packages/cufflinks/package.py +++ b/var/spack/repos/builtin/packages/cufflinks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/cups/package.py b/var/spack/repos/builtin/packages/cups/package.py index bfccd89ff4..b2688064da 100644 --- a/var/spack/repos/builtin/packages/cups/package.py +++ b/var/spack/repos/builtin/packages/cups/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py index 4ab1b53a27..e0e964893f 100644 --- a/var/spack/repos/builtin/packages/curl/package.py +++ b/var/spack/repos/builtin/packages/curl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,7 @@ class Curl(AutotoolsPackage): # URL must remain http:// so Spack can bootstrap curl url = "http://curl.haxx.se/download/curl-7.60.0.tar.bz2" + version('7.68.0', sha256='207f54917dd6a2dc733065ccf18d61bb5bebeaceb5df49cd9445483e8623eeb9') version('7.63.0', sha256='9bab7ed4ecff77020a312d84cc5fb7eb02d58419d218f267477a724a17fd8dd8') version('7.60.0', sha256='897dfb2204bd99be328279f88f55b7c61592216b0542fcbe995c60aa92871e9b') version('7.59.0', sha256='b5920ffd6a8c95585fb95070e0ced38322790cb335c39d0dab852d12e157b5a0') diff --git a/var/spack/repos/builtin/packages/cvs/package.py b/var/spack/repos/builtin/packages/cvs/package.py index 0ddf296eb3..9d117a3e49 100644 --- a/var/spack/repos/builtin/packages/cvs/package.py +++ b/var/spack/repos/builtin/packages/cvs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,10 +7,10 @@ from spack import * -class Cvs(AutotoolsPackage): +class Cvs(AutotoolsPackage, GNUMirrorPackage): """CVS a very traditional source control system""" homepage = "http://www.nongnu.org/cvs/" - url = "https://ftpmirror.gnu.org/non-gnu/cvs/source/feature/1.12.13/cvs-1.12.13.tar.bz2" + gnu_mirror_path = "non-gnu/cvs/source/feature/1.12.13/cvs-1.12.13.tar.bz2" version('1.12.13', sha256='78853613b9a6873a30e1cc2417f738c330e75f887afdaf7b3d0800cb19ca515e') diff --git a/var/spack/repos/builtin/packages/cxxopts/package.py b/var/spack/repos/builtin/packages/cxxopts/package.py index cb3ff6e800..e5bd1d68ef 100644 --- a/var/spack/repos/builtin/packages/cxxopts/package.py +++ b/var/spack/repos/builtin/packages/cxxopts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py index b92de9106a..acd128adc1 100644 --- a/var/spack/repos/builtin/packages/czmq/package.py +++ b/var/spack/repos/builtin/packages/czmq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,8 +19,8 @@ class Czmq(AutotoolsPackage): depends_on('automake', type='build') depends_on('autoconf', type='build') depends_on('pkgconfig', type='build') - depends_on("libuuid") - depends_on('zeromq') + depends_on('libuuid') + depends_on('libzmq') def autoreconf(self, spec, prefix): autogen = Executable('./autogen.sh') diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py index fc3a31ebc2..a7f58229c1 100644 --- a/var/spack/repos/builtin/packages/dakota/package.py +++ b/var/spack/repos/builtin/packages/dakota/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/daligner/package.py b/var/spack/repos/builtin/packages/daligner/package.py index 2abfb2c74e..8f05e8b9c0 100644 --- a/var/spack/repos/builtin/packages/daligner/package.py +++ b/var/spack/repos/builtin/packages/daligner/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/damageproto/package.py b/var/spack/repos/builtin/packages/damageproto/package.py index db748f547d..1b1e9f71f4 100644 --- a/var/spack/repos/builtin/packages/damageproto/package.py +++ b/var/spack/repos/builtin/packages/damageproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/damaris/package.py b/var/spack/repos/builtin/packages/damaris/package.py index 6c3ec891bd..13616e1d78 100644 --- a/var/spack/repos/builtin/packages/damaris/package.py +++ b/var/spack/repos/builtin/packages/damaris/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,10 +12,10 @@ class Damaris(CMakePackage): targeting large-scale, MPI-based HPC simulations.""" homepage = "https://project.inria.fr/damaris/" - url = "https://gitlab.inria.fr/Damaris/damaris" + git = "https://gitlab.inria.fr/Damaris/damaris.git" - version('master', git='https://gitlab.inria.fr/Damaris/damaris.git') - version('1.3.1', git='https://gitlab.inria.fr/Damaris/damaris.git', tag='v1.3.1', preferred=True) + version('master', branch='master') + version('1.3.1', tag='v1.3.1') variant('fortran', default=True, description='Enables Fortran support') variant('hdf5', default=False, description='Enables the HDF5 storage plugin') diff --git a/var/spack/repos/builtin/packages/damselfly/package.py b/var/spack/repos/builtin/packages/damselfly/package.py index 66156fbf61..5629b94efa 100644 --- a/var/spack/repos/builtin/packages/damselfly/package.py +++ b/var/spack/repos/builtin/packages/damselfly/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,3 +14,4 @@ class Damselfly(CMakePackage): version('1.0', sha256='560e1b800c9036766396a1033c00914bd8d181b911e87140c3ac8879baf6545a') depends_on('cmake@2.6:', type='build') + depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/darshan-runtime/package.py b/var/spack/repos/builtin/packages/darshan-runtime/package.py index 0b3c770ded..d728bf4037 100644 --- a/var/spack/repos/builtin/packages/darshan-runtime/package.py +++ b/var/spack/repos/builtin/packages/darshan-runtime/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -54,7 +54,7 @@ class DarshanRuntime(Package): make() make('install') - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # default path for log file, could be user or site specific setting - darshan_log_dir = '%s' % os.environ['HOME'] - run_env.set('DARSHAN_LOG_DIR_PATH', darshan_log_dir) + darshan_log_dir = os.environ['HOME'] + env.set('DARSHAN_LOG_DIR_PATH', darshan_log_dir) diff --git a/var/spack/repos/builtin/packages/darshan-util/package.py b/var/spack/repos/builtin/packages/darshan-util/package.py index 33041161dd..4acc4452fd 100644 --- a/var/spack/repos/builtin/packages/darshan-util/package.py +++ b/var/spack/repos/builtin/packages/darshan-util/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dash/package.py b/var/spack/repos/builtin/packages/dash/package.py index 8ce374c6ca..57323d6721 100644 --- a/var/spack/repos/builtin/packages/dash/package.py +++ b/var/spack/repos/builtin/packages/dash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/datamash/package.py b/var/spack/repos/builtin/packages/datamash/package.py index dd79b61af8..65fcddbe0a 100644 --- a/var/spack/repos/builtin/packages/datamash/package.py +++ b/var/spack/repos/builtin/packages/datamash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,13 +6,13 @@ from spack import * -class Datamash(AutotoolsPackage): +class Datamash(AutotoolsPackage, GNUMirrorPackage): """GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files. """ homepage = "https://www.gnu.org/software/datamash/" - url = "https://ftpmirror.gnu.org/datamash/datamash-1.0.5.tar.gz" + gnu_mirror_path = "datamash/datamash-1.0.5.tar.gz" version('1.3', sha256='eebb52171a4353aaad01921384098cf54eb96ebfaf99660e017f6d9fc96657a6') version('1.1.0', sha256='a9e5acc86af4dd64c7ac7f6554718b40271aa67f7ff6e9819bdd919a25904bb0') diff --git a/var/spack/repos/builtin/packages/dataspaces/package.py b/var/spack/repos/builtin/packages/dataspaces/package.py index d227d4ea3c..6e2120d399 100644 --- a/var/spack/repos/builtin/packages/dataspaces/package.py +++ b/var/spack/repos/builtin/packages/dataspaces/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,9 +20,7 @@ class Dataspaces(AutotoolsPackage): homepage = "http://www.dataspaces.org" url = "https://dataspaces.rdi2.rutgers.edu/downloads/dataspaces-1.6.2.tar.gz" - git = "https://github.com/melrom/dataspaces.git" - version('develop', branch='master') version('1.8.0', sha256='7f204bb3c03c2990f5a2d76a29185466b584793c63ada03e5e694627e6060605') version('1.6.2', sha256='3c43d551c1e8198a4ab269c83928e1dc6f8054e6d41ceaee45155d91a48cf9bf') diff --git a/var/spack/repos/builtin/packages/dateutils/package.py b/var/spack/repos/builtin/packages/dateutils/package.py index f921865b87..39e616876b 100644 --- a/var/spack/repos/builtin/packages/dateutils/package.py +++ b/var/spack/repos/builtin/packages/dateutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/davix/package.py b/var/spack/repos/builtin/packages/davix/package.py index 381251a62d..0510b794d9 100644 --- a/var/spack/repos/builtin/packages/davix/package.py +++ b/var/spack/repos/builtin/packages/davix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class Davix(CMakePackage): """High-performance file management over WebDAV/HTTP.""" homepage = "https://dmc.web.cern.ch/projects/davix" - url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.7/davix-0.6.7.tar.gz" + url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.8/davix-0.6.8.tar.gz" list_url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/" list_depth = 1 diff --git a/var/spack/repos/builtin/packages/dbcsr/package.py b/var/spack/repos/builtin/packages/dbcsr/package.py index 0fef73b8fa..c917ba010b 100644 --- a/var/spack/repos/builtin/packages/dbcsr/package.py +++ b/var/spack/repos/builtin/packages/dbcsr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,9 +10,9 @@ class Dbcsr(CMakePackage): """Distributed Block Compressed Sparse Row matrix library.""" homepage = "https://github.com/cp2k/dbcsr" - url = "https://github.com/cp2k/dbcsr/archive/v1.0.0-rc.0.tar.gz" + git = "https://github.com/cp2k/dbcsr.git" - version('develop', git='https://github.com/cp2k/dbcsr.git', branch='develop') + version('develop', branch='develop') variant('mpi', default=True, description='Compile with MPI') variant('openmp', default=False, description='Build with OpenMP support') diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py index 3a578e0708..31495a06b5 100644 --- a/var/spack/repos/builtin/packages/dbus/package.py +++ b/var/spack/repos/builtin/packages/dbus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dcmtk/package.py b/var/spack/repos/builtin/packages/dcmtk/package.py index 3e7b6465fe..de7a4c6ef2 100644 --- a/var/spack/repos/builtin/packages/dcmtk/package.py +++ b/var/spack/repos/builtin/packages/dcmtk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dd4hep/package.py b/var/spack/repos/builtin/packages/dd4hep/package.py index a88cdd1529..46d64b9a82 100644 --- a/var/spack/repos/builtin/packages/dd4hep/package.py +++ b/var/spack/repos/builtin/packages/dd4hep/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,16 +18,18 @@ class Dd4hep(CMakePackage): homepage = "https://dd4hep.web.cern.ch/dd4hep/" git = "https://github.com/AIDASoft/DD4hep.git" - version('develop', branch='master') - version('1.10.0', commit='9835d1813c07d9d5850d1e68276c0171d1726801') + version('master', branch='master') + version('1.11.0', commit='280c7d748d56a704699408ac8e57815d029b169a') + version('1.10.0', commit='9835d1813c07d9d5850d1e68276c0171d1726801') variant('xercesc', default=False, description="Enable 'Detector Builders' based on XercesC") variant('geant4', default=False, description="Enable the simulation part based on Geant4") variant('testing', default=False, description="Enable and build tests") - depends_on('cmake @3.3:', type='build') - depends_on('root @6.08: +gdml +opengl +x') + depends_on('cmake @3.12:', type='build') depends_on('boost @1.49:') + depends_on('root @6.08: +gdml +math +opengl +python +x') + depends_on('python') depends_on('xerces-c', when='+xercesc') depends_on('geant4@10.2.2:', when='+geant4') @@ -38,6 +40,9 @@ class Dd4hep(CMakePackage): "-DCMAKE_CXX_STANDARD={0}".format(cxxstd), "-DDD4HEP_USE_XERCESC={0}".format(spec.satisfies('+xercesc')), "-DDD4HEP_USE_GEANT4={0}".format(spec.satisfies('+geant4')), - "-DBUILD_TESTING={0}".format(spec.satisfies('+testing')) + "-DBUILD_TESTING={0}".format(spec.satisfies('+testing')), + "-DBOOST_ROOT={0}".format(spec['boost'].prefix), + "-DBoost_NO_BOOST_CMAKE=ON", + "-DPYTHON_EXECUTABLE={0}".format(spec['python'].command.path), ] return args diff --git a/var/spack/repos/builtin/packages/dealii-parameter-gui/package.py b/var/spack/repos/builtin/packages/dealii-parameter-gui/package.py index 53329fcfc6..f6e6cdcaaa 100644 --- a/var/spack/repos/builtin/packages/dealii-parameter-gui/package.py +++ b/var/spack/repos/builtin/packages/dealii-parameter-gui/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,5 +17,5 @@ class DealiiParameterGui(CMakePackage): depends_on('qt') - def setup_environment(self, spack_env, run_env): - run_env.set('PARAMETER_GUI_DIR', self.prefix) + def setup_run_environment(self, env): + env.set('PARAMETER_GUI_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 109b67da2d..797931052e 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -66,6 +66,8 @@ class Dealii(CMakePackage, CudaPackage): description='Compile with Slepc (only with Petsc and MPI)') variant('symengine', default=True, description='Compile with SymEngine') + variant('threads', default=True, + description='Compile with multi-threading via TBB') variant('trilinos', default=True, description='Compile with Trilinos (only with MPI)') variant('python', default=False, @@ -95,7 +97,7 @@ class Dealii(CMakePackage, CudaPackage): patch('boost_1.68.0.patch', level=1, when='@1.68.0'), - ], + ], when='~python') depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams+python', patches=[patch('boost_1.65.1_singleton.patch', @@ -104,13 +106,12 @@ class Dealii(CMakePackage, CudaPackage): patch('boost_1.68.0.patch', level=1, when='@1.68.0'), - ], + ], when='+python') # bzip2 is not needed since 9.0 depends_on('bzip2', when='@:8.99') depends_on('lapack') depends_on('suite-sparse') - depends_on('tbb') depends_on('zlib') # optional dependencies @@ -137,7 +138,7 @@ class Dealii(CMakePackage, CudaPackage): depends_on('metis@5:~int64', when='+metis~int64') depends_on('muparser', when='+muparser') depends_on('nanoflann', when='@9.0:+nanoflann') - depends_on('netcdf+mpi', when='+netcdf+mpi') + depends_on('netcdf-c+mpi', when='+netcdf+mpi') depends_on('netcdf-cxx', when='+netcdf+mpi') depends_on('oce', when='+oce') depends_on('p4est', when='+p4est+mpi') @@ -159,6 +160,7 @@ class Dealii(CMakePackage, CudaPackage): # depends_on("symengine@0.4: build_type=Release", when="@9.1:+symengine+trilinos^trilinos~debug") # NOQA: ignore=E501 # depends_on("symengine@0.4: build_type=Debug", when="@9.1:+symengine+trilinos^trilinos+debug") # NOQA: ignore=E501 depends_on('symengine@0.4:', when='@9.1:+symengine') + depends_on('tbb', when='+threads') # do not require +rol to make concretization of xsdk possible depends_on('trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos', when='+trilinos+mpi~int64~cuda') depends_on('trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos~hypre', when='+trilinos+mpi+int64~cuda') @@ -178,6 +180,12 @@ class Dealii(CMakePackage, CudaPackage): sha256='61f217744b70f352965be265d2f06e8c1276685e2944ca0a88b7297dd55755da', when='@9.0.1 ^boost@1.70.0:') + # Fix TBB version check + # https://github.com/dealii/dealii/pull/9208 + patch('https://github.com/dealii/dealii/commit/80b13fe5a2eaefc77fa8c9266566fa8a2de91edf.patch', + sha256='6f876dc8eadafe2c4ec2a6673864fb451c6627ca80511b6e16f3c401946fdf33', + when='@9.0.0:9.1.1') + # check that the combination of variants makes sense # 64-bit BLAS: for p in ['openblas', 'intel-mkl', 'intel-parallel-studio+mkl']: @@ -233,7 +241,6 @@ class Dealii(CMakePackage, CudaPackage): lapack_blas_headers = spec['lapack'].headers + spec['blas'].headers options.extend([ '-DDEAL_II_COMPONENT_EXAMPLES=ON', - '-DDEAL_II_WITH_THREADS:BOOL=ON', '-DBOOST_DIR=%s' % spec['boost'].prefix, # CMake's FindBlas/Lapack may pickup system's blas/lapack instead # of Spack's. Be more specific to avoid this. @@ -247,7 +254,13 @@ class Dealii(CMakePackage, CudaPackage): '-DDEAL_II_ALLOW_BUNDLED=OFF' ]) - if (spec.satisfies('^intel-parallel-studio+tbb')): + if '+threads' in spec: + options.append('-DDEAL_II_WITH_THREADS:BOOL=ON') + else: + options.extend(['-DDEAL_II_WITH_THREADS:BOOL=OFF']) + + if (spec.satisfies('^intel-parallel-studio+tbb') + and '+threads' in spec): # deal.II/cmake will have hard time picking up TBB from Intel. tbb_ver = '.'.join(('%s' % spec['tbb'].version).split('.')[1:]) options.extend([ @@ -393,13 +406,13 @@ class Dealii(CMakePackage, CudaPackage): # since Netcdf is spread among two, need to do it by hand: if '+netcdf' in spec and '+mpi' in spec: - netcdf = spec['netcdf-cxx'].libs + spec['netcdf'].libs + netcdf = spec['netcdf-cxx'].libs + spec['netcdf-c'].libs options.extend([ '-DNETCDF_FOUND=true', '-DNETCDF_LIBRARIES=%s' % netcdf.joined(';'), '-DNETCDF_INCLUDE_DIRS=%s;%s' % ( spec['netcdf-cxx'].prefix.include, - spec['netcdf'].prefix.include), + spec['netcdf-c'].prefix.include), ]) else: options.extend([ @@ -447,5 +460,5 @@ class Dealii(CMakePackage, CudaPackage): return options - def setup_environment(self, spack_env, run_env): - run_env.set('DEAL_II_DIR', self.prefix) + def setup_run_environment(self, env): + env.set('DEAL_II_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/deconseq-standalone/package.py b/var/spack/repos/builtin/packages/deconseq-standalone/package.py index ac451ff95a..82409198eb 100644 --- a/var/spack/repos/builtin/packages/deconseq-standalone/package.py +++ b/var/spack/repos/builtin/packages/deconseq-standalone/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -37,5 +37,5 @@ class DeconseqStandalone(Package): chmod('+x', join_path(prefix.bin, 'deconseq.pl')) chmod('+x', join_path(prefix.bin, 'splitFasta.pl')) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PERL5LIB', prefix) + def setup_run_environment(self, env): + env.prepend_path('PERL5LIB', self.prefix) diff --git a/var/spack/repos/builtin/packages/dejagnu/package.py b/var/spack/repos/builtin/packages/dejagnu/package.py index b7a8606469..6826b947ec 100644 --- a/var/spack/repos/builtin/packages/dejagnu/package.py +++ b/var/spack/repos/builtin/packages/dejagnu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Dejagnu(AutotoolsPackage): +class Dejagnu(AutotoolsPackage, GNUMirrorPackage): """DejaGnu is a framework for testing other programs. Its purpose is to provide a single front end for all tests.""" homepage = "https://www.gnu.org/software/dejagnu/" - url = "https://ftpmirror.gnu.org/dejagnu/dejagnu-1.6.tar.gz" + gnu_mirror_path = "dejagnu/dejagnu-1.6.tar.gz" version('1.6', sha256='00b64a618e2b6b581b16eb9131ee80f721baa2669fa0cdee93c500d1a652d763') version('1.4.4', sha256='d0fbedef20fb0843318d60551023631176b27ceb1e11de7468a971770d0e048d') diff --git a/var/spack/repos/builtin/packages/delly2/package.py b/var/spack/repos/builtin/packages/delly2/package.py index 47146faf3c..0bd2f4f6f4 100644 --- a/var/spack/repos/builtin/packages/delly2/package.py +++ b/var/spack/repos/builtin/packages/delly2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/denovogear/package.py b/var/spack/repos/builtin/packages/denovogear/package.py index 55c1213e38..8f475492c1 100644 --- a/var/spack/repos/builtin/packages/denovogear/package.py +++ b/var/spack/repos/builtin/packages/denovogear/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dftfe/package.py b/var/spack/repos/builtin/packages/dftfe/package.py index 37f0324f53..a463aa7ccb 100644 --- a/var/spack/repos/builtin/packages/dftfe/package.py +++ b/var/spack/repos/builtin/packages/dftfe/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py index b0fe51553e..19f3897013 100644 --- a/var/spack/repos/builtin/packages/dia/package.py +++ b/var/spack/repos/builtin/packages/dia/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dialign-tx/package.py b/var/spack/repos/builtin/packages/dialign-tx/package.py index 7c9df36972..4c1d538531 100644 --- a/var/spack/repos/builtin/packages/dialign-tx/package.py +++ b/var/spack/repos/builtin/packages/dialign-tx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dialign/package.py b/var/spack/repos/builtin/packages/dialign/package.py index 5a8e6b7d7c..406a524fab 100644 --- a/var/spack/repos/builtin/packages/dialign/package.py +++ b/var/spack/repos/builtin/packages/dialign/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,5 +24,5 @@ class Dialign(MakefilePackage): mkdirp(prefix.share) install_tree('dialign2_dir', prefix.share) - def setup_environment(self, spack_env, run_env): - run_env.set('DIALIGN2_DIR', self.prefix.share) + def setup_run_environment(self, env): + env.set('DIALIGN2_DIR', self.prefix.share) diff --git a/var/spack/repos/builtin/packages/diamond/fix_narrowing_error.patch b/var/spack/repos/builtin/packages/diamond/fix_narrowing_error.patch new file mode 100644 index 0000000000..597f245918 --- /dev/null +++ b/var/spack/repos/builtin/packages/diamond/fix_narrowing_error.patch @@ -0,0 +1,18 @@ +--- diamond-0.9.25/src/basic/score_matrix.cpp.org 2019-12-10 15:16:46.549126025 +0900 ++++ diamond-0.9.25/src/basic/score_matrix.cpp 2019-12-10 15:17:08.721466092 +0900 +@@ -36,7 +36,7 @@ + + const double INT2_MAX = std::numeric_limits<double>::max(); + +-const char DNA_scores[5 * 5] = { ++const signed char DNA_scores[5 * 5] = { + 2, -3, -3, -3, -3, + -3,2,-3,-3,-3, + -3,-3,2,-3,-3, +@@ -317,4 +317,4 @@ + constants[3] = lambda; + constants[4] = K; + constants_ = constants; +-} +\ No newline at end of file ++} diff --git a/var/spack/repos/builtin/packages/diamond/package.py b/var/spack/repos/builtin/packages/diamond/package.py index 2d52d22e23..b008750981 100644 --- a/var/spack/repos/builtin/packages/diamond/package.py +++ b/var/spack/repos/builtin/packages/diamond/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,3 +24,7 @@ class Diamond(CMakePackage): version('0.8.26', sha256='00d2be32dad76511a767ab8e917962c0ecc572bc808080be60dec028df45439f') depends_on('zlib') + + # fix error [-Wc++11-narrowing] + # Ref: https://github.com/bbuchfink/diamond/commit/155e076d662b0e9268e2b00bef6d33d90aede7ff + patch('fix_narrowing_error.patch') diff --git a/var/spack/repos/builtin/packages/diffsplice/package.py b/var/spack/repos/builtin/packages/diffsplice/package.py index cca9e0cc9c..dc3c9f2023 100644 --- a/var/spack/repos/builtin/packages/diffsplice/package.py +++ b/var/spack/repos/builtin/packages/diffsplice/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/diffutils/package.py b/var/spack/repos/builtin/packages/diffutils/package.py index 961fcf1390..c8f2dca83f 100644 --- a/var/spack/repos/builtin/packages/diffutils/package.py +++ b/var/spack/repos/builtin/packages/diffutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Diffutils(AutotoolsPackage): +class Diffutils(AutotoolsPackage, GNUMirrorPackage): """GNU Diffutils is a package of several programs related to finding differences between files.""" homepage = "https://www.gnu.org/software/diffutils/" - url = "https://ftpmirror.gnu.org/diffutils/diffutils-3.7.tar.xz" + gnu_mirror_path = "diffutils/diffutils-3.7.tar.xz" version('3.7', sha256='b3a7a6221c3dc916085f0d205abf6b8e1ba443d4dd965118da364a1dc1cb3a26') version('3.6', sha256='d621e8bdd4b573918c8145f7ae61817d1be9deb4c8d2328a65cea8e11d783bd6') @@ -19,3 +19,8 @@ class Diffutils(AutotoolsPackage): build_directory = 'spack-build' depends_on('libiconv') + + def setup_build_environment(self, env): + if self.spec.satisfies('%fj'): + env.append_flags('CFLAGS', + '-Qunused-arguments') diff --git a/var/spack/repos/builtin/packages/dimemas/package.py b/var/spack/repos/builtin/packages/dimemas/package.py index 6973151cf7..6b5ba9690d 100644 --- a/var/spack/repos/builtin/packages/dimemas/package.py +++ b/var/spack/repos/builtin/packages/dimemas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/direnv/package.py b/var/spack/repos/builtin/packages/direnv/package.py index d00c811dbb..a021905849 100644 --- a/var/spack/repos/builtin/packages/direnv/package.py +++ b/var/spack/repos/builtin/packages/direnv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/discovar/package.py b/var/spack/repos/builtin/packages/discovar/package.py index 16484efe1b..7b9acfc0e4 100644 --- a/var/spack/repos/builtin/packages/discovar/package.py +++ b/var/spack/repos/builtin/packages/discovar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/discovardenovo/package.py b/var/spack/repos/builtin/packages/discovardenovo/package.py index d62b523bcb..bf14043f83 100644 --- a/var/spack/repos/builtin/packages/discovardenovo/package.py +++ b/var/spack/repos/builtin/packages/discovardenovo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dislin/package.py b/var/spack/repos/builtin/packages/dislin/package.py index cfdffeb9ba..518db4eba9 100644 --- a/var/spack/repos/builtin/packages/dislin/package.py +++ b/var/spack/repos/builtin/packages/dislin/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,7 +14,7 @@ class Dislin(Package): homepage = "http://www.mps.mpg.de/dislin" url = "ftp://ftp.gwdg.de/pub/grafik/dislin/linux/i586_64/dislin-11.0.linux.i586_64.tar.gz" - version('11.2.linux.i586_64', sha256='13d28188924e0b0b803d72aa4b48be4067e98e890701b0aa6f54a11c7d34dd10') + version('11.0', sha256='13d28188924e0b0b803d72aa4b48be4067e98e890701b0aa6f54a11c7d34dd10') depends_on('motif') depends_on('gl') @@ -39,16 +39,18 @@ class Dislin(Package): libraries, root=self.prefix, shared=True, recursive=True ) - def setup_environment(self, spack_env, run_env): - spack_env.set('DISLIN', self.prefix) - run_env.set('DISLIN', self.prefix) - run_env.prepend_path('PATH', self.prefix) - run_env.prepend_path('LD_LIBRARY_PATH', self.prefix) - run_env.prepend_path('LD_LIBRARY_PATH', self.spec['motif'].prefix.lib) - run_env.prepend_path('LD_LIBRARY_PATH', self.spec['mesa'].prefix.lib) + def setup_build_environment(self, env): + env.set('DISLIN', self.prefix) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - run_env.prepend_path('LD_LIBRARY_PATH', self.prefix) + def setup_run_environment(self, env): + env.set('DISLIN', self.prefix) + env.prepend_path('PATH', self.prefix) + env.prepend_path('LD_LIBRARY_PATH', self.prefix) + env.prepend_path('LD_LIBRARY_PATH', self.spec['motif'].prefix.lib) + env.prepend_path('LD_LIBRARY_PATH', self.spec['mesa'].prefix.lib) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path('LD_LIBRARY_PATH', self.prefix) def install(self, spec, prefix): install = Executable('./INSTALL') diff --git a/var/spack/repos/builtin/packages/diy/package.py b/var/spack/repos/builtin/packages/diy/package.py index 4eb511fbf5..efd581f1ba 100644 --- a/var/spack/repos/builtin/packages/diy/package.py +++ b/var/spack/repos/builtin/packages/diy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,6 +16,10 @@ class Diy(CMakePackage): version('3.5.0', sha256='b3b5490441d521b6e9b33471c782948194bf95c7c3df3eb97bc5cf4530b91576') version('master', branch='master') + depends_on('mpi') + def cmake_args(self): - args = ['-Dbuild_examples=off', '-Dbuild_tests=off'] + args = ['-Dbuild_examples=off', + '-Dbuild_tests=off', + '-DCMAKE_CXX_COMPILER=%s' % self.spec['mpi'].mpicxx] return args diff --git a/var/spack/repos/builtin/packages/dlpack/package.py b/var/spack/repos/builtin/packages/dlpack/package.py index d057f6ead8..4e4b74e102 100644 --- a/var/spack/repos/builtin/packages/dlpack/package.py +++ b/var/spack/repos/builtin/packages/dlpack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dmd/package.py b/var/spack/repos/builtin/packages/dmd/package.py index 5755524476..b18ab86cf1 100644 --- a/var/spack/repos/builtin/packages/dmd/package.py +++ b/var/spack/repos/builtin/packages/dmd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -32,10 +32,13 @@ class Dmd(MakefilePackage): sha256='71fa249dbfd278eec2b95ce577af32e623e44caf0d993905ddc189e3beec21d0', placement='tools') - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix.linux.bin64) - run_env.prepend_path('LIBRARY_PATH', self.prefix.linux.lib64) - run_env.prepend_path('LD_LIBRARY_PATH', self.prefix.linux.lib64) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix.linux.bin64) + env.prepend_path('LIBRARY_PATH', self.prefix.linux.lib64) + env.prepend_path('LD_LIBRARY_PATH', self.prefix.linux.lib64) + + def setup_dependent_build_environment(self, env, dependent_spec): + self.setup_run_environment(env) def edit(self, spec, prefix): # Move contents to dmd/ diff --git a/var/spack/repos/builtin/packages/dmlc-core/package.py b/var/spack/repos/builtin/packages/dmlc-core/package.py index 706d3b6e2e..ed65eab682 100644 --- a/var/spack/repos/builtin/packages/dmlc-core/package.py +++ b/var/spack/repos/builtin/packages/dmlc-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dmtcp/package.py b/var/spack/repos/builtin/packages/dmtcp/package.py index 42a92c4683..0e8ee12d21 100644 --- a/var/spack/repos/builtin/packages/dmtcp/package.py +++ b/var/spack/repos/builtin/packages/dmtcp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,7 @@ class Dmtcp(AutotoolsPackage): with no modifications to user code or to the O/S.""" homepage = "http://dmtcp.sourceforge.net/" - url = "https://sourceforge.net/projects/dmtcp/files/2.5.2/dmtcp-2.5.2.tar.gz/download" + url = "https://sourceforge.net/projects/dmtcp/files/2.6.0/dmtcp-2.6.0.tar.gz/download" + version('2.6.0', sha256='3ed62a86dd0cb9c828b93ee8c7c852d6f9c96a0efa48bcfe867521adf7bced68') version('2.5.2', sha256='0e3e5e15bd401b7b6937f2b678cd7d6a252eab0a143d5740b89cc3bebb4282be') diff --git a/var/spack/repos/builtin/packages/dmxproto/package.py b/var/spack/repos/builtin/packages/dmxproto/package.py index 0106b5eb8f..4c18d6de98 100644 --- a/var/spack/repos/builtin/packages/dmxproto/package.py +++ b/var/spack/repos/builtin/packages/dmxproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/docbook-xml/package.py b/var/spack/repos/builtin/packages/docbook-xml/package.py index 0a24a5d2b6..257d2566f8 100644 --- a/var/spack/repos/builtin/packages/docbook-xml/package.py +++ b/var/spack/repos/builtin/packages/docbook-xml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/docbook-xsl/package.py b/var/spack/repos/builtin/packages/docbook-xsl/package.py index 99bfb06d66..9533f3950c 100644 --- a/var/spack/repos/builtin/packages/docbook-xsl/package.py +++ b/var/spack/repos/builtin/packages/docbook-xsl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,10 +26,10 @@ class DocbookXsl(Package): def catalog(self): return os.path.join(self.prefix, 'catalog.xml') - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): catalog = self.catalog - run_env.set('XML_CATALOG_FILES', catalog, separator=' ') + env.set('XML_CATALOG_FILES', catalog, separator=' ') - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): catalog = self.catalog - spack_env.prepend_path("XML_CATALOG_FILES", catalog) + env.prepend_path("XML_CATALOG_FILES", catalog) diff --git a/var/spack/repos/builtin/packages/dos2unix/package.py b/var/spack/repos/builtin/packages/dos2unix/package.py index d9c5daed75..926bc5f65f 100644 --- a/var/spack/repos/builtin/packages/dos2unix/package.py +++ b/var/spack/repos/builtin/packages/dos2unix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py index 5d9a3ef014..16b5a22643 100644 --- a/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py +++ b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,19 +12,17 @@ class DotnetCoreSdk(Package): applications for all types of infrastructure.""" homepage = "https://www.microsoft.com/net/" - url = "https://github.com/dotnet/core/" version('2.1.300', - url='https://download.microsoft.com/download/8/8/5/88544F33-836A' - '-49A5-8B67-451C24709A8F/dotnet-sdk-2.1.300-linux-x64.tar.gz', + url='https://download.microsoft.com/download/8/8/5/88544F33-836A-49A5-8B67-451C24709A8F/dotnet-sdk-2.1.300-linux-x64.tar.gz', sha256='fabca4c8825182ff18e5a2f82dfe75aecd10260ee9e7c85a8c4b3d108e5d8e1b') variant('telemetry', default=False, description='allow collection of telemetry data') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if '-telemetry' in self.spec: - spack_env.set('DOTNET_CLI_TELEMETRY_OPTOUT', 1) + env.set('DOTNET_CLI_TELEMETRY_OPTOUT', 1) def install(self, spec, prefix): mkdirp('bin') diff --git a/var/spack/repos/builtin/packages/double-conversion/package.py b/var/spack/repos/builtin/packages/double-conversion/package.py index 8b0ba30815..70ef475aaa 100644 --- a/var/spack/repos/builtin/packages/double-conversion/package.py +++ b/var/spack/repos/builtin/packages/double-conversion/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py index 53ff0efcd7..aa99ca73ee 100644 --- a/var/spack/repos/builtin/packages/doxygen/package.py +++ b/var/spack/repos/builtin/packages/doxygen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,6 +28,8 @@ class Doxygen(CMakePackage): description='Build with dot command support from Graphviz.') depends_on("cmake@2.8.12:", type='build') + depends_on("python", type='build') # 2 or 3 OK; used in CMake build + depends_on("libiconv") depends_on("flex", type='build') # code.l just checks subminor version <=2.5.4 or >=2.5.33 # but does not recognize 2.6.x as newer...could be patched if needed @@ -41,3 +43,13 @@ class Doxygen(CMakePackage): # https://github.com/Sleepyowl/doxygen/commit/6c380ba91ae41c6d5c409a5163119318932ae2a3?diff=unified # Also - https://github.com/doxygen/doxygen/pull/6588 patch('shared_ptr.patch', when='@1.8.14') + + def patch(self): + # On Linux systems, iconv is provided by libc. Since CMake finds the + # symbol in libc, it does not look for libiconv, which leads to linker + # errors. This makes sure that CMake always looks for the external + # libconv instead. + filter_file('check_function_exists(iconv_open ICONV_IN_GLIBC)', + 'set(ICONV_IN_GLIBC FALSE)', + join_path('cmake', 'FindIconv.cmake'), + string=True) diff --git a/var/spack/repos/builtin/packages/draco/d710-python2.patch b/var/spack/repos/builtin/packages/draco/d710-python2.patch new file mode 100644 index 0000000000..7f50f5d782 --- /dev/null +++ b/var/spack/repos/builtin/packages/draco/d710-python2.patch @@ -0,0 +1,62 @@ +diff --git a/config/ApplicationUnitTest.cmake b/config/ApplicationUnitTest.cmake +index a0a79858..0c47b72a 100644 +--- a/config/ApplicationUnitTest.cmake ++++ b/config/ApplicationUnitTest.cmake +@@ -249,7 +249,7 @@ macro( aut_register_test ) + endif(VERBOSE_DEBUG) + + # Look for python, which is used to drive application unit tests +- if( NOT PYTHONINTERP_FOUND ) ++ if( NOT Python_Interpreter_FOUND ) + # python should have been found when vendor_libraries.cmake was run. + message( FATAL_ERROR "Draco requires python. Python not found in PATH.") + endif() +@@ -289,7 +289,7 @@ macro( aut_register_test ) + if (${PYTHON_TEST}) + add_test( + NAME ${ctestname_base}${argname} +- COMMAND "${PYTHON_EXECUTABLE}" ++ COMMAND "${Python_EXECUTABLE}" + ${aut_DRIVER} + ${SHARED_ARGUMENTS} + ) +diff --git a/config/draco-config-install.cmake.in b/config/draco-config-install.cmake.in +index c5bf1c75..a16f72f4 100644 +--- a/config/draco-config-install.cmake.in ++++ b/config/draco-config-install.cmake.in +@@ -107,8 +107,9 @@ set( WITH_CUDA "@WITH_CUDA@" ) + #endif() + + # Python +-set( PYTHONINTERP_FOUND "@PYTHONINTERP_FOUND@" ) +-set( PYTHON_EXECUTABLE "@PYTHON_EXECUTABLE@" ) ++set( Python_FOUND "@Python_FOUND@" ) ++set( Python_Interpreter_FOUND "@Python_Interpreter_FOUND@" ) ++set( Python_EXECUTABLE "@Python_EXECUTABLE@" ) + + ## --------------------------------------------------------------------------- + ## Set useful general variables +diff --git a/config/vendor_libraries.cmake b/config/vendor_libraries.cmake +index c3e079bc..6b393eb4 100644 +--- a/config/vendor_libraries.cmake ++++ b/config/vendor_libraries.cmake +@@ -16,7 +16,7 @@ include( setupMPI ) # defines the macros setupMPILibrariesUnix|Windows + macro( setupPython ) + + message( STATUS "Looking for Python...." ) +- find_package(PythonInterp 2.7 QUIET REQUIRED) ++ find_package(Python 2.7 QUIET REQUIRED COMPONENTS Interpreter) + # PYTHONINTERP_FOUND - Was the Python executable found + # PYTHON_EXECUTABLE - path to the Python interpreter + set_package_properties( PythonInterp PROPERTIES +@@ -25,8 +25,8 @@ macro( setupPython ) + TYPE REQUIRED + PURPOSE "Required for running tests and accessing features that rely on matplotlib." + ) +- if( PYTHONINTERP_FOUND ) +- message( STATUS "Looking for Python....found ${PYTHON_EXECUTABLE}" ) ++ if( Python_Interpreter_FOUND ) ++ message( STATUS "Looking for Python....found ${Python_EXECUTABLE}" ) + else() + message( STATUS "Looking for Python....not found" ) + endif() diff --git a/var/spack/repos/builtin/packages/draco/d710.patch b/var/spack/repos/builtin/packages/draco/d710.patch new file mode 100644 index 0000000000..1f4e8d5656 --- /dev/null +++ b/var/spack/repos/builtin/packages/draco/d710.patch @@ -0,0 +1,62 @@ +diff --git a/config/ApplicationUnitTest.cmake b/config/ApplicationUnitTest.cmake +index a0a79858..0c47b72a 100644 +--- a/config/ApplicationUnitTest.cmake ++++ b/config/ApplicationUnitTest.cmake +@@ -249,7 +249,7 @@ macro( aut_register_test ) + endif(VERBOSE_DEBUG) + + # Look for python, which is used to drive application unit tests +- if( NOT PYTHONINTERP_FOUND ) ++ if( NOT Python_Interpreter_FOUND ) + # python should have been found when vendor_libraries.cmake was run. + message( FATAL_ERROR "Draco requires python. Python not found in PATH.") + endif() +@@ -289,7 +289,7 @@ macro( aut_register_test ) + if (${PYTHON_TEST}) + add_test( + NAME ${ctestname_base}${argname} +- COMMAND "${PYTHON_EXECUTABLE}" ++ COMMAND "${Python_EXECUTABLE}" + ${aut_DRIVER} + ${SHARED_ARGUMENTS} + ) +diff --git a/config/draco-config-install.cmake.in b/config/draco-config-install.cmake.in +index c5bf1c75..a16f72f4 100644 +--- a/config/draco-config-install.cmake.in ++++ b/config/draco-config-install.cmake.in +@@ -107,8 +107,9 @@ set( WITH_CUDA "@WITH_CUDA@" ) + #endif() + + # Python +-set( PYTHONINTERP_FOUND "@PYTHONINTERP_FOUND@" ) +-set( PYTHON_EXECUTABLE "@PYTHON_EXECUTABLE@" ) ++set( Python_FOUND "@Python_FOUND@" ) ++set( Python_Interpreter_FOUND "@Python_Interpreter_FOUND@" ) ++set( Python_EXECUTABLE "@Python_EXECUTABLE@" ) + + ## --------------------------------------------------------------------------- + ## Set useful general variables +diff --git a/config/vendor_libraries.cmake b/config/vendor_libraries.cmake +index c3e079bc..6b393eb4 100644 +--- a/config/vendor_libraries.cmake ++++ b/config/vendor_libraries.cmake +@@ -16,7 +16,7 @@ include( setupMPI ) # defines the macros setupMPILibrariesUnix|Windows + macro( setupPython ) + + message( STATUS "Looking for Python...." ) +- find_package(PythonInterp 2.7 QUIET REQUIRED) ++ find_package(Python 3.5 QUIET REQUIRED COMPONENTS Interpreter) + # PYTHONINTERP_FOUND - Was the Python executable found + # PYTHON_EXECUTABLE - path to the Python interpreter + set_package_properties( PythonInterp PROPERTIES +@@ -25,8 +25,8 @@ macro( setupPython ) + TYPE REQUIRED + PURPOSE "Required for running tests and accessing features that rely on matplotlib." + ) +- if( PYTHONINTERP_FOUND ) +- message( STATUS "Looking for Python....found ${PYTHON_EXECUTABLE}" ) ++ if( Python_Interpreter_FOUND ) ++ message( STATUS "Looking for Python....found ${Python_EXECUTABLE}" ) + else() + message( STATUS "Looking for Python....not found" ) + endif() diff --git a/var/spack/repos/builtin/packages/draco/d730.patch b/var/spack/repos/builtin/packages/draco/d730.patch new file mode 100644 index 0000000000..926b205e64 --- /dev/null +++ b/var/spack/repos/builtin/packages/draco/d730.patch @@ -0,0 +1,34 @@ +diff --git a/config/platform_checks.cmake b/config/platform_checks.cmake +index c9841b0d..84bf07f5 100644 +--- a/config/platform_checks.cmake ++++ b/config/platform_checks.cmake +@@ -85,6 +85,7 @@ macro( query_craype ) + set( CRAY_PE ON CACHE BOOL + "Are we building in a Cray Programming Environment?") + ++ if (FALSE) + # We expect developers to use the Cray compiler wrappers (especially in + # setupMPI.cmake). See also + # https://cmake.org/cmake/help/latest/module/FindMPI.html +@@ -111,6 +112,7 @@ macro( query_craype ) + "Otherwise please email this error message and other related information to" + " draco@lanl.gov.\n" ) + endif() ++ endif() + message( STATUS + "Looking to see if we are building in a Cray Environment..." + "found version $ENV{CRAYPE_VERSION}.") + +diff --git a/config/setupMPI.cmake b/config/setupMPI.cmake +index da522499..5b5e27c5 100644 +--- a/config/setupMPI.cmake ++++ b/config/setupMPI.cmake +@@ -51,7 +51,7 @@ function( setMPIflavorVer ) + if( DEFINED ENV{CRAY_MPICH2_VER} ) + set( MPI_VERSION $ENV{CRAY_MPICH2_VER} ) + endif() +- elseif( ${MPI_FLAVOR} STREQUAL "spectrum" ) ++ elseif( "${MPI_FLAVOR}" STREQUAL "spectrum" ) + if( DEFINED ENV{LMOD_MPI_VERSION} ) + set( LMOD_MPI_VERSION $ENV{LMOD_MPI_VERSION} ) + endif() diff --git a/var/spack/repos/builtin/packages/draco/d740.patch b/var/spack/repos/builtin/packages/draco/d740.patch new file mode 100644 index 0000000000..684158474a --- /dev/null +++ b/var/spack/repos/builtin/packages/draco/d740.patch @@ -0,0 +1,21 @@ +diff --git a/config/platform_checks.cmake b/config/platform_checks.cmake +index c9841b0d..aeecc767 100644 +--- a/config/platform_checks.cmake ++++ b/config/platform_checks.cmake +@@ -88,6 +88,8 @@ macro( query_craype ) + # We expect developers to use the Cray compiler wrappers (especially in + # setupMPI.cmake). See also + # https://cmake.org/cmake/help/latest/module/FindMPI.html ++ if( NOT "$ENV{CXX}" MATCHES "/lib/spack/env/" ) ++ # skip this check if building from within spack. + if( NOT "$ENV{CXX}" MATCHES "CC$" OR + NOT "$ENV{CC}" MATCHES "cc$" OR + NOT "$ENV{FC}" MATCHES "ftn$" OR +@@ -110,6 +112,7 @@ macro( query_craype ) + " export CRAYPE_LINK_TYPE=dynamic\n" + "Otherwise please email this error message and other related information to" + " draco@lanl.gov.\n" ) ++ endif() + endif() + message( STATUS + "Looking to see if we are building in a Cray Environment..." diff --git a/var/spack/repos/builtin/packages/draco/package.py b/var/spack/repos/builtin/packages/draco/package.py index 0834ada36e..de1e3696b5 100644 --- a/var/spack/repos/builtin/packages/draco/package.py +++ b/var/spack/repos/builtin/packages/draco/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,42 +15,52 @@ class Draco(CMakePackage): homepage = "https://github.com/lanl/draco" url = "https://github.com/lanl/Draco/archive/draco-7_1_0.zip" git = "https://github.com/lanl/Draco.git" + maintainers = ['KineticTheory'] version('develop', branch='develop') + version('7.4.0', sha256='61da2c3feace0e92c5410c9e9e613708fdf8954b1367cdc62c415329b0ddab6e') + version('7.3.0', sha256='dc47ef6c1e04769ea177a10fc6ddf506f3e1e8d36eb5d49f4bc38cc509e24f10') version('7.2.0', sha256='ac4eac03703d4b7344fa2390a54140533c5e1f6ea0d59ef1f1d525c434ebe639') - version('7_1_0', sha256='eca6bb86eb930837fb5e09b76c85c200b2c1522267cc66f81f2ec11a8262b5c9') - version('6_25_0', sha256='e27eba44f397e7d111ff9a45b518b186940f75facfc6f318d76bd0e72f987440') - version('6_23_0', sha256='edf20308746c06647087cb4e6ae7656fd057a89091a22bcba8f17a52e28b7849') - version('6_22_0', sha256='4d1ed54944450c4ec7d00d7ba371469506c6985922f48f780bae2580c9335b86') - version('6_21_0', sha256='f1ac88041606cdb1dfddd3bc74db0f1e15d8fc9d0a1eed939c8aa0fa63a85b55') - version('6_20_1', sha256='b1c51000c9557e0818014713fce70d681869c50ed9c4548dcfb2e9219c354ebe') - version('6_20_0', sha256='a6e3142c1c90b09c4ff8057bfee974369b815122b01d1f7b57888dcb9b1128f6') + version('7.1.0', sha256='eca6bb86eb930837fb5e09b76c85c200b2c1522267cc66f81f2ec11a8262b5c9') + version('6.25.0', sha256='e27eba44f397e7d111ff9a45b518b186940f75facfc6f318d76bd0e72f987440') + version('6.23.0', sha256='edf20308746c06647087cb4e6ae7656fd057a89091a22bcba8f17a52e28b7849') + version('6.22.0', sha256='4d1ed54944450c4ec7d00d7ba371469506c6985922f48f780bae2580c9335b86') + version('6.21.0', sha256='f1ac88041606cdb1dfddd3bc74db0f1e15d8fc9d0a1eed939c8aa0fa63a85b55') + version('6.20.1', sha256='b1c51000c9557e0818014713fce70d681869c50ed9c4548dcfb2e9219c354ebe') + version('6.20.0', sha256='a6e3142c1c90b09c4ff8057bfee974369b815122b01d1f7b57888dcb9b1128f6') variant('build_type', default='Release', description='CMake build type', values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel')) - variant('eospac', default=False, description='Enable EOSPAC Support') - variant('lapack', default=False, description='Enable LAPACK Wrapper') - variant('parmetis', default=False, description='Enable Parmetis Support') - variant('qt', default=False, description='Enable Qt Support') - variant('superlu_dist', default=False, description='Enable SuperLU-DIST Support') + variant('eospac', default=True, description='Enable EOSPAC support') + variant('lapack', default=True, description='Enable LAPACK wrapper') + variant('libquo', default=True, description='Enable Quo wrapper') + variant('parmetis', default=True, description='Enable Parmetis support') + variant('qt', default=False, description='Enable Qt support') + variant('superlu_dist', default=True, description='Enable SuperLU-DIST support') - depends_on('gsl', type=('build', 'link')) - depends_on('mpi@3:', type=('build', 'link', 'run')) - depends_on('numdiff', type='build') + depends_on('gsl') + depends_on('mpi@3:', type=('build', 'link', 'run')) + depends_on('numdiff', type='build') depends_on('python@2.7:', type=('build', 'run')) - depends_on('random123', type='build') + depends_on('random123', type='build') - depends_on('cmake@3.9:', when='@:6.99', type='build') - depends_on('cmake@3.11:', when='@7.0.0:7.1.9', type='build') - depends_on('cmake@3.14:', when='@7.2:', type='build') - depends_on('eospac@6.3:', when='+eospac', type=('build', 'link')) - depends_on('lapack', when='+lapack', type=('build', 'link')) - depends_on('metis', when='+parmetis', type=('build', 'link')) - depends_on('parmetis', when='+parmetis', type=('build', 'link')) + depends_on('cmake@3.9:', when='@:6.99', type='build') + depends_on('cmake@3.11:', when='@7.0.0:7.1.99', type='build') + depends_on('cmake@3.14:', when='@7.2:', type='build') + depends_on('eospac@6.3:', when='+eospac') + depends_on('lapack', when='+lapack') + depends_on('libquo', when='@7.4.0:+libquo') + depends_on('metis', when='+parmetis') + depends_on('parmetis', when='+parmetis') depends_on('qt', when='+qt', type=('build', 'link', 'run')) - depends_on('superlu-dist@:5.99', when='+superlu-dist', - type=('build', 'link')) + depends_on('superlu-dist@:5.99', when='+superlu_dist') + + # Fix python discovery. + patch('d710.patch', when='@7.1.0^python@3:') + patch('d710-python2.patch', when='@7.1.0^python@2.7:2.99') + patch('d730.patch', when='@7.3.0:7.3.99') + patch('d740.patch', when='@7.4.0:7.4.99') def url_for_version(self, version): url = "https://github.com/lanl/Draco/archive/draco-{0}.zip" @@ -63,11 +73,3 @@ class Draco(CMakePackage): '-DBUILD_TESTING={0}'.format('ON' if self.run_tests else 'OFF') ]) return options - - @run_after('build') - @on_package_attributes(run_tests=True) - def check(self): - """Run ctest after building project.""" - - with working_dir(self.build_directory): - ctest() diff --git a/var/spack/repos/builtin/packages/dri2proto/package.py b/var/spack/repos/builtin/packages/dri2proto/package.py index 8fc3c35c5a..fb535220e0 100644 --- a/var/spack/repos/builtin/packages/dri2proto/package.py +++ b/var/spack/repos/builtin/packages/dri2proto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dri3proto/package.py b/var/spack/repos/builtin/packages/dri3proto/package.py index 2e210afa65..c3955f41be 100644 --- a/var/spack/repos/builtin/packages/dri3proto/package.py +++ b/var/spack/repos/builtin/packages/dri3proto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/drill/package.py b/var/spack/repos/builtin/packages/drill/package.py new file mode 100644 index 0000000000..01925ec337 --- /dev/null +++ b/var/spack/repos/builtin/packages/drill/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Drill(Package): + """ + Apache Drill is a distributed MPP query layer that supports SQL and + alternative query languages against NoSQL and Hadoop data storage + systems. + """ + + homepage = "http://drill.apache.org/" + url = "https://www-eu.apache.org/dist/drill/drill-1.17.0/apache-drill-1.17.0.tar.gz" + + version('1.17.0', sha256='a3d2d544bcc32b915fb53fced0f982670bd6fe2abd764423e566a5f6b54debf1') + version('1.16.0', sha256='fd195d2b38f393459b37d8f13ac1f36cdbe38495eabb08252da38e3544e87839') + version('1.15.0', sha256='188c1d0df28e50f0265f4bc3c5871b4e7abc9450a4e5a7dbe7f0b23146bec76b') + version('1.14.0', sha256='1145bdbb723119f271d32daf4cdd77cdeebe88ddcb7d04facd585b715bb5723b') + version('1.13.0', sha256='8da6d56f75ae01e0bee6176095d32760e7183dd0200f10ee68b8cd3f882def6a') + + depends_on('java@7:', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/ds/package.py b/var/spack/repos/builtin/packages/ds/package.py index f371ddb924..1906450f4c 100644 --- a/var/spack/repos/builtin/packages/ds/package.py +++ b/var/spack/repos/builtin/packages/ds/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dsdp/package.py b/var/spack/repos/builtin/packages/dsdp/package.py index c12c1d1c92..f10c9c2756 100644 --- a/var/spack/repos/builtin/packages/dsdp/package.py +++ b/var/spack/repos/builtin/packages/dsdp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dsrc/package.py b/var/spack/repos/builtin/packages/dsrc/package.py index d8d6f2c609..5635fc4423 100644 --- a/var/spack/repos/builtin/packages/dsrc/package.py +++ b/var/spack/repos/builtin/packages/dsrc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dtcmp/package.py b/var/spack/repos/builtin/packages/dtcmp/package.py index 43679fa6c2..1ff4c23775 100644 --- a/var/spack/repos/builtin/packages/dtcmp/package.py +++ b/var/spack/repos/builtin/packages/dtcmp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dyninst/package.py b/var/spack/repos/builtin/packages/dyninst/package.py index 84a0575bc5..6f43c1eb7b 100644 --- a/var/spack/repos/builtin/packages/dyninst/package.py +++ b/var/spack/repos/builtin/packages/dyninst/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/dysco/package.py b/var/spack/repos/builtin/packages/dysco/package.py index b594b48147..c7d4978b24 100644 --- a/var/spack/repos/builtin/packages/dysco/package.py +++ b/var/spack/repos/builtin/packages/dysco/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ea-utils/package.py b/var/spack/repos/builtin/packages/ea-utils/package.py index 6eae29bc78..2b044dc23e 100644 --- a/var/spack/repos/builtin/packages/ea-utils/package.py +++ b/var/spack/repos/builtin/packages/ea-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/easybuild/package.py b/var/spack/repos/builtin/packages/easybuild/package.py index 8ada721adc..7f9ba11fdb 100644 --- a/var/spack/repos/builtin/packages/easybuild/package.py +++ b/var/spack/repos/builtin/packages/easybuild/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ebms/package.py b/var/spack/repos/builtin/packages/ebms/package.py index f2721c4f79..1afb5c33d6 100644 --- a/var/spack/repos/builtin/packages/ebms/package.py +++ b/var/spack/repos/builtin/packages/ebms/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/eccodes/package.py b/var/spack/repos/builtin/packages/eccodes/package.py index 5bbc02f96b..8638463740 100644 --- a/var/spack/repos/builtin/packages/eccodes/package.py +++ b/var/spack/repos/builtin/packages/eccodes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -49,7 +49,7 @@ class Eccodes(CMakePackage): # tests are enabled but the testing scripts don't use it. # depends_on('valgrind', type='test', when='+test') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('openjpeg@1.5.0:1.5.999,2.1.0:2.1.999', when='jp2k=openjpeg') depends_on('jasper', when='jp2k=jasper') depends_on('libpng', when='+png') @@ -100,7 +100,7 @@ class Eccodes(CMakePackage): '-DHDF5_ROOT=' + self.spec['hdf5'].prefix, # Prevent possible overriding by environment variables # NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH. - '-DNETCDF_PATH=' + self.spec['netcdf'].prefix]) + '-DNETCDF_PATH=' + self.spec['netcdf-c'].prefix]) else: args.append('-DENABLE_NETCDF=OFF') diff --git a/var/spack/repos/builtin/packages/ecflow/package.py b/var/spack/repos/builtin/packages/ecflow/package.py index 5613138d9e..467076382f 100644 --- a/var/spack/repos/builtin/packages/ecflow/package.py +++ b/var/spack/repos/builtin/packages/ecflow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py b/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py index ef517b92d2..11054b409c 100644 --- a/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py +++ b/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -45,6 +45,3 @@ class EclipseGcjParser(Package): def install(self, spec, prefix): mkdirp(spec.prefix.bin) install('ecj1', spec.prefix.bin) - - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/ecos/package.py b/var/spack/repos/builtin/packages/ecos/package.py new file mode 100644 index 0000000000..7ce3427a3f --- /dev/null +++ b/var/spack/repos/builtin/packages/ecos/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Ecos(MakefilePackage): + """A lightweight conic solver for second-order cone programming.""" + + homepage = "https://github.com/embotech/ecos" + url = "https://github.com/embotech/ecos/archive/2.0.7.tar.gz" + + version('2.0.7', sha256='bdb6a84f7d150820459bd0a796cb64ffbb019afb95dc456d22acc2dafb2e70e0') + + build_targets = ['all', 'shared'] + + def install(self, spec, prefix): + install_tree('include', prefix.include) + + mkdir(prefix.lib) + install('libecos.a', prefix.lib) + install('libecos_bb.a', prefix.lib) + install('libecos.so', prefix.lib) + + mkdir(prefix.bin) + install('runecos', prefix.bin) + install('runecosexp', prefix.bin) diff --git a/var/spack/repos/builtin/packages/ecp-io-sdk/package.py b/var/spack/repos/builtin/packages/ecp-io-sdk/package.py index 774704ff0f..ffc09974f1 100644 --- a/var/spack/repos/builtin/packages/ecp-io-sdk/package.py +++ b/var/spack/repos/builtin/packages/ecp-io-sdk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py b/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py index 68586070c8..c3f79c33bb 100644 --- a/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py +++ b/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py b/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py index f86330613c..505121e0e9 100644 --- a/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py +++ b/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -37,7 +37,7 @@ class EcpVizSdk(CMakePackage): depends_on('paraview', when='+paraview') depends_on('sz', when='+sz') depends_on('visit', when='+visit') - depends_on('vtkm', when='+vtkm') + depends_on('vtk-m', when='+vtkm') depends_on('zfp', when='+zfp') def cmake_args(self): diff --git a/var/spack/repos/builtin/packages/ed/package.py b/var/spack/repos/builtin/packages/ed/package.py index 9c84e64262..21a29bd497 100644 --- a/var/spack/repos/builtin/packages/ed/package.py +++ b/var/spack/repos/builtin/packages/ed/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,13 +6,13 @@ from spack import * -class Ed(AutotoolsPackage): +class Ed(AutotoolsPackage, GNUMirrorPackage): """GNU ed is a line-oriented text editor. It is used to create, display, modify and otherwise manipulate text files, both interactively and via shell scripts.""" homepage = "https://www.gnu.org/software/ed" - url = "https://ftpmirror.gnu.org/ed/ed-1.4.tar.gz" + gnu_mirror_path = "ed/ed-1.4.tar.gz" version('1.4', sha256='db36da85ee1a9d8bafb4b041bd4c8c11becba0c43ec446353b67045de1634fda') diff --git a/var/spack/repos/builtin/packages/editline/package.py b/var/spack/repos/builtin/packages/editline/package.py index 22a48659d4..393b0fac59 100644 --- a/var/spack/repos/builtin/packages/editline/package.py +++ b/var/spack/repos/builtin/packages/editline/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/editres/package.py b/var/spack/repos/builtin/packages/editres/package.py index d32e221bd3..0aa661a682 100644 --- a/var/spack/repos/builtin/packages/editres/package.py +++ b/var/spack/repos/builtin/packages/editres/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/eem/package.py b/var/spack/repos/builtin/packages/eem/package.py index a14b215a39..8e904b0c8c 100644 --- a/var/spack/repos/builtin/packages/eem/package.py +++ b/var/spack/repos/builtin/packages/eem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index 0c1a86d676..9b01807bad 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -48,9 +48,8 @@ class Eigen(CMakePackage): patch('find-ptscotch.patch', when='@3.3.4') - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('CPATH', - join_path(self.prefix, 'include', 'eigen3')) + def setup_run_environment(self, env): + env.prepend_path('CPATH', self.prefix.include.eigen3) @property def headers(self): diff --git a/var/spack/repos/builtin/packages/elasticsearch/package.py b/var/spack/repos/builtin/packages/elasticsearch/package.py index 6b7be6715e..6879cdd5df 100644 --- a/var/spack/repos/builtin/packages/elasticsearch/package.py +++ b/var/spack/repos/builtin/packages/elasticsearch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/elemental/package.py b/var/spack/repos/builtin/packages/elemental/package.py index 42e7992d66..a46e31ff11 100644 --- a/var/spack/repos/builtin/packages/elemental/package.py +++ b/var/spack/repos/builtin/packages/elemental/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/elfutils/package.py b/var/spack/repos/builtin/packages/elfutils/package.py index 80e39e3e8f..07d852f254 100644 --- a/var/spack/repos/builtin/packages/elfutils/package.py +++ b/var/spack/repos/builtin/packages/elfutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,10 +17,11 @@ class Elfutils(AutotoolsPackage): version of elfutils.""" homepage = "https://fedorahosted.org/elfutils/" - url = "https://sourceware.org/elfutils/ftp/0.177/elfutils-0.177.tar.bz2" + url = "https://sourceware.org/elfutils/ftp/0.178/elfutils-0.178.tar.bz2" list_url = "https://sourceware.org/elfutils/ftp" list_depth = 1 + version('0.178', sha256='31e7a00e96d4e9c4bda452e1f2cdac4daf8abd24f5e154dee232131899f3a0f2') version('0.177', sha256='fa489deccbcae7d8c920f60d85906124c1989c591196d90e0fd668e3dc05042e') version('0.176', sha256='eb5747c371b0af0f71e86215a5ebb88728533c3a104a43d4231963f308cd1023') version('0.175', sha256='f7ef925541ee32c6d15ae5cb27da5f119e01a5ccdbe9fe57bf836730d7b7a65b') @@ -88,6 +89,11 @@ class Elfutils(AutotoolsPackage): else: args.append('--disable-nls') + # The experimental debuginfod server requires libmicrohttpd + # which doesn't have a spack package + if spec.satisfies('@0.178:'): + args.append('--disable-debuginfod') + return args # Install elf.h to include directory. diff --git a/var/spack/repos/builtin/packages/elk/package.py b/var/spack/repos/builtin/packages/elk/package.py index 4a210fe328..1367eda296 100644 --- a/var/spack/repos/builtin/packages/elk/package.py +++ b/var/spack/repos/builtin/packages/elk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/elmer-fem/package.py b/var/spack/repos/builtin/packages/elmerfem/package.py index a22c1226f2..464611eaf4 100644 --- a/var/spack/repos/builtin/packages/elmer-fem/package.py +++ b/var/spack/repos/builtin/packages/elmerfem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class ElmerFem(CMakePackage): +class Elmerfem(CMakePackage): """Elmer is an open source multiphysical simulation software. It includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics.""" @@ -15,6 +15,7 @@ class ElmerFem(CMakePackage): url = "https://github.com/ElmerCSC/elmerfem/archive/release-8.4.tar.gz" version('8.4', sha256='cc3ce807d76798361592cc14952cdc3db1ad8f9bac038017514033ce9badc5b3') + version('devel', git='https://github.com/ElmerCSC/elmerfem.git', branch='devel') variant('openmp', default=True, description='Enable OpenMP support.') variant('mumps', default=False, description='Enable MUMPS support.') @@ -83,5 +84,5 @@ class ElmerFem(CMakePackage): return args - def setup_environment(self, spack_env, run_env): - run_env.set('ELMER_HOME', self.prefix) + def setup_run_environment(self, env): + env.set('ELMER_HOME', self.prefix) diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py index 699431d2b5..3aad567fe5 100644 --- a/var/spack/repos/builtin/packages/elpa/package.py +++ b/var/spack/repos/builtin/packages/elpa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,6 +14,7 @@ class Elpa(AutotoolsPackage): homepage = 'http://elpa.mpcdf.mpg.de/' url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz' + version('2019.05.002', sha256='d2eab5e5d74f53601220b00d18185670da8c00c13e1c1559ecfb0cd7cb2c4e8d') version('2018.11.001', sha256='cc27fe8ba46ce6e6faa8aea02c8c9983052f8e73a00cfea38abf7613cb1e1b16') version('2018.05.001.rc1', sha256='598c01da20600a4514ea4d503b93e977ac0367e797cab7a7c1b0e0e3e86490db') @@ -21,7 +22,7 @@ class Elpa(AutotoolsPackage): version('2017.05.003', sha256='bccd49ce35a323bd734b17642aed8f2588fea4cc78ee8133d88554753bc3bf1b') version('2017.05.002', sha256='568b71024c094d667b5cbb23045ad197ed5434071152ac608dae490ace5eb0aa') version('2016.11.001.pre', sha256='69b67f0f6faaa2b3b5fd848127b632be32771636d2ad04583c5269d550956f92') - version('2016.05.004', sha256='08c59dc9da458bab856f489d779152e5506e04f0d4b8d6dcf114ca5fbbe46c58', preferred=True) + version('2016.05.004', sha256='08c59dc9da458bab856f489d779152e5506e04f0d4b8d6dcf114ca5fbbe46c58') version('2016.05.003', sha256='c8da50c987351514e61491e14390cdea4bdbf5b09045261991876ed5b433fca4') version('2015.11.001', sha256='c0761a92a31c08a4009c9688c85fc3fc8fde9b6ce05e514c3e1587cf045e9eba') @@ -61,32 +62,40 @@ class Elpa(AutotoolsPackage): build_directory = 'spack-build' - def setup_build_environment(self, env): + def configure_args(self): spec = self.spec + options = [] - env.set('CC', spec['mpi'].mpicc) - env.set('FC', spec['mpi'].mpifc) - env.set('CXX', spec['mpi'].mpicxx) + # TODO: add --enable-gpu, --disable-sse-assembly, --enable-sparc64 + # and --enable-neon-arch64 + simd_features = ['vsx', 'sse', 'avx', 'avx2', 'avx512', 'bgp', 'bgq'] - env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags) - env.append_flags('LIBS', spec['lapack'].libs.link_flags) - env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined()) + for feature in simd_features: + msg = '--enable-{0}' if feature in spec.target else '--disable-{0}' + options.append(msg.format(feature)) - def configure_args(self): - # TODO: set optimum flags for platform+compiler combo, see - # https://github.com/hfp/xconfigure/tree/master/elpa - # also see: - # https://src.fedoraproject.org/cgit/rpms/elpa.git/ - # https://packages.qa.debian.org/e/elpa.html - options = [] - # without -march=native there is configure error for 2017.05.02 - # Could not compile test program, try with --disable-sse, or - # adjust the C compiler or CFLAGS - if '+optflags' in self.spec: + # If no features are found, enable the generic ones + if not any(f in spec.target for f in simd_features): + options.append('--enable-generic') + + if '+optflags' in spec: options.extend([ 'FCFLAGS=-O2 -ffree-line-length-none', 'CFLAGS=-O2' ]) - if '+openmp' in self.spec: + + if '+openmp' in spec: options.append('--enable-openmp') + else: + options.append('--disable-openmp') + + options.extend([ + 'CC={0}'.format(spec['mpi'].mpicc), + 'FC={0}'.format(spec['mpi'].mpifc), + 'CXX={0}'.format(spec['mpi'].mpicxx), + 'LDFLAGS={0}'.format(spec['lapack'].libs.search_flags), + 'LIBS={0}'.format(spec['lapack'].libs.link_flags), + 'SCALAPACK_LDFLAGS={0}'.format(spec['scalapack'].libs.joined()) + ]) + return options diff --git a/var/spack/repos/builtin/packages/elsd/package.py b/var/spack/repos/builtin/packages/elsd/package.py index 479f183ddb..f625b80dda 100644 --- a/var/spack/repos/builtin/packages/elsd/package.py +++ b/var/spack/repos/builtin/packages/elsd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/elsdc/package.py b/var/spack/repos/builtin/packages/elsdc/package.py index b32394842f..c41e5ece66 100644 --- a/var/spack/repos/builtin/packages/elsdc/package.py +++ b/var/spack/repos/builtin/packages/elsdc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/elsi/package.py b/var/spack/repos/builtin/packages/elsi/package.py index 34aeacffbe..db5d4714f6 100644 --- a/var/spack/repos/builtin/packages/elsi/package.py +++ b/var/spack/repos/builtin/packages/elsi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py index c556c446ce..cd82dcb75f 100644 --- a/var/spack/repos/builtin/packages/emacs/package.py +++ b/var/spack/repos/builtin/packages/emacs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,12 +8,13 @@ from spack import * import sys -class Emacs(AutotoolsPackage): +class Emacs(AutotoolsPackage, GNUMirrorPackage): """The Emacs programmable text editor.""" homepage = "https://www.gnu.org/software/emacs" - url = "https://ftpmirror.gnu.org/emacs/emacs-24.5.tar.gz" + gnu_mirror_path = "emacs/emacs-24.5.tar.gz" + version('26.3', sha256='09c747e048137c99ed35747b012910b704e0974dde4db6696fde7054ce387591') version('26.2', sha256='4f99e52a38a737556932cc57479e85c305a37a8038aaceb5156625caf102b4eb') version('26.1', sha256='760382d5e8cdc5d0d079e8f754bce1136fbe1473be24bb885669b0e38fc56aa3') version('25.3', sha256='f72c6a1b48b6fbaca2b991eed801964a208a2f8686c70940013db26cd37983c9') diff --git a/var/spack/repos/builtin/packages/ember/package.py b/var/spack/repos/builtin/packages/ember/package.py index e31eec7289..d80ac91efd 100644 --- a/var/spack/repos/builtin/packages/ember/package.py +++ b/var/spack/repos/builtin/packages/ember/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/emboss/package.py b/var/spack/repos/builtin/packages/emboss/package.py index 2ec381cd41..62f043694a 100644 --- a/var/spack/repos/builtin/packages/emboss/package.py +++ b/var/spack/repos/builtin/packages/emboss/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/enchant/package.py b/var/spack/repos/builtin/packages/enchant/package.py index 44d15e3608..4592a2a671 100644 --- a/var/spack/repos/builtin/packages/enchant/package.py +++ b/var/spack/repos/builtin/packages/enchant/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,8 @@ class Enchant(AutotoolsPackage): homepage = "https://abiword.github.io/enchant/" url = "https://github.com/AbiWord/enchant/releases/download/v2.2.5/enchant-2.2.5.tar.gz" + version('2.2.7', sha256='1b22976135812b35cb5b8d21a53ad11d5e7c1426c93f51e7a314a2a42cab3a09') + version('2.2.6', sha256='8048c5bd26190b21279745cfecd05808c635bc14912e630340cd44a49b87d46d') version('2.2.5', sha256='ffce4ea00dbda1478d91c3e1538cadfe5761d9d6c0ceb27bc3dba51882fe1c47') version('2.2.4', sha256='f5d6b689d23c0d488671f34b02d07b84e408544b2f9f6e74fb7221982b1ecadc') version('2.2.3', sha256='abd8e915675cff54c0d4da5029d95c528362266557c61c7149d53fa069b8076d') diff --git a/var/spack/repos/builtin/packages/energyplus/package.py b/var/spack/repos/builtin/packages/energyplus/package.py index 358c7fe8da..ca534999f9 100644 --- a/var/spack/repos/builtin/packages/energyplus/package.py +++ b/var/spack/repos/builtin/packages/energyplus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/entrezdirect/package.py b/var/spack/repos/builtin/packages/entrezdirect/package.py index 04aa202d54..038a57035f 100644 --- a/var/spack/repos/builtin/packages/entrezdirect/package.py +++ b/var/spack/repos/builtin/packages/entrezdirect/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/environment-modules/package.py b/var/spack/repos/builtin/packages/environment-modules/package.py index 3f47fa8c2b..14670da0ae 100644 --- a/var/spack/repos/builtin/packages/environment-modules/package.py +++ b/var/spack/repos/builtin/packages/environment-modules/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,10 +12,12 @@ class EnvironmentModules(Package): """ homepage = 'https://cea-hpc.github.io/modules/' - url = 'https://github.com/cea-hpc/modules/releases/download/v4.3.1/modules-4.3.1.tar.gz' + url = 'https://github.com/cea-hpc/modules/releases/download/v4.4.1/modules-4.4.1.tar.gz' maintainers = ['xdelaruelle'] + version('4.4.1', sha256='3c20cfb2ff8a4d74ac6d566e7b5fa9dd220d96d17e6d8a4ae29b1ec0107ee407') + version('4.4.0', sha256='4dd55ad6cc684905e891ad1ba9e3c542e79eea0a9cd9a0e99cd77abe6ed63fab') version('4.3.1', sha256='979efb5b3d3c8df2c3c364aaba61f97a459456fc5bbc092dfc02677da63e5654') version('4.3.0', sha256='231f059c4109a2d3028c771f483f6c92f1f3689eb0033648ce00060dad00e103') version('4.2.5', sha256='3375b454568e7bbec7748cd6173516ef9f30a3d8e13c3e99c02794a6a3bc3c8c') @@ -68,6 +70,13 @@ class EnvironmentModules(Package): if '~X' in spec: config_args = ['--without-x'] + config_args + if '@4.4.0:' in self.spec: + config_args.extend([ + '--with-icase=search', + '--enable-extended-default', + '--enable-advanced-version-spec' + ]) + if '@4.3.0:' in self.spec: config_args.extend([ '--enable-color' diff --git a/var/spack/repos/builtin/packages/eospac/package.py b/var/spack/repos/builtin/packages/eospac/package.py index 1ee01f6f21..f73274ca46 100644 --- a/var/spack/repos/builtin/packages/eospac/package.py +++ b/var/spack/repos/builtin/packages/eospac/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,21 +12,21 @@ class Eospac(Package): library. """ - homepage = "http://laws-green.lanl.gov/projects/data/eos.html" - list_url = "http://laws-green.lanl.gov/projects/data/eos/eospacReleases.php" + homepage = "http://laws.lanl.gov/projects/data/eos.html" + list_url = "http://laws.lanl.gov/projects/data/eos/eospacReleases.php" version('6.4.0', sha256='15a953beac735c68431afe86ffe33323d540d0fbbbec03ba79438dd29736051d', - url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0_612ea8c9b8ffa6d9175d9118955571d9107f1e3c.tgz") + url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0_612ea8c9b8ffa6d9175d9118955571d9107f1e3c.tgz") version('6.4.0beta.4', sha256='0ebfd8badff575ea77444aa978629dbdca3135a0b5eb373b8daba058773d4635', - url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.4_aff6429bb6868de31a980278bafa13487c2ce83f.tgz") + url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.4_aff6429bb6868de31a980278bafa13487c2ce83f.tgz") version('6.4.0beta.3', sha256='9f387ca5356519494c6f3f27adb0c165cf9f9e15e3355a67bf940a4a92eebdab', - url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.3_90ff265f62aa1780bfcd0a62dad807b6be6ed461.tgz") + url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.3_90ff265f62aa1780bfcd0a62dad807b6be6ed461.tgz") version('6.4.0beta.2', sha256='f9db46cd6c62a6f83960d802350f3e37675921af102969b293c02eb797558a53', - url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.2_69196eadbc77506561eef711f19d2f03b4ab0ffa.tgz") + url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.2_69196eadbc77506561eef711f19d2f03b4ab0ffa.tgz") version('6.4.0beta.1', sha256='14c5c804e5f628f41e8ed80bcee5a80adeb6c6f3d130715421ca99a30c7eb7e2', - url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz") + url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz") version('6.3.1', sha256='aa1112c4251c9c3c2883a7ab2c7f2abff2c339f29dbbf8421ef88b0c9df904f8', preferred=True, - url="http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.3.1_r20161202150449.tgz") + url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.3.1_r20161202150449.tgz") # This patch allows the use of spack's compile wrapper 'flang' patch('flang.patch', when='@:6.4.0beta.2%clang') diff --git a/var/spack/repos/builtin/packages/eqr/package.py b/var/spack/repos/builtin/packages/eq-r/package.py index e31f88bb39..8270489368 100644 --- a/var/spack/repos/builtin/packages/eqr/package.py +++ b/var/spack/repos/builtin/packages/eq-r/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,20 +7,18 @@ from spack import * import os -class Eqr(AutotoolsPackage): +class EqR(AutotoolsPackage): """ EMEWS Queues for R (EQ/R) Installs EQ/R. """ - git = "https://github.com/emews/EQ-R" - - version('develop', branch='master') - - configure_directory = 'src' - homepage = "http://emews.org" url = "https://github.com/emews/EQ-R/archive/1.0.tar.gz" + git = "https://github.com/emews/EQ-R.git" + + version('master', branch='master') + version('1.0', sha256='68047cb0edf088eaaefc5e36cefda9818292e5c832593e10a1dd9c73c27661b6') depends_on('autoconf', type='build') @@ -34,11 +32,13 @@ class Eqr(AutotoolsPackage): depends_on('tcl') depends_on('swig') - def setup_environment(self, spack_env, run_env): + configure_directory = 'src' + + def setup_build_environment(self, env): spec = self.spec - spack_env.set('CC', spec['mpi'].mpicc) - spack_env.set('CXX', spec['mpi'].mpicxx) - spack_env.set('CXXLD', spec['mpi'].mpicxx) + env.set('CC', spec['mpi'].mpicc) + env.set('CXX', spec['mpi'].mpicxx) + env.set('CXXLD', spec['mpi'].mpicxx) def configure_args(self): args = ['--with-tcl=' + self.spec['tcl'].prefix] @@ -46,7 +46,7 @@ class Eqr(AutotoolsPackage): if not os.path.exists(r_location): rscript = which('Rscript') if rscript is not None: - r_location = rscript('-e', 'cat(R.home())') + r_location = rscript('-e', 'cat(R.home())', output=str) else: msg = 'couldn\'t locate Rscript on your PATH' raise RuntimeError(msg) diff --git a/var/spack/repos/builtin/packages/er/package.py b/var/spack/repos/builtin/packages/er/package.py index 2edc201b97..55e5067f12 100644 --- a/var/spack/repos/builtin/packages/er/package.py +++ b/var/spack/repos/builtin/packages/er/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class Er(CMakePackage): """Encoding and redundancy on a file set""" homepage = "https://github.com/ECP-VeloC/er" - url = "https://github.com/ECP-VeloC/er/archive/v0.0.2.zip" + url = "https://github.com/ECP-VeloC/er/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/er.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/erfa/package.py b/var/spack/repos/builtin/packages/erfa/package.py index 870c8a3427..dd2e838c18 100644 --- a/var/spack/repos/builtin/packages/erfa/package.py +++ b/var/spack/repos/builtin/packages/erfa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/erlang/package.py b/var/spack/repos/builtin/packages/erlang/package.py new file mode 100644 index 0000000000..1101bee787 --- /dev/null +++ b/var/spack/repos/builtin/packages/erlang/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Erlang(AutotoolsPackage): + """ + Erlang is a programming language and runtime system for building + massively scalable soft real-time systems with requirements on + high availability. + """ + + homepage = "https://erlang.org/" + url = "https://erlang.org/download/otp_src_22.2.tar.gz" + + version('22.2', sha256='89c2480cdac566065577c82704a48e10f89cf2e6ca5ab99e1cf80027784c678f') + version('22.1', sha256='cd33a102cbac6dd1c7b1e7a9a0d82d13587771fac4e96e8fff92e403d15e32c8') + version('22.0', sha256='042e168d74055a501c75911694758a30597446accd8c82ec569552b9e9fcd272') + version('21.3', sha256='69a743c4f23b2243e06170b1937558122142e47c8ebe652be143199bfafad6e4') + version('21.2', sha256='f6b07bf8e6705915679a63363ce80faaa6b7c231e7236cde443d6445f7430334') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('m4', type='build') + depends_on('libtool', type='build') diff --git a/var/spack/repos/builtin/packages/ermod/package.py b/var/spack/repos/builtin/packages/ermod/package.py index d9d8586d71..38c2ab6963 100644 --- a/var/spack/repos/builtin/packages/ermod/package.py +++ b/var/spack/repos/builtin/packages/ermod/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/erne/package.py b/var/spack/repos/builtin/packages/erne/package.py index 7eee817d22..3a9e276851 100644 --- a/var/spack/repos/builtin/packages/erne/package.py +++ b/var/spack/repos/builtin/packages/erne/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/es/package.py b/var/spack/repos/builtin/packages/es-shell/package.py index 99b846e96f..c8f7bcc83c 100644 --- a/var/spack/repos/builtin/packages/es/package.py +++ b/var/spack/repos/builtin/packages/es-shell/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,8 +6,7 @@ from spack import * -class Es(AutotoolsPackage): - +class EsShell(AutotoolsPackage): """Es is an extensible shell. The language was derived from the Plan 9 shell, rc, and was influenced by functional programming languages, such as Scheme, and the Tcl embeddable programming language. This diff --git a/var/spack/repos/builtin/packages/esmf/package.py b/var/spack/repos/builtin/packages/esmf/package.py index bfe35d9f19..d63af514ff 100644 --- a/var/spack/repos/builtin/packages/esmf/package.py +++ b/var/spack/repos/builtin/packages/esmf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -34,7 +34,7 @@ class Esmf(MakefilePackage): # Optional dependencies depends_on('mpi', when='+mpi') depends_on('lapack@3:', when='+lapack') - depends_on('netcdf@3.6:', when='+netcdf') + depends_on('netcdf-c@3.6:', when='+netcdf') depends_on('netcdf-fortran@3.6:', when='+netcdf') depends_on('parallel-netcdf@1.2.0:', when='+pnetcdf') depends_on('xerces-c@3.1.0:', when='+xerces') @@ -200,7 +200,7 @@ class Esmf(MakefilePackage): if '+netcdf' in spec: # ESMF provides the ability to read Grid and Mesh data in # NetCDF format. - if spec.satisfies('^netcdf@4.2:'): + if spec.satisfies('^netcdf-c@4.2:'): # ESMF_NETCDF_LIBS will be set to "-lnetcdff -lnetcdf". # This option is useful for systems which have the Fortran # and C bindings archived in seperate library files. diff --git a/var/spack/repos/builtin/packages/essl/package.py b/var/spack/repos/builtin/packages/essl/package.py index f6d477b0f8..29ba3958e7 100644 --- a/var/spack/repos/builtin/packages/essl/package.py +++ b/var/spack/repos/builtin/packages/essl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ethminer/package.py b/var/spack/repos/builtin/packages/ethminer/package.py index 996532f878..bc57f2630d 100644 --- a/var/spack/repos/builtin/packages/ethminer/package.py +++ b/var/spack/repos/builtin/packages/ethminer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ethtool/package.py b/var/spack/repos/builtin/packages/ethtool/package.py new file mode 100644 index 0000000000..bbf53f505f --- /dev/null +++ b/var/spack/repos/builtin/packages/ethtool/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Ethtool(AutotoolsPackage): + """Ethtool is a small utility for examining and tuning your ethernet-based + network interface.""" + + homepage = "https://github.com/Distrotech/ethtool" + url = "https://github.com/Distrotech/ethtool/archive/v4.8.tar.gz" + + version('4.8', sha256='e4443c612b01b6c4891e21f55a59aa2d6da1c9915edcf067bb66a0855590e143') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + + def autoreconf(self, spec, prefix): + autoreconf('--install', '--verbose', '--force') diff --git a/var/spack/repos/builtin/packages/etsf-io/package.py b/var/spack/repos/builtin/packages/etsf-io/package.py index 62096ace0f..a878894db3 100644 --- a/var/spack/repos/builtin/packages/etsf-io/package.py +++ b/var/spack/repos/builtin/packages/etsf-io/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/everytrace-example/package.py b/var/spack/repos/builtin/packages/everytrace-example/package.py index f5ccf381b8..6ba1271522 100644 --- a/var/spack/repos/builtin/packages/everytrace-example/package.py +++ b/var/spack/repos/builtin/packages/everytrace-example/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,6 +18,3 @@ class EverytraceExample(CMakePackage): # Currently the only MPI this everytrace works with. depends_on('openmpi') - - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', join_path(self.prefix, 'bin')) diff --git a/var/spack/repos/builtin/packages/everytrace/package.py b/var/spack/repos/builtin/packages/everytrace/package.py index 1de226bdac..f07607fc12 100644 --- a/var/spack/repos/builtin/packages/everytrace/package.py +++ b/var/spack/repos/builtin/packages/everytrace/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,6 +31,3 @@ class Everytrace(CMakePackage): '-DUSE_MPI=%s' % ('YES' if '+mpi' in spec else 'NO'), '-DUSE_FORTRAN=%s' % ('YES' if '+fortran' in spec else 'NO'), '-DUSE_CXX=%s' % ('YES' if '+cxx' in spec else 'NO')] - - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', join_path(self.prefix, 'bin')) diff --git a/var/spack/repos/builtin/packages/evieext/package.py b/var/spack/repos/builtin/packages/evieext/package.py index 4b292ebe2b..af7386dca6 100644 --- a/var/spack/repos/builtin/packages/evieext/package.py +++ b/var/spack/repos/builtin/packages/evieext/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/exabayes/package.py b/var/spack/repos/builtin/packages/exabayes/package.py index 379f829810..c8ef56717d 100644 --- a/var/spack/repos/builtin/packages/exabayes/package.py +++ b/var/spack/repos/builtin/packages/exabayes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/examinimd/package.py b/var/spack/repos/builtin/packages/examinimd/package.py index 4d92266f2b..a6250b0dcb 100644 --- a/var/spack/repos/builtin/packages/examinimd/package.py +++ b/var/spack/repos/builtin/packages/examinimd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/exampm/package.py b/var/spack/repos/builtin/packages/exampm/package.py index 7d86270320..bf1ae7f545 100644 --- a/var/spack/repos/builtin/packages/exampm/package.py +++ b/var/spack/repos/builtin/packages/exampm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/exasp2/package.py b/var/spack/repos/builtin/packages/exasp2/package.py index bc9c452046..4ff5251579 100644 --- a/var/spack/repos/builtin/packages/exasp2/package.py +++ b/var/spack/repos/builtin/packages/exasp2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/exchanger/package.py b/var/spack/repos/builtin/packages/exchanger/package.py index 46047ed658..018459d8c3 100644 --- a/var/spack/repos/builtin/packages/exchanger/package.py +++ b/var/spack/repos/builtin/packages/exchanger/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/exiv2/package.py b/var/spack/repos/builtin/packages/exiv2/package.py index 0149701b2c..05d6de7bd8 100644 --- a/var/spack/repos/builtin/packages/exiv2/package.py +++ b/var/spack/repos/builtin/packages/exiv2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/exmcutils/package.py b/var/spack/repos/builtin/packages/exmcutils/package.py index 8d53b7a71a..860f0518e7 100644 --- a/var/spack/repos/builtin/packages/exmcutils/package.py +++ b/var/spack/repos/builtin/packages/exmcutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class Exmcutils(AutotoolsPackage): """ExM C-Utils: Generic C utility library for ADLB/X and Swift/T""" homepage = 'http://swift-lang.org/Swift-T' - url = 'http://swift-lang.github.io/swift-t-downloads/spack/exmcutils-0.0.0.tar.gz' + url = 'http://swift-lang.github.io/swift-t-downloads/spack/exmcutils-0.5.7.tar.gz' git = "https://github.com/swift-lang/swift-t.git" version('master', branch='master') diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py index 6472b7b997..7a163dcffb 100644 --- a/var/spack/repos/builtin/packages/exodusii/package.py +++ b/var/spack/repos/builtin/packages/exodusii/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,8 +30,8 @@ class Exodusii(CMakePackage): depends_on('mpi', when='+mpi') # https://github.com/gsjaardema/seacas/blob/master/NetCDF-Mapping.md - depends_on('netcdf@4.6.1:+mpi', when='+mpi') - depends_on('netcdf@4.6.1:~mpi', when='~mpi') + depends_on('netcdf-c@4.6.1:+mpi', when='+mpi') + depends_on('netcdf-c@4.6.1:~mpi', when='~mpi') def cmake_args(self): spec = self.spec @@ -49,7 +49,7 @@ class Exodusii(CMakePackage): '-DSEACASProj_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=ON', '-DSEACASProj_ENABLE_CXX11:BOOL=OFF', '-DSEACASProj_ENABLE_Zoltan:BOOL=OFF', - '-DNetCDF_DIR:PATH={0}'.format(spec['netcdf'].prefix), + '-DNetCDF_DIR:PATH={0}'.format(spec['netcdf-c'].prefix), # MPI Flags # '-DTPL_ENABLE_MPI={0}'.format('ON' if '+mpi' in spec else 'OFF'), diff --git a/var/spack/repos/builtin/packages/exonerate/package.py b/var/spack/repos/builtin/packages/exonerate/package.py index c7eadef01f..2d4c3f7b1b 100644 --- a/var/spack/repos/builtin/packages/exonerate/package.py +++ b/var/spack/repos/builtin/packages/exonerate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py index da3aa5b0eb..7eb816923f 100644 --- a/var/spack/repos/builtin/packages/expat/package.py +++ b/var/spack/repos/builtin/packages/expat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/expect/package.py b/var/spack/repos/builtin/packages/expect/package.py index ad6e24bdb9..4cab48a064 100644 --- a/var/spack/repos/builtin/packages/expect/package.py +++ b/var/spack/repos/builtin/packages/expect/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/express/package.py b/var/spack/repos/builtin/packages/express/package.py index 45a05cffa8..d434a866c1 100644 --- a/var/spack/repos/builtin/packages/express/package.py +++ b/var/spack/repos/builtin/packages/express/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -40,6 +40,6 @@ class Express(CMakePackage): edit.filter(r'\${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/' 'libbamtools.a', '%s' % self.spec['bamtools'].libs) - def setup_environment(self, spack_env, run_env): - spack_env.prepend_path('CPATH', self.spec[ - 'bamtools'].prefix.include.bamtools) + def setup_build_environment(self, env): + env.prepend_path('CPATH', + self.spec['bamtools'].prefix.include.bamtools) diff --git a/var/spack/repos/builtin/packages/extrae/package.py b/var/spack/repos/builtin/packages/extrae/package.py index 54c3622b06..4ea5928b02 100644 --- a/var/spack/repos/builtin/packages/extrae/package.py +++ b/var/spack/repos/builtin/packages/extrae/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -101,10 +101,10 @@ class Extrae(AutotoolsPackage): else: make('install', parallel=False) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # set EXTRAE_HOME in the module file - run_env.set('EXTRAE_HOME', self.prefix) + env.set('EXTRAE_HOME', self.prefix) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): # set EXTRAE_HOME for everyone using the Extrae package - spack_env.set('EXTRAE_HOME', self.prefix) + env.set('EXTRAE_HOME', self.prefix) diff --git a/var/spack/repos/builtin/packages/exuberant-ctags/package.py b/var/spack/repos/builtin/packages/exuberant-ctags/package.py index dc76106827..6efb00602c 100644 --- a/var/spack/repos/builtin/packages/exuberant-ctags/package.py +++ b/var/spack/repos/builtin/packages/exuberant-ctags/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/eztrace/package.py b/var/spack/repos/builtin/packages/eztrace/package.py index fc56e6fa1d..9468ce8214 100644 --- a/var/spack/repos/builtin/packages/eztrace/package.py +++ b/var/spack/repos/builtin/packages/eztrace/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/f18/package.py b/var/spack/repos/builtin/packages/f18/package.py index fce4359cf0..b766a8f17c 100644 --- a/var/spack/repos/builtin/packages/f18/package.py +++ b/var/spack/repos/builtin/packages/f18/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/f90cache/package.py b/var/spack/repos/builtin/packages/f90cache/package.py index 1de70bafa7..32aaff590f 100644 --- a/var/spack/repos/builtin/packages/f90cache/package.py +++ b/var/spack/repos/builtin/packages/f90cache/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fabtests/package.py b/var/spack/repos/builtin/packages/fabtests/package.py index f11e27a79d..a71a69ab37 100644 --- a/var/spack/repos/builtin/packages/fabtests/package.py +++ b/var/spack/repos/builtin/packages/fabtests/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fairlogger/package.py b/var/spack/repos/builtin/packages/fairlogger/package.py new file mode 100644 index 0000000000..3190f1702c --- /dev/null +++ b/var/spack/repos/builtin/packages/fairlogger/package.py @@ -0,0 +1,65 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# Copyright 2020 GSI Helmholtz Centre for Heavy Ion Research GmbH, +# Darmstadt, Germany +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Fairlogger(CMakePackage): + """Lightweight and fast C++ Logging Library""" + + homepage = 'https://github.com/FairRootGroup/FairLogger' + url = "https://github.com/FairRootGroup/FairLogger/archive/v1.2.0.tar.gz" + git = 'https://github.com/FairRootGroup/FairLogger.git' + maintainers = ['dennisklein', 'ChristianTackeGSI'] + # generator = 'Ninja' + + version('develop', branch='dev') + version('1.6.1', sha256='3894580f4c398d724ba408e410e50f70c9f452e8cfaf7c3ff8118c08df28eaa8') + version('1.6.0', sha256='721e8cadfceb2f63014c2a727e098babc6deba653baab8866445a772385d0f5b') + version('1.5.0', sha256='8e74e0b1e50ee86f4fca87a44c6b393740b32099ac3880046bf252c31c58dd42') + version('1.4.0', sha256='75457e86984cc03ce87d6ad37adc5aab1910cabd39a9bbe5fb21ce2475a91138') + version('1.3.0', sha256='5cedea2773f7091d69aae9fd8f724e6e47929ee3784acdd295945a848eb36b93') + version('1.2.0', sha256='bc0e049cf84ceb308132d8679e7f22fcdca5561dda314d5233d0d5fe2b0f8c62') + version('1.1.0', sha256='e185e5bd07df648224f85e765d18579fae0de54adaab9a194335e3ad6d3d29f7') + version('1.0.6', sha256='2fc266a6e494adda40837be406aef8d9838f385ffd64fbfafb1164833906b4e0') + + variant('build_type', default='RelWithDebInfo', + values=('Debug', 'Release', 'RelWithDebInfo'), + multi=False, + description='CMake build type') + variant('cxxstd', default='11', + values=('11', '14', '17'), + multi=False, + description='Use the specified C++ standard when building.') + variant('pretty', + default=False, + description='Use BOOST_PRETTY_FUNCTION macro.') + conflicts('+pretty', when='@:1.3.99') + + depends_on('cmake@3.9.4:', type='build') + depends_on('git', type='build', when='@develop') + depends_on('boost', when='+pretty') + depends_on('fmt@5.3.0:', when='@1.6.0:') + + def patch(self): + """FairLogger gets its version number from git. + But the tarball doesn't have that information, so + we patch the spack version into CMakeLists.txt""" + if not self.spec.satisfies("@develop"): + filter_file(r'(get_git_version\(.*)\)', + r'\1 DEFAULT_VERSION %s)' % self.spec.version, + 'CMakeLists.txt') + + def cmake_args(self): + cxxstd = self.spec.variants['cxxstd'].value + args = [] + args.append('-DCMAKE_CXX_STANDARD=%s' % cxxstd) + args.append('-DUSE_BOOST_PRETTY_FUNCTION=%s' % + ('ON' if '+pretty' in self.spec else 'OFF')) + if self.spec.satisfies('@1.6:'): + args.append('-DUSE_EXTERNAL_FMT=ON') + return args diff --git a/var/spack/repos/builtin/packages/falcon/Py_None.patch b/var/spack/repos/builtin/packages/falcon/Py_None.patch new file mode 100644 index 0000000000..6f7ed073e7 --- /dev/null +++ b/var/spack/repos/builtin/packages/falcon/Py_None.patch @@ -0,0 +1,10 @@ +--- spack-src/src/c/ext_falcon.c.org 2020-01-15 17:40:41.279400137 +0900 ++++ spack-src/src/c/ext_falcon.c 2020-01-15 17:44:47.785718088 +0900 +@@ -9,5 +9,6 @@ + + m = Py_InitModule("ext_falcon", SpamMethods); + if (m == NULL) +- return; ++ Py_INCREF(Py_None); ++ return Py_None; + } diff --git a/var/spack/repos/builtin/packages/falcon/package.py b/var/spack/repos/builtin/packages/falcon/package.py index 4d8784926c..36649dd7e6 100644 --- a/var/spack/repos/builtin/packages/falcon/package.py +++ b/var/spack/repos/builtin/packages/falcon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,3 +28,7 @@ class Falcon(PythonPackage): depends_on('pacbio-daligner', type='run') depends_on('pacbio-dextractor', type='run') depends_on('pacbio-damasker', type='run') + + # Python version 3 and later should return + # a value of PyObject type. [-Wreturn-type] + patch('Py_None.patch', when='^python@3:') diff --git a/var/spack/repos/builtin/packages/fann/package.py b/var/spack/repos/builtin/packages/fann/package.py index ec5a69f91d..b6c7c0d07c 100644 --- a/var/spack/repos/builtin/packages/fann/package.py +++ b/var/spack/repos/builtin/packages/fann/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/faodel/package.py b/var/spack/repos/builtin/packages/faodel/package.py index 701a40b405..63f5798a02 100644 --- a/var/spack/repos/builtin/packages/faodel/package.py +++ b/var/spack/repos/builtin/packages/faodel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fast-global-file-status/package.py b/var/spack/repos/builtin/packages/fast-global-file-status/package.py index c805638fe1..afc2ef23de 100644 --- a/var/spack/repos/builtin/packages/fast-global-file-status/package.py +++ b/var/spack/repos/builtin/packages/fast-global-file-status/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fasta/package.py b/var/spack/repos/builtin/packages/fasta/package.py index d211d15c47..49ff18bede 100644 --- a/var/spack/repos/builtin/packages/fasta/package.py +++ b/var/spack/repos/builtin/packages/fasta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fastdfs/package.py b/var/spack/repos/builtin/packages/fastdfs/package.py new file mode 100644 index 0000000000..688308e910 --- /dev/null +++ b/var/spack/repos/builtin/packages/fastdfs/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Fastdfs(Package): + """ + FastDFS is an open source high performance distributed file system. + It's major functions include: file storing, file syncing and file + accessing (file uploading and file downloading), and it can resolve + the high capacity and load balancing problem. FastDFS should meet + the requirement of the website whose service based on files such + as photo sharing site and video sharing site. + """ + + homepage = "https://github.com/happyfish100/fastdfs" + url = "https://github.com/happyfish100/fastdfs/archive/V6.05.tar.gz" + + version('6.05', sha256='00b736a1a7bd9cb5733aa51969efaa3b46df3764988c1edb43f06d72c4d575d9') + version('6.04', sha256='76090f6bbd0add08b049ce17f30a7507a44ef0d883784cad774b380ba4906916') + version('6.03', sha256='142be123eb389335b3b3793f0765494bdad3a632e4352af57861ed29098ec8d1') + version('6.02', sha256='b1801f80da9ebce1d84e7e05356c4614190651cb6a5cb4f5662d9196fe243e21') + version('6.01', sha256='b72f4ff6beb21a83af59aeba9f1904e727fa2c1e960e0a9c2b969138d2804148') + + depends_on('perl', type='build') + depends_on('libfastcommon', type='build') + + def install(self, spec, prefix): + sh = which('sh') + sh('make.sh') + sh('make.sh', 'install') + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/fastjar/package.py b/var/spack/repos/builtin/packages/fastjar/package.py index 1211b4b97b..a0e0490020 100644 --- a/var/spack/repos/builtin/packages/fastjar/package.py +++ b/var/spack/repos/builtin/packages/fastjar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fastmath/package.py b/var/spack/repos/builtin/packages/fastmath/package.py index bc04da7237..e2c177832b 100644 --- a/var/spack/repos/builtin/packages/fastmath/package.py +++ b/var/spack/repos/builtin/packages/fastmath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,24 +6,22 @@ from spack import * -class Fastmath(Package): +class Fastmath(BundlePackage): """FASTMath is a suite of ~15 numerical libraries frequently used together in various SciDAC and CSE applications. The suite includes discretization libraries for structured, AMR and unstructured grids as well as solver libraries for ODE's, Time Integrators, Iterative, Non-Linear, and Direct Solvers.""" - homepage = "www.fastmath-scidac.org/" - url = "https://github.com/citibeth/dummy/tarball/v1.0" + homepage = "https://fastmath-scidac.org/" - version('1.0', sha256='402a2198e40b7e9022a99ab88ba6f0ee1c04b103fc15589b22c892859f14b60a') + version('latest') - # BundlePackage depends_on('amrex') # default is 3 dimensions depends_on('chombo@3.2') depends_on('hypre~internal-superlu') -# depends_on('ml-trilinos') # hoping for stripped down install of just ml -# depends_on('nox-trilinos') # hoping for stripped down install of just nox + # depends_on('ml-trilinos') # hoping for stripped down install of just ml + # depends_on('nox-trilinos') # hoping for stripped down install of just nox depends_on('mpi') depends_on('arpack-ng') depends_on('petsc') @@ -33,12 +31,3 @@ class Fastmath(Package): depends_on('superlu-dist') depends_on('trilinos') depends_on('zoltan') - - # Dummy install for now, will be removed when metapackage is available - def install(self, spec, prefix): - # Prevent the error message - # ==> Error: Install failed for fastmath. Nothing was installed! - # ==> Error: Installation process had nonzero exit code : 256 - with open(join_path(spec.prefix, 'bundle-package.txt'), 'w') as out: - out.write('This is a bundle\n') - out.close() diff --git a/var/spack/repos/builtin/packages/fastme/package.py b/var/spack/repos/builtin/packages/fastme/package.py index 2b678b9ac0..83e5169088 100644 --- a/var/spack/repos/builtin/packages/fastme/package.py +++ b/var/spack/repos/builtin/packages/fastme/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fastp/package.py b/var/spack/repos/builtin/packages/fastp/package.py index 5d129e32d2..1fa7efb535 100644 --- a/var/spack/repos/builtin/packages/fastp/package.py +++ b/var/spack/repos/builtin/packages/fastp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fastphase/package.py b/var/spack/repos/builtin/packages/fastphase/package.py index 381ca0a973..2639cb2d6a 100644 --- a/var/spack/repos/builtin/packages/fastphase/package.py +++ b/var/spack/repos/builtin/packages/fastphase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fastq-screen/package.py b/var/spack/repos/builtin/packages/fastq-screen/package.py index ef651a4c9d..2b2096d343 100644 --- a/var/spack/repos/builtin/packages/fastq-screen/package.py +++ b/var/spack/repos/builtin/packages/fastq-screen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,7 +17,7 @@ class FastqScreen(Package): version('0.11.2', sha256='a179df1f5803b42bbbb2b50af05ea18ae6fefcbf7020ca2feeb0d3c598a65207') depends_on('perl', type='run') - depends_on('perl-gd-graph', type='run') + depends_on('perl-gdgraph', type='run') depends_on('bowtie') depends_on('bowtie2') depends_on('bwa') diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py index 289cda53bb..be4770d2a8 100644 --- a/var/spack/repos/builtin/packages/fastqc/package.py +++ b/var/spack/repos/builtin/packages/fastqc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -34,8 +34,8 @@ class Fastqc(Package): # In theory the 'run' dependency on 'jdk' above should take # care of this for me. In practice, it does not. - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Add <prefix> to the path; the package has a script at the top level. """ - run_env.prepend_path('PATH', self.spec['java'].prefix.bin) + env.prepend_path('PATH', self.spec['java'].prefix.bin) diff --git a/var/spack/repos/builtin/packages/fastqvalidator/package.py b/var/spack/repos/builtin/packages/fastqvalidator/package.py index 9397eec2a0..54d0b329bb 100644 --- a/var/spack/repos/builtin/packages/fastqvalidator/package.py +++ b/var/spack/repos/builtin/packages/fastqvalidator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fasttree/package.py b/var/spack/repos/builtin/packages/fasttree/package.py index b6b2f9e2a3..34ef2d7281 100644 --- a/var/spack/repos/builtin/packages/fasttree/package.py +++ b/var/spack/repos/builtin/packages/fasttree/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fastx-toolkit/fix_pragma_pack.patch b/var/spack/repos/builtin/packages/fastx-toolkit/fix_pragma_pack.patch new file mode 100644 index 0000000000..5f4d178d03 --- /dev/null +++ b/var/spack/repos/builtin/packages/fastx-toolkit/fix_pragma_pack.patch @@ -0,0 +1,19 @@ +--- spack-src/src/libfastx/fastx.h.org 2019-12-19 12:05:37.497936486 +0900 ++++ spack-src/src/libfastx/fastx.h 2019-12-19 13:44:55.481837853 +0900 +@@ -58,7 +58,7 @@ + OUTPUT_SAME_AS_INPUT=3 + } OUTPUT_FILE_TYPE; + +-#pragma pack(1) ++#pragma pack(push, 1) + typedef struct + { + /* Record data - common for FASTA/FASTQ */ +@@ -115,6 +115,7 @@ + FILE* input; + FILE* output; + } FASTX ; ++#pragma pack(pop) + + + void fastx_init_reader(FASTX *pFASTX, const char* filename, diff --git a/var/spack/repos/builtin/packages/fastx-toolkit/package.py b/var/spack/repos/builtin/packages/fastx-toolkit/package.py index a291cb4385..8ad93ddad5 100644 --- a/var/spack/repos/builtin/packages/fastx-toolkit/package.py +++ b/var/spack/repos/builtin/packages/fastx-toolkit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,3 +19,5 @@ class FastxToolkit(AutotoolsPackage): # patch implicit fallthrough patch("pr-22.patch") + # fix error [-Werror,-Wpragma-pack] + patch('fix_pragma_pack.patch', when='%fj') diff --git a/var/spack/repos/builtin/packages/feh/package.py b/var/spack/repos/builtin/packages/feh/package.py new file mode 100644 index 0000000000..4d82263494 --- /dev/null +++ b/var/spack/repos/builtin/packages/feh/package.py @@ -0,0 +1,34 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class Feh(MakefilePackage): + """ + feh is an X11 image viewer aimed mostly at console users. Unlike most + other viewers, it does not have a fancy GUI, but simply displays images. It + is controlled via commandline arguments and configurable key/mouse + actions. + """ + + homepage = "https://feh.finalrewind.org/" + url = "https://feh.finalrewind.org/feh-3.3.tar.bz2" + + maintainers = ['TheQueasle'] + + version('3.3', sha256='f3959958258111d5f7c9fbe2e165c52b9d5987f07fd1f37540a4abf9f9638811') + version('3.1.1', sha256='61d0242e3644cf7c5db74e644f0e8a8d9be49b7bd01034265cc1ebb2b3f9c8eb') + + depends_on('imlib2') + depends_on('curl') + depends_on('libxinerama') + depends_on('libexif') + depends_on('libxt') + + def build(self, spec, prefix): + make('PREFIX={0}'.format(prefix), 'exif=1', 'help=1') + + def install(self, spec, prefix): + make('install', 'PREFIX={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py index 896edb583b..722d5c45be 100644 --- a/var/spack/repos/builtin/packages/fenics/package.py +++ b/var/spack/repos/builtin/packages/fenics/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fermi/package.py b/var/spack/repos/builtin/packages/fermi/package.py index 461b6d71d2..bf97d8fba1 100644 --- a/var/spack/repos/builtin/packages/fermi/package.py +++ b/var/spack/repos/builtin/packages/fermi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fermikit/package.py b/var/spack/repos/builtin/packages/fermikit/package.py index 3f746cf80e..6775c1c0e5 100644 --- a/var/spack/repos/builtin/packages/fermikit/package.py +++ b/var/spack/repos/builtin/packages/fermikit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fermisciencetools/package.py b/var/spack/repos/builtin/packages/fermisciencetools/package.py index ce2ae604b1..81719b4fd9 100644 --- a/var/spack/repos/builtin/packages/fermisciencetools/package.py +++ b/var/spack/repos/builtin/packages/fermisciencetools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ferret/package.py b/var/spack/repos/builtin/packages/ferret/package.py index 0113dfba3a..1ad1978240 100644 --- a/var/spack/repos/builtin/packages/ferret/package.py +++ b/var/spack/repos/builtin/packages/ferret/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,7 +19,7 @@ class Ferret(Package): version('6.96', sha256='7eb87156aa586cfe838ab83f08b2102598f9ab62062d540a5da8c9123816331a') depends_on("hdf5+hl") - depends_on("netcdf") + depends_on("netcdf-c") depends_on("netcdf-fortran") depends_on("readline") depends_on("zlib") @@ -63,7 +63,7 @@ class Ferret(Package): "-L%s -lnetcdff" % self.spec['netcdf-fortran'].prefix.lib, 'FERRET/platform_specific.mk.x86_64-linux') filter_file(r'\$\(NETCDF4_DIR\)/lib64/libnetcdf.a', - "-L%s -lnetcdf" % self.spec['netcdf'].prefix.lib, + "-L%s -lnetcdf" % self.spec['netcdf-c'].prefix.lib, 'FERRET/platform_specific.mk.x86_64-linux') filter_file(r'\$\(HDF5_DIR\)/lib64/libhdf5_hl.a', "-L%s -lhdf5_hl" % self.spec['hdf5'].prefix.lib, diff --git a/var/spack/repos/builtin/packages/ffmpeg/package.py b/var/spack/repos/builtin/packages/ffmpeg/package.py index 3a1983213e..b4ef8cc790 100644 --- a/var/spack/repos/builtin/packages/ffmpeg/package.py +++ b/var/spack/repos/builtin/packages/ffmpeg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py index 895bb53c3e..961c4cfc66 100644 --- a/var/spack/repos/builtin/packages/fftw/package.py +++ b/var/spack/repos/builtin/packages/fftw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fgsl/package.py b/var/spack/repos/builtin/packages/fgsl/package.py index 60d3580f25..1af9b2a0fa 100644 --- a/var/spack/repos/builtin/packages/fgsl/package.py +++ b/var/spack/repos/builtin/packages/fgsl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -34,6 +34,6 @@ class Fgsl(AutotoolsPackage): def create_m4_dir(self): mkdir('m4') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if self.compiler.name == 'gcc': - spack_env.append_flags('FCFLAGS', "-ffree-line-length-none") + env.append_flags('FCFLAGS', "-ffree-line-length-none") diff --git a/var/spack/repos/builtin/packages/figtree/package.py b/var/spack/repos/builtin/packages/figtree/package.py index 64e64c02e1..b96ccba7fa 100644 --- a/var/spack/repos/builtin/packages/figtree/package.py +++ b/var/spack/repos/builtin/packages/figtree/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/file/package.py b/var/spack/repos/builtin/packages/file/package.py new file mode 100644 index 0000000000..06ccfe4c33 --- /dev/null +++ b/var/spack/repos/builtin/packages/file/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class File(AutotoolsPackage): + """The file command is "a file type guesser", that is, a command-line + tool that tells you in words what kind of data a file contains""" + + homepage = "http://www.darwinsys.com/file/" + url = "https://astron.com/pub/file/file-5.37.tar.gz" + + version('5.37', sha256='e9c13967f7dd339a3c241b7710ba093560b9a33013491318e88e6b8b57bae07f') diff --git a/var/spack/repos/builtin/packages/filebench/package.py b/var/spack/repos/builtin/packages/filebench/package.py new file mode 100644 index 0000000000..0cb5e93a1f --- /dev/null +++ b/var/spack/repos/builtin/packages/filebench/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Filebench(AutotoolsPackage): + """ + Filebench is a file system and storage benchmark that can generate a + large variety of workloads. Unlike typical benchmarks it is extremely + flexible and allows to specify application's I/O behavior using its + extensive Workload Model Language (WML). Users can either describe + desired workloads from scratch or use(with or without modifications) + workload personalities shipped with Filebench(e.g., mail-, web-, file-, + and database-server workloads). Filebench is equally good for micro + and macro-benchmarking, quick to setup, and relatively easy to use. + """ + + homepage = "https://github.com/filebench/filebench" + url = "https://github.com/filebench/filebench/archive/1.4.9.1.tar.gz" + + version('1.4.9.1', sha256='77ae91b83c828ded1219550aec74fbbd6975dce02cb5ab13c3b99ac2154e5c2e') + version('1.4.9', sha256='61b8a838c1450b51a4ce61481a19a1bf0d6e3993180c524ff4051f7c18bd9c6a') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('flex', type='build') + depends_on('bison', type='build') + + def autoreconf(self, spec, prefix): + sh = which('sh') + sh('libtoolize') + sh('aclocal') + sh('autoheader') + sh('automake', '--add-missing') + sh('autoconf') diff --git a/var/spack/repos/builtin/packages/fimpute/package.py b/var/spack/repos/builtin/packages/fimpute/package.py index 7ee5f361f6..3f2bb658ea 100644 --- a/var/spack/repos/builtin/packages/fimpute/package.py +++ b/var/spack/repos/builtin/packages/fimpute/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/find-circ/package.py b/var/spack/repos/builtin/packages/find-circ/package.py new file mode 100644 index 0000000000..eef0f314aa --- /dev/null +++ b/var/spack/repos/builtin/packages/find-circ/package.py @@ -0,0 +1,34 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class FindCirc(Package): + """Find-circ is a collection of python scripts + detecting head-to-tail spliced (back-spliced) sequencing reads, + indicative of circular RNA (circRNA) in RNA-seq data.""" + + homepage = "https://github.com/marvin-jens/find_circ" + url = "https://github.com/marvin-jens/find_circ/archive/v1.2.tar.gz" + + version('1.2', sha256='f88bf9b5d0cc818313074982d4460c96706f555d924e2821832c3d03bf67743e') + + depends_on('python@2.7:2.8', type=('build', 'run')) + depends_on('py-pysam', type=('build', 'run')) + # Higher version of py-pandas and py-numpy + # depends on python@3: which conflicts with py-rnacocktail + depends_on('py-numpy@:1.16.5', type=('build', 'run')) + + def install(self, spec, prefix): + mkdir(prefix.bin) + install('cmp_bed.py', prefix.bin) + install('find_circ.py', prefix.bin) + install('maxlength.py', prefix.bin) + install('unmapped2anchors.py', prefix.bin) + install('README.md', prefix) + install('README.pdf', prefix) + install('LICENSE', prefix) + install_tree('test_data', prefix.test_data) diff --git a/var/spack/repos/builtin/packages/findutils/package.py b/var/spack/repos/builtin/packages/findutils/package.py index eb8009623a..f4a36dbb46 100644 --- a/var/spack/repos/builtin/packages/findutils/package.py +++ b/var/spack/repos/builtin/packages/findutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Findutils(AutotoolsPackage): +class Findutils(AutotoolsPackage, GNUMirrorPackage): """The GNU Find Utilities are the basic directory searching utilities of the GNU operating system.""" homepage = "https://www.gnu.org/software/findutils/" - url = "https://ftpmirror.gnu.org/findutils/findutils-4.6.0.tar.gz" + gnu_mirror_path = "findutils/findutils-4.6.0.tar.gz" version('4.6.0', sha256='ded4c9f73731cd48fec3b6bdaccce896473b6d8e337e9612e16cf1431bb1169d') version('4.4.2', sha256='434f32d171cbc0a5e72cfc5372c6fc4cb0e681f8dce566a0de5b6fccd702b62a') diff --git a/var/spack/repos/builtin/packages/fio/package.py b/var/spack/repos/builtin/packages/fio/package.py index 7e52b98c30..90064be1d5 100644 --- a/var/spack/repos/builtin/packages/fio/package.py +++ b/var/spack/repos/builtin/packages/fio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fish/package.py b/var/spack/repos/builtin/packages/fish/package.py index 4f8d8d3aae..57ca658a18 100644 --- a/var/spack/repos/builtin/packages/fish/package.py +++ b/var/spack/repos/builtin/packages/fish/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fixesproto/package.py b/var/spack/repos/builtin/packages/fixesproto/package.py index 15f8b2c8e0..14cbf18d26 100644 --- a/var/spack/repos/builtin/packages/fixesproto/package.py +++ b/var/spack/repos/builtin/packages/fixesproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fl/package.py b/var/spack/repos/builtin/packages/fl/package.py index 3b60495a53..f314ca6cdc 100644 --- a/var/spack/repos/builtin/packages/fl/package.py +++ b/var/spack/repos/builtin/packages/fl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/flac/package.py b/var/spack/repos/builtin/packages/flac/package.py index 7fd7761cd2..5a35abda8a 100644 --- a/var/spack/repos/builtin/packages/flac/package.py +++ b/var/spack/repos/builtin/packages/flac/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/flang/package.py b/var/spack/repos/builtin/packages/flang/package.py index a09e25b5be..853a8dfb35 100644 --- a/var/spack/repos/builtin/packages/flang/package.py +++ b/var/spack/repos/builtin/packages/flang/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,40 +13,65 @@ class Flang(CMakePackage): homepage = "https://github.com/flang-compiler/flang" - url = "https://github.com/flang-compiler/flang/archive/flang_20180612.tar.gz" + url = "https://github.com/flang-compiler/flang/archive/flang_20190329.tar.gz" git = "https://github.com/flang-compiler/flang.git" - version('develop', branch='master') + maintainers = ['naromero77'] + + version('master', branch='master') + version('20190329', sha256='b8c621da53829f8c53bad73125556fb1839c9056d713433b05741f7e445199f2') + version('20181226', sha256='00e716bea258c3bb60d6a5bb0c82bc79f67000062dc89939693e75f501883c36') version('20180921', sha256='f33bd1f054e474f1e8a204bb6f78d42f8f6ecf7a894fdddc3999f7c272350784') version('20180612', sha256='6af858bea013548e091371a97726ac784edbd4ff876222575eaae48a3c2920ed') - depends_on('llvm@flang-develop', when='@develop') - depends_on('llvm@flang-20180921', when='@20180921 target=x86_64:') - depends_on('llvm@flang-20180612', when='@20180612 target=x86_64:') + # Variants + variant('nvptx', + default=False, + description='Target OpenMP offload to NVidia GPUs') - depends_on('llvm@flang-20180921', when='@20180921 target=aarch64:') + # Build dependency + depends_on('cmake@3.8:', type='build') + depends_on('python@2.7:', type='build') - # LLVM version specific to OpenPOWER. - depends_on('llvm@flang-ppc64le-20180921', when='@20180921 target=ppc64le:') - depends_on('llvm@flang-ppc64le-20180612', when='@20180612 target=ppc64le:') + depends_on('llvm-flang@release_70', when='@master') + depends_on('llvm-flang@20190329', when='@20190329') + depends_on('llvm-flang@20181226_70', when='@20181226') + depends_on('llvm-flang@20180921', when='@20180921') + depends_on('llvm-flang@20180612', when='@20180612') - depends_on('pgmath@develop', when='@develop') + depends_on('pgmath@master', when='@master') + depends_on('pgmath@20190329', when='@20190329') + depends_on('pgmath@20181226', when='@20181226') depends_on('pgmath@20180921', when='@20180921') depends_on('pgmath@20180612', when='@20180612') + depends_on('cuda', when='+nvptx', type=('run')) + + # conflicts + conflicts('+nvptx', when='@:20181226', + msg='OMP offload to NVidia GPUs available March 2019 or later') + def cmake_args(self): + spec = self.spec options = [ '-DWITH_WERROR=OFF', '-DCMAKE_C_COMPILER=%s' % os.path.join( - self.spec['llvm'].prefix.bin, 'clang'), + spec['llvm-flang'].prefix.bin, 'clang'), '-DCMAKE_CXX_COMPILER=%s' % os.path.join( - self.spec['llvm'].prefix.bin, 'clang++'), + spec['llvm-flang'].prefix.bin, 'clang++'), '-DCMAKE_Fortran_COMPILER=%s' % os.path.join( - self.spec['llvm'].prefix.bin, 'flang'), + spec['llvm-flang'].prefix.bin, 'flang'), '-DFLANG_LIBOMP=%s' % find_libraries( - 'libomp', root=self.spec['llvm'].prefix.lib) + 'libomp', root=spec['llvm-flang'].prefix.lib), + '-DPYTHON_EXECUTABLE={0}'.format( + spec['python'].command.path) ] + if '+nvptx' in spec: + options.append('-DFLANG_OPENMP_GPU_NVIDIA=ON') + else: + options.append('-DFLANG_OPENMP_GPU_NVIDIA=OFF') + return options @run_after('install') @@ -61,7 +86,7 @@ class Flang(CMakePackage): out.write('#!/bin/bash\n') out.write( '{0} -I{1} -L{2} -L{3} {4}{5} {6}{7} -B{8} "$@"\n'.format( - self.spec['llvm'].prefix.bin.flang, + self.spec['llvm-flang'].prefix.bin.flang, self.prefix.include, self.prefix.lib, self.spec['pgmath'].prefix.lib, self.compiler.fc_rpath_arg, self.prefix.lib, @@ -71,9 +96,11 @@ class Flang(CMakePackage): chmod = which('chmod') chmod('+x', flang) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # to find llvm's libc++.so - spack_env.set('LD_LIBRARY_PATH', self.spec['llvm'].prefix.lib) - run_env.set('FC', join_path(self.spec.prefix.bin, 'flang')) - run_env.set('F77', join_path(self.spec.prefix.bin, 'flang')) - run_env.set('F90', join_path(self.spec.prefix.bin, 'flang')) + env.set('LD_LIBRARY_PATH', self.spec['llvm-flang'].prefix.lib) + + def setup_run_environment(self, env): + env.set('FC', self.spec.prefix.bin.flang) + env.set('F77', self.spec.prefix.bin.flang) + env.set('F90', self.spec.prefix.bin.flang) diff --git a/var/spack/repos/builtin/packages/flann/package.py b/var/spack/repos/builtin/packages/flann/package.py index 8746f764d6..fc69246518 100644 --- a/var/spack/repos/builtin/packages/flann/package.py +++ b/var/spack/repos/builtin/packages/flann/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -68,13 +68,13 @@ class Flann(CMakePackage): depends_on("boost+mpi+system+serialization+thread", when="+mpi ^hdf5+mpi") # Doc deps - depends_on("latex", when="+doc") + depends_on("texlive", when="+doc") # Example uses hdf5. depends_on("hdf5", when="+examples") depends_on('hdf5', type='test') - depends_on('gtest', type='test') + depends_on('googletest', type='test') # See: https://github.com/mariusmuja/flann/issues/369 patch('linux-gcc-cmakev3.11-plus.patch', when='%gcc^cmake@3.11:') diff --git a/var/spack/repos/builtin/packages/flash/package.py b/var/spack/repos/builtin/packages/flash/package.py index 4021f76360..79a27b46d4 100644 --- a/var/spack/repos/builtin/packages/flash/package.py +++ b/var/spack/repos/builtin/packages/flash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/flatbuffers/package.py b/var/spack/repos/builtin/packages/flatbuffers/package.py index e2386155d8..538922a7de 100644 --- a/var/spack/repos/builtin/packages/flatbuffers/package.py +++ b/var/spack/repos/builtin/packages/flatbuffers/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ class Flatbuffers(CMakePackage): homepage = "http://google.github.io/flatbuffers/" url = "https://github.com/google/flatbuffers/archive/v1.9.0.tar.gz" + version('1.11.0', sha256='3f4a286642094f45b1b77228656fbd7ea123964f19502f9ecfd29933fd23a50b') version('1.10.0', sha256='3714e3db8c51e43028e10ad7adffb9a36fc4aa5b1a363c2d0c4303dd1be59a7c') version('1.9.0', sha256='5ca5491e4260cacae30f1a5786d109230db3f3a6e5a0eb45d0d0608293d247e3') version('1.8.0', sha256='c45029c0a0f1a88d416af143e34de96b3091642722aa2d8c090916c6d1498c2e') diff --git a/var/spack/repos/builtin/packages/flatcc/package.py b/var/spack/repos/builtin/packages/flatcc/package.py index 2cc71b8381..ce3fc222fc 100644 --- a/var/spack/repos/builtin/packages/flatcc/package.py +++ b/var/spack/repos/builtin/packages/flatcc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/flecsale/package.py b/var/spack/repos/builtin/packages/flecsale/package.py index bb32fac5e2..2a05562752 100644 --- a/var/spack/repos/builtin/packages/flecsale/package.py +++ b/var/spack/repos/builtin/packages/flecsale/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/flecsi/package.py b/var/spack/repos/builtin/packages/flecsi/package.py index 3616de5a97..d78f350c59 100644 --- a/var/spack/repos/builtin/packages/flecsi/package.py +++ b/var/spack/repos/builtin/packages/flecsi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,13 +17,29 @@ class Flecsi(CMakePackage): n-dimensional hashed-tree data structures, graph partitioning interfaces,and dependency closures. ''' - homepage = 'http://flecsi.lanl.gov/' + homepage = 'http://flecsi.org/' git = 'https://github.com/laristra/flecsi.git' - version('develop', branch='master', submodules=False, preferred=True) + version('master', branch='master', submodules=False, preferred=True) - variant('backend', default='mpi', values=('serial', 'mpi', 'legion'), - description='Backend to use for distributed memory') + variant('build_type', default='Release', values=('Debug', 'Release'), + description='The build type to build', multi=False) + variant('backend', default='mpi', values=('serial', 'mpi', 'legion', 'hpx'), + description='Backend to use for distributed memory', multi=False) + variant('minimal', default=False, + description='Disable FindPackageMetis') + variant('shared', default=True, + description='Build shared libraries') + variant('flog', default=False, + description='Enable flog testing') + variant('doxygen', default=False, + description='Enable doxygen') + variant('doc', default=False, + description='Enable documentation') + variant('coverage', default=False, + description='Enable coverage build') + variant('hdf5', default=False, + description='Enable HDF5 Support') variant('caliper', default=False, description='Enable Caliper Support') variant('graphviz', default=False, @@ -33,50 +49,97 @@ class Flecsi(CMakePackage): variant('flecstan', default=False, description='Build FleCSI Static Analyzer') - depends_on('cmake@3.1:', type='build') + depends_on('cmake@3.12:', type='build') # Requires cinch > 1.0 due to cinchlog installation issue depends_on('cinch@1.01:', type='build') depends_on('mpi', when='backend=mpi') depends_on('mpi', when='backend=legion') - depends_on('gasnet@2019.3.0 ~pshm', when='backend=legion') - depends_on('legion@ctrl-rep +shared +mpi', when='backend=legion') - depends_on('boost@1.59.0: cxxstd=11 +program_options') + depends_on('mpi', when='backend=hpx') + depends_on('legion@ctrl-rep +shared +mpi +hdf5', when='backend=legion +hdf5') + depends_on('legion@ctrl-rep +shared +mpi', when='backend=legion ~hdf5') + depends_on('hpx@1.3.0 cxxstd=14', when='backend=hpx') + depends_on('boost@1.70.0: cxxstd=14 +program_options') depends_on('metis@5.1.0:') depends_on('parmetis@4.0.3:') + depends_on('hdf5', when='+hdf5') depends_on('caliper', when='+caliper') depends_on('graphviz', when='+graphviz') depends_on('python@3.0:', when='+tutorial') depends_on('llvm', when='+flecstan') + conflicts('+tutorial', when='backend=hpx') +# conflicts('+hdf5', when='backend=hpx') +# conflicts('+hdf5', when='backend=mpi') + def cmake_args(self): - options = ['-DCMAKE_BUILD_TYPE=debug'] - options.append('-DCINCH_SOURCE_DIR=' + self.spec['cinch'].prefix) + spec = self.spec + options = ['-DENABLE_OPENMP=ON', + '-DCXX_CONFORMANCE_STANDARD=c++17', + '-DENABLE_METIS=ON', + '-DENABLE_PARMETIS=ON', + '-DENABLE_COLORING=ON', + '-DENABLE_DEVEL_TARGETS=ON' + ] + options.append('-DCINCH_SOURCE_DIR=' + spec['cinch'].prefix) - if self.spec.variants['backend'].value == 'legion': + if spec.variants['backend'].value == 'legion': options.append('-DFLECSI_RUNTIME_MODEL=legion') - elif self.spec.variants['backend'].value == 'mpi': + options.append('-DENABLE_MPI=ON') + elif spec.variants['backend'].value == 'mpi': options.append('-DFLECSI_RUNTIME_MODEL=mpi') + options.append('-DENABLE_MPI=ON') + elif spec.variants['backend'].value == 'hpx': + options.append('-DFLECSI_RUNTIME_MODEL=hpx') + options.append('-DENABLE_MPI=ON') else: options.append('-DFLECSI_RUNTIME_MODEL=serial') - options.append( - '-DENABLE_MPI=OFF', - ) + options.append('-DENABLE_MPI=OFF') - if '+tutorial' in self.spec: - options.append('-DENABLE_FLECSIT=ON') - options.append('-DENABLE_FLECSI_TUTORIAL=ON') + if '+minimal' in spec: + options.append('-DCMAKE_DISABLE_FIND_PACKAGE_METIS=ON') else: - options.append('-DENABLE_FLECSIT=OFF') - options.append('-DENABLE_FLECSI_TUTORIAL=OFF') + options.append('-DCMAKE_DISABLE_FIND_PACKAGE_METIS=OFF') + if '+shared' in spec: + options.append('-DBUILD_SHARED_LIBS=ON') + else: + options.append('-DBUILD_SHARED_LIBS=OFF') + + if self.run_tests: + options.append('-DENABLE_UNIT_TESTS=ON') + else: + options.append('-DENABLE_UNIT_TESTS=OFF') - if '+caliper' in self.spec: + if '+hdf5' in spec and spec.variants['backend'].value == 'legion': + options.append('-DENABLE_HDF5=ON') + else: + options.append('-DENABLE_HDF5=OFF') + if '+caliper' in spec: options.append('-DENABLE_CALIPER=ON') else: options.append('-DENABLE_CALIPER=OFF') + if '+tutorial' in spec: + options.append('-DENABLE_FLECSIT=ON') + options.append('-DENABLE_FLECSI_TUTORIAL=ON') + else: + options.append('-DENABLE_FLECSIT=OFF') + options.append('-DENABLE_FLECSI_TUTORIAL=OFF') - if '+flecstan' in self.spec: + if '+flecstan' in spec: options.append('-DENABLE_FLECSTAN=ON') else: options.append('-DENABLE_FLECSTAN=OFF') + if '+doxygen' in spec: + options.append('-DENABLE_DOXYGEN=ON') + else: + options.append('-DENABLE_DOXYGEN=OFF') + if '+doc' in spec: + options.append('-DENABLE_DOCUMENTATION=ON') + else: + options.append('-DENABLE_DOCUMENTATION=OFF') + if '+coverage' in spec: + options.append('-DENABLE_COVERAGE_BUILD=ON') + else: + options.append('-DENABLE_COVERAGE_BUILD=OFF') + return options diff --git a/var/spack/repos/builtin/packages/flecsph/package.py b/var/spack/repos/builtin/packages/flecsph/package.py index 705c9eaecc..fee1e36c64 100644 --- a/var/spack/repos/builtin/packages/flecsph/package.py +++ b/var/spack/repos/builtin/packages/flecsph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py index 64e9bb69dc..3c9f51a0eb 100644 --- a/var/spack/repos/builtin/packages/flex/package.py +++ b/var/spack/repos/builtin/packages/flex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,6 +27,8 @@ class Flex(AutotoolsPackage): depends_on('bison', type='build') depends_on('gettext@0.19:', type='build') depends_on('help2man', type='build') + depends_on('findutils', type='build') + depends_on('diffutils', type='build') # Older tarballs don't come with a configure script and the patch for # 2.6.4 touches configure diff --git a/var/spack/repos/builtin/packages/flibcpp/package.py b/var/spack/repos/builtin/packages/flibcpp/package.py index b03fa79cbb..2e50100d4a 100644 --- a/var/spack/repos/builtin/packages/flibcpp/package.py +++ b/var/spack/repos/builtin/packages/flibcpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,7 +12,7 @@ class Flibcpp(CMakePackage): homepage = "https://flibcpp.readthedocs.io/en/latest" git = "https://github.com/swig-fortran/flibcpp.git" - url = "https://github.com/swig-fortran/flibcpp/archive/v0.3.0.tar.gz" + url = "https://github.com/swig-fortran/flibcpp/archive/v0.3.1.tar.gz" version('master', branch='master') version('0.3.1', sha256='871570124122c18018478275d5040b4b787d1966e50ee95b634b0b5e0cd27e91') diff --git a/var/spack/repos/builtin/packages/flink/package.py b/var/spack/repos/builtin/packages/flink/package.py new file mode 100644 index 0000000000..d07391f756 --- /dev/null +++ b/var/spack/repos/builtin/packages/flink/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Flink(Package): + """ + Apache Flink is an open source stream processing framework with + powerful stream- and batch-processing capabilities. + """ + + homepage = "https://flink.apache.org/" + url = "http://archive.apache.org/dist/flink/flink-1.9.1/flink-1.9.1-bin-scala_2.11.tgz" + + version('1.9.1', sha256='f69de344cd593e92f8261e19ae8a47b3910e9a70a7cd1ccfb1ecd1ff000b93ea') + version('1.9.0', sha256='a2245f68309e94ed54d86a680232a518aed9c5ea030bcc0b298bc8f27165eeb7') + version('1.8.3', sha256='1ba90e99f70ad7e2583d48d1404d1c09e327e8fb8fa716b1823e427464cc8dc0') + version('1.8.2', sha256='1a315f4f1fab9d651702d177b1741439ac98e6d06e9e13f9d410b34441eeda1c') + version('1.8.1', sha256='4fc0d0f163174ec43e160fdf21a91674979b978793e60361e2fce5dddba4ddfa') + + depends_on('java@8:', type='run') + + def url_for_version(self, version): + url = "http://archive.apache.org/dist/flink/flink-{0}/flink-{0}-bin-scala_2.11.tgz" + return url.format(version) + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/flint/package.py b/var/spack/repos/builtin/packages/flint/package.py index c83e4f0cd2..11c3afbdf0 100644 --- a/var/spack/repos/builtin/packages/flint/package.py +++ b/var/spack/repos/builtin/packages/flint/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/flit/package.py b/var/spack/repos/builtin/packages/flit/package.py index 7b3364ef13..66f4c43452 100644 --- a/var/spack/repos/builtin/packages/flit/package.py +++ b/var/spack/repos/builtin/packages/flit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fltk/package.py b/var/spack/repos/builtin/packages/fltk/package.py index 9b4aaa6de9..c1971899bf 100644 --- a/var/spack/repos/builtin/packages/fltk/package.py +++ b/var/spack/repos/builtin/packages/fltk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/flume/package.py b/var/spack/repos/builtin/packages/flume/package.py new file mode 100644 index 0000000000..f672aa3b79 --- /dev/null +++ b/var/spack/repos/builtin/packages/flume/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Flume(Package): + """ + Apache Flume is a distributed, reliable, and available service for + efficiently collecting, aggregating, and moving large amounts of log + data. It has a simple and flexible architecture based on streaming + data flows. It is robust and fault tolerant with tunable reliability + mechanisms and many failover and recovery mechanisms. The system is + centrally managed and allows for intelligent dynamic management. It + uses a simple extensible data model that allows for online analytic + application. + """ + + homepage = "https://cwiki.apache.org/FLUME" + url = "https://www.apache.org/dist/flume/1.9.0/apache-flume-1.9.0-bin.tar.gz" + + version('1.9.0', sha256='0373ed5abfd44dc4ab23d9a02251ffd7e3b32c02d83a03546e97ec15a7b23619') + version('1.8.0', sha256='be1b554a5e23340ecc5e0b044215bf7828ff841f6eabe647b526d31add1ab5fa') + version('1.7.0', sha256='b97254cf37c36b6e5045f764095d86fc6d9a8043dda169e950547fcae35681ec') + version('1.6.0', sha256='0f7cef2f0128249893498a23401a0c8cb261e4516bc60f1885f8a3ae4475ed80') + version('1.5.2', sha256='649f07c41d0e77acd661c683146a0c5e395bfb3f23df198196fe8058a7b01426') + + depends_on('java@8:', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/flux-core/package.py b/var/spack/repos/builtin/packages/flux-core/package.py index 11cb14d23c..04ce1eceeb 100644 --- a/var/spack/repos/builtin/packages/flux-core/package.py +++ b/var/spack/repos/builtin/packages/flux-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,7 +14,10 @@ class FluxCore(AutotoolsPackage): url = "https://github.com/flux-framework/flux-core/releases/download/v0.8.0/flux-core-0.8.0.tar.gz" git = "https://github.com/flux-framework/flux-core.git" - version('master', branch='master') + version('master', branch='master') + version('0.11.3', sha256='91b5d7dca8fc28a77777c4e4cb8717fc3dc2c174e70611740689a71901c6de7e') + version('0.11.2', sha256='ab8637428cd9b74b2dff4842d10e0fc4acc8213c4e51f31d32a4cbfbdf730412') + version('0.11.1', sha256='3c8495db0f3b701f6dfe3e2a75aed794fc561e9f28284e8c02ac67693bfe890e') version('0.11.0', sha256='a4d8ff92e79b4ca19d556395bb8c5f8dc02fd9d5a8cc38c4a2c66867a96de5ea') version('0.10.0', sha256='a70cdd228077af60c9443a5c69d3da932e447dd11697f5fef9028c48dabb3041') version('0.9.0', sha256='7b5b4aa72704b3c4432136b9e515e0d663568e6dbfc3ecd2f91c83b65841104e') @@ -27,10 +30,10 @@ class FluxCore(AutotoolsPackage): variant('docs', default=False, description='Build flux manpages') variant('cuda', default=False, description='Build dependencies with support for CUDA') - depends_on("zeromq@4.0.4:") + depends_on("libzmq@4.0.4:") depends_on("czmq") - depends_on("czmq@2.2:3.99", when="@0.1:0.6.99") - depends_on("czmq@3.0.1:", when="@0.7:,master") + depends_on("czmq@2.2:3.99", when="@0.1:0.6") + depends_on("czmq@3.0.1:", when="@0.7:") depends_on("hwloc@1.11.1:1.99") depends_on("hwloc +cuda", when='+cuda') # Provide version hints for lua so that the concretizer succeeds when no @@ -42,15 +45,15 @@ class FluxCore(AutotoolsPackage): depends_on("munge", when="@0.1.0:0.10.0") depends_on("python", type=('build', 'run')) depends_on("python@2.7:2.99", when="@0.1.0:0.11.0") - depends_on("python@2.7:", when="@0.11.1:,master") + depends_on("python@2.7:", when="@0.11.1:") depends_on("py-cffi", type=('build', 'run')) - depends_on("py-six", type=('build', 'run'), when="@0.11.0:,master") - depends_on("py-pyyaml", type=('build', 'run'), when="@0.11.0:,master") - depends_on("py-jsonschema", type=('build', 'run'), when="@master") + depends_on("py-six", type=('build', 'run'), when="@0.11.0:") + depends_on("py-pyyaml", type=('build', 'run'), when="@0.11.0:") + depends_on("py-jsonschema", type=('build', 'run'), when="@0.12.0:") depends_on("jansson") depends_on("pkgconfig") - depends_on("yaml-cpp", when="@:0.11.0") - depends_on("lz4", when="@0.11.0:,master") + depends_on("yaml-cpp", when="@:0.11") + depends_on("lz4", when="@0.11.0:") # versions up to 0.8.0 uses pylint to check Flux's python binding # later versions provide a configure flag and disable the check by default @@ -63,6 +66,29 @@ class FluxCore(AutotoolsPackage): depends_on("automake", type='build', when='@master') depends_on("libtool", type='build', when='@master') + # Testing Dependencies + depends_on("mpich pmi=pmi", type="test") + depends_on("valgrind", type="test") + depends_on("jq", type="test", when='@0.12.0:') + + def url_for_version(self, version): + ''' + Flux uses a fork of ZeroMQ's Collective Code Construction Contract + (https://github.com/flux-framework/rfc/blob/master/spec_1.adoc). + This model requires a repository fork for every stable release that has + patch releases. For example, 0.8.0 and 0.9.0 are both tags within the + main repository, but 0.8.1 and 0.9.5 would be releases on the v0.8 and + v0.9 forks, respectively. + + Rather than provide an explicit URL for each patch release, make Spack + aware of this repo structure. + ''' + if version[-1] == 0: + url = "https://github.com/flux-framework/flux-core/releases/download/v{0}/flux-core-{0}.tar.gz" + else: + url = "https://github.com/flux-framework/flux-core-v{1}/releases/download/v{0}/flux-core-{0}.tar.gz" + return url.format(version.up_to(3), version.up_to(2)) + def setup(self): pass @@ -95,28 +121,49 @@ class FluxCore(AutotoolsPackage): def lua_lib_dir(self): return os.path.join('lib', 'lua', str(self.lua_version)) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Ensure ./fluxometer.lua can be found during flux's make check - spack_env.append_path('LUA_PATH', './?.lua', separator=';') + env.append_path('LUA_PATH', './?.lua', separator=';') - run_env.prepend_path( + def setup_run_environment(self, env): + env.prepend_path( 'LUA_PATH', os.path.join(self.spec.prefix, self.lua_share_dir, '?.lua'), separator=';') - run_env.prepend_path( + env.prepend_path( 'LUA_CPATH', os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'), separator=';') - run_env.prepend_path( + env.prepend_path( 'PYTHONPATH', os.path.join( self.spec.prefix.lib, "python{0}".format(self.spec['python'].version.up_to(2)), "site-packages"), ) - run_env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules) - run_env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd) - run_env.prepend_path('FLUX_RC_PATH', self.prefix.etc.flux) + env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules) + env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd) + env.prepend_path('FLUX_RC_PATH', self.prefix.etc.flux) + env.prepend_path('FLUX_RC1_PATH', self.prefix.etc.flux.rc1) + env.prepend_path('FLUX_RC3_PATH', self.prefix.etc.flux.rc3) + env.prepend_path( + 'FLUX_CONNECTOR_PATH', + self.prefix.lib.flux.connectors + ) + env.prepend_path( + 'FLUX_PMI_LIBRARY_PATH', + os.path.join(self.prefix.lib.flux, "libpmi.so") + ) + # Wreck was removed in 0.12 + if self.version < Version("0.12.0"): + env.prepend_path( + 'FLUX_WREXECD_PATH', + self.prefix.libexec.flux.wrexecd + ) + env.prepend_path( + 'FLUX_WRECK_LUA_PATTERN', + os.path.join(self.prefix.etc.wreck, "lua.d", "*.lua") + ) def configure_args(self): args = ['--enable-pylint=no'] diff --git a/var/spack/repos/builtin/packages/flux-sched/package.py b/var/spack/repos/builtin/packages/flux-sched/package.py index 5a77ed46ff..60001e7b89 100644 --- a/var/spack/repos/builtin/packages/flux-sched/package.py +++ b/var/spack/repos/builtin/packages/flux-sched/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,7 @@ class FluxSched(AutotoolsPackage): git = "https://github.com/flux-framework/flux-sched.git" version('master', branch='master') + version('0.7.1', sha256='a35e555a353feed6b7b814ae83d05362356f9ee33ffa75d7dfb7e2fe86c21294') version('0.7.0', sha256='69267a3aaacaedd9896fd90cfe17aef266cba4fb28c77f8123d95a31ce739a7b') version('0.6.0', sha256='3301d4c10810414228e5969b84b75fe1285abb97453070eb5a77f386d8184f8d') version('0.5.0', sha256='d6347f5c85c12c76364dccb39d63c007094ca9cbbbae4e8f4e98d8b1c0b07e89') @@ -26,9 +27,9 @@ class FluxSched(AutotoolsPackage): variant('cuda', default=False, description='Build dependencies with support for CUDA') - depends_on("boost+graph@1.53.0,1.59.0:", when='@0.5.0:,master') - depends_on("py-pyyaml", when="@0.7.0:,master") - depends_on("libxml2@2.9.1:", when="@0.6.0,master") + depends_on("boost+graph@1.53.0,1.59.0:", when='@0.5.0:') + depends_on("py-pyyaml", when="@0.7.0:") + depends_on("libxml2@2.9.1:", when="@0.6.0") depends_on("yaml-cpp", when="@0.7.0:") depends_on("libuuid") depends_on("pkgconfig") @@ -39,6 +40,7 @@ class FluxSched(AutotoolsPackage): depends_on("flux-core@0.9.0", when='@0.5.0') depends_on("flux-core@0.10.0", when='@0.6.0') depends_on("flux-core@0.11.0", when='@0.7.0') + depends_on("flux-core@0.11.2:0.11.99", when='@0.7.1') depends_on("flux-core@master", when='@master') # Need autotools when building on master: @@ -46,6 +48,24 @@ class FluxSched(AutotoolsPackage): depends_on("automake", type='build', when='@master') depends_on("libtool", type='build', when='@master') + def url_for_version(self, version): + ''' + Flux uses a fork of ZeroMQ's Collective Code Construction Contract + (https://github.com/flux-framework/rfc/blob/master/spec_1.adoc). + This model requires a repository fork for every stable release that has + patch releases. For example, 0.8.0 and 0.9.0 are both tags within the + main repository, but 0.8.1 and 0.9.5 would be releases on the v0.8 and + v0.9 forks, respectively. + + Rather than provide an explicit URL for each patch release, make Spack + aware of this repo structure. + ''' + if version[-1] == 0: + url = "https://github.com/flux-framework/flux-sched/releases/download/v{0}/flux-sched-{0}.tar.gz" + else: + url = "https://github.com/flux-framework/flux-sched-v{1}/releases/download/v{0}/flux-sched-{0}.tar.gz" + return url.format(version.up_to(3), version.up_to(2)) + def setup(self): pass @@ -86,18 +106,18 @@ class FluxSched(AutotoolsPackage): def lua_lib_dir(self): return os.path.join('lib', 'lua', str(self.lua_version)) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path( + def setup_run_environment(self, env): + env.prepend_path( 'LUA_PATH', os.path.join(self.spec.prefix, self.lua_share_dir, '?.lua'), separator=';') - run_env.prepend_path( + env.prepend_path( 'LUA_CPATH', os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'), separator=';') - run_env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules) - run_env.prepend_path('FLUX_MODULE_PATH', - self.prefix.lib.flux.modules.sched) - run_env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd) - run_env.prepend_path('FLUX_RC_EXTRA', self.prefix.etc.flux) + env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules) + env.prepend_path('FLUX_MODULE_PATH', + self.prefix.lib.flux.modules.sched) + env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd) + env.prepend_path('FLUX_RC_EXTRA', self.prefix.etc.flux) diff --git a/var/spack/repos/builtin/packages/fluxbox/fix_zero_comparison.patch b/var/spack/repos/builtin/packages/fluxbox/fix_zero_comparison.patch new file mode 100644 index 0000000000..53c2367a3a --- /dev/null +++ b/var/spack/repos/builtin/packages/fluxbox/fix_zero_comparison.patch @@ -0,0 +1,11 @@ +--- spack-src/util/fluxbox-remote.cc.org 2019-11-08 16:22:55.647747144 +0900 ++++ spack-src/util/fluxbox-remote.cc 2019-11-08 16:23:15.709859444 +0900 +@@ -73,7 +73,7 @@ + if (strcmp(cmd, "result") == 0) { + XTextProperty text_prop; + if (XGetTextProperty(disp, root, &text_prop, atom_result) != 0 +- && text_prop.value > 0 ++ && text_prop.value != 0 + && text_prop.nitems > 0) { + + printf("%s", text_prop.value); diff --git a/var/spack/repos/builtin/packages/fluxbox/package.py b/var/spack/repos/builtin/packages/fluxbox/package.py index d4499612ba..04dc39196b 100644 --- a/var/spack/repos/builtin/packages/fluxbox/package.py +++ b/var/spack/repos/builtin/packages/fluxbox/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,6 +19,9 @@ class Fluxbox(AutotoolsPackage): version('1.3.7', sha256='c99e2baa06fff1e96342b20415059d12ff1fa2917ade0173c75b2fa570295b9f') + # Referenced:https://sourceforge.net/p/fluxbox/bugs/1171/ + patch('fix_zero_comparison.patch') + depends_on('pkgconfig', type='build') depends_on('freetype') depends_on('libxrender') diff --git a/var/spack/repos/builtin/packages/fmt/package.py b/var/spack/repos/builtin/packages/fmt/package.py index b410b568b6..8cba74d000 100644 --- a/var/spack/repos/builtin/packages/fmt/package.py +++ b/var/spack/repos/builtin/packages/fmt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/foam-extend/package.py b/var/spack/repos/builtin/packages/foam-extend/package.py index 8932c4cc07..e0c9a5ded9 100644 --- a/var/spack/repos/builtin/packages/foam-extend/package.py +++ b/var/spack/repos/builtin/packages/foam-extend/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -118,7 +118,7 @@ class FoamExtend(Package): # - End of definitions / setup - # - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Add environment variables to the generated module file. These environment variables come from running: @@ -126,13 +126,6 @@ class FoamExtend(Package): $ . $WM_PROJECT_DIR/etc/bashrc """ - - # NOTE: Spack runs setup_environment twice. - # 1) pre-build to set up the build environment - # 2) post-install to determine runtime environment variables - # The etc/bashrc is only available (with corrrect content) - # post-installation. - bashrc = join_path(self.projectdir, 'etc', 'bashrc') minimal = True if os.path.isfile(bashrc): @@ -173,7 +166,7 @@ class FoamExtend(Package): 'PYTHON_BIN_DIR', ]) - run_env.extend(mods) + env.extend(mods) minimal = False tty.info('foam-extend env: {0}'.format(bashrc)) except Exception: @@ -182,19 +175,19 @@ class FoamExtend(Package): if minimal: # pre-build or minimal environment tty.info('foam-extend minimal env {0}'.format(self.prefix)) - run_env.set('FOAM_INST_DIR', os.path.dirname(self.projectdir)), - run_env.set('FOAM_PROJECT_DIR', self.projectdir) - run_env.set('WM_PROJECT_DIR', self.projectdir) + env.set('FOAM_INST_DIR', os.path.dirname(self.projectdir)), + env.set('FOAM_PROJECT_DIR', self.projectdir) + env.set('WM_PROJECT_DIR', self.projectdir) for d in ['wmake', self.archbin]: # bin added automatically - run_env.prepend_path('PATH', join_path(self.projectdir, d)) + env.prepend_path('PATH', join_path(self.projectdir, d)) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Location of the OpenFOAM project. This is identical to the WM_PROJECT_DIR value, but we avoid that variable since it would mask the normal OpenFOAM cleanup of previous versions. """ - spack_env.set('FOAM_PROJECT_DIR', self.projectdir) + env.set('FOAM_PROJECT_DIR', self.projectdir) @property def projectdir(self): diff --git a/var/spack/repos/builtin/packages/folly/package.py b/var/spack/repos/builtin/packages/folly/package.py index e49b04b42a..c61b82024f 100644 --- a/var/spack/repos/builtin/packages/folly/package.py +++ b/var/spack/repos/builtin/packages/folly/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/font-util/package.py b/var/spack/repos/builtin/packages/font-util/package.py index 11635276fa..41923f5ad1 100644 --- a/var/spack/repos/builtin/packages/font-util/package.py +++ b/var/spack/repos/builtin/packages/font-util/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -77,10 +77,9 @@ class FontUtil(AutotoolsPackage): default=','.join(fonts), multi=True) - def setup_environment(self, spack_env, run_env): - spack_env.prepend_path('PATH', self.prefix.bin) - spack_env.prepend_path('PKG_CONFIG_PATH', - join_path(self.prefix.lib, 'pkgconfig')) + def setup_build_environment(self, env): + env.prepend_path('PATH', self.prefix.bin) + env.prepend_path('PKG_CONFIG_PATH', self.prefix.lib.pkgconfig) @run_after('install') def font_install(self): diff --git a/var/spack/repos/builtin/packages/fontcacheproto/package.py b/var/spack/repos/builtin/packages/fontcacheproto/package.py index 3c7328a14c..52d1a23fe0 100644 --- a/var/spack/repos/builtin/packages/fontcacheproto/package.py +++ b/var/spack/repos/builtin/packages/fontcacheproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fontconfig/package.py b/var/spack/repos/builtin/packages/fontconfig/package.py index 1b6f1e7738..d6fd7f9085 100644 --- a/var/spack/repos/builtin/packages/fontconfig/package.py +++ b/var/spack/repos/builtin/packages/fontconfig/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fontsproto/package.py b/var/spack/repos/builtin/packages/fontsproto/package.py index 7165eab558..419984c624 100644 --- a/var/spack/repos/builtin/packages/fontsproto/package.py +++ b/var/spack/repos/builtin/packages/fontsproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fonttosfnt/package.py b/var/spack/repos/builtin/packages/fonttosfnt/package.py index b47f89b873..74b870ca64 100644 --- a/var/spack/repos/builtin/packages/fonttosfnt/package.py +++ b/var/spack/repos/builtin/packages/fonttosfnt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fp16/package.py b/var/spack/repos/builtin/packages/fp16/package.py index 7260b4cb9f..7ce6c7742d 100644 --- a/var/spack/repos/builtin/packages/fp16/package.py +++ b/var/spack/repos/builtin/packages/fp16/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fpc/package.py b/var/spack/repos/builtin/packages/fpc/package.py index ccaaee5b8d..5e1be34992 100644 --- a/var/spack/repos/builtin/packages/fpc/package.py +++ b/var/spack/repos/builtin/packages/fpc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fpocket/package.py b/var/spack/repos/builtin/packages/fpocket/package.py index 5d5e92dc4d..029e150db9 100644 --- a/var/spack/repos/builtin/packages/fpocket/package.py +++ b/var/spack/repos/builtin/packages/fpocket/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,11 +14,11 @@ class Fpocket(MakefilePackage): version('master', branch='master', git='https://github.com/Discngine/fpocket.git') - depends_on("netcdf") + depends_on("netcdf-c") - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if self.compiler.name == 'gcc': - spack_env.set('CXX', 'g++') + env.set('CXX', 'g++') def edit(self): makefile = FileFilter('makefile') diff --git a/var/spack/repos/builtin/packages/fqtrim/package.py b/var/spack/repos/builtin/packages/fqtrim/package.py index fb02c9c89c..b9dfd16360 100644 --- a/var/spack/repos/builtin/packages/fqtrim/package.py +++ b/var/spack/repos/builtin/packages/fqtrim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fr-hit/package.py b/var/spack/repos/builtin/packages/fr-hit/package.py index f1ea5774c0..e3547a3111 100644 --- a/var/spack/repos/builtin/packages/fr-hit/package.py +++ b/var/spack/repos/builtin/packages/fr-hit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/freebayes/package.py b/var/spack/repos/builtin/packages/freebayes/package.py index 9b047247a8..338ca3c26c 100644 --- a/var/spack/repos/builtin/packages/freebayes/package.py +++ b/var/spack/repos/builtin/packages/freebayes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/freeglut/package.py b/var/spack/repos/builtin/packages/freeglut/package.py index bea45b795f..72ab7986d1 100644 --- a/var/spack/repos/builtin/packages/freeglut/package.py +++ b/var/spack/repos/builtin/packages/freeglut/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/freeimage/package.py b/var/spack/repos/builtin/packages/freeimage/package.py index a7be20f9ec..0243d39b2d 100644 --- a/var/spack/repos/builtin/packages/freeimage/package.py +++ b/var/spack/repos/builtin/packages/freeimage/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/freetype/package.py b/var/spack/repos/builtin/packages/freetype/package.py index 0f522ab2c8..a4662cfa9c 100644 --- a/var/spack/repos/builtin/packages/freetype/package.py +++ b/var/spack/repos/builtin/packages/freetype/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/freexl/package.py b/var/spack/repos/builtin/packages/freexl/package.py index aef3a885d3..20348e5581 100644 --- a/var/spack/repos/builtin/packages/freexl/package.py +++ b/var/spack/repos/builtin/packages/freexl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fribidi/package.py b/var/spack/repos/builtin/packages/fribidi/package.py index 4af15714bf..d356e465c3 100644 --- a/var/spack/repos/builtin/packages/fribidi/package.py +++ b/var/spack/repos/builtin/packages/fribidi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fseq/package.py b/var/spack/repos/builtin/packages/fseq/package.py index 4858114ef0..8bbd4f176f 100644 --- a/var/spack/repos/builtin/packages/fseq/package.py +++ b/var/spack/repos/builtin/packages/fseq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fsl/package.py b/var/spack/repos/builtin/packages/fsl/package.py index 642f09644a..35f4978698 100644 --- a/var/spack/repos/builtin/packages/fsl/package.py +++ b/var/spack/repos/builtin/packages/fsl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -51,33 +51,33 @@ class Fsl(Package): install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if not self.stage.source_path: self.stage.fetch() self.stage.expand_archive() - spack_env.set('FSLDIR', self.stage.source_path) - - # Here, run-time environment variables are being set manually. - # Normally these would be added to the modulefile at build-time - # by sourcing fsl.sh, but incorrect paths were being set, pointing to - # the staging directory rather than the install directory. - run_env.set('FSLDIR', self.prefix) - run_env.set('FSLOUTPUTTYPE', 'NIFTI_GZ') - run_env.set('FSLMULTIFILEQUIT', 'TRUE') - run_env.set('FSLTCLSH', self.prefix.bin.fsltclsh) - run_env.set('FSLWISH', self.prefix.bin.fslwish) - run_env.set('FSLLOCKDIR', '') - run_env.set('FSLMACHINELIST', '') - run_env.set('FSLREMOTECALL', '') - run_env.set('FSLGECUDAQ', 'cuda.q') - - run_env.prepend_path('PATH', self.prefix) + env.set('FSLDIR', self.stage.source_path) # Below is for sourcing purposes during building fslsetup = join_path(self.stage.source_path, 'etc', 'fslconf', 'fsl.sh') if os.path.isfile(fslsetup): - spack_env.extend(EnvironmentModifications.from_sourcing_file( - fslsetup)) + env.extend(EnvironmentModifications.from_sourcing_file(fslsetup)) + + def setup_run_environment(self, env): + # Here, run-time environment variables are being set manually. + # Normally these would be added to the modulefile at build-time + # by sourcing fsl.sh, but incorrect paths were being set, pointing to + # the staging directory rather than the install directory. + env.set('FSLDIR', self.prefix) + env.set('FSLOUTPUTTYPE', 'NIFTI_GZ') + env.set('FSLMULTIFILEQUIT', 'TRUE') + env.set('FSLTCLSH', self.prefix.bin.fsltclsh) + env.set('FSLWISH', self.prefix.bin.fslwish) + env.set('FSLLOCKDIR', '') + env.set('FSLMACHINELIST', '') + env.set('FSLREMOTECALL', '') + env.set('FSLGECUDAQ', 'cuda.q') + + env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/fslsfonts/package.py b/var/spack/repos/builtin/packages/fslsfonts/package.py index c01b606f8a..32083f58dc 100644 --- a/var/spack/repos/builtin/packages/fslsfonts/package.py +++ b/var/spack/repos/builtin/packages/fslsfonts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fstobdf/package.py b/var/spack/repos/builtin/packages/fstobdf/package.py index b5704593b8..76ee5a731e 100644 --- a/var/spack/repos/builtin/packages/fstobdf/package.py +++ b/var/spack/repos/builtin/packages/fstobdf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fstrack/package.py b/var/spack/repos/builtin/packages/fstrack/package.py index 297af6dbac..d6a0f5e4de 100644 --- a/var/spack/repos/builtin/packages/fstrack/package.py +++ b/var/spack/repos/builtin/packages/fstrack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,25 +20,25 @@ class Fstrack(MakefilePackage): variant('flow', default=True, description='Build the flow tracker') depends_on('gmt@4.0:4.999', when='+flow') - depends_on('netcdf', when='+flow') + depends_on('netcdf-c', when='+flow') parallel = False - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Compilers - spack_env.set('F90', spack_fc) + env.set('F90', spack_fc) # Compiler flags (assumes GCC) - spack_env.set('CFLAGS', '-O2') - spack_env.set('FFLAGS', '-ffixed-line-length-132 -x f77-cpp-input -O2') - spack_env.set('FFLAGS_DEBUG', '-g -x f77-cpp-input') - spack_env.set('F90FLAGS', '-O2 -x f95-cpp-input') - spack_env.set('F90FLAGS_DEBUG', '-g -x f95-cpp-input') - spack_env.set('LDFLAGS', '-lm') + env.set('CFLAGS', '-O2') + env.set('FFLAGS', '-ffixed-line-length-132 -x f77-cpp-input -O2') + env.set('FFLAGS_DEBUG', '-g -x f77-cpp-input') + env.set('F90FLAGS', '-O2 -x f95-cpp-input') + env.set('F90FLAGS_DEBUG', '-g -x f95-cpp-input') + env.set('LDFLAGS', '-lm') if '+flow' in self.spec: - spack_env.set('GMTHOME', self.spec['gmt'].prefix) - spack_env.set('NETCDFDIR', self.spec['netcdf'].prefix) + env.set('GMTHOME', self.spec['gmt'].prefix) + env.set('NETCDFDIR', self.spec['netcdf-c'].prefix) def build(self, spec, prefix): with working_dir('eispack'): diff --git a/var/spack/repos/builtin/packages/ftgl/ftgl-2.1.3-rc5-ldflags.patch b/var/spack/repos/builtin/packages/ftgl/ftgl-2.1.3-rc5-ldflags.patch deleted file mode 100644 index 871990a234..0000000000 --- a/var/spack/repos/builtin/packages/ftgl/ftgl-2.1.3-rc5-ldflags.patch +++ /dev/null @@ -1,118 +0,0 @@ -diff -up ftgl-2.1.3~rc5/demo/Makefile.am.ldflags ftgl-2.1.3~rc5/demo/Makefile.am ---- ftgl-2.1.3~rc5/demo/Makefile.am.ldflags 2008-06-02 03:10:10.000000000 +0200 -+++ ftgl-2.1.3~rc5/demo/Makefile.am 2010-02-14 15:02:19.670081290 +0100 -@@ -9,14 +9,14 @@ simple_SOURCES = \ - simple.cpp \ - $(NULL) - simple_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --simple_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -+simple_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) - simple_LDADD = ../src/libftgl.la - - c_demo_SOURCES = \ - c-demo.c \ - $(NULL) - c_demo_CFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --c_demo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -+c_demo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) -lm - c_demo_LDADD = ../src/libftgl.la - - FTGLDemo_SOURCES = \ -@@ -27,7 +27,7 @@ FTGLDemo_SOURCES = \ - trackball.h \ - $(NULL) - FTGLDemo_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --FTGLDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -+FTGLDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) - FTGLDemo_LDADD = ../src/libftgl.la - - FTGLMFontDemo_SOURCES = \ -@@ -38,7 +38,7 @@ FTGLMFontDemo_SOURCES = \ - trackball.h \ - $(NULL) - FTGLMFontDemo_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --FTGLMFontDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -+FTGLMFontDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) - FTGLMFontDemo_LDADD = ../src/libftgl.la - - NULL = -diff -up ftgl-2.1.3~rc5/demo/Makefile.in.ldflags ftgl-2.1.3~rc5/demo/Makefile.in ---- ftgl-2.1.3~rc5/demo/Makefile.in.ldflags 2008-06-12 16:33:01.000000000 +0200 -+++ ftgl-2.1.3~rc5/demo/Makefile.in 2010-02-14 15:02:01.866831398 +0100 -@@ -242,14 +242,14 @@ simple_SOURCES = \ - $(NULL) - - simple_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --simple_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -+simple_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) - simple_LDADD = ../src/libftgl.la - c_demo_SOURCES = \ - c-demo.c \ - $(NULL) - - c_demo_CFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --c_demo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -+c_demo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) -lm - c_demo_LDADD = ../src/libftgl.la - FTGLDemo_SOURCES = \ - FTGLDemo.cpp \ -@@ -260,7 +260,7 @@ FTGLDemo_SOURCES = \ - $(NULL) - - FTGLDemo_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --FTGLDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -+FTGLDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) - FTGLDemo_LDADD = ../src/libftgl.la - FTGLMFontDemo_SOURCES = \ - FTGLMFontDemo.cpp \ -@@ -271,7 +271,7 @@ FTGLMFontDemo_SOURCES = \ - $(NULL) - - FTGLMFontDemo_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --FTGLMFontDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -+FTGLMFontDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) - FTGLMFontDemo_LDADD = ../src/libftgl.la - NULL = - all: all-am -diff -up ftgl-2.1.3~rc5/test/Makefile.am.ldflags ftgl-2.1.3~rc5/test/Makefile.am ---- ftgl-2.1.3~rc5/test/Makefile.am.ldflags 2010-02-14 14:43:14.819077822 +0100 -+++ ftgl-2.1.3~rc5/test/Makefile.am 2010-02-14 14:43:49.227081230 +0100 -@@ -51,7 +51,7 @@ AM_CPPFLAGS = \ - $(NULL) - - CXXTest_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --CXXTest_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -lcppunit -+CXXTest_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) -lcppunit - CXXTest_LDADD = ../src/libftgl.la - - CTest_SOURCES = \ -@@ -64,7 +64,7 @@ CTest_CPPFLAGS = \ - -I$(top_srcdir)/src/FTFont \ - -I$(top_srcdir)/src/FTLayout - CTest_CFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --CTest_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -+CTest_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) - CTest_LDADD = ../src/libftgl.la - - NULL = -diff -up ftgl-2.1.3~rc5/test/Makefile.in.ldflags ftgl-2.1.3~rc5/test/Makefile.in ---- ftgl-2.1.3~rc5/test/Makefile.in.ldflags 2010-02-14 14:43:20.365077958 +0100 -+++ ftgl-2.1.3~rc5/test/Makefile.in 2010-02-14 14:44:13.653078013 +0100 -@@ -294,7 +294,7 @@ AM_CPPFLAGS = \ - $(NULL) - - CXXTest_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --CXXTest_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -lcppunit -+CXXTest_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) -lcppunit - CXXTest_LDADD = ../src/libftgl.la - CTest_SOURCES = \ - CTest.c \ -@@ -308,7 +308,7 @@ CTest_CPPFLAGS = \ - -I$(top_srcdir)/src/FTLayout - - CTest_CFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) --CTest_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -+CTest_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) - CTest_LDADD = ../src/libftgl.la - NULL = - all: all-am diff --git a/var/spack/repos/builtin/packages/ftgl/package.py b/var/spack/repos/builtin/packages/ftgl/package.py index 5e6641005b..bf77dd663a 100644 --- a/var/spack/repos/builtin/packages/ftgl/package.py +++ b/var/spack/repos/builtin/packages/ftgl/package.py @@ -1,76 +1,49 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import os -import sys from spack import * -class Ftgl(AutotoolsPackage): +class Ftgl(CMakePackage): """Library to use arbitrary fonts in OpenGL applications.""" - homepage = "http://ftgl.sourceforge.net/docs/html/" - url = "https://sourceforge.net/projects/ftgl/files/FTGL%20Source/2.1.2/ftgl-2.1.2.tar.gz/download" - list_url = "https://sourceforge.net/projects/ftgl/files/FTGL%20Source/" - list_depth = 1 + homepage = "https://github.com/frankheckenbach/ftgl" + git = "https://github.com/frankheckenbach/ftgl.git" - version('2.1.3-rc5', sha256='5458d62122454869572d39f8aa85745fc05d5518001bcefa63bd6cbb8d26565b') - version('2.1.2', sha256='2759cbd5fac0b631e8b012923cd0d2add320f6e541b399a7cda37163ad034075') + version('master', branch='master') + version('2.4.0', commit='483639219095ad080538e07ceb5996de901d4e74') + version('2.3.1', commit='3c0fdf367824b6381f29df3d8b4590240db62ab7') - variant('doc', default=False, description='Build docs') - conflicts('+doc', when='@2.1.3-rc5') - - # Ftgl does not come with a configure script - depends_on('autoconf', type='build') - depends_on('automake', type='build') - depends_on('libtool', type='build') - depends_on('m4', type='build') + # FIXME: Doc generation is broken in upstream build system + # variant('doc', default=False, description='Build the documentation') + variant('shared', default=True, description='Build as a shared library') + depends_on('cmake@2.8:', type='build') + # depends_on('doxygen', type='build', when='+doc') -- FIXME, see above depends_on('pkgconfig', type='build') depends_on('gl') depends_on('glu') depends_on('freetype@2.0.9:') - depends_on('doxygen', type='build', when='+doc') - - # Fix unnecessary qualifier in 2.1.2. - patch('remove-extra-qualifier.diff', when='@2.1.2') - # Add missing GL libraries to LDFLAGS. - patch('ftgl-2.1.3-rc5-ldflags.patch', when='@2.1.3-rc5') - - # Deactivate docs if we're not building them. - @when('@2.1.2~doc') - def patch(self): - filter_file('SUBDIRS = src demo docs', - 'SUBDIRS = src demo', os.path.join('unix', 'Makefile')) - @when('@2.1.3-rc5~doc') - def patch(self): - filter_file('SUBDIRS = src test demo docs', - 'SUBDIRS = src test demo', 'Makefile.am') - filter_file('SUBDIRS = src test demo docs', - 'SUBDIRS = src test demo', 'Makefile.in') + # Fix oversight in CMakeLists + patch('remove-ftlibrary-from-sources.diff', when='@:2.4.0') - @property - def configure_directory(self): - if self.spec.satisfies('@2.1.2'): - subdir = 'mac' if sys.platform == 'darwin' else 'unix' - return os.path.join(self.stage.source_path, subdir) - else: - return self.stage.source_path - - def configure_args(self): - args = ['--enable-shared', '--disable-static', - '--with-gl-inc={0}'.format( - self.spec['gl'].prefix.include), - '--with-gl-lib={0}'.format( - self.spec['gl'].prefix.lib), - '--with-freetype={0}'.format( - self.spec['freetype'].prefix), - '--with-glut-inc={0}'.format( - self.spec['glu'].prefix.include), - '--with-glut-lib={0}'.format( - self.spec['glu'].prefix.lib), - '--with-x'] + def cmake_args(self): + spec = self.spec + args = ['-DBUILD_SHARED_LIBS={0}'.format(spec.satisfies('+shared'))] return args + + # FIXME: See doc variant comment + # @run_after('build') + # def build_docs(self): + # if '+doc' in self.spec: + # cmake = self.spec['cmake'].command + # cmake('--build', '../spack-build', '--target', 'doc') + # + # @run_after('install') + # def install_docs(self): + # if '+doc' in self.spec: + # cmake = self.spec['cmake'].command + # cmake('--install', '../spack-build', '--target', 'doc') diff --git a/var/spack/repos/builtin/packages/ftgl/remove-extra-qualifier.diff b/var/spack/repos/builtin/packages/ftgl/remove-extra-qualifier.diff deleted file mode 100644 index cff9a3836e..0000000000 --- a/var/spack/repos/builtin/packages/ftgl/remove-extra-qualifier.diff +++ /dev/null @@ -1,11 +0,0 @@ ---- FTGL/include/FTTextureGlyph.h 2018-07-26 08:30:55.144488976 +0000 -+++ FTGL/include/FTTextureGlyph.h 2018-07-26 08:29:42.072489186 +0000 -@@ -52,7 +52,7 @@ - * Reset the currently active texture to zero to get into a known state before - * drawing a string. This is to get round possible threading issues. - */ -- static void FTTextureGlyph::ResetActiveTexture(){ activeTextureID = 0;} -+ static void ResetActiveTexture(){ activeTextureID = 0;} - - private: - /** diff --git a/var/spack/repos/builtin/packages/ftgl/remove-ftlibrary-from-sources.diff b/var/spack/repos/builtin/packages/ftgl/remove-ftlibrary-from-sources.diff new file mode 100644 index 0000000000..0d1c6c3e2a --- /dev/null +++ b/var/spack/repos/builtin/packages/ftgl/remove-ftlibrary-from-sources.diff @@ -0,0 +1,10 @@ +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -26,7 +26,6 @@ SET(libftgl_la_SOURCES + FTGlyphContainer.h + FTInternals.h + FTLibrary.cpp +- FTLibrary.h + FTList.h + FTPoint.cpp + FTSize.cpp diff --git a/var/spack/repos/builtin/packages/fujitsu-mpi/package.py b/var/spack/repos/builtin/packages/fujitsu-mpi/package.py index 3370cc3b21..62da3aab01 100644 --- a/var/spack/repos/builtin/packages/fujitsu-mpi/package.py +++ b/var/spack/repos/builtin/packages/fujitsu-mpi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -33,8 +33,8 @@ class FujitsuMpi(Package): self.spec.mpif77 = self.prefix.bin.mpifrt self.spec.mpifc = self.prefix.bin.mpifrt - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('MPICC', self.prefix.bin.mpifcc) - spack_env.set('MPICXX', self.prefix.bin.mpiFCC) - spack_env.set('MPIF77', self.prefix.bin.mpifrt) - spack_env.set('MPIF90', self.prefix.bin.mpifrt) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('MPICC', self.prefix.bin.mpifcc) + env.set('MPICXX', self.prefix.bin.mpiFCC) + env.set('MPIF77', self.prefix.bin.mpifrt) + env.set('MPIF90', self.prefix.bin.mpifrt) diff --git a/var/spack/repos/builtin/packages/funhpc/package.py b/var/spack/repos/builtin/packages/funhpc/package.py index ed69e4f88e..18175119f8 100644 --- a/var/spack/repos/builtin/packages/funhpc/package.py +++ b/var/spack/repos/builtin/packages/funhpc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class Funhpc(CMakePackage): """FunHPC: Functional HPC Programming""" homepage = "https://github.com/eschnett/FunHPC.cxx" - url = "https://github.com/eschnett/FunHPC.cxx/archive/version/0.1.0.tar.gz" + url = "https://github.com/eschnett/FunHPC.cxx/archive/version/1.3.0.tar.gz" git = "https://github.com/eschnett/FunHPC.cxx.git" version('develop', branch='master') diff --git a/var/spack/repos/builtin/packages/fyba/package.py b/var/spack/repos/builtin/packages/fyba/package.py index 4c63ac84c5..9439140bf0 100644 --- a/var/spack/repos/builtin/packages/fyba/package.py +++ b/var/spack/repos/builtin/packages/fyba/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/fzf/package.py b/var/spack/repos/builtin/packages/fzf/package.py index 708b856cb0..5d654ddedc 100644 --- a/var/spack/repos/builtin/packages/fzf/package.py +++ b/var/spack/repos/builtin/packages/fzf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/g4abla/package.py b/var/spack/repos/builtin/packages/g4abla/package.py index ecbedea255..2ce2f6ece1 100644 --- a/var/spack/repos/builtin/packages/g4abla/package.py +++ b/var/spack/repos/builtin/packages/g4abla/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/g4emlow/package.py b/var/spack/repos/builtin/packages/g4emlow/package.py index 3838fa5c74..81e6b856d4 100644 --- a/var/spack/repos/builtin/packages/g4emlow/package.py +++ b/var/spack/repos/builtin/packages/g4emlow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/g4ensdfstate/package.py b/var/spack/repos/builtin/packages/g4ensdfstate/package.py index ad065f9233..514593f34c 100644 --- a/var/spack/repos/builtin/packages/g4ensdfstate/package.py +++ b/var/spack/repos/builtin/packages/g4ensdfstate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,8 +21,8 @@ class G4ensdfstate(Package): .format(self.version)) install_tree(self.stage.source_path, install_path) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - run_env.set('G4ENSDFSTATEDATA', join_path(prefix.share, 'data')) + def setup_dependent_run_environment(self, env, dependent_spec): + env.set('G4ENSDFSTATEDATA', self.prefix.share.data) def url_for_version(self, version): """Handle version string.""" diff --git a/var/spack/repos/builtin/packages/g4ndl/package.py b/var/spack/repos/builtin/packages/g4ndl/package.py index 05c3d292d7..909f732b5c 100644 --- a/var/spack/repos/builtin/packages/g4ndl/package.py +++ b/var/spack/repos/builtin/packages/g4ndl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/g4neutronxs/package.py b/var/spack/repos/builtin/packages/g4neutronxs/package.py index 650823c488..f853780c35 100644 --- a/var/spack/repos/builtin/packages/g4neutronxs/package.py +++ b/var/spack/repos/builtin/packages/g4neutronxs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/g4photonevaporation/package.py b/var/spack/repos/builtin/packages/g4photonevaporation/package.py index 29f18d05d7..ff47072c50 100644 --- a/var/spack/repos/builtin/packages/g4photonevaporation/package.py +++ b/var/spack/repos/builtin/packages/g4photonevaporation/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/g4pii/package.py b/var/spack/repos/builtin/packages/g4pii/package.py index a58c638b62..65ca27aba2 100644 --- a/var/spack/repos/builtin/packages/g4pii/package.py +++ b/var/spack/repos/builtin/packages/g4pii/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/g4radioactivedecay/package.py b/var/spack/repos/builtin/packages/g4radioactivedecay/package.py index d69dda6218..e36b0464e1 100644 --- a/var/spack/repos/builtin/packages/g4radioactivedecay/package.py +++ b/var/spack/repos/builtin/packages/g4radioactivedecay/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/g4realsurface/package.py b/var/spack/repos/builtin/packages/g4realsurface/package.py index dd68dcdd25..d20e6fddc5 100644 --- a/var/spack/repos/builtin/packages/g4realsurface/package.py +++ b/var/spack/repos/builtin/packages/g4realsurface/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/g4saiddata/package.py b/var/spack/repos/builtin/packages/g4saiddata/package.py index dc40f6024f..0565276d90 100644 --- a/var/spack/repos/builtin/packages/g4saiddata/package.py +++ b/var/spack/repos/builtin/packages/g4saiddata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/g4tendl/package.py b/var/spack/repos/builtin/packages/g4tendl/package.py index cc2b0f0666..04ad834271 100644 --- a/var/spack/repos/builtin/packages/g4tendl/package.py +++ b/var/spack/repos/builtin/packages/g4tendl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gams/package.py b/var/spack/repos/builtin/packages/gams/package.py index c900c6aad8..e7e652f381 100644 --- a/var/spack/repos/builtin/packages/gams/package.py +++ b/var/spack/repos/builtin/packages/gams/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,10 +20,9 @@ class Gams(Package): def url_for_version(self, version): return "file://{0}/linux_x64_64_sfx.exe".format(os.getcwd()) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path("PATH", join_path(self.prefix, - 'gams{0}_linux_x64_64_sfx' - .format(self.version))) + def setup_run_environment(self, env): + env.prepend_path("PATH", join_path( + self.prefix, 'gams{0}_linux_x64_64_sfx'.format(self.version))) def install(self, spec, prefix): os.chmod(join_path(self.stage.source_path, diff --git a/var/spack/repos/builtin/packages/gapbs/package.py b/var/spack/repos/builtin/packages/gapbs/package.py index c587c3f5b8..c992a6eed0 100644 --- a/var/spack/repos/builtin/packages/gapbs/package.py +++ b/var/spack/repos/builtin/packages/gapbs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gapcloser/package.py b/var/spack/repos/builtin/packages/gapcloser/package.py index 99e7ec6584..e8c060c260 100644 --- a/var/spack/repos/builtin/packages/gapcloser/package.py +++ b/var/spack/repos/builtin/packages/gapcloser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gapfiller/package.py b/var/spack/repos/builtin/packages/gapfiller/package.py index 6e97434f87..c2fa5b025e 100644 --- a/var/spack/repos/builtin/packages/gapfiller/package.py +++ b/var/spack/repos/builtin/packages/gapfiller/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -33,7 +33,7 @@ class Gapfiller(Package): def patch(self): with working_dir('.'): - files = glob.iglob("*.pl") + files = glob.glob("*.pl") + glob.glob('bwa/*.pl') for file in files: change = FileFilter(file) change.filter('usr/bin/perl', 'usr/bin/env perl') diff --git a/var/spack/repos/builtin/packages/gasnet/package.py b/var/spack/repos/builtin/packages/gasnet/package.py index e98593f632..d705344b39 100644 --- a/var/spack/repos/builtin/packages/gasnet/package.py +++ b/var/spack/repos/builtin/packages/gasnet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py index 8f620daba5..78436f3873 100644 --- a/var/spack/repos/builtin/packages/gatk/package.py +++ b/var/spack/repos/builtin/packages/gatk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -87,7 +87,7 @@ class Gatk(Package): **kwargs ) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path( - "GATK", join_path(self.prefix, "bin", "GenomeAnalysisTK.jar") + def setup_run_environment(self, env): + env.prepend_path( + "GATK", join_path(self.prefix.bin, "GenomeAnalysisTK.jar") ) diff --git a/var/spack/repos/builtin/packages/gaudi/package.py b/var/spack/repos/builtin/packages/gaudi/package.py index 29b9e1710a..20f7c0f28b 100644 --- a/var/spack/repos/builtin/packages/gaudi/package.py +++ b/var/spack/repos/builtin/packages/gaudi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gaussian/package.py b/var/spack/repos/builtin/packages/gaussian/package.py index 3acb95974d..f32b9b2b38 100644 --- a/var/spack/repos/builtin/packages/gaussian/package.py +++ b/var/spack/repos/builtin/packages/gaussian/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -38,15 +38,14 @@ class Gaussian(Package): filter_file('/usr/bin/linda', prefix.bin, join_path(prefix.bin, filename), string='True') - def setup_environment(self, spack_env, run_env): - run_env.set('g09root', self.prefix) - run_env.set('GAUSSIANHOME', self.prefix) - run_env.set('GAUSS_EXEDIR', self.prefix.bin) - run_env.set('G09_BASIS', join_path(self.prefix.bin, 'basis')) - run_env.set('GAUSS_LEXEDIR', join_path(self.prefix.bin, - 'linda-exe')) - run_env.set('GAUSS_ARCHDIR', join_path(self.prefix.bin, 'arch')) - run_env.set('GAUSS_BSDDIR', join_path(self.prefix.bin, 'bsd')) - run_env.prepend_path('LD_LIBRARY_PATH', join_path(self.prefix.bin, - 'linda8.2/opteron-linux/lib')) - run_env.prepend_path('LD_LIBRARY_PATH', self.prefix.bin) + def setup_run_environment(self, env): + env.set('g09root', self.prefix) + env.set('GAUSSIANHOME', self.prefix) + env.set('GAUSS_EXEDIR', self.prefix.bin) + env.set('G09_BASIS', self.prefix.bin.basis) + env.set('GAUSS_LEXEDIR', join_path(self.prefix.bin, 'linda-exe')) + env.set('GAUSS_ARCHDIR', self.prefix.bin.arch) + env.set('GAUSS_BSDDIR', self.prefix.bin.bsd) + env.prepend_path('LD_LIBRARY_PATH', join_path(self.prefix.bin, + 'linda8.2', 'opteron-linux', 'lib')) + env.prepend_path('LD_LIBRARY_PATH', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/gawk/package.py b/var/spack/repos/builtin/packages/gawk/package.py index a3e7268fc8..d567dfdcdc 100644 --- a/var/spack/repos/builtin/packages/gawk/package.py +++ b/var/spack/repos/builtin/packages/gawk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Gawk(AutotoolsPackage): +class Gawk(AutotoolsPackage, GNUMirrorPackage): """If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the @@ -21,8 +21,9 @@ class Gawk(AutotoolsPackage): """ homepage = "https://www.gnu.org/software/gawk/" - url = "https://ftpmirror.gnu.org/gawk/gawk-4.1.4.tar.xz" + gnu_mirror_path = "gawk/gawk-4.1.4.tar.xz" + version('5.0.1', sha256='8e4e86f04ed789648b66f757329743a0d6dfb5294c3b91b756a474f1ce05a794') version('4.1.4', sha256='53e184e2d0f90def9207860531802456322be091c7b48f23fdc79cda65adc266') depends_on('gettext') diff --git a/var/spack/repos/builtin/packages/gblocks/package.py b/var/spack/repos/builtin/packages/gblocks/package.py index 08b732d906..5b41ffc215 100644 --- a/var/spack/repos/builtin/packages/gblocks/package.py +++ b/var/spack/repos/builtin/packages/gblocks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 836c018604..df87800ff2 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,12 +13,12 @@ import os import sys -class Gcc(AutotoolsPackage): +class Gcc(AutotoolsPackage, GNUMirrorPackage): """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.""" homepage = 'https://gcc.gnu.org' - url = 'https://ftpmirror.gnu.org/gcc/gcc-7.1.0/gcc-7.1.0.tar.bz2' + gnu_mirror_path = 'gcc/gcc-9.2.0/gcc-9.2.0.tar.xz' svn = 'svn://gcc.gnu.org/svn/gcc/' list_url = 'http://ftp.gnu.org/gnu/gcc/' list_depth = 1 @@ -96,11 +96,12 @@ class Gcc(AutotoolsPackage): # GCC 5.4 https://github.com/spack/spack/issues/6902#issuecomment-433072097 # GCC 7.3 https://github.com/spack/spack/issues/6902#issuecomment-433030376 # GCC 9+ https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86724 - depends_on('isl@0.15', when='@5:5.9') + depends_on('isl@0.14', when='@5.0:5.2') + depends_on('isl@0.15', when='@5.3:5.9') depends_on('isl@0.15:0.18', when='@6:8.9') depends_on('isl@0.15:0.20', when='@9:') depends_on('zlib', when='@6:') - depends_on('libiconv') + depends_on('libiconv', when='platform=darwin') depends_on('gnat', when='languages=ada') depends_on('binutils~libiberty', when='+binutils') depends_on('zip', type='build', when='languages=java') @@ -228,16 +229,14 @@ class Gcc(AutotoolsPackage): build_directory = 'spack-build' def url_for_version(self, version): - url = 'https://ftpmirror.gnu.org/gcc/gcc-{0}/gcc-{0}.tar.{1}' - suffix = 'xz' - - if version < Version('6.4.0') or version == Version('7.1.0'): - suffix = 'bz2' - - if version == Version('5.5.0'): - suffix = 'xz' - - return url.format(version, suffix) + # This function will be called when trying to fetch from url, before + # mirrors are tried. It takes care of modifying the suffix of gnu + # mirror path so that Spack will also look for the correct file in + # the mirrors + if (version < Version('6.4.0')and version != Version('5.5.0')) \ + or version == Version('7.1.0'): + self.gnu_mirror_path = self.gnu_mirror_path.replace('xz', 'bz2') + return super(Gcc, self).url_for_version(version) def patch(self): spec = self.spec @@ -279,7 +278,6 @@ class Gcc(AutotoolsPackage): ','.join(spec.variants['languages'].value)), # Drop gettext dependency '--disable-nls', - '--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix), '--with-mpfr={0}'.format(spec['mpfr'].prefix), '--with-gmp={0}'.format(spec['gmp'].prefix), ] @@ -328,7 +326,8 @@ class Gcc(AutotoolsPackage): if sys.platform == 'darwin': options.extend([ '--with-native-system-header-dir=/usr/include', - '--with-sysroot={0}'.format(macos_sdk_path()) + '--with-sysroot={0}'.format(macos_sdk_path()), + '--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix) ]) return options @@ -424,7 +423,7 @@ class Gcc(AutotoolsPackage): self.prefix.lib, self.prefix.lib64)) set_install_permissions(specs_file) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # Search prefix directory for possibly modified compiler names from spack.compilers.gcc import Gcc as Compiler @@ -450,6 +449,6 @@ class Gcc(AutotoolsPackage): continue # Set the proper environment variable - run_env.set(lang.upper(), abspath) + env.set(lang.upper(), abspath) # Stop searching filename/regex combos for this language break diff --git a/var/spack/repos/builtin/packages/gccmakedep/package.py b/var/spack/repos/builtin/packages/gccmakedep/package.py index de623d4b38..ffe068a35f 100644 --- a/var/spack/repos/builtin/packages/gccmakedep/package.py +++ b/var/spack/repos/builtin/packages/gccmakedep/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gccxml/package.py b/var/spack/repos/builtin/packages/gccxml/package.py index 399182c716..a7a885bcd3 100644 --- a/var/spack/repos/builtin/packages/gccxml/package.py +++ b/var/spack/repos/builtin/packages/gccxml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gconf/package.py b/var/spack/repos/builtin/packages/gconf/package.py index a3ed72b9cb..e1f2162686 100644 --- a/var/spack/repos/builtin/packages/gconf/package.py +++ b/var/spack/repos/builtin/packages/gconf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gcta/package.py b/var/spack/repos/builtin/packages/gcta/package.py index 952e41a835..1736055f88 100644 --- a/var/spack/repos/builtin/packages/gcta/package.py +++ b/var/spack/repos/builtin/packages/gcta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py index 32e746472d..2182811233 100644 --- a/var/spack/repos/builtin/packages/gdal/package.py +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,7 +18,7 @@ class Gdal(AutotoolsPackage): """ homepage = "https://www.gdal.org/" - url = "https://download.osgeo.org/gdal/3.0.1/gdal-3.0.1.tar.xz" + url = "https://download.osgeo.org/gdal/3.0.4/gdal-3.0.4.tar.xz" list_url = "https://download.osgeo.org/gdal/" list_depth = 1 @@ -29,8 +29,13 @@ class Gdal(AutotoolsPackage): 'osgeo.gdal_array', 'osgeo.gdalconst' ] + version('3.0.4', sha256='5569a4daa1abcbba47a9d535172fc335194d9214fdb96cd0f139bb57329ae277') + version('3.0.3', sha256='e20add5802265159366f197a8bb354899e1693eab8dbba2208de14a457566109') + version('3.0.2', sha256='c3765371ce391715c8f28bd6defbc70b57aa43341f6e94605f04fe3c92468983') version('3.0.1', sha256='45b4ae25dbd87282d589eca76481c426f72132d7a599556470d5c38263b09266') version('3.0.0', sha256='ad316fa052d94d9606e90b20a514b92b2dd64e3142dfdbd8f10981a5fcd5c43e') + version('2.4.4', sha256='a383bd3cf555d6e1169666b01b5b3025b2722ed39e834f1b65090f604405dcd8') + version('2.4.3', sha256='d52dc3e0cff3af3e898d887c4151442989f416e839948e73f0994f0224bbff60') version('2.4.2', sha256='dcc132e469c5eb76fa4aaff238d32e45a5d947dc5b6c801a123b70045b618e0c') version('2.4.1', sha256='fd51b4900b2fc49b98d8714f55fc8a78ebfd07218357f93fb796791115a5a1ad') version('2.4.0', sha256='c3791dcc6d37e59f6efa86e2df2a55a4485237b0a48e330ae08949f0cdf00f27') @@ -93,9 +98,9 @@ class Gdal(AutotoolsPackage): # Required dependencies depends_on('libtiff@3.6.0:') # 3.9.0+ needed to pass testsuite - depends_on('libgeotiff@1.2.1:') - depends_on('libgeotiff@:1.4', when='@:2.4') - depends_on('libgeotiff@1.5:', when='@3:') + depends_on('libgeotiff@1.2.1:1.4', when='@:2.4.0') + depends_on('libgeotiff@1.2.1:1.5', when='@2.4.1:2.4.99') + depends_on('libgeotiff@1.5:', when='@3.0.0:') depends_on('json-c') depends_on('json-c@0.12.1', when='@:2.2') @@ -114,7 +119,7 @@ class Gdal(AutotoolsPackage): depends_on('hdf', when='+hdf4') depends_on('hdf5', when='+hdf5') depends_on('kealib', when='+kea @2:') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('jasper@1.900.1', patches='uuid.patch', when='+jasper') depends_on('openjpeg', when='+openjpeg') depends_on('xerces-c', when='+xerces') @@ -157,12 +162,12 @@ class Gdal(AutotoolsPackage): conflicts('+mdb', when='~java', msg='MDB driver requires Java') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Needed to install Python bindings to GDAL installation # prefix instead of Python installation prefix. # See swig/python/GNUmakefile for more details. - spack_env.set('PREFIX', self.prefix) - spack_env.set('DESTDIR', '/') + env.set('PREFIX', self.prefix) + env.set('DESTDIR', '/') # https://trac.osgeo.org/gdal/wiki/BuildHints def configure_args(self): @@ -299,7 +304,7 @@ class Gdal(AutotoolsPackage): # https://trac.osgeo.org/gdal/wiki/NetCDF if '+netcdf' in spec: - args.append('--with-netcdf={0}'.format(spec['netcdf'].prefix)) + args.append('--with-netcdf={0}'.format(spec['netcdf-c'].prefix)) else: args.append('--with-netcdf=no') diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index 1d26562f06..b683579a43 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,15 +6,16 @@ from spack import * -class Gdb(AutotoolsPackage): +class Gdb(AutotoolsPackage, GNUMirrorPackage): """GDB, the GNU Project debugger, allows you to see what is going on 'inside' another program while it executes -- or what another program was doing at the moment it crashed. """ homepage = "https://www.gnu.org/software/gdb" - url = "https://ftpmirror.gnu.org/gdb/gdb-7.10.tar.gz" + gnu_mirror_path = "gdb/gdb-7.10.tar.gz" + version('8.3.1', sha256='26ce655216cd03f4611518a7a1c31d80ec8e884c16715e9ba8b436822e51434b') version('8.3', sha256='b2266ec592440d0eec18ee1790f8558b3b8a2845b76cc83a872e39b501ce8a28') version('8.2.1', sha256='0107985f1edb8dddef6cdd68a4f4e419f5fec0f488cc204f0b7d482c0c6c9282') version('8.2', sha256='847e4b65e5a7b872e86019dd59659029e2b06cae962e0ef345f169dcb4b851b8') diff --git a/var/spack/repos/builtin/packages/gdbm/package.py b/var/spack/repos/builtin/packages/gdbm/package.py index 478772d87c..8469cc4fb5 100644 --- a/var/spack/repos/builtin/packages/gdbm/package.py +++ b/var/spack/repos/builtin/packages/gdbm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,15 +7,14 @@ from spack import * -class Gdbm(AutotoolsPackage): +class Gdbm(AutotoolsPackage, GNUMirrorPackage): """GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database.""" homepage = "http://www.gnu.org.ua/software/gdbm/gdbm.html" - # URL must remain http:// so Spack can bootstrap curl - url = "http://ftpmirror.gnu.org/gdbm/gdbm-1.13.tar.gz" + gnu_mirror_path = "gdbm/gdbm-1.13.tar.gz" version('1.18.1', sha256='86e613527e5dba544e73208f42b78b7c022d4fa5a6d5498bf18c8d6f745b91dc') version('1.14.1', sha256='cdceff00ffe014495bed3aed71c7910aa88bf29379f795abc0f46d4ee5f8bc5f') diff --git a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py index 5981d6381e..04fd4d6030 100644 --- a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py +++ b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -46,11 +46,11 @@ class GdkPixbuf(Package): url = "https://ftp.acc.umu.se/pub/gnome/sources/gdk-pixbuf/{0}/gdk-pixbuf-{1}.tar.xz" return url.format(version.up_to(2), version) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path("XDG_DATA_DIRS", - self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", - self.prefix.share) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) def install(self, spec, prefix): with working_dir('spack-build', create=True): @@ -81,7 +81,7 @@ class GdkPixbuf(Package): if self.run_tests: make('installcheck') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # The "post-install.sh" script uses gdk-pixbuf-query-loaders, # which was installed earlier. - spack_env.prepend_path('PATH', self.prefix.bin) + env.prepend_path('PATH', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/gdl/package.py b/var/spack/repos/builtin/packages/gdl/package.py index eef7ada1c0..956061f4fa 100644 --- a/var/spack/repos/builtin/packages/gdl/package.py +++ b/var/spack/repos/builtin/packages/gdl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -57,7 +57,7 @@ class Gdl(CMakePackage): depends_on('libsm') depends_on('libxinerama') depends_on('libxxf86vm') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('pslib') depends_on('readline') diff --git a/var/spack/repos/builtin/packages/geant4-data/package.py b/var/spack/repos/builtin/packages/geant4-data/package.py index cd11e18e59..c1372dee1a 100644 --- a/var/spack/repos/builtin/packages/geant4-data/package.py +++ b/var/spack/repos/builtin/packages/geant4-data/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py index d0a4c111e7..6fb2318479 100644 --- a/var/spack/repos/builtin/packages/geant4/package.py +++ b/var/spack/repos/builtin/packages/geant4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,7 @@ class Geant4(CMakePackage): homepage = "http://geant4.cern.ch/" url = "http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz" + version('10.05.p01', sha256='f4a292220500fad17e0167ce3153e96e3410ecbe96284e572dc707f63523bdff') version('10.04', sha256='f6d883132f110eb036c69da2b21df51f13c585dc7b99d4211ddd32f4ccee1670') version('10.03.p03', sha256='a164f49c038859ab675eec474d08c9d02be8c4be9c0c2d3aa8e69adf89e1e138') @@ -61,7 +62,7 @@ class Geant4(CMakePackage): depends_on("libx11", when='+x11') depends_on("libxmu", when='+x11') depends_on("motif", when='+motif') - depends_on("qt@4.8:4.999", when="+qt") + depends_on("qt@4.8:", when="+qt") # if G4 data not installed with geant4 # depend on G4 data packages @@ -70,6 +71,7 @@ class Geant4(CMakePackage): depends_on('geant4-data@10.03.p03', when='@10.03.p03 ~data') depends_on('geant4-data@10.04', when='@10.04 ~data') + depends_on('geant4-data@10.05.p01', when='@10.05.p01 ~data') # As released, 10.03.03 has issues with respect to using external # CLHEP. @@ -145,7 +147,7 @@ class Geant4(CMakePackage): target = os.readlink(d) os.symlink(target, os.path.basename(target)) - def setup_dependent_environment(self, spack_env, run_env, dep_spec): + def setup_dependent_build_environment(self, env, dependent_spec): version = self.version major = version[0] minor = version[1] @@ -154,6 +156,5 @@ class Geant4(CMakePackage): else: patch = 0 datadir = 'Geant4-%s.%s.%s' % (major, minor, patch) - spack_env.append_path('CMAKE_MODULE_PATH', - '{0}/{1}/Modules'.format( - self.prefix.lib64, datadir)) + env.append_path('CMAKE_MODULE_PATH', join_path( + self.prefix.lib64, datadir, 'Modules')) diff --git a/var/spack/repos/builtin/packages/gearshifft/package.py b/var/spack/repos/builtin/packages/gearshifft/package.py index d889b05384..2222db91c7 100644 --- a/var/spack/repos/builtin/packages/gearshifft/package.py +++ b/var/spack/repos/builtin/packages/gearshifft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gemmlowp/package.py b/var/spack/repos/builtin/packages/gemmlowp/package.py index cce4c73f82..67dd3d7b07 100644 --- a/var/spack/repos/builtin/packages/gemmlowp/package.py +++ b/var/spack/repos/builtin/packages/gemmlowp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/genemark-et/package.py b/var/spack/repos/builtin/packages/genemark-et/package.py index a66cfa87a0..efa09e657e 100644 --- a/var/spack/repos/builtin/packages/genemark-et/package.py +++ b/var/spack/repos/builtin/packages/genemark-et/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -55,5 +55,5 @@ class GenemarkEt(Package): for file in files: filter_file(pattern, repl, *files, backup=False) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PERL5LIB', prefix.lib) + def setup_run_environment(self, env): + env.prepend_path('PERL5LIB', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/genomefinisher/package.py b/var/spack/repos/builtin/packages/genomefinisher/package.py index ed8f28650f..efaec44d12 100644 --- a/var/spack/repos/builtin/packages/genomefinisher/package.py +++ b/var/spack/repos/builtin/packages/genomefinisher/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/genometools/package.py b/var/spack/repos/builtin/packages/genometools/package.py index e76b0df92c..082fc77741 100644 --- a/var/spack/repos/builtin/packages/genometools/package.py +++ b/var/spack/repos/builtin/packages/genometools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,5 +25,5 @@ class Genometools(MakefilePackage): def install(self, spec, prefix): make('install', 'prefix=%s' % prefix) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('CPATH', self.prefix.include.genometools) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('CPATH', self.prefix.include.genometools) diff --git a/var/spack/repos/builtin/packages/genrich/package.py b/var/spack/repos/builtin/packages/genrich/package.py new file mode 100644 index 0000000000..a703259968 --- /dev/null +++ b/var/spack/repos/builtin/packages/genrich/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Genrich(MakefilePackage): + """Genrich is a peak-caller for genomic enrichment assays.""" + + homepage = "https://github.com/jsh58/Genrich" + url = "https://github.com/jsh58/Genrich/archive/v0.6.tar.gz" + + version('0.6', sha256='4c87aca8b7789f28b0c5c2c0ccea75668f19fa6a4cb38cd3c06d80ffd98d396f') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('Genrich', prefix.bin) diff --git a/var/spack/repos/builtin/packages/geode/package.py b/var/spack/repos/builtin/packages/geode/package.py new file mode 100644 index 0000000000..33581a1a87 --- /dev/null +++ b/var/spack/repos/builtin/packages/geode/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Geode(Package): + """ + Apache Geode is a data management platform that provides real-time, + consistent access to data-intensive applications throughout widely + distributed cloud architectures. + """ + + homepage = "https://geode.apache.org/" + url = "https://archive.apache.org/dist/geode/1.9.2/apache-geode-1.9.2.tgz" + + version('1.9.2', sha256='4b8118114ef43166f6bf73af56b93aadbf9108fcab06d1fbbb8e27f7d559d7e0') + version('1.9.0', sha256='8794808ebc89bc855f0b989b32e91e890d446cfd058e123f6ccb9e12597c1c4f') + version('1.8.0', sha256='58edc41edac4eabd899322b73a24727eac41f6253274c2ce7d0a82227121ae3e') + version('1.7.0', sha256='91eec04420f46e949d32104479c4a4b5b34a4e5570dca7b98ca067a30d5a783d') + version('1.6.0', sha256='79e8d81d058b1c4edd5fb414ff30ac530f7913b978f5abc899c353fcb06e5ef3') + + depends_on('java', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/geopm/package.py b/var/spack/repos/builtin/packages/geopm/package.py index 154d9e4ceb..95888343b9 100644 --- a/var/spack/repos/builtin/packages/geopm/package.py +++ b/var/spack/repos/builtin/packages/geopm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,16 +18,14 @@ class Geopm(AutotoolsPackage): msr-safe kernel module by your administrator.""" homepage = "https://geopm.github.io" - url = "https://github.com/geopm/geopm/releases/download/v0.4.0/geopm-0.4.0.tar.gz" + url = "https://github.com/geopm/geopm/releases/download/v1.0.0/geopm-1.0.0.tar.gz" git = "https://github.com/geopm/geopm.git" # Add additional proper versions and checksums here. "spack checksum geopm" version('develop', branch='dev') version('master', branch='master') - version('1.0.0-rc2', sha256='c6637df54728ded31fd682f39a07dffee45883f350e6dbd13e1496dd50243ffd', - url='https://github.com/geopm/geopm/releases/download/v1.0.0%2Brc2/geopm-1.0.0+rc2.tar.gz') - version('1.0.0-rc1', sha256='f8a2e5c384a15e9663f409de478b6372cd63e63a28d4701a33ac043fc27905e0', - url='https://github.com/geopm/geopm/releases/download/v1.0.0-rc1/geopm-1.0.0+rc1.tar.gz') + version('1.1.0', sha256='5f9a4df37ef0d64c53d64829d46736803c9fe614afd8d2c70fe7a5ebea09f88e') + version('1.0.0', sha256='24fe72265a7e44d62bdfe49467c49f0b7a649131ddda402d763c00a49765e1cb') version('0.6.1', sha256='0ca42853f90885bf213df190c3462b8675c143cc843aee0d8b8a0e30802b55a9') version('0.6.0', sha256='95ccf256c2b7cb35838978152479569d154347c3065af1639ed17be1399182d3') version('0.5.1', sha256='db247af55f7000b6e4628af099956349b68a637500b9d4fe8d8fb13687124d53') @@ -45,27 +43,44 @@ class Geopm(AutotoolsPackage): variant('doc', default=True, description='Create man pages with ruby-ronn.') variant('openmp', default=True, description='Build with OpenMP.') variant('ompt', default=False, description='Use OpenMP Tools Interface.') - variant('hwloc', default=False, description='Build with hwloc, deprecated and ignored after v0.5.1.') variant('gnu-ld', default=False, description='Assume C compiler uses gnu-ld.') # Added dependencies. + depends_on('ruby-ronn', type='build', when='+doc') + depends_on('doxygen', type='build', when='+doc') + depends_on('mpi@2.2:', when='+mpi') + depends_on('m4', type='build') - depends_on('automake', type='build') depends_on('autoconf', type='build') + depends_on('automake', type='build') depends_on('libtool', type='build') depends_on('ruby-ronn', type='build', when='+doc') depends_on('doxygen', type='build', when='+doc') - depends_on('numactl') + depends_on('numactl', when="@:1.0.0-rc2") depends_on('mpi', when='+mpi') depends_on('hwloc@1.11.9', when='@:0.5.1+hwloc') - depends_on('json-c') - depends_on('py-pandas', type='run') - depends_on('py-numpy', type='run') - depends_on('py-natsort', type='run') - depends_on('py-matplotlib@2.2.3', type='run') + depends_on('json-c', when='@:0.9.9') + depends_on('py-cycler@0.10.0:', when="@1.0.0:", type=('build', 'run')) + depends_on('py-pandas@0.22.0:', type=('build', 'run')) + depends_on('py-tables@3.4.3:3.5.2', when="@1.0.0:", type=('build', 'run')) + depends_on('py-cffi@1.6.0:', when="@1.1.0:", type=('build', 'run')) + depends_on('py-pyyaml@5.1.0:', when="@1.1.0:", type=('build', 'run')) + depends_on('py-mock@3.0.0:', when="@1.1.0:", type=('build', 'run')) + depends_on('py-future@0.17.1:', when="@1.1.0:", type=('build', 'run')) + depends_on('py-numpy@1.14.3:', type=('build', 'run')) + depends_on('py-setuptools@39.2.0:', when="@1.0.0:", type='build') + depends_on('py-natsort@5.3.2:', type=('build', 'run')) + depends_on('py-psutil@5.4.8:', when="@1.0.0:", type=('build', 'run')) + depends_on('py-pylint@1.9.5:', when="@1.1.0:", type=('build', 'run')) + depends_on('py-matplotlib@2.2.3', when="@:1.0.0-rc2", type=('build', 'run')) + depends_on('py-matplotlib@2.2.3:', when="@1.1.0:", type=('build', 'run')) parallel = False + def autoreconf(self, spec, prefix): + bash = which("bash") + bash('./autogen.sh') + def configure_args(self): args = [] args.extend(self.enable_or_disable('debug')) @@ -77,10 +92,6 @@ class Geopm(AutotoolsPackage): args.extend(self.enable_or_disable('doc')) args.extend(self.enable_or_disable('openmp')) args.extend(self.enable_or_disable('ompt')) - if self.version <= Version('0.5.1'): - args.extend(self.with_or_without( - 'hwloc', - activation_value='prefix')) args.extend(self.with_or_without('gnu-ld')) return args diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py index 2100b95d20..7c0ae0ea2e 100644 --- a/var/spack/repos/builtin/packages/geos/package.py +++ b/var/spack/repos/builtin/packages/geos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py index 070ad06781..8eb0ad6f09 100644 --- a/var/spack/repos/builtin/packages/gettext/package.py +++ b/var/spack/repos/builtin/packages/gettext/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,11 @@ from spack import * -class Gettext(AutotoolsPackage): +class Gettext(AutotoolsPackage, GNUMirrorPackage): """GNU internationalization (i18n) and localization (l10n) library.""" homepage = "https://www.gnu.org/software/gettext/" - url = "https://ftpmirror.gnu.org/gettext/gettext-0.20.1.tar.xz" + gnu_mirror_path = "gettext/gettext-0.20.1.tar.xz" version('0.20.1', sha256='53f02fbbec9e798b0faaf7c73272f83608e835c6288dd58be6c9bb54624a3800') version('0.19.8.1', sha256='105556dbc5c3fbbc2aa0edb46d22d055748b6f5c7cd7a8d99f8e7eb84e938be4') diff --git a/var/spack/repos/builtin/packages/gflags/package.py b/var/spack/repos/builtin/packages/gflags/package.py index 8baa8667a0..1870b728e5 100644 --- a/var/spack/repos/builtin/packages/gflags/package.py +++ b/var/spack/repos/builtin/packages/gflags/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ghost/package.py b/var/spack/repos/builtin/packages/ghost/package.py index d8b9b678aa..a02e070115 100644 --- a/var/spack/repos/builtin/packages/ghost/package.py +++ b/var/spack/repos/builtin/packages/ghost/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ghostscript-fonts/package.py b/var/spack/repos/builtin/packages/ghostscript-fonts/package.py index be37b5347f..62fadcd4c7 100644 --- a/var/spack/repos/builtin/packages/ghostscript-fonts/package.py +++ b/var/spack/repos/builtin/packages/ghostscript-fonts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ghostscript/package.py b/var/spack/repos/builtin/packages/ghostscript/package.py index 3ccf0de51f..72f3e6f3e0 100644 --- a/var/spack/repos/builtin/packages/ghostscript/package.py +++ b/var/spack/repos/builtin/packages/ghostscript/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,8 @@ class Ghostscript(AutotoolsPackage): homepage = "http://ghostscript.com/" url = "https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs926/ghostscript-9.26.tar.gz" + version('9.50', sha256='0f53e89fd647815828fc5171613e860e8535b68f7afbc91bf89aee886769ce89') + version('9.27', sha256='9760e8bdd07a08dbd445188a6557cb70e60ccb6a5601f7dbfba0d225e28ce285') version('9.26', sha256='831fc019bd477f7cc2d481dc5395ebfa4a593a95eb2fe1eb231a97e450d7540d') version('9.21', sha256='02bceadbc4dddeb6f2eec9c8b1623d945d355ca11b8b4df035332b217d58ce85') version('9.18', sha256='5fc93079749a250be5404c465943850e3ed5ffbc0d5c07e10c7c5ee8afbbdb1b') diff --git a/var/spack/repos/builtin/packages/giflib/package.py b/var/spack/repos/builtin/packages/giflib/package.py index 3f31891c70..71a0cb7965 100644 --- a/var/spack/repos/builtin/packages/giflib/package.py +++ b/var/spack/repos/builtin/packages/giflib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ginkgo/package.py b/var/spack/repos/builtin/packages/ginkgo/package.py index 23d2b53495..8440be2516 100644 --- a/var/spack/repos/builtin/packages/ginkgo/package.py +++ b/var/spack/repos/builtin/packages/ginkgo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,14 +12,14 @@ class Ginkgo(CMakePackage, CudaPackage): with a focus on sparse solution of linear systems.""" homepage = "https://ginkgo-project.github.io/" - url = "https://github.com/ginkgo-project/ginkgo.git" git = "https://github.com/ginkgo-project/ginkgo.git" maintainers = ['tcojean', 'hartwiganzt'] version('develop', branch='develop') version('master', branch='master') - version('1.0.0', commit='4524464') # v1.0.0 + version('1.1.0', commit='b9bec8225442b3eb2a85a870efa112ab767a17fb') # v1.1.0 + version('1.0.0', commit='45244641e0c2b19ba33aecd25153c0bddbcbe1a0') # v1.0.0 variant('shared', default=True, description='Build shared libraries') variant('full_optimizations', default=False, description='Compile with all optimizations') @@ -32,6 +32,8 @@ class Ginkgo(CMakePackage, CudaPackage): depends_on('cmake@3.9:', type='build') depends_on('cuda@9:', when='+cuda') + conflicts('%gcc@:5.2.9') + def cmake_args(self): spec = self.spec return [ diff --git a/var/spack/repos/builtin/packages/git-fat-git/package.py b/var/spack/repos/builtin/packages/git-fat-git/package.py index b992a428ea..2c089190f6 100644 --- a/var/spack/repos/builtin/packages/git-fat-git/package.py +++ b/var/spack/repos/builtin/packages/git-fat-git/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/git-imerge/package.py b/var/spack/repos/builtin/packages/git-imerge/package.py index 67ef3ea614..4e5bb20b3b 100644 --- a/var/spack/repos/builtin/packages/git-imerge/package.py +++ b/var/spack/repos/builtin/packages/git-imerge/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,7 +31,7 @@ class GitImerge(MakefilePackage): version('1.0.0', sha256='2ef3a49a6d54c4248ef2541efc3c860824fc8295a7226760f24f0bb2c5dd41f2') depends_on('python@2.6:') - depends_on('py-argparse', when='^python@2.6') + depends_on('py-argparse', when='^python@:2.6') depends_on('git') # Package copies a Python script and bash-completion files, so diff --git a/var/spack/repos/builtin/packages/git-lfs/package.py b/var/spack/repos/builtin/packages/git-lfs/package.py index 180e01b97d..870c98fa0a 100644 --- a/var/spack/repos/builtin/packages/git-lfs/package.py +++ b/var/spack/repos/builtin/packages/git-lfs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index 8828d68238..c77c1fa916 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,6 +25,11 @@ class Git(AutotoolsPackage): releases = [ { + 'version': '2.25.0', + 'sha256': 'a98c9b96d91544b130f13bf846ff080dda2867e77fe08700b793ab14ba5346f6', + 'sha256_manpages': '22b2380842ef75e9006c0358de250ead449e1376d7e5138070b9a3073ef61d44' + }, + { 'version': '2.21.0', 'sha256': '85eca51c7404da75e353eba587f87fea9481ba41e162206a6f70ad8118147bee', 'sha256_manpages': '14c76ebb4e31f9e55cf5338a04fd3a13bced0323cd51794ccf45fc74bd0c1080' @@ -175,7 +180,7 @@ class Git(AutotoolsPackage): depends_on('libiconv') depends_on('openssl') depends_on('pcre', when='@:2.13') - depends_on('pcre+jit', when='@2.14:') + depends_on('pcre2', when='@2.14:') depends_on('perl') depends_on('zlib') @@ -185,13 +190,13 @@ class Git(AutotoolsPackage): depends_on('m4', type='build') depends_on('tk', type=('build', 'link'), when='+tcltk') - # See the comment in setup_environment re EXTLIBS. + # See the comment in setup_build_environment re EXTLIBS. def patch(self): filter_file(r'^EXTLIBS =$', '#EXTLIBS =', 'Makefile') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # We use EXTLIBS rather than LDFLAGS so that git's Makefile # inserts the information into the proper place in the link commands # (alongside the # other libraries/paths that configure discovers). @@ -204,9 +209,9 @@ class Git(AutotoolsPackage): # In that case the node in the DAG gets truncated and git DOES NOT # have a gettext dependency. if 'gettext' in self.spec: - spack_env.append_flags('EXTLIBS', '-L{0} -lintl'.format( + env.append_flags('EXTLIBS', '-L{0} -lintl'.format( self.spec['gettext'].prefix.lib)) - spack_env.append_flags('CFLAGS', '-I{0}'.format( + env.append_flags('CFLAGS', '-I{0}'.format( self.spec['gettext'].prefix.include)) def configure_args(self): @@ -216,12 +221,17 @@ class Git(AutotoolsPackage): '--with-curl={0}'.format(spec['curl'].prefix), '--with-expat={0}'.format(spec['expat'].prefix), '--with-iconv={0}'.format(spec['libiconv'].prefix), - '--with-libpcre={0}'.format(spec['pcre'].prefix), '--with-openssl={0}'.format(spec['openssl'].prefix), '--with-perl={0}'.format(spec['perl'].command.path), '--with-zlib={0}'.format(spec['zlib'].prefix), ] + if '^pcre' in self.spec: + configure_args.append('--with-libpcre={0}'.format( + spec['pcre'].prefix)) + if '^pcre2' in self.spec: + configure_args.append('--with-libpcre2={0}'.format( + spec['pcre2'].prefix)) if '+tcltk' in self.spec: configure_args.append('--with-tcltk={0}'.format( self.spec['tk'].prefix.bin.wish)) diff --git a/var/spack/repos/builtin/packages/gl2ps/package.py b/var/spack/repos/builtin/packages/gl2ps/package.py index 6a9f5b7b2e..eed6ef3119 100644 --- a/var/spack/repos/builtin/packages/gl2ps/package.py +++ b/var/spack/repos/builtin/packages/gl2ps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ class Gl2ps(CMakePackage): homepage = "http://www.geuz.org/gl2ps/" url = "http://geuz.org/gl2ps/src/gl2ps-1.3.9.tgz" + version('1.4.0', sha256='03cb5e6dfcd87183f3b9ba3b22f04cd155096af81e52988cc37d8d8efe6cf1e2') version('1.3.9', sha256='8a680bff120df8bcd78afac276cdc38041fed617f2721bade01213362bcc3640') variant('png', default=True, description='Enable PNG support') diff --git a/var/spack/repos/builtin/packages/glew/package.py b/var/spack/repos/builtin/packages/glew/package.py index d2fe265380..a5ca6f65da 100644 --- a/var/spack/repos/builtin/packages/glew/package.py +++ b/var/spack/repos/builtin/packages/glew/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/glfmultiples/package.py b/var/spack/repos/builtin/packages/glfmultiples/package.py index 74162517e6..d5423a6bd5 100644 --- a/var/spack/repos/builtin/packages/glfmultiples/package.py +++ b/var/spack/repos/builtin/packages/glfmultiples/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index f883508449..e43a9d1728 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/glibmm/package.py b/var/spack/repos/builtin/packages/glibmm/package.py index 5e43576f6f..71b9388532 100644 --- a/var/spack/repos/builtin/packages/glibmm/package.py +++ b/var/spack/repos/builtin/packages/glibmm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/glimmer/package.py b/var/spack/repos/builtin/packages/glimmer/package.py index f6543f1236..ee8bdbb658 100644 --- a/var/spack/repos/builtin/packages/glimmer/package.py +++ b/var/spack/repos/builtin/packages/glimmer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py index 4e9f8194e8..faa3d6e294 100644 --- a/var/spack/repos/builtin/packages/glm/package.py +++ b/var/spack/repos/builtin/packages/glm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/global/package.py b/var/spack/repos/builtin/packages/global/package.py index 3d8231491f..7a252e7add 100644 --- a/var/spack/repos/builtin/packages/global/package.py +++ b/var/spack/repos/builtin/packages/global/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/globalarrays/package.py b/var/spack/repos/builtin/packages/globalarrays/package.py index a42d95f0c9..918163191f 100644 --- a/var/spack/repos/builtin/packages/globalarrays/package.py +++ b/var/spack/repos/builtin/packages/globalarrays/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/glog/package.py b/var/spack/repos/builtin/packages/glog/package.py index 362e6c9a02..d7edf3cad7 100644 --- a/var/spack/repos/builtin/packages/glog/package.py +++ b/var/spack/repos/builtin/packages/glog/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gloo/package.py b/var/spack/repos/builtin/packages/gloo/package.py index eeef5750f9..af8ec7824f 100644 --- a/var/spack/repos/builtin/packages/gloo/package.py +++ b/var/spack/repos/builtin/packages/gloo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/glpk/package.py b/var/spack/repos/builtin/packages/glpk/package.py index 05ed3fdc7e..14f47357bf 100644 --- a/var/spack/repos/builtin/packages/glpk/package.py +++ b/var/spack/repos/builtin/packages/glpk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Glpk(AutotoolsPackage): +class Glpk(AutotoolsPackage, GNUMirrorPackage): """The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written @@ -14,7 +14,7 @@ class Glpk(AutotoolsPackage): """ homepage = "https://www.gnu.org/software/glpk" - url = "https://ftpmirror.gnu.org/glpk/glpk-4.65.tar.gz" + gnu_mirror_path = "glpk/glpk-4.65.tar.gz" version('4.65', sha256='4281e29b628864dfe48d393a7bedd781e5b475387c20d8b0158f329994721a10') version('4.61', sha256='9866de41777782d4ce21da11b88573b66bb7858574f89c28be6967ac22dfaba9') diff --git a/var/spack/repos/builtin/packages/glproto/package.py b/var/spack/repos/builtin/packages/glproto/package.py index 9ef4427303..ff78f859bd 100644 --- a/var/spack/repos/builtin/packages/glproto/package.py +++ b/var/spack/repos/builtin/packages/glproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/glvis/package.py b/var/spack/repos/builtin/packages/glvis/package.py index e893c12730..07b33d82b8 100644 --- a/var/spack/repos/builtin/packages/glvis/package.py +++ b/var/spack/repos/builtin/packages/glvis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gmake/package.py b/var/spack/repos/builtin/packages/gmake/package.py index baa4aa5080..fe6e58f15e 100644 --- a/var/spack/repos/builtin/packages/gmake/package.py +++ b/var/spack/repos/builtin/packages/gmake/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Gmake(AutotoolsPackage): +class Gmake(AutotoolsPackage, GNUMirrorPackage): """GNU Make is a tool which controls the generation of executables and other non-source files of a program from the program's source files.""" homepage = "https://www.gnu.org/software/make/" - url = "https://ftpmirror.gnu.org/make/make-4.2.1.tar.gz" + gnu_mirror_path = "make/make-4.2.1.tar.gz" version('4.2.1', sha256='e40b8f018c1da64edd1cc9a6fce5fa63b2e707e404e20cad91fbae337c98a5b7') version('4.0', sha256='fc42139fb0d4b4291929788ebaf77e2a4de7eaca95e31f3634ef7d4932051f69') @@ -22,6 +22,8 @@ class Gmake(AutotoolsPackage): depends_on('gettext', when='+nls') depends_on('guile', when='+guile') + depends_on('texinfo', type='build') + build_directory = 'spack-build' patch('https://src.fedoraproject.org/rpms/make/raw/519a7c5bcbead22e6ea2d2c2341d981ef9e25c0d/f/make-4.2.1-glob-fix-2.patch', level=1, sha256='fe5b60d091c33f169740df8cb718bf4259f84528b42435194ffe0dd5b79cd125', when='@4.2.1') diff --git a/var/spack/repos/builtin/packages/gmap-gsnap/package.py b/var/spack/repos/builtin/packages/gmap-gsnap/package.py index ba938f0981..f87f4121c7 100644 --- a/var/spack/repos/builtin/packages/gmap-gsnap/package.py +++ b/var/spack/repos/builtin/packages/gmap-gsnap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gmime/package.py b/var/spack/repos/builtin/packages/gmime/package.py index 7b8a66298f..8455a67822 100644 --- a/var/spack/repos/builtin/packages/gmime/package.py +++ b/var/spack/repos/builtin/packages/gmime/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gmodel/fix_gmodel.cpp.patch b/var/spack/repos/builtin/packages/gmodel/fix_gmodel.cpp.patch new file mode 100644 index 0000000000..c4e1cae15e --- /dev/null +++ b/var/spack/repos/builtin/packages/gmodel/fix_gmodel.cpp.patch @@ -0,0 +1,54 @@ +--- spack-src/gmodel.cpp.org 2019-12-13 10:43:51.578849661 +0900 ++++ spack-src/gmodel.cpp 2019-12-13 10:54:55.467737618 +0900 +@@ -30,9 +30,9 @@ + /* PLANE = */ "Physical Surface", + /* RULED = */ "Physical Surface", + /* VOLUME = */ "Physical Volume", +- /* LOOP = */ 0, +- /* SHELL = */ 0, +- /* GROUP = */ 0}; ++ /* LOOP = */ nullptr, ++ /* SHELL = */ nullptr, ++ /* GROUP = */ nullptr}; + + int const type_dims[NTYPES] = { + /* POINT = */ 0, +@@ -63,11 +63,6 @@ + return v.at(std::size_t(i)); + } + +-template <typename T> +-static int size(std::vector<T> const& v) { +- return int(v.size()); +-} +- + int is_entity(int t) { return t <= VOLUME; } + + int is_face(int t) { return t == PLANE || t == RULED; } +@@ -452,7 +447,7 @@ + auto loop = new_loop(); + add_use(loop, FORWARD, start); + add_use(loop, FORWARD, right.middle); +- ObjPtr end = 0; ++ ObjPtr end = nullptr; + switch (start->type) { + case LINE: { + end = new_line2(std::dynamic_pointer_cast<Point>(left.end), +@@ -492,7 +487,7 @@ + break; + } + default: +- end = 0; ++ end = nullptr; + break; + } + add_use(loop, REVERSE, end); +@@ -508,7 +503,7 @@ + middle = new_ruled2(loop); + break; + default: +- middle = 0; ++ middle = nullptr; + break; + } + return Extruded{middle, end}; diff --git a/var/spack/repos/builtin/packages/gmodel/package.py b/var/spack/repos/builtin/packages/gmodel/package.py index fecf45a967..0af31f92e7 100644 --- a/var/spack/repos/builtin/packages/gmodel/package.py +++ b/var/spack/repos/builtin/packages/gmodel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,3 +18,8 @@ class Gmodel(CMakePackage): url = "https://github.com/ibaned/gmodel/archive/v2.1.0.tar.gz" version('2.1.0', sha256='80df0c6dc413a9ffa0f0e7b65118b05b643ba3e1bfcac28fb91d2d3ad017fda0') + + # fix error [-Werror,-Wzero-as-null-pointer-constant] + # fix error [-Werror,-Wunused-template] + # Ref: https://github.com/ibaned/gmodel/commit/6b81ec190cf2ce9a6554a99cb6d759b023393cdd + patch('fix_gmodel.cpp.patch') diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py index 5e333f8b22..8c24853950 100644 --- a/var/spack/repos/builtin/packages/gmp/package.py +++ b/var/spack/repos/builtin/packages/gmp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Gmp(AutotoolsPackage): +class Gmp(AutotoolsPackage, GNUMirrorPackage): """GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.""" homepage = "https://gmplib.org" - url = "https://ftpmirror.gnu.org/gmp/gmp-6.1.2.tar.bz2" + gnu_mirror_path = "gmp/gmp-6.1.2.tar.bz2" version('6.1.2', sha256='5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2') version('6.1.1', sha256='a8109865f2893f1373b0a8ed5ff7429de8db696fc451b1036bd7bdf95bbeffd6') diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index 1e1d197295..b5d677bd99 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,7 +17,7 @@ class Gmsh(CMakePackage): """ homepage = 'http://gmsh.info' - url = 'http://gmsh.info/src/gmsh-2.11.0-source.tgz' + url = 'http://gmsh.info/src/gmsh-4.4.1-source.tgz' version('4.4.1', sha256='853c6438fc4e4b765206e66a514b09182c56377bb4b73f1d0d26eda7eb8af0dc') version('4.2.2', sha256='e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc') diff --git a/var/spack/repos/builtin/packages/gmt/package.py b/var/spack/repos/builtin/packages/gmt/package.py index 045f4e11f6..b9bb7b71d9 100644 --- a/var/spack/repos/builtin/packages/gmt/package.py +++ b/var/spack/repos/builtin/packages/gmt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -33,7 +33,7 @@ class Gmt(Package): depends_on('ghostscript') depends_on('subversion') depends_on('cmake@2.8.5:', type='build', when='@5:') - depends_on('netcdf@4:') + depends_on('netcdf-c@4:') depends_on('curl', when='@5.4:') # Optional dependencies @@ -58,7 +58,7 @@ class Gmt(Package): def install(self, spec, prefix): args = [ '--prefix={0}'.format(prefix), - '--enable-netcdf={0}'.format(spec['netcdf'].prefix), + '--enable-netcdf={0}'.format(spec['netcdf-c'].prefix), '--enable-shared', '--without-x' ] diff --git a/var/spack/repos/builtin/packages/gmtsar/package.py b/var/spack/repos/builtin/packages/gmtsar/package.py index 844914e960..1a299a0c89 100644 --- a/var/spack/repos/builtin/packages/gmtsar/package.py +++ b/var/spack/repos/builtin/packages/gmtsar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gnat/package.py b/var/spack/repos/builtin/packages/gnat/package.py index 5fe1b8488f..58a93932d1 100644 --- a/var/spack/repos/builtin/packages/gnat/package.py +++ b/var/spack/repos/builtin/packages/gnat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gnome-common/package.py b/var/spack/repos/builtin/packages/gnome-common/package.py index 0e8036f1e6..1132f6c858 100644 --- a/var/spack/repos/builtin/packages/gnome-common/package.py +++ b/var/spack/repos/builtin/packages/gnome-common/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gnupg/package.py b/var/spack/repos/builtin/packages/gnupg/package.py index 255b9e0b4b..65005a4bba 100644 --- a/var/spack/repos/builtin/packages/gnupg/package.py +++ b/var/spack/repos/builtin/packages/gnupg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gnuplot/package.py b/var/spack/repos/builtin/packages/gnuplot/package.py index ff2fdd5376..17ee973eee 100644 --- a/var/spack/repos/builtin/packages/gnuplot/package.py +++ b/var/spack/repos/builtin/packages/gnuplot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,6 +26,7 @@ class Gnuplot(AutotoolsPackage): # dependency of readline. Fix it with a small patch patch('term_include.patch') + version('5.2.8', sha256='60a6764ccf404a1668c140f11cc1f699290ab70daa1151bb58fed6139a28ac37') version('5.2.7', sha256='97fe503ff3b2e356fe2ae32203fc7fd2cf9cef1f46b60fe46dc501a228b9f4ed') version('5.2.5', sha256='039db2cce62ddcfd31a6696fe576f4224b3bc3f919e66191dfe2cdb058475caa') version('5.2.2', sha256='a416d22f02bdf3873ef82c5eb7f8e94146795811ef808e12b035ada88ef7b1a1') diff --git a/var/spack/repos/builtin/packages/gnutls/package.py b/var/spack/repos/builtin/packages/gnutls/package.py index 8511065177..aa9c863499 100644 --- a/var/spack/repos/builtin/packages/gnutls/package.py +++ b/var/spack/repos/builtin/packages/gnutls/package.py @@ -1,10 +1,9 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * -import os class Gnutls(AutotoolsPackage): @@ -49,11 +48,10 @@ class Gnutls(AutotoolsPackage): url = "https://www.gnupg.org/ftp/gcrypt/gnutls/v{0}/gnutls-{1}.tar.xz" return url.format(version.up_to(2), version) - def setup_environment(self, build_env, run_env): + def setup_build_environment(self, env): spec = self.spec if '+guile' in spec: - build_env.set('GUILE', os.path.join(spec["guile"].prefix.bin, - 'guile')) + env.set('GUILE', spec["guile"].prefix.bin.guile) def configure_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/go-bootstrap/package.py b/var/spack/repos/builtin/packages/go-bootstrap/package.py index e5bfcef380..2d53d30176 100644 --- a/var/spack/repos/builtin/packages/go-bootstrap/package.py +++ b/var/spack/repos/builtin/packages/go-bootstrap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -55,8 +55,8 @@ class GoBootstrap(Package): install_tree('.', prefix) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('GOROOT_BOOTSTRAP', self.spec.prefix) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('GOROOT_BOOTSTRAP', self.spec.prefix) - def setup_environment(self, spack_env, run_env): - spack_env.set('GOROOT_FINAL', self.spec.prefix) + def setup_build_environment(self, env): + env.set('GOROOT_FINAL', self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/go-md2man/package.py b/var/spack/repos/builtin/packages/go-md2man/package.py index 0986d41661..e7c5e95016 100644 --- a/var/spack/repos/builtin/packages/go-md2man/package.py +++ b/var/spack/repos/builtin/packages/go-md2man/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index 1090718ea3..f2d0e94f87 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -35,8 +35,19 @@ class Go(Package): extendable = True + version('1.13.7', sha256='e4ad42cc5f5c19521fbbbde3680995f2546110b5c6aa2b48c3754ff7af9b41f4') + version('1.13.6', sha256='aae5be954bdc40bcf8006eb77e8d8a5dde412722bc8effcdaf9772620d06420c') + version('1.13.5', sha256='27d356e2a0b30d9983b60a788cf225da5f914066b37a6b4f69d457ba55a626ff') + version('1.13.4', sha256='95dbeab442ee2746b9acf0934c8e2fc26414a0565c008631b04addb8c02e7624') + version('1.13.3', sha256='4f7123044375d5c404280737fbd2d0b17064b66182a65919ffe20ffe8620e3df') + version('1.13.2', sha256='1ea68e01472e4276526902b8817abd65cf84ed921977266f0c11968d5e915f44') version('1.13.1', sha256='81f154e69544b9fa92b1475ff5f11e64270260d46e7e36c34aafc8bc96209358') version('1.13', sha256='3fc0b8b6101d42efd7da1da3029c0a13f22079c0c37ef9730209d8ec665bf122') + version('1.12.15', sha256='8aba74417e527524ad5724e6e6c21016795d1017692db76d1b0851c6bdec84c3') + version('1.12.14', sha256='39dbf05f7e2ffcb19b08f07d53dcc96feadeb1987fef9e279e7ff0c598213064') + version('1.12.13', sha256='5383d3b8db4baa48284ffcb14606d9cad6f03e9db843fa6d835b94d63cccf5a7') + version('1.12.12', sha256='fcb33b5290fa9bcc52be3211501540df7483d7276b031fc77528672a3c705b99') + version('1.12.11', sha256='fcf58935236802929f5726e96cd1d900853b377bec2c51b2e37219c658a4950f') version('1.12.10', sha256='f56e48fce80646d3c94dcf36d3e3f490f6d541a92070ad409b87b6bbb9da3954') version('1.12.9', sha256='ab0e56ed9c4732a653ed22e232652709afbf573e710f56a07f7fdeca578d62fc') version('1.12.8', sha256='11ad2e2e31ff63fcf8a2bdffbe9bfa2e1845653358daed593c8c2d03453c9898') @@ -104,12 +115,12 @@ class Go(Package): install_tree(wd, prefix) - def setup_environment(self, spack_env, run_env): - spack_env.set('GOROOT_FINAL', self.spec.prefix) + def setup_build_environment(self, env): + env.set('GOROOT_FINAL', self.spec.prefix) # We need to set CC/CXX_FOR_TARGET, otherwise cgo will use the # internal Spack wrappers and fail. - spack_env.set('CC_FOR_TARGET', self.compiler.cc) - spack_env.set('CXX_FOR_TARGET', self.compiler.cxx) + env.set('CC_FOR_TARGET', self.compiler.cc) + env.set('CXX_FOR_TARGET', self.compiler.cxx) def setup_dependent_package(self, module, dependent_spec): """Called before go modules' install() methods. @@ -123,19 +134,24 @@ class Go(Package): # Add a go command/compiler for extensions module.go = self.spec['go'].command - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def generate_path_components(self, dependent_spec): if os.environ.get('GOROOT', False): tty.warn('GOROOT is set, this is not recommended') + # Set to include paths of dependencies path_components = [] - # Set GOPATH to include paths of dependencies for d in dependent_spec.traverse(): if d.package.extends(self.spec): path_components.append(d.prefix) + return path_components + def setup_dependent_build_environment(self, env, dependent_spec): # This *MUST* be first, this is where new code is installed - spack_env.set('GOPATH', ':'.join(path_components)) + env.set('GOPATH', ':'.join(self.generate_path_components( + dependent_spec))) + def setup_dependent_run_environment(self, env, dependent_spec): # Allow packages to find this when using module files - run_env.prepend_path('GOPATH', ':'.join( - [dependent_spec.prefix] + path_components)) + env.prepend_path('GOPATH', ':'.join( + [dependent_spec.prefix] + self.generate_path_components( + dependent_spec))) diff --git a/var/spack/repos/builtin/packages/gobject-introspection/package.py b/var/spack/repos/builtin/packages/gobject-introspection/package.py index 20996c981f..294d1ba46e 100644 --- a/var/spack/repos/builtin/packages/gobject-introspection/package.py +++ b/var/spack/repos/builtin/packages/gobject-introspection/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -57,9 +57,11 @@ class GobjectIntrospection(Package): url = 'http://ftp.gnome.org/pub/gnome/sources/gobject-introspection/{0}/gobject-introspection-{1}.tar.xz' return url.format(version.up_to(2), version) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) def install(self, spec, prefix): configure("--prefix=%s" % prefix) @@ -69,5 +71,5 @@ class GobjectIntrospection(Package): make() make("install") - def setup_environment(self, spack_env, run_env): - spack_env.set('SPACK_SBANG', "%s/bin/sbang" % spack_root) + def setup_build_environment(self, env): + env.set('SPACK_SBANG', "%s/bin/sbang" % spack_root) diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py index 26cd097149..1480339e93 100644 --- a/var/spack/repos/builtin/packages/googletest/package.py +++ b/var/spack/repos/builtin/packages/googletest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gotcha/package.py b/var/spack/repos/builtin/packages/gotcha/package.py index 44d22bcc7e..006b74a49a 100644 --- a/var/spack/repos/builtin/packages/gotcha/package.py +++ b/var/spack/repos/builtin/packages/gotcha/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gource/package.py b/var/spack/repos/builtin/packages/gource/package.py index a47bfc6821..f4455e1853 100644 --- a/var/spack/repos/builtin/packages/gource/package.py +++ b/var/spack/repos/builtin/packages/gource/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gpdb/package.py b/var/spack/repos/builtin/packages/gpdb/package.py new file mode 100644 index 0000000000..07ced439bd --- /dev/null +++ b/var/spack/repos/builtin/packages/gpdb/package.py @@ -0,0 +1,41 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Gpdb(AutotoolsPackage): + """ + Greenplum Database (GPDB) is an advanced, fully featured, open source + data warehouse, based on PostgreSQL. It provides powerful and rapid + analytics on petabyte scale data volumes. Uniquely geared toward big + data analytics, Greenplum Database is powered by the world's most + advanced cost-based query optimizer delivering high analytical query + performance on large data volumes. + """ + + homepage = "https://github.com/greenplum-db/gpdb" + url = "https://github.com/greenplum-db/gpdb/archive/6.2.1.tar.gz" + + version('6.2.1', sha256='60c81d71665d623ea98a0e9bd8e6df7fecf6b30eb60a5881ccef781ff5214438') + version('6.1.0', sha256='81fa854b0ac5fe4e0de5fdee9a7b7c2514e1ea1feefa4e4d10518538a5c5b2a8') + version('6.0.1', sha256='8902f5d64386447f61c25686f283a785858760e0dcf9a049266db058d3597156') + version('6.0.0', sha256='8514140bee9db514d18a769034562e7f3464f74828595903a64dbf3d175ab71a') + version('5.24.0', sha256='4ea5cfcc20f149669bb3713378158e15b5c5949b367351a0f497ba1602d61fc1') + version('5.23.0', sha256='b06a797eb941362d5473b84d5def349b5ce12ce87ab116bea7c74ad193738ae9') + + depends_on('zstd') + depends_on('apr') + depends_on('libevent') + depends_on('curl') + depends_on('xerces-c') + depends_on('bison', type='build') + depends_on('libxml2') + depends_on('flex') + depends_on('readline') + + def configure_args(self): + args = ['--disable-orca'] + return args diff --git a/var/spack/repos/builtin/packages/gperf/package.py b/var/spack/repos/builtin/packages/gperf/package.py index 1262f8a5c0..9d58b8fe33 100644 --- a/var/spack/repos/builtin/packages/gperf/package.py +++ b/var/spack/repos/builtin/packages/gperf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Gperf(AutotoolsPackage): +class Gperf(AutotoolsPackage, GNUMirrorPackage): """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the @@ -15,7 +15,7 @@ class Gperf(AutotoolsPackage): single string comparison only.""" homepage = "https://www.gnu.org/software/gperf/" - url = "https://ftpmirror.gnu.org/gperf/gperf-3.0.4.tar.gz" + gnu_mirror_path = "gperf/gperf-3.0.4.tar.gz" version('3.0.4', sha256='767112a204407e62dbc3106647cf839ed544f3cf5d0f0523aaa2508623aad63e') diff --git a/var/spack/repos/builtin/packages/gperftools/package.py b/var/spack/repos/builtin/packages/gperftools/package.py index e2452c871d..dfc0a9503d 100644 --- a/var/spack/repos/builtin/packages/gperftools/package.py +++ b/var/spack/repos/builtin/packages/gperftools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gpgme/package.py b/var/spack/repos/builtin/packages/gpgme/package.py index 434c75450d..e7844aa3c3 100644 --- a/var/spack/repos/builtin/packages/gpgme/package.py +++ b/var/spack/repos/builtin/packages/gpgme/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gplates/package.py b/var/spack/repos/builtin/packages/gplates/package.py index 7e4022b3a8..150134f11b 100644 --- a/var/spack/repos/builtin/packages/gplates/package.py +++ b/var/spack/repos/builtin/packages/gplates/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gprolog/package.py index d332711077..49aabd195a 100644 --- a/var/spack/repos/builtin/packages/gnu-prolog/package.py +++ b/var/spack/repos/builtin/packages/gprolog/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class GnuProlog(Package): +class Gprolog(Package): """A free Prolog compiler with constraint solving over finite domains.""" homepage = "http://www.gprolog.org/" url = "http://www.gprolog.org/gprolog-1.4.5.tar.gz" diff --git a/var/spack/repos/builtin/packages/gpu-burn/package.py b/var/spack/repos/builtin/packages/gpu-burn/package.py index fd11176baa..62ef82eb05 100644 --- a/var/spack/repos/builtin/packages/gpu-burn/package.py +++ b/var/spack/repos/builtin/packages/gpu-burn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -51,5 +51,5 @@ class GpuBurn(MakefilePackage, CudaPackage): # The gpu_burn program looks for the compare.ptx file in the current # working directory. Create an environment variable that can be pointed to # so that it can be copied or linked. - def setup_environment(self, spack_env, run_env): - run_env.set('COMPARE_PTX', join_path(self.prefix.share, 'compare.ptx')) + def setup_run_environment(self, env): + env.set('COMPARE_PTX', join_path(self.prefix.share, 'compare.ptx')) diff --git a/var/spack/repos/builtin/packages/grackle/package.py b/var/spack/repos/builtin/packages/grackle/package.py index c6db417c67..f0647393ad 100644 --- a/var/spack/repos/builtin/packages/grackle/package.py +++ b/var/spack/repos/builtin/packages/grackle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gradle/package.py b/var/spack/repos/builtin/packages/gradle/package.py index 7566cbf7be..2c4354ebad 100644 --- a/var/spack/repos/builtin/packages/gradle/package.py +++ b/var/spack/repos/builtin/packages/gradle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/grandr/package.py b/var/spack/repos/builtin/packages/grandr/package.py index 7e3becc72f..aa5f96976e 100644 --- a/var/spack/repos/builtin/packages/grandr/package.py +++ b/var/spack/repos/builtin/packages/grandr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/graph500/package.py b/var/spack/repos/builtin/packages/graph500/package.py index 2367a7a623..8e650673af 100644 --- a/var/spack/repos/builtin/packages/graph500/package.py +++ b/var/spack/repos/builtin/packages/graph500/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/graphicsmagick/package.py b/var/spack/repos/builtin/packages/graphicsmagick/package.py index 24015ea045..5e32b05e14 100644 --- a/var/spack/repos/builtin/packages/graphicsmagick/package.py +++ b/var/spack/repos/builtin/packages/graphicsmagick/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,6 +18,11 @@ class Graphicsmagick(AutotoolsPackage): homepage = "http://www.graphicsmagick.org/" url = "https://sourceforge.net/projects/graphicsmagick/files/graphicsmagick/1.3.29/GraphicsMagick-1.3.29.tar.xz/download" + version('1.3.34', sha256='df009d5173ed0d6a0c6457234256c5a8aeaace782afa1cbab015d5a12bd4f7a4') + version('1.3.33', sha256='130cb330a633580b5124eba5c125bbcbc484298423a97b9bed37ccd50d6dc778') + version('1.3.32', sha256='b842a5a0d6c84fd6c5f161b5cd8e02bbd210b0c0b6728dd762b7c53062ba94e1') + version('1.3.31', sha256='096bbb59d6f3abd32b562fc3b34ea90d88741dc5dd888731d61d17e100394278') + version('1.3.30', sha256='d965e5c6559f55eec76c20231c095d4ae682ea0cbdd8453249ae8771405659f1') version('1.3.29', sha256='e18df46a6934c8c12bfe274d09f28b822f291877f9c81bd9a506f879a7610cd4') depends_on('bzip2') diff --git a/var/spack/repos/builtin/packages/graphite2/package.py b/var/spack/repos/builtin/packages/graphite2/package.py new file mode 100644 index 0000000000..544f3a53d3 --- /dev/null +++ b/var/spack/repos/builtin/packages/graphite2/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Graphite2(CMakePackage): + """Graphite is a system that can be used to create "smart fonts" capable of + displaying writing systems with various complex behaviors. A smart font + contains not only letter shapes but also additional instructions indicating + how to combine and position the letters in complex ways.""" + + homepage = "https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home" + url = "https://github.com/silnrsi/graphite/releases/download/1.3.13/graphite2-1.3.13.tgz" + + version('1.3.13', sha256='dd63e169b0d3cf954b397c122551ab9343e0696fb2045e1b326db0202d875f06') + + patch('regparm.patch') diff --git a/var/spack/repos/builtin/packages/graphite2/regparm.patch b/var/spack/repos/builtin/packages/graphite2/regparm.patch new file mode 100644 index 0000000000..0f6ca1ec48 --- /dev/null +++ b/var/spack/repos/builtin/packages/graphite2/regparm.patch @@ -0,0 +1,11 @@ +--- a/src/inc/Machine.h 2018-12-20 00:28:50.000000000 -0600 ++++ b/src/inc/Machine.h 2020-01-26 19:15:29.965965418 -0600 +@@ -46,7 +46,7 @@ + #endif + #else + #define HOT __attribute__((hot)) +-#if defined(__x86_64) ++#if defined(__x86_64) && !defined(__INTEL_COMPILER) + #define REGPARM(n) __attribute__((hot, regparm(n))) + #else + #define REGPARM(n) diff --git a/var/spack/repos/builtin/packages/graphlib/package.py b/var/spack/repos/builtin/packages/graphlib/package.py index c5f4d8bae7..1452616c4d 100644 --- a/var/spack/repos/builtin/packages/graphlib/package.py +++ b/var/spack/repos/builtin/packages/graphlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/graphmap/package.py b/var/spack/repos/builtin/packages/graphmap/package.py index 28dab0f28d..8d14d80734 100644 --- a/var/spack/repos/builtin/packages/graphmap/package.py +++ b/var/spack/repos/builtin/packages/graphmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py index 8e7a12e303..5e9032b388 100644 --- a/var/spack/repos/builtin/packages/graphviz/package.py +++ b/var/spack/repos/builtin/packages/graphviz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,6 +24,11 @@ class Graphviz(AutotoolsPackage): # This commit hash is tag='stable_release_2.40.1' version('2.40.1', commit='67cd2e5121379a38e0801cc05cce5033f8a2a609') + conflicts('%gcc@:5.9', + when='@2.40.1+qt ^qt@5:', + msg='graphviz-2.40.1 needs gcc-6 or greater to compile with QT5 ' + 'suppport') + # Language bindings language_bindings = ['java'] @@ -57,16 +62,16 @@ class Graphviz(AutotoolsPackage): variant('x', default=False, description='Use the X Window System') - patch('http://www.linuxfromscratch.org/patches/blfs/svn/graphviz-2.40.1-qt5-1.patch', + patch('http://www.linuxfromscratch.org/patches/blfs/9.0/graphviz-2.40.1-qt5-1.patch', sha256='bd532df325df811713e311d17aaeac3f5d6075ea4fd0eae8d989391e6afba930', - when='+qt^qt@5:') + when='@:2.40+qt^qt@5:') patch('https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/master/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0_icc_sfio.patch', sha256='393a0a772315a89dcc970b5efd4765d22dba83493d7956303673eb89c45b949f', level=0, - when='%intel') + when='@:2.40%intel') patch('https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/master/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1_icc_vmalloc.patch', sha256='813e6529e79161a18b0f24a969b7de22f8417b2e942239e658b5402884541bc2', - when='%intel') + when='@:2.40%intel') if not MACOS_VERSION: conflicts('+quartz', @@ -95,7 +100,7 @@ class Graphviz(AutotoolsPackage): depends_on('libpng', when='+pangocairo') depends_on('pango', when='+pangocairo') depends_on('zlib') - depends_on('qt@4', when='+qt') + depends_on('qt', when='+qt') depends_on('libx11', when="+x") # Build dependencies @@ -118,9 +123,9 @@ class Graphviz(AutotoolsPackage): bash = which('bash') bash('./autogen.sh', 'NOCONFIG') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if '+quartz' in self.spec: - spack_env.set('OBJC', self.compiler.cc) + env.set('OBJC', self.compiler.cc) @when('%clang platform=darwin') def patch(self): diff --git a/var/spack/repos/builtin/packages/grass/package.py b/var/spack/repos/builtin/packages/grass/package.py index f480d95fe3..c80255fb43 100644 --- a/var/spack/repos/builtin/packages/grass/package.py +++ b/var/spack/repos/builtin/packages/grass/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,84 +12,104 @@ class Grass(AutotoolsPackage): used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization.""" - homepage = "http://grass.osgeo.org" - - version('7.6.1', sha256='9e25c99cafd16ed8f5e2dca75b5a10dc2af0568dbedf3fc39f1c5a0a9c840b0b') - version('7.4.4', sha256='96a39e273103f7375a670eba94fa3e5dad2819c5c5664c9aee8f145882a94e8c') - version('7.4.3', sha256='004e65693ee97fd4d5dc7ad244e3286a115dccd88964d04be61c07db6574b399') - version('7.4.2', sha256='18eb19bc0aa4cd7be3f30f79ac83f9d0a29c63657f4c1b05bf4c5d5d57a8f46d') - version('7.4.1', sha256='560b8669caaafa9e8dbd4bbf2b4b4bbab7dca1cc46ee828eaf26c744fe0635fc') - version('7.4.0', sha256='cb6fa188e030a3a447fc5451fbe0ecbeb4069ee2fd1bf52ed8e40e9b89e293cc') - - variant('cxx', default=True, description='Add c++ functionality') - variant('tiff', default=True, description='Add TIFF functionality') - variant('png', default=True, description='Add PNG functionality') - variant('postgres', default=False, description='Add PostgreSQL functionality') - variant('mysql', default=False, description='Add MySQL functionality') - variant('sqlite', default=True, description='Add SQLite functionality') - variant('opengl', default=True, description='Add OpenGL functionality') - variant('fftw', default=True, description='Add FFTW functionality') - variant('blas', default=False, description='Add BLAS functionality') - variant('lapack', default=False, description='Add LAPACK functionality') - variant('cairo', default=True, description='Add Cairo functionality') - variant('freetype', default=True, description='Add FreeType functionality') - variant('readline', default=False, description='Add Readline functionality') - variant('regex', default=True, description='Add regex functionality') - variant('pthread', default=False, description='Add POSIX threads functionality') - variant('openmp', default=False, description='Add OpenMP functionality') - variant('opencl', default=False, description='Add OpenCL functionality') - variant('bzlib', default=False, description='Add BZIP2 functionality') + homepage = "https://grass.osgeo.org" + url = "https://grass.osgeo.org/grass78/source/grass-7.8.2.tar.gz" + list_url = "https://grass.osgeo.org/download/software/sources/" + + maintainers = ['adamjstewart'] + + version('7.8.2', sha256='33576f7078f805b39ca20c2fa416ac79c64260c0581072a6dc7d813f53aa9abb') + version('7.8.1', sha256='6ae578fd67afcce7abec4ba4505dcc55b3d2dfe0ca46b99d966cb148c654abb3') + version('7.8.0', sha256='4b1192294e959ffd962282344e4ff325c4472f73abe605e246a1da3beda7ccfa') + version('7.6.1', sha256='9e25c99cafd16ed8f5e2dca75b5a10dc2af0568dbedf3fc39f1c5a0a9c840b0b') + version('7.4.4', sha256='96a39e273103f7375a670eba94fa3e5dad2819c5c5664c9aee8f145882a94e8c') + version('7.4.3', sha256='004e65693ee97fd4d5dc7ad244e3286a115dccd88964d04be61c07db6574b399') + version('7.4.2', sha256='18eb19bc0aa4cd7be3f30f79ac83f9d0a29c63657f4c1b05bf4c5d5d57a8f46d') + version('7.4.1', sha256='560b8669caaafa9e8dbd4bbf2b4b4bbab7dca1cc46ee828eaf26c744fe0635fc') + version('7.4.0', sha256='cb6fa188e030a3a447fc5451fbe0ecbeb4069ee2fd1bf52ed8e40e9b89e293cc') + + variant('cxx', default=True, description='Support C++ functionality') + variant('tiff', default=False, description='Support TIFF functionality') + variant('png', default=False, description='Support PNG functionality') + variant('postgres', default=False, description='Support PostgreSQL functionality') + variant('mysql', default=False, description='Support MySQL functionality') + variant('sqlite', default=False, description='Support SQLite functionality') + variant('opengl', default=False, description='Support OpenGL functionality') + variant('odbc', default=False, description='Support ODBC functionality') + variant('fftw', default=False, description='Support FFTW functionality') + variant('blas', default=False, description='Support BLAS functionality') + variant('lapack', default=False, description='Support LAPACK functionality') + variant('cairo', default=False, description='Support Cairo functionality') + variant('freetype', default=False, description='Support FreeType functionality') + variant('readline', default=False, description='Support Readline functionality') + variant('regex', default=False, description='Support regex functionality') + variant('pthread', default=False, description='Support POSIX threads functionality') + variant('openmp', default=False, description='Support OpenMP functionality') + variant('opencl', default=False, description='Support OpenCL functionality') + variant('bzlib', default=False, description='Support BZIP2 functionality') + variant('zstd', default=False, description='Support Zstandard functionality') + variant('gdal', default=True, description='Enable GDAL/OGR support') + variant('liblas', default=False, description='Enable libLAS support') + variant('wxwidgets', default=False, description='Enable wxWidgets support') variant('netcdf', default=False, description='Enable NetCDF support') - variant('geos', default=False, description='Geometry Engine for v.buffer') + variant('geos', default=False, description='Enable GEOS support') + variant('x', default=False, description='Use the X Window System') - # required components - depends_on('gmake@3.8.1:', type='build') + # http://htmlpreview.github.io/?https://github.com/OSGeo/grass/blob/master/REQUIREMENTS.html + # General requirements + depends_on('gmake@3.81:', type='build') + depends_on('libiconv') depends_on('zlib') depends_on('flex', type='build') depends_on('bison', type='build') depends_on('proj') depends_on('proj@:4', when='@:7.5') - depends_on('proj@:5', when='@:7.7') - depends_on('gdal') - depends_on('python@2.7:2.9', type=('build', 'run')) - depends_on('libx11') - - # optional pieces + # GRASS 7.8.0 was supposed to support PROJ 6, but it still checks for + # share/proj/epsg, which was removed in PROJ 6 + depends_on('proj@:5', when='@:7.8') + depends_on('python@2.7:', type=('build', 'run')) + depends_on('python@2.7:2.8', when='@:7.6', type=('build', 'run')) + depends_on('py-six', when='@7.8:', type=('build', 'run')) + + # Optional packages depends_on('libtiff', when='+tiff') depends_on('libpng', when='+png') depends_on('postgresql', when='+postgres') depends_on('mariadb', when='+mysql') depends_on('sqlite', when='+sqlite') depends_on('gl', when='+opengl') + depends_on('unixodbc', when='+odbc') depends_on('fftw', when='+fftw') depends_on('blas', when='+blas') depends_on('lapack', when='+lapack') - depends_on('cairo', when='+cairo') + depends_on('cairo@1.5.8:', when='+cairo') depends_on('freetype', when='+freetype') depends_on('readline', when='+readline') depends_on('opencl', when='+opencl') depends_on('bzip2', when='+bzlib') - depends_on('netcdf', when='+netcdf') + depends_on('zstd', when='+zstd') + depends_on('gdal', when='+gdal') # required? + depends_on('liblas', when='+liblas') + depends_on('wxwidgets', when='+wxwidgets') + depends_on('py-wxpython@2.8.10.1:', when='+wxwidgets', type=('build', 'run')) + depends_on('netcdf-c', when='+netcdf') depends_on('geos', when='+geos') + depends_on('libx11', when='+x') def url_for_version(self, version): - base = 'https://grass.osgeo.org' - return '{0}/grass{1}/source/grass-{2}.tar.gz'.format( - base, version.up_to(2).joined, version.dotted - ) + url = "https://grass.osgeo.org/grass{0}/source/grass-{1}.tar.gz" + return url.format(version.up_to(2).joined, version) + # https://grasswiki.osgeo.org/wiki/Compile_and_Install def configure_args(self): spec = self.spec args = [ - '--without-odbc', '--without-nls', + # TODO: add packages for these optional dependencies '--without-opendwg', - '--with-x', - '--with-gdal={0}/bin/gdal-config'.format( - spec['gdal'].prefix), - '--with-proj-share={0}/share/proj'.format( - spec['proj'].prefix), + '--without-pdal', + '--with-proj-share={0}'.format(spec['proj'].prefix.share.proj), ] if '+cxx' in spec: @@ -127,6 +147,11 @@ class Grass(AutotoolsPackage): else: args.append('--without-opengl') + if '+odbc' in spec: + args.append('--with-odbc') + else: + args.append('--without-odbc') + if '+fftw' in spec: args.append('--with-fftw') else: @@ -182,9 +207,32 @@ class Grass(AutotoolsPackage): else: args.append('--without-bzlib') + if '+zstd' in spec: + args.append('--with-zstd') + else: + args.append('--without-zstd') + + if '+gdal' in spec: + args.append('--with-gdal={0}/gdal-config'.format( + spec['gdal'].prefix.bin)) + else: + args.append('--without-gdal') + + if '+liblas' in spec: + args.append('--with-liblas={0}/liblas-config'.format( + spec['liblas'].prefix.bin)) + else: + args.append('--without-liblas') + + if '+wxwidgets' in spec: + args.append('--with-wxwidgets={0}/wx-config'.format( + spec['wxwidgets'].prefix.bin)) + else: + args.append('--without-wxwidgets') + if '+netcdf' in spec: args.append('--with-netcdf={0}/bin/nc-config'.format( - spec['netcdf'].prefix)) + spec['netcdf-c'].prefix)) else: args.append('--without-netcdf') @@ -194,6 +242,11 @@ class Grass(AutotoolsPackage): else: args.append('--without-geos') + if '+x' in spec: + args.append('--with-x') + else: + args.append('--without-x') + return args # see issue: https://github.com/spack/spack/issues/11325 @@ -202,5 +255,4 @@ class Grass(AutotoolsPackage): @run_after('configure') def fix_iconv_linking(self): makefile = FileFilter('include/Make/Platform.make') - makefile.filter(r'^ICONVLIB\s*=\s*', 'ICONVLIB = -liconv') - return None + makefile.filter(r'^ICONVLIB\s*=.*', 'ICONVLIB = -liconv') diff --git a/var/spack/repos/builtin/packages/grep/package.py b/var/spack/repos/builtin/packages/grep/package.py new file mode 100644 index 0000000000..7d4bded3f8 --- /dev/null +++ b/var/spack/repos/builtin/packages/grep/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class Grep(AutotoolsPackage): + """Grep searches one or more input files for lines containing a match to + a specified pattern""" + + homepage = "https://www.gnu.org/software/grep/" + url = "https://ftp.gnu.org/gnu/grep/grep-3.3.tar.xz" + + version('3.3', sha256='b960541c499619efd6afe1fa795402e4733c8e11ebf9fafccc0bb4bccdc5b514') diff --git a/var/spack/repos/builtin/packages/grib-api/package.py b/var/spack/repos/builtin/packages/grib-api/package.py index b54e909367..6c4a15116a 100644 --- a/var/spack/repos/builtin/packages/grib-api/package.py +++ b/var/spack/repos/builtin/packages/grib-api/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -50,7 +50,7 @@ class GribApi(CMakePackage): # tests are enabled but the testing scripts don't use it. # depends_on('valgrind', type='test', when='+test') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('openjpeg@1.5.0:1.5.999', when='jp2k=openjpeg') depends_on('jasper', when='jp2k=jasper') depends_on('libpng', when='+png') @@ -100,7 +100,7 @@ class GribApi(CMakePackage): '-DHDF5_ROOT=' + self.spec['hdf5'].prefix, # Prevent possible overriding by environment variables # NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH. - '-DNETCDF_PATH=' + self.spec['netcdf'].prefix]) + '-DNETCDF_PATH=' + self.spec['netcdf-c'].prefix]) else: args.append('-DENABLE_NETCDF=OFF') diff --git a/var/spack/repos/builtin/packages/grnboost/package.py b/var/spack/repos/builtin/packages/grnboost/package.py index 442fa77746..600c65ed40 100644 --- a/var/spack/repos/builtin/packages/grnboost/package.py +++ b/var/spack/repos/builtin/packages/grnboost/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,16 +25,16 @@ class Grnboost(Package): depends_on('xgboost+jvm-packages', type='run') depends_on('spark+hadoop', type='run') - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): grnboost_jar = join_path(self.prefix, 'target', 'scala-2.11', 'GRNBoost.jar') xgboost_version = self.spec['xgboost'].version.string xgboost_jar = join_path(self.spec['xgboost'].prefix, 'xgboost4j-' + xgboost_version + '.jar') - run_env.set('GRNBOOST_JAR', grnboost_jar) - run_env.set('JAVA_HOME', self.spec['java'].prefix) - run_env.set('CLASSPATH', xgboost_jar) - run_env.set('XGBOOST_JAR', xgboost_jar) + env.set('GRNBOOST_JAR', grnboost_jar) + env.set('JAVA_HOME', self.spec['java'].prefix) + env.set('CLASSPATH', xgboost_jar) + env.set('XGBOOST_JAR', xgboost_jar) def install(self, spec, prefix): sbt = which('sbt') diff --git a/var/spack/repos/builtin/packages/groff/package.py b/var/spack/repos/builtin/packages/groff/package.py index 7ec685b5a1..f67f1c901b 100644 --- a/var/spack/repos/builtin/packages/groff/package.py +++ b/var/spack/repos/builtin/packages/groff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,14 +6,14 @@ from spack import * -class Groff(AutotoolsPackage): +class Groff(AutotoolsPackage, GNUMirrorPackage): """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. Output may be PostScript or PDF, html, or ASCII/UTF8 for display at the terminal.""" homepage = "https://www.gnu.org/software/groff/" - url = "https://ftpmirror.gnu.org/groff/groff-1.22.3.tar.gz" + gnu_mirror_path = "groff/groff-1.22.3.tar.gz" # TODO: add html variant, spack doesn't have netpbm and its too # complicated for me to find out at this point in time. diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py index 43cecbec81..bc61efdbe9 100644 --- a/var/spack/repos/builtin/packages/gromacs/package.py +++ b/var/spack/repos/builtin/packages/gromacs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,14 +25,21 @@ class Gromacs(CMakePackage): maintainers = ['junghans', 'marvinbernhardt'] version('develop', branch='master') + version('2020', sha256='477e56142b3dcd9cb61b8f67b24a55760b04d1655e8684f979a75a5eec40ba01') + version('2019.5', sha256='438061a4a2d45bbb5cf5c3aadd6c6df32d2d77ce8c715f1c8ffe56156994083a') + version('2019.4', sha256='ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867') + version('2019.3', sha256='4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573') version('2019.2', sha256='bcbf5cc071926bc67baa5be6fb04f0986a2b107e1573e15fadcb7d7fc4fb9f7e') version('2019.1', sha256='b2c37ed2fcd0e64c4efcabdc8ee581143986527192e6e647a197c76d9c4583ec') version('2019', sha256='c5b281a5f0b5b4eeb1f4c7d4dc72f96985b566561ca28acc9c7c16f6ee110d0b') + version('2018.8', sha256='776923415df4bc78869d7f387c834141fdcda930b2e75be979dc59ecfa6ebecf') + version('2018.5', sha256='32261df6f7ec4149fc0508f9af416953d056e281590359838c1ed6644ba097b8') version('2018.4', sha256='6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891') version('2018.3', sha256='4423a49224972969c52af7b1f151579cea6ab52148d8d7cbae28c183520aa291') version('2018.2', sha256='4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857') version('2018.1', sha256='4d3533340499323fece83b4a2d4251fa856376f2426c541e00b8e6b4c0d705cd') version('2018', sha256='deb5d0b749a52a0c6083367b5f50a99e08003208d81954fb49e7009e1b1fd0e9') + version('2016.6', sha256='bac0117d2cad21f9b94fe5b854fb9ae7435b098a6da4e732ee745f18e52473d7') version('2016.5', sha256='57db26c6d9af84710a1e0c47a1f5bf63a22641456448dcd2eeb556ebd14e0b7c') version('2016.4', sha256='4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264') version('2016.3', sha256='7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27') @@ -65,6 +72,7 @@ class Gromacs(CMakePackage): ' of libgromacs and/or the mdrun program') variant('openmp', default=True, description='Enables OpenMP at configure time') variant('double_precision', default=False, description='Enables a double-precision configuration') + variant('hwloc', default=True, description='Use the hwloc portable hardware locality library') depends_on('mpi', when='+mpi') depends_on('plumed+mpi', when='+plumed+mpi') @@ -74,7 +82,10 @@ class Gromacs(CMakePackage): depends_on('cmake@3.4.3:3.99.99', type='build', when='@2018:') depends_on('cuda', when='+cuda') - patch('gmxDetectCpu-cmake-3.14.patch', when='@2018:^cmake@3.14.0:') + # TODO: openmpi constraint; remove when concretizer is fixed + depends_on('hwloc@:1.999', when='+hwloc') + + patch('gmxDetectCpu-cmake-3.14.patch', when='@2018:2019.3^cmake@3.14.0:') patch('gmxDetectSimd-cmake-3.14.patch', when='@:2017.99^cmake@3.14.0:') def patch(self): @@ -94,6 +105,11 @@ class Gromacs(CMakePackage): if '~shared' in self.spec: options.append('-DBUILD_SHARED_LIBS:BOOL=OFF') + if '+hwloc' in self.spec: + options.append('-DGMX_HWLOC:BOOL=ON') + else: + options.append('-DGMX_HWLOC:BOOL=OFF') + if '+cuda' in self.spec: options.append('-DGMX_GPU:BOOL=ON') options.append('-DCUDA_TOOLKIT_ROOT_DIR:STRING=' + diff --git a/var/spack/repos/builtin/packages/grpc/package.py b/var/spack/repos/builtin/packages/grpc/package.py index 20d09541ff..8cbfe77328 100644 --- a/var/spack/repos/builtin/packages/grpc/package.py +++ b/var/spack/repos/builtin/packages/grpc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,8 +9,12 @@ class Grpc(CMakePackage): """A high performance, open-source universal RPC framework.""" homepage = "https://grpc.io" - url = "https://github.com/grpc/grpc/archive/v1.23.1.tar.gz" + url = "https://github.com/grpc/grpc/archive/v1.27.0.tar.gz" + version('1.27.0', sha256='3ccc4e5ae8c1ce844456e39cc11f1c991a7da74396faabe83d779836ef449bce') + version('1.26.0', sha256='2fcb7f1ab160d6fd3aaade64520be3e5446fc4c6fa7ba6581afdc4e26094bd81') + version('1.25.0', sha256='ffbe61269160ea745e487f79b0fd06b6edd3d50c6d9123f053b5634737cf2f69') + version('1.24.3', sha256='c84b3fa140fcd6cce79b3f9de6357c5733a0071e04ca4e65ba5f8d306f10f033') version('1.23.1', sha256='dd7da002b15641e4841f20a1f3eb1e359edb69d5ccf8ac64c362823b05f523d9') variant('codegen', default=True, @@ -20,7 +24,7 @@ class Grpc(CMakePackage): depends_on('protobuf') depends_on('openssl') depends_on('zlib') - depends_on('cares') + depends_on('c-ares') def cmake_args(self): args = [ diff --git a/var/spack/repos/builtin/packages/gsl/package.py b/var/spack/repos/builtin/packages/gsl/package.py index 021bf26e91..3ad7b11971 100644 --- a/var/spack/repos/builtin/packages/gsl/package.py +++ b/var/spack/repos/builtin/packages/gsl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,7 +7,7 @@ from spack import * -class Gsl(AutotoolsPackage): +class Gsl(AutotoolsPackage, GNUMirrorPackage): """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random @@ -15,7 +15,7 @@ class Gsl(AutotoolsPackage): over 1000 functions in total with an extensive test suite.""" homepage = "http://www.gnu.org/software/gsl" - url = "https://ftpmirror.gnu.org/gsl/gsl-2.3.tar.gz" + gnu_mirror_path = "gsl/gsl-2.3.tar.gz" version('2.5', sha256='0460ad7c2542caaddc6729762952d345374784100223995eb14d614861f2258d') version('2.4', sha256='4d46d07b946e7b31c19bbf33dda6204d7bedc2f5462a1bae1d4013426cd1ce9b') diff --git a/var/spack/repos/builtin/packages/gslib/package.py b/var/spack/repos/builtin/packages/gslib/package.py index 59a077b628..1bdffc3ecf 100644 --- a/var/spack/repos/builtin/packages/gslib/package.py +++ b/var/spack/repos/builtin/packages/gslib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gtkmm/package.py b/var/spack/repos/builtin/packages/gtkmm/package.py index 13ac610740..12a149e7ab 100644 --- a/var/spack/repos/builtin/packages/gtkmm/package.py +++ b/var/spack/repos/builtin/packages/gtkmm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gtkorvo-atl/package.py b/var/spack/repos/builtin/packages/gtkorvo-atl/package.py index e609cee178..80dc12e34b 100644 --- a/var/spack/repos/builtin/packages/gtkorvo-atl/package.py +++ b/var/spack/repos/builtin/packages/gtkorvo-atl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py b/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py index 094ede18fd..19a57f122b 100644 --- a/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py +++ b/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gtkorvo-dill/package.py b/var/spack/repos/builtin/packages/gtkorvo-dill/package.py index effb7f8c1c..cb5920ae5b 100644 --- a/var/spack/repos/builtin/packages/gtkorvo-dill/package.py +++ b/var/spack/repos/builtin/packages/gtkorvo-dill/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gtkorvo-enet/package.py b/var/spack/repos/builtin/packages/gtkorvo-enet/package.py index 9f6c6b5f59..7b86f292c7 100644 --- a/var/spack/repos/builtin/packages/gtkorvo-enet/package.py +++ b/var/spack/repos/builtin/packages/gtkorvo-enet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/gtkplus/package.py b/var/spack/repos/builtin/packages/gtkplus/package.py index dcd3e36529..619879ea0a 100644 --- a/var/spack/repos/builtin/packages/gtkplus/package.py +++ b/var/spack/repos/builtin/packages/gtkplus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -48,11 +48,11 @@ class Gtkplus(AutotoolsPackage): filter_file(r'CFLAGS="-DGDK_PIXBUF_DISABLE_DEPRECATED $CFLAGS"', '', 'configure', string=True) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path("XDG_DATA_DIRS", - self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", - self.prefix.share) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) def configure_args(self): args = [] diff --git a/var/spack/repos/builtin/packages/gtksourceview/package.py b/var/spack/repos/builtin/packages/gtksourceview/package.py index 9907a95255..01876610b2 100644 --- a/var/spack/repos/builtin/packages/gtksourceview/package.py +++ b/var/spack/repos/builtin/packages/gtksourceview/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -42,13 +42,17 @@ class Gtksourceview(AutotoolsPackage): url += '{0}/gtksourceview-{1}.tar.xz' return url.format(version.up_to(2), version) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) - def setup_environment(self, spack_env, run_env): - spack_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + + def setup_build_environment(self, env): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + + def setup_run_environment(self, env): + env.prepend_path("XDG_DATA_DIRS", self.prefix.share) # TODO: If https://github.com/spack/spack/pull/12344 is merged, this # method is unnecessary. diff --git a/var/spack/repos/builtin/packages/gts/package.py b/var/spack/repos/builtin/packages/gts/package.py index c4b2beb8f8..13698ec27a 100644 --- a/var/spack/repos/builtin/packages/gts/package.py +++ b/var/spack/repos/builtin/packages/gts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/guidance/package.py b/var/spack/repos/builtin/packages/guidance/package.py index ef4de4596c..e0015b7f32 100644 --- a/var/spack/repos/builtin/packages/guidance/package.py +++ b/var/spack/repos/builtin/packages/guidance/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,7 +17,7 @@ class Guidance(MakefilePackage): version('2.02', sha256='825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844') depends_on('perl', type=('build', 'run')) - depends_on('perl-bio-perl', type=('build', 'run')) + depends_on('perl-bioperl', type=('build', 'run')) depends_on('ruby') depends_on('prank') depends_on('clustalw') @@ -43,5 +43,5 @@ class Guidance(MakefilePackage): install('guidance.pl', join_path(prefix.bin.www.Guidance, 'guidance')) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', prefix.bin.www.Guidance) + def setup_run_environment(self, env): + env.prepend_path('PATH', prefix.bin.www.Guidance) diff --git a/var/spack/repos/builtin/packages/guile/package.py b/var/spack/repos/builtin/packages/guile/package.py index de15b1848d..47bfa38125 100644 --- a/var/spack/repos/builtin/packages/guile/package.py +++ b/var/spack/repos/builtin/packages/guile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Guile(AutotoolsPackage): +class Guile(AutotoolsPackage, GNUMirrorPackage): """Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.""" homepage = "https://www.gnu.org/software/guile/" - url = "https://ftpmirror.gnu.org/guile/guile-2.2.0.tar.gz" + gnu_mirror_path = "guile/guile-2.2.0.tar.gz" version('2.2.6', sha256='08c0e7487777740b61cdd97949b69e8a5e2997d8c2fe6c7e175819eb18444506') version('2.2.5', sha256='c3c7a2f6ae0d8321a240c7ebc532a1d47af8c63214157a73789e2b2305b4c927') @@ -24,20 +24,29 @@ class Guile(AutotoolsPackage): version('2.0.11', sha256='e6786c934346fa2e38e46d8d81a622bb1c16d130153523f6129fcd79ef1fb040') variant('readline', default=True, description='Use the readline library') - variant('threads', default=True, description='Use the thread interface') + variant( + 'threads', + default='none', + values=('none', 'posix', 'dgux386'), + multi=False, + description='Use the thread interface' + ) + depends_on('bdw-gc@7.0: threads=none', when='threads=none') + depends_on('bdw-gc@7.0: threads=posix', when='threads=posix') + depends_on('bdw-gc@7.0: threads=dgux386', when='threads=dgux386') depends_on('gmp@4.2:') depends_on('gettext') depends_on('libtool@1.5.6:') depends_on('libunistring@0.9.3:') - depends_on('bdw-gc@7.0:') depends_on('libffi') depends_on('readline', when='+readline') depends_on('pkgconfig', type='build') build_directory = 'spack-build' - conflicts('+threads', when='%intel') + conflicts('threads=posix', when='%intel') + conflicts('threads=dgux386', when='%intel') def configure_args(self): spec = self.spec @@ -49,7 +58,11 @@ class Guile(AutotoolsPackage): '--with-libgmp-prefix={0}'.format(spec['gmp'].prefix), '--with-libintl-prefix={0}'.format(spec['gettext'].prefix), ] - config_args += self.with_or_without('threads') + + if 'threads=none' in spec: + config_args.append('--without-threads') + else: + config_args.append('--with-threads') if '+readline' in spec: config_args.append('--with-libreadline-prefix={0}'.format( diff --git a/var/spack/repos/builtin/packages/gurobi/package.py b/var/spack/repos/builtin/packages/gurobi/package.py index b9c416e46b..4922d23678 100644 --- a/var/spack/repos/builtin/packages/gurobi/package.py +++ b/var/spack/repos/builtin/packages/gurobi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -35,8 +35,8 @@ class Gurobi(Package): def url_for_version(self, version): return "file://{0}/gurobi{1}_linux64.tar.gz".format(os.getcwd(), version) - def setup_environment(self, spack_env, run_env): - run_env.set('GUROBI_HOME', self.prefix) + def setup_run_environment(self, env): + env.set('GUROBI_HOME', self.prefix) def install(self, spec, prefix): install_tree('linux64', prefix) diff --git a/var/spack/repos/builtin/packages/gzip/package.py b/var/spack/repos/builtin/packages/gzip/package.py new file mode 100644 index 0000000000..7a99424c3b --- /dev/null +++ b/var/spack/repos/builtin/packages/gzip/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class Gzip(AutotoolsPackage): + """GNU Gzip is a popular data compression program originally written by + Jean-loup Gailly for the GNU project.""" + + homepage = "https://www.gnu.org/software/gzip/" + url = "https://ftp.gnu.org/gnu/gzip/gzip-1.10.tar.gz" + + version('1.10', sha256='c91f74430bf7bc20402e1f657d0b252cb80aa66ba333a25704512af346633c68') diff --git a/var/spack/repos/builtin/packages/h5cpp/package.py b/var/spack/repos/builtin/packages/h5cpp/package.py new file mode 100644 index 0000000000..373aa1303d --- /dev/null +++ b/var/spack/repos/builtin/packages/h5cpp/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class H5cpp(CMakePackage): + """Easy to use HDF5 C++ templates for Serial and Parallel HDF5""" + + homepage = "http://h5cpp.org" + url = "https://github.com/steven-varga/h5cpp/archive/v1.10.4-5.tar.gz" + git = "https://github.com/steven-varga/h5cpp.git" + + maintainers = ['eschnett'] + + version('master', branch='master') + version('1.10.4-5', sha256='42d0ca1aaff1ead8998a26d892a51c12b1b89023382f191dc438bd0fa4513455') + + variant('mpi', default=True, description='Include MPI support') + + depends_on('cmake @3.10:', type='build') + depends_on('hdf5 @1.10.4:') + depends_on('hdf5 +mpi', when='+mpi') + depends_on('mpi', when='+mpi') + + def cmake_args(self): + return ['-DH5CPP_BUILD_TESTS=OFF'] diff --git a/var/spack/repos/builtin/packages/h5hut/package.py b/var/spack/repos/builtin/packages/h5hut/package.py index 48c5fa2020..09497c6d68 100644 --- a/var/spack/repos/builtin/packages/h5hut/package.py +++ b/var/spack/repos/builtin/packages/h5hut/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/h5part/package.py b/var/spack/repos/builtin/packages/h5part/package.py index d08f37c82c..74246a6ea9 100644 --- a/var/spack/repos/builtin/packages/h5part/package.py +++ b/var/spack/repos/builtin/packages/h5part/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/h5utils/package.py b/var/spack/repos/builtin/packages/h5utils/package.py index 5ffb6e9805..78fd397311 100644 --- a/var/spack/repos/builtin/packages/h5utils/package.py +++ b/var/spack/repos/builtin/packages/h5utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/h5z-zfp/package.py b/var/spack/repos/builtin/packages/h5z-zfp/package.py index 683bc168d4..f36f48d5b7 100644 --- a/var/spack/repos/builtin/packages/h5z-zfp/package.py +++ b/var/spack/repos/builtin/packages/h5z-zfp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hacckernels/package.py b/var/spack/repos/builtin/packages/hacckernels/package.py index 0a7e69954a..b15e2ac9cb 100644 --- a/var/spack/repos/builtin/packages/hacckernels/package.py +++ b/var/spack/repos/builtin/packages/hacckernels/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hadoop/package.py b/var/spack/repos/builtin/packages/hadoop/package.py index 04b00e0a85..26acecfc89 100644 --- a/var/spack/repos/builtin/packages/hadoop/package.py +++ b/var/spack/repos/builtin/packages/hadoop/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,9 +13,14 @@ class Hadoop(Package): """ homepage = "http://hadoop.apache.org/" - url = "http://apache-mirror.8birdsvideo.com/hadoop/common/hadoop-3.1.2/hadoop-3.1.2-src.tar.gz" - - version('3.1.2', sha256='02f277c9fc75d4b13c7697ed6be30dba41667841ab5e37442855267c39bec6b6') + url = "https://www.apache.org/dist/hadoop/common/hadoop-3.2.1/hadoop-3.2.1.tar.gz" + + version('3.2.1', sha256='f66a3a4115b8f16c1077d1a198a06854dbef0e4233291712ed08d0a10629ed37') + version('3.1.3', sha256='1e8b7ca4e3911f8ec999595f71921390e9ad7a27255fbd36af1f3a1628b67e2b') + version('2.10.0', sha256='131750c258368be4baff5d4a83b4de2cd119bda3774ed26d1d233b6fdf33f07f') + version('2.9.2', sha256='3d2023c46b1156c1b102461ad08cbc17c8cc53004eae95dab40a1f659839f28a') + version('2.8.5', sha256='f9c726df693ce2daa4107886f603270d66e7257f77a92c9886502d6cd4a884a4') + version('2.7.7', sha256='d129d08a2c9dafec32855a376cbd2ab90c6a42790898cabbac6be4d29f9c2026') depends_on('java', type='run') diff --git a/var/spack/repos/builtin/packages/halc/package.py b/var/spack/repos/builtin/packages/halc/package.py index 23545f48d5..e9b4ffc0aa 100644 --- a/var/spack/repos/builtin/packages/halc/package.py +++ b/var/spack/repos/builtin/packages/halc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/half/package.py b/var/spack/repos/builtin/packages/half/package.py new file mode 100644 index 0000000000..f1ec03c4e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/half/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Half(Package): + """This is a C++ header-only library to provide an IEEE-754 conformant + half-precision floating point type along with corresponding + arithmetic operators, type conversions and common mathematical + functions. It aims for both efficiency and ease of use, trying to + accurately mimic the behaviour of the builtin floating point types + at the best performance possible. It automatically uses and + provides C++11 features when possible, but stays completely + C++98-compatible when neccessary.""" + + homepage = "https://sourceforge.net/projects/half/" + url = "https://downloads.sourceforge.net/project/half/half/2.1.0/half-2.1.0.zip" + + maintainers = ['bvanessen'] + + version('2.1.0', sha256='ad1788afe0300fa2b02b0d1df128d857f021f92ccf7c8bddd07812685fa07a25') + + def install(self, spec, prefix): + mkdirp(prefix.include) + install_tree('include', prefix.include) diff --git a/var/spack/repos/builtin/packages/hama/package.py b/var/spack/repos/builtin/packages/hama/package.py new file mode 100644 index 0000000000..6883155f7f --- /dev/null +++ b/var/spack/repos/builtin/packages/hama/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Hama(Package): + """ + Apache Hama is a framework for Big Data analytics which uses the Bulk + Synchronous Parallel (BSP) computing model, which was established in + 2012 as a Top-Level Project of The Apache Software Foundation. + """ + + homepage = "https://www-eu.apache.org" + url = "https://www-eu.apache.org/dist/hama/hama-0.7.1/hama-dist-0.7.1.tar.gz" + + version('0.7.1', sha256='c7466c2a70a949609a501e868f6a288b7142725c407e24649ea6f7121632bc89') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/hapcut2/package.py b/var/spack/repos/builtin/packages/hapcut2/package.py index 69eb5073d5..a4581647cd 100644 --- a/var/spack/repos/builtin/packages/hapcut2/package.py +++ b/var/spack/repos/builtin/packages/hapcut2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hapdip/package.py b/var/spack/repos/builtin/packages/hapdip/package.py index 45d5b9f697..7e1446a0c9 100644 --- a/var/spack/repos/builtin/packages/hapdip/package.py +++ b/var/spack/repos/builtin/packages/hapdip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/haploview/package.py b/var/spack/repos/builtin/packages/haploview/package.py index 328b5e8205..298ecf6edb 100644 --- a/var/spack/repos/builtin/packages/haploview/package.py +++ b/var/spack/repos/builtin/packages/haploview/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/haproxy/package.py b/var/spack/repos/builtin/packages/haproxy/package.py new file mode 100644 index 0000000000..2b8d46c315 --- /dev/null +++ b/var/spack/repos/builtin/packages/haproxy/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Haproxy(MakefilePackage): + """ + HAProxy is a single-threaded, event-driven, non-blocking engine + combining a very fast I/O layer with a priority-based scheduler. + """ + + homepage = "https://www.haproxy.org" + url = "https://www.haproxy.org/download/2.1/src/haproxy-2.1.0.tar.gz" + + version('2.1.1', sha256='57e75c1a380fc6f6aa7033f71384370899443c7f4e8a4ba289b5d4350bc76d1a') + version('2.1.0', sha256='f268efb360a0e925137b4b8ed431f2f8f3b68327efb2c418b266e535d8e335a0') + + def url_for_version(self, version): + url = "https://www.haproxy.org/download/{0}/src/haproxy-{1}.tar.gz" + return url.format(version.up_to(2), version) + + def build(self, spec, prefix): + make('TARGET=generic', 'PREFIX=' + prefix) + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/harfbuzz/package.py b/var/spack/repos/builtin/packages/harfbuzz/package.py index deef607ec4..4ab6005dbf 100644 --- a/var/spack/repos/builtin/packages/harfbuzz/package.py +++ b/var/spack/repos/builtin/packages/harfbuzz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,12 +17,18 @@ class Harfbuzz(AutotoolsPackage): version('1.4.6', sha256='21a78b81cd20cbffdb04b59ac7edfb410e42141869f637ae1d6778e74928d293') version('0.9.37', sha256='255f3b3842dead16863d1d0c216643d97b80bfa087aaa8fc5926da24ac120207') + variant('graphite2', default=False, description='enable support for graphite2 font engine') + depends_on("pkgconfig", type="build") depends_on("glib") depends_on("icu4c") depends_on("freetype") depends_on("cairo") depends_on("zlib") + depends_on("graphite2", when='+graphite2') + + conflicts('%intel', when='@2.3.1:', + msg='harfbuzz-2.3.1 does not build with the Intel compiler') def configure_args(self): args = [] @@ -34,6 +40,8 @@ class Harfbuzz(AutotoolsPackage): args.append('GTKDOC_CHECK_PATH={0}'.format(true)) args.append('GTKDOC_MKPDF={0}'.format(true)) args.append('GTKDOC_REBASE={0}'.format(true)) + args.extend(self.with_or_without('graphite2')) + return args def patch(self): diff --git a/var/spack/repos/builtin/packages/harminv/package.py b/var/spack/repos/builtin/packages/harminv/package.py index 3570f87fe1..7aab4053ab 100644 --- a/var/spack/repos/builtin/packages/harminv/package.py +++ b/var/spack/repos/builtin/packages/harminv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hbase/package.py b/var/spack/repos/builtin/packages/hbase/package.py new file mode 100644 index 0000000000..d34fe2f9f1 --- /dev/null +++ b/var/spack/repos/builtin/packages/hbase/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Hbase(Package): + """ + Apache HBase is an open-source, distributed, versioned, column-oriented + store modeled after Google' Bigtable: A Distributed Storage System for + Structured Data by Chang et al. Just as Bigtable leverages the distributed + data storage provided by the Google File System, HBase provides + Bigtable-like capabilities on top of Apache Hadoop. + """ + + homepage = "https://github.com/apache/hbase" + url = "https://github.com/apache/hbase/archive/rel/2.2.2.tar.gz" + + version('2.2.2', sha256='e9a58946e9adff1cac23a0b261ecf32da32f8d2ced0706af1d04e8a67d582926') + version('2.1.8', sha256='121cea4c554879c8401f676c8eb49e39bd35d41c358e919379ad4a318844c8de') + + depends_on('java@7:', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/hc/package.py b/var/spack/repos/builtin/packages/hc/package.py index 19fd4c6b4f..ac7de94062 100644 --- a/var/spack/repos/builtin/packages/hc/package.py +++ b/var/spack/repos/builtin/packages/hc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,7 +17,7 @@ class Hc(MakefilePackage): version('1.0.7', sha256='7499ea76ac4739a9c0941bd57d124fb681fd387c8d716ebb358e6af3395103ed') depends_on('gmt@4.2.1:4.999') - depends_on('netcdf') + depends_on('netcdf-c') # Build phase fails in parallel with the following error messages: # /usr/bin/ld: cannot find -lrick @@ -25,11 +25,11 @@ class Hc(MakefilePackage): # /usr/bin/ld: cannot find -lggrd parallel = False - def setup_environment(self, spack_env, run_env): - spack_env.set('GMTHOME', self.spec['gmt'].prefix) - spack_env.set('NETCDFHOME', self.spec['netcdf'].prefix) - spack_env.set('HC_HOME', self.prefix) - spack_env.unset('ARCH') + def setup_build_environment(self, env): + env.set('GMTHOME', self.spec['gmt'].prefix) + env.set('NETCDFHOME', self.spec['netcdf-c'].prefix) + env.set('HC_HOME', self.prefix) + env.unset('ARCH') def install(self, spec, prefix): # Most files are installed during the build stage. diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py index ef8be65084..0c30501560 100644 --- a/var/spack/repos/builtin/packages/hdf/package.py +++ b/var/spack/repos/builtin/packages/hdf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py index 7516ca6e4f..2a535f5e69 100644 --- a/var/spack/repos/builtin/packages/hdf5-blosc/package.py +++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -183,10 +183,14 @@ Done. raise RuntimeError("HDF5 Blosc plugin check failed") shutil.rmtree(checkdir) - def setup_environment(self, spack_env, run_env): - spack_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib) - run_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib) + def setup_build_environment(self, env): + env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib) - run_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib) + def setup_run_environment(self, env): + env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib) + + def setup_dependent_build_environment(self, env, dependent_spec): + env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib) diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index 715f57dd72..cbc445edf0 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,6 +23,7 @@ class Hdf5(AutotoolsPackage): version('develop', branch='develop') + version('1.10.6', sha256='5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa') version('1.10.5', sha256='6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8') version('1.10.4', sha256='8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2') version('1.10.3', sha256='b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39') @@ -113,7 +114,7 @@ class Hdf5(AutotoolsPackage): # Disable MPI C++ interface when C++ is disabled, otherwise downstream # libraries fail to link; see https://github.com/spack/spack/issues/12586 - patch('h5public-skip-mpicxx.patch', when='+mpi~cxx', + patch('h5public-skip-mpicxx.patch', when='@:1.8.21,1.10.0:1.10.5+mpi~cxx', sha256='b61e2f058964ad85be6ee5ecea10080bf79e73f83ff88d1fa4b602d00209da9c') filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc', relative_root='bin') diff --git a/var/spack/repos/builtin/packages/heaptrack/package.py b/var/spack/repos/builtin/packages/heaptrack/package.py index 7c0b254f00..bdb6a90b76 100644 --- a/var/spack/repos/builtin/packages/heaptrack/package.py +++ b/var/spack/repos/builtin/packages/heaptrack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/heffte/package.py b/var/spack/repos/builtin/packages/heffte/package.py new file mode 100644 index 0000000000..e3bb7e4961 --- /dev/null +++ b/var/spack/repos/builtin/packages/heffte/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Heffte(CMakePackage): + """Highly Efficient FFT for Exascale""" + + homepage = "https://bitbucket.org/icl/heffte" + url = "https://bitbucket.org/icl/heffte/get/v0.1.tar.gz" + git = "https://bitbucket.org/icl/heffte.git" + + version('master', branch='master') + version('0.1', sha256='d279a03298d2dc76574b1ae1031acb4ea964348cf359273d1afa4668b5bfe748') + + variant('cuda', default=False, description='Builds with support for GPUs via CUDA') + + depends_on('fftw') + depends_on('mpi') + depends_on('cuda', when="+cuda") + + def cmake_args(self): + args = ['-DBUILD_SHARED=ON'] + if '+cuda' in self.spec: + args.append('-DBUILD_GPU=ON') + else: + args.append('-DBUILD_GPU=OFF') + return args diff --git a/var/spack/repos/builtin/packages/help2man/package.py b/var/spack/repos/builtin/packages/help2man/package.py index d1365016b0..5ec6a24f95 100644 --- a/var/spack/repos/builtin/packages/help2man/package.py +++ b/var/spack/repos/builtin/packages/help2man/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Help2man(AutotoolsPackage): +class Help2man(AutotoolsPackage, GNUMirrorPackage): """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" homepage = "https://www.gnu.org/software/help2man/" - url = "https://ftpmirror.gnu.org/help2man/help2man-1.47.11.tar.xz" + gnu_mirror_path = "help2man/help2man-1.47.11.tar.xz" version('1.47.11', sha256='5985b257f86304c8791842c0c807a37541d0d6807ee973000cf8a3fe6ad47b88') version('1.47.8', sha256='528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc') diff --git a/var/spack/repos/builtin/packages/henson/package.py b/var/spack/repos/builtin/packages/henson/package.py index 11701e62d4..4e6bb04755 100644 --- a/var/spack/repos/builtin/packages/henson/package.py +++ b/var/spack/repos/builtin/packages/henson/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,10 +10,9 @@ class Henson(CMakePackage): """Cooperative multitasking for in situ processing.""" homepage = "https://github.com/henson-insitu/henson" - url = "https://github.com/henson-insitu/henson" git = "https://github.com/henson-insitu/henson.git" - version('develop', branch='master') + version('master', branch='master') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/hepmc/package.py b/var/spack/repos/builtin/packages/hepmc/package.py index 8a003e042a..fe8502d097 100644 --- a/var/spack/repos/builtin/packages/hepmc/package.py +++ b/var/spack/repos/builtin/packages/hepmc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/heppdt/package.py b/var/spack/repos/builtin/packages/heppdt/package.py index a9f4e1e3ff..ee2d77f56d 100644 --- a/var/spack/repos/builtin/packages/heppdt/package.py +++ b/var/spack/repos/builtin/packages/heppdt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hic-pro/package.py b/var/spack/repos/builtin/packages/hic-pro/package.py index c4fc45bdb1..2d6bdf63a8 100644 --- a/var/spack/repos/builtin/packages/hic-pro/package.py +++ b/var/spack/repos/builtin/packages/hic-pro/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/highfive/package.py b/var/spack/repos/builtin/packages/highfive/package.py index bd8aac37b4..aed6d1e51e 100644 --- a/var/spack/repos/builtin/packages/highfive/package.py +++ b/var/spack/repos/builtin/packages/highfive/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/highwayhash/package.py b/var/spack/repos/builtin/packages/highwayhash/package.py index 9dc6e9d1e9..f3666ce991 100644 --- a/var/spack/repos/builtin/packages/highwayhash/package.py +++ b/var/spack/repos/builtin/packages/highwayhash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hiop/package.py b/var/spack/repos/builtin/packages/hiop/package.py index 7286321119..f0603381dd 100644 --- a/var/spack/repos/builtin/packages/hiop/package.py +++ b/var/spack/repos/builtin/packages/hiop/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hisat2/package.py b/var/spack/repos/builtin/packages/hisat2/package.py index 64c756a9e8..93b54e9ed5 100644 --- a/var/spack/repos/builtin/packages/hisat2/package.py +++ b/var/spack/repos/builtin/packages/hisat2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -40,5 +40,5 @@ class Hisat2(MakefilePackage): if os.path.isfile(file): install(file, prefix.bin) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.spec.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/hisea/package.py b/var/spack/repos/builtin/packages/hisea/package.py index f934edbee5..c78fe166a0 100644 --- a/var/spack/repos/builtin/packages/hisea/package.py +++ b/var/spack/repos/builtin/packages/hisea/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,7 +12,6 @@ class Hisea(MakefilePackage): among others.""" homepage = "https://doi.org/10.1186/s12859-017-1953-9" - url = "https://github.com/lucian-ilie/HISEA" version('2017.12.26', sha256='3c6ddfb8490a327cc5f9e45f64cd4312abc6ef5719661ce8892db8a20a1e9c5e', url='https://github.com/lucian-ilie/HISEA/tarball/39e01e98caa0f2101da806ca59306296effe789c') diff --git a/var/spack/repos/builtin/packages/hive/package.py b/var/spack/repos/builtin/packages/hive/package.py new file mode 100644 index 0000000000..a32e08a80c --- /dev/null +++ b/var/spack/repos/builtin/packages/hive/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Hive(Package): + """ + The Apache Hive data warehouse software facilitates reading, writing, + and managing large datasets residing in distributed storage using SQL. + Structure can be projected onto data already in storage. A command line + tool and JDBC driver are provided to connect users to Hive. + """ + + homepage = "https://hive.apache.org/" + url = "https://www.apache.org/dist/hive/hive-3.1.2/apache-hive-3.1.2-bin.tar.gz" + + version('3.1.2', sha256='d75dcf36908b4e7b9b0ec9aec57a46a6628b97b276c233cb2c2f1a3e89b13462') + version('2.3.6', sha256='0b3736edc8d15f01ed649bfce7d74346c35fd57567411e9d0c3f48578f76610d') + version('1.2.2', sha256='763b246a1a1ceeb815493d1e5e1d71836b0c5b9be1c4cd9c8d685565113771d1') + + depends_on('hadoop', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/hmmer/package.py b/var/spack/repos/builtin/packages/hmmer/package.py index 197c58bc0d..9e808a7eb5 100644 --- a/var/spack/repos/builtin/packages/hmmer/package.py +++ b/var/spack/repos/builtin/packages/hmmer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,8 +12,9 @@ class Hmmer(Package): probabilistic models called profile hidden Markov models (profile HMMs). """ homepage = 'http://www.hmmer.org' - url = 'http://eddylab.org/software/hmmer/hmmer-3.2.1.tar.gz' + url = 'http://eddylab.org/software/hmmer/hmmer-3.3.tar.gz' + version('3.3', sha256='0186bf40af67032666014971ed8ddc3cf2834bebc2be5b3bc0304a93e763736c') version('3.2.1', sha256='a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c') version('3.1b2', sha256='dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536') version('3.0', sha256='6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83') diff --git a/var/spack/repos/builtin/packages/homer/package.py b/var/spack/repos/builtin/packages/homer/package.py index bf190eb055..2f5fffdcce 100644 --- a/var/spack/repos/builtin/packages/homer/package.py +++ b/var/spack/repos/builtin/packages/homer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class Homer(Package): """Software for motif discovery and next generation sequencing analysis""" homepage = "http://homer.ucsd.edu/homer" - url = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.zip" + url = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.1.zip" version('4.9.1', sha256='ad1303b0b0400dc8a88dbeae1ee03a94631977b751a3d335326c4febf0eec3a9') diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py index e06bf00071..34d180e5cf 100644 --- a/var/spack/repos/builtin/packages/hoomd-blue/package.py +++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hotspot/package.py b/var/spack/repos/builtin/packages/hotspot/package.py index eea323ea37..99a79d771e 100644 --- a/var/spack/repos/builtin/packages/hotspot/package.py +++ b/var/spack/repos/builtin/packages/hotspot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hpccg/package.py b/var/spack/repos/builtin/packages/hpccg/package.py index 9fdf084e3a..67eb4c1941 100644 --- a/var/spack/repos/builtin/packages/hpccg/package.py +++ b/var/spack/repos/builtin/packages/hpccg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,7 @@ class Hpccg(MakefilePackage): """ homepage = "https://mantevo.org/about/applications/" - url = "http://mantevo.org/downloads/releaseTarballs/miniapps/HPCCG/HPCCG-1.0.tar.gz" + url = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/HPCCG-1.0.tar.gz" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py index e10b447dca..2347e3bb6a 100644 --- a/var/spack/repos/builtin/packages/hpctoolkit/package.py +++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,7 +19,8 @@ class Hpctoolkit(AutotoolsPackage): maintainers = ['mwkrentel'] version('master', branch='master') - version('gpu', branch='master-gpu') + version('gpu', branch='gpu') + version('2019.12.28', commit='b4e1877ff96069fd8ed0fdf0e36283a5b4b62240') version('2019.08.14', commit='6ea44ed3f93ede2d0a48937f288a2d41188a277c') version('2018.12.28', commit='8dbf0d543171ffa9885344f32f23cc6f7f6e39bc') version('2018.11.05', commit='d0c43e39020e67095b1f1d8bb89b75f22b12aee9') @@ -35,7 +36,7 @@ class Hpctoolkit(AutotoolsPackage): variant('bgq', default=False, description='Build for Blue Gene compute nodes, including ' - 'hpcprof-mpi.') + 'hpcprof-mpi (up to 2019.12.28 only).') variant('mpi', default=False, description='Build hpcprof-mpi, the MPI version of hpcprof.') @@ -52,39 +53,45 @@ class Hpctoolkit(AutotoolsPackage): 'for the compute nodes.') variant('cuda', default=False, - description='Support CUDA on NVIDIA GPUs (gpu branch only).') + description='Support CUDA on NVIDIA GPUs (master or gpu branch).') - boost_libs = '+atomic +chrono +date_time +filesystem +system +thread' \ - '+timer +graph +regex +shared +multithreaded' + boost_libs = ( + '+atomic +chrono +date_time +filesystem +system +thread +timer' + ' +graph +regex +shared +multithreaded visibility=global' + ) depends_on('binutils+libiberty~nls', type='link') depends_on('boost' + boost_libs) - depends_on('boost' + ' visibility=global', when='@gpu') depends_on('bzip2', type='link') depends_on('dyninst') depends_on('elfutils~nls', type='link') depends_on('intel-tbb') depends_on('libdwarf') - depends_on('libmonitor+hpctoolkit', when='~bgq') - depends_on('libmonitor+hpctoolkit+bgq', when='+bgq') + depends_on('libmonitor+hpctoolkit') + depends_on('libmonitor+bgq', when='+bgq') depends_on('libunwind@2018.10.0:') + depends_on('mbedtls+pic') depends_on('xerces-c transcoder=iconv') depends_on('xz', type='link') depends_on('zlib') depends_on('cuda', when='+cuda') depends_on('intel-xed', when='target=x86_64:') - depends_on('mbedtls+pic', when='@gpu') depends_on('papi', when='+papi') depends_on('libpfm4', when='~papi') depends_on('mpi', when='+mpi') conflicts('%gcc@:4.7.99', when='^dyninst@10.0.0:', msg='hpctoolkit requires gnu gcc 4.8.x or later') + conflicts('%gcc@:4.99.99', when='@gpu', msg='the gpu branch requires gnu gcc 5.x or later') - conflicts('+cuda', when='@2018.0.0:', - msg='cuda is only available on the gpu branch') + + conflicts('%gcc@:4.99.99', when='@master', + msg='the master branch requires gnu gcc 5.x or later') + + conflicts('+cuda', when='@2018.0.0:2019.99.99', + msg='cuda is only available on the master or gpu branches') flag_handler = AutotoolsPackage.build_system_flags @@ -101,6 +108,7 @@ class Hpctoolkit(AutotoolsPackage): '--with-libdwarf=%s' % spec['libdwarf'].prefix, '--with-libmonitor=%s' % spec['libmonitor'].prefix, '--with-libunwind=%s' % spec['libunwind'].prefix, + '--with-mbedtls=%s' % spec['mbedtls'].prefix, '--with-xerces=%s' % spec['xerces-c'].prefix, '--with-lzma=%s' % spec['xz'].prefix, '--with-zlib=%s' % spec['zlib'].prefix, @@ -113,9 +121,6 @@ class Hpctoolkit(AutotoolsPackage): '--with-cupti=%s' % cupti_path, ]) - if spec.satisfies('@gpu'): - args.append('--with-mbedtls=%s' % spec['mbedtls'].prefix) - if spec.target.family == 'x86_64': args.append('--with-xed=%s' % spec['intel-xed'].prefix) diff --git a/var/spack/repos/builtin/packages/hpcviewer/package.py b/var/spack/repos/builtin/packages/hpcviewer/package.py index a0b8e04f04..21cfa67daa 100644 --- a/var/spack/repos/builtin/packages/hpcviewer/package.py +++ b/var/spack/repos/builtin/packages/hpcviewer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -37,6 +37,15 @@ class Hpcviewer(Package): maintainers = ['mwkrentel'] viewer_sha = { + ('2020.01', 'x86_64'): '3cd5a2a382cec1d64c8bd0abaf2b1461dcd4092a4b4074ddbdc1b96d2a0b4220', + ('2020.01', 'ppc64'): '814394a5f410033cc1019526c268ef98b5b381e311fcd39ae8b2bde6c6ff017c', + ('2020.01', 'ppc64le'): 'e830e956b8088c415fb25ef44a8aca16ebcb27bcd34536866612343217e3f9e4', + ('2019.12', 'x86_64'): '6ba149c8d23d9913291655602894f7a91f9c838e69ae5682fd7b605467255c2d', + ('2019.12', 'ppc64'): '787257272381fac26401e1013952bea94635172503e7abf8063081fe03f08384', + ('2019.12', 'ppc64le'): 'fd20891fdae6dd5c2313cdd98e53c52023a0cf146a1121d0c889ebedc08a8bb9', + ('2019.09', 'x86_64'): '40982a43880fe646b7f9d03ac4911b55f8a4464510eb8c7304ffaf4d4205ecc6', + ('2019.09', 'ppc64'): '3972d604bd160c058185b6f8f3f3a63c4031046734b29cc386c24e40831e6798', + ('2019.09', 'ppc64le'): 'c348f442b7415aadb94ead06bd35e96442a49a9768fd8c972ca707d77d61e0c3', ('2019.08', 'x86_64'): '249aae6a23dca19286ee15909afbeba5e515388f1c1ad87f572454534fccb9f2', ('2019.08', 'ppc64'): 'f91b4772c92c05a4a35c88eec094604f3c233c7233adeede97acba38592da379', ('2019.08', 'ppc64le'): 'b1bd5c76b37f225a01631193e0a62524bd41a54b3354a658fdfd0f66c444cc28', @@ -52,6 +61,15 @@ class Hpcviewer(Package): } trace_sha = { + ('2020.01', 'x86_64'): '9459177a2445e85d648384e2ccee20524592e91a74d615262f32d0876831cd7c', + ('2020.01', 'ppc64'): '02366a2ba30b9b2450d50cf44933288f04fae5bf9868eef7bb2ae1b49d4f454e', + ('2020.01', 'ppc64le'): '39970e84e397ed96bc994e7b8db3b7b3aab4e3155fa7ca8e68b9274bb58115f0', + ('2019.12', 'x86_64'): '6339b36e655e2c2b07af4cb40946f325acc46da3ec590d36069661e69b046a92', + ('2019.12', 'ppc64'): 'fe4ee5af22a983fa0ddbfbd97fa6676f07492400536e900188455f21e489c59b', + ('2019.12', 'ppc64le'): '2688ea834c546b9e2c6e9d69d271a62dd00f6bc7ff4cb874563ba8d0ae5824e3', + ('2019.09', 'x86_64'): '8d7ce0710570bb8cd424d88cc4b5bfe821330f24fef84bbbbb370fa291b60a14', + ('2019.09', 'ppc64'): 'dfb3fe8283cbaeaa1653e8c8bf68267a3f25886bc452309b10f88a7b1e713ec6', + ('2019.09', 'ppc64le'): 'c1b6ab4f6c91e3a226e8629de62e718c92318ffd83d03db3c40678d578b99b20', ('2019.08', 'x86_64'): '6cefed6a397298ab31cadd10831f5d5533d3f634a4a76bb93f686e603a42c5ed', ('2019.08', 'ppc64'): '64ca5605c89dd3065cacaeee4a8e2ac14b47953530711ed9e04666c8435e44e8', ('2019.08', 'ppc64le'): 'bee03b5cb2de7e8556cf1249f98ece7848c13a0de6b8ba71786c430da68f7bcc', @@ -66,19 +84,19 @@ class Hpcviewer(Package): ('2019.02', 'ppc64le'): '01a159306e7810efe07157ec823ac6ca7570ec2014c95db599a3f90eee33355c', } - version_list = ['2019.02', '2019.04', '2019.07', '2019.08'] - - for ver in version_list: - key = (ver, platform.machine()) - if key in viewer_sha and key in trace_sha: - version(ver, url=viewer_url(*key), sha256=viewer_sha[key]) + for key in viewer_sha.keys(): + if key in trace_sha and key[1] == platform.machine(): + version(key[0], url=viewer_url(*key), sha256=viewer_sha[key]) resource(name='hpctraceviewer', url=trace_url(*key), sha256=trace_sha[key], placement='TRACE', - when='@{0}'.format(ver)) + when='@{0}'.format(key[0])) depends_on('java@8', type=('build', 'run')) + conflicts('target=aarch64:', msg='hpcviewer is not available on arm') + conflicts('platform=darwin', msg='hpcviewer requires a manual install on MacOS, see homepage') + # Both hpcviewer and trace viewer have an install script. def install(self, spec, prefix): args = [ diff --git a/var/spack/repos/builtin/packages/hpgmg/package.py b/var/spack/repos/builtin/packages/hpgmg/package.py index 1805315130..e701d1c212 100644 --- a/var/spack/repos/builtin/packages/hpgmg/package.py +++ b/var/spack/repos/builtin/packages/hpgmg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,7 +17,7 @@ class Hpgmg(Package): """ homepage = "https://bitbucket.org/hpgmg/hpgmg" - url = "https://hpgmg.org/static/hpgmg-0.tar.gz" + url = "https://hpgmg.org/static/hpgmg-0.4.tar.gz" git = "https://bitbucket.org/hpgmg/hpgmg.git" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/hpl/package.py b/var/spack/repos/builtin/packages/hpl/package.py index 22c9096e40..05909653c0 100644 --- a/var/spack/repos/builtin/packages/hpl/package.py +++ b/var/spack/repos/builtin/packages/hpl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hpx/git_external.patch b/var/spack/repos/builtin/packages/hpx/git_external.patch new file mode 100644 index 0000000000..72d203e7fa --- /dev/null +++ b/var/spack/repos/builtin/packages/hpx/git_external.patch @@ -0,0 +1,81 @@ +--- hpx/cmake/GitExternal.cmake.orig 2019-08-16 17:27:04.856315000 +0200 ++++ hpx/cmake/GitExternal.cmake 2019-08-16 17:27:47.362709000 +0200 +@@ -19,12 +19,12 @@ + # + # [optional] Flags which control behaviour + # NO_UPDATE +-# When set, GitExternal will not change a repo that has already been checked out. +-# The purpose of this is to allow one to set a default branch to be checked out, +-# but stop GitExternal from changing back to that branch if the user has checked ++# When set, GitExternal will not change a repo that has already been checked out. ++# The purpose of this is to allow one to set a default branch to be checked out, ++# but stop GitExternal from changing back to that branch if the user has checked + # out and is working on another. +-# VERBOSE +-# When set, displays information about git commands that are executed ++# VERBOSE ++# When set, displays information about git commands that are executed + # + + find_package(Git) +@@ -55,17 +55,21 @@ + if(nok) + message(FATAL_ERROR "${DIR} git clone failed: ${error}\n") + endif() +- endif() + +- if(IS_DIRECTORY "${DIR}/.git") ++ # checkout requested tag ++ GIT_EXTERNAL_MESSAGE("git checkout -q ${TAG}") ++ execute_process( ++ COMMAND "${GIT_EXECUTABLE}" checkout -q "${TAG}" ++ RESULT_VARIABLE nok ERROR_VARIABLE error ++ WORKING_DIRECTORY "${DIR}" ++ ) ++ if(nok) ++ message(STATUS "${DIR} git checkout ${TAG} failed: ${error}\n") ++ endif() ++ elseif(IS_DIRECTORY "${DIR}/.git") + if (${GIT_EXTERNAL_NO_UPDATE}) + GIT_EXTERNAL_MESSAGE("Update branch disabled by user") + else() +- GIT_EXTERNAL_MESSAGE("current ref is \"${currentref}\" and tag is \"${TAG}\"") +- if(currentref STREQUAL TAG) # nothing to do +- return() +- endif() +- + # reset generated files + foreach(GIT_EXTERNAL_RESET_FILE ${GIT_EXTERNAL_RESET}) + GIT_EXTERNAL_MESSAGE("git reset -q ${GIT_EXTERNAL_RESET_FILE}") +@@ -100,15 +104,24 @@ + message(STATUS "${DIR} git checkout ${TAG} failed: ${error}\n") + endif() + +- # update tag +- GIT_EXTERNAL_MESSAGE("git rebase FETCH_HEAD") +- execute_process(COMMAND ${GIT_EXECUTABLE} rebase FETCH_HEAD +- RESULT_VARIABLE RESULT OUTPUT_VARIABLE OUTPUT ERROR_VARIABLE OUTPUT ++ # check if this is a branch ++ GIT_EXTERNAL_MESSAGE("git symbolic-ref -q HEAD") ++ execute_process(COMMAND "${GIT_EXECUTABLE}" symbolic-ref -q HEAD ++ RESULT_VARIABLE nok ERROR_VARIABLE error + WORKING_DIRECTORY "${DIR}") +- if(RESULT) +- message(STATUS "git rebase failed, aborting ${DIR} merge") +- execute_process(COMMAND ${GIT_EXECUTABLE} rebase --abort ++ if(nok) ++ message(STATUS "${TAG} is not a branch") ++ else() ++ # update tag ++ GIT_EXTERNAL_MESSAGE("git rebase FETCH_HEAD") ++ execute_process(COMMAND ${GIT_EXECUTABLE} rebase FETCH_HEAD ++ RESULT_VARIABLE RESULT OUTPUT_VARIABLE OUTPUT ERROR_VARIABLE OUTPUT + WORKING_DIRECTORY "${DIR}") ++ if(RESULT) ++ message(STATUS "git rebase failed, aborting ${DIR} merge") ++ execute_process(COMMAND ${GIT_EXECUTABLE} rebase --abort ++ WORKING_DIRECTORY "${DIR}") ++ endif() + endif() + endif() + else() diff --git a/var/spack/repos/builtin/packages/hpx/package.py b/var/spack/repos/builtin/packages/hpx/package.py index 6863689f23..9d24fc0e88 100644 --- a/var/spack/repos/builtin/packages/hpx/package.py +++ b/var/spack/repos/builtin/packages/hpx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,8 +12,10 @@ class Hpx(CMakePackage, CudaPackage): homepage = "http://stellar.cct.lsu.edu/tag/hpx/" url = "https://github.com/STEllAR-GROUP/hpx/archive/1.2.1.tar.gz" + maintainers = ['msimberg', 'albestro'] version('master', git='https://github.com/STEllAR-GROUP/hpx.git', branch='master') + version('1.4.0', sha256='241a1c47fafba751848fac12446e7bf4ad3d342d5eb2fa1ef94dd904acc329ed') version('1.3.0', sha256='cd34da674064c4cc4a331402edbd65c5a1f8058fb46003314ca18fa08423c5ad') version('1.2.1', sha256='8cba9b48e919035176d3b7bbfc2c110df6f07803256626f1dad8d9dde16ab77a') version('1.2.0', sha256='20942314bd90064d9775f63b0e58a8ea146af5260a4c84d0854f9f968077c170') @@ -30,6 +32,10 @@ class Hpx(CMakePackage, CudaPackage): values=('system', 'tcmalloc', 'jemalloc', 'tbbmalloc') ) + variant('max_cpu_count', default='64', + description='Max number of OS-threads for HPX applications', + values=lambda x: isinstance(x, str) and x.isdigit()) + variant('instrumentation', values=any_combination_of( 'apex', 'google_perftools', 'papi', 'valgrind' ), description='Add support for various kind of instrumentation') @@ -43,7 +49,6 @@ class Hpx(CMakePackage, CudaPackage): variant('tools', default=False, description='Build HPX tools') variant('examples', default=False, description='Build examples') - depends_on('boost') depends_on('hwloc') depends_on('python', type=('build', 'test', 'run')) depends_on('pkgconfig', type='build') @@ -72,15 +77,13 @@ class Hpx(CMakePackage, CudaPackage): depends_on('mpi', when='networking=mpi') # Instrumentation - depends_on('apex', when='instrumentation=apex') + depends_on('otf2', when='instrumentation=apex') depends_on('gperftools', when='instrumentation=google_perftools') depends_on('papi', when='instrumentation=papi') depends_on('valgrind', when='instrumentation=valgrind') - # TODO: hpx can build perfectly fine in parallel, except that each - # TODO: process might need more than 2GB to compile. This is just the - # TODO: most conservative approach to ensure a sane build. - parallel = False + # Patches APEX + patch('git_external.patch', when='@1.3.0 instrumentation=apex') def cxx_standard(self): value = self.spec.variants['cxxstd'].value @@ -109,6 +112,10 @@ class Hpx(CMakePackage, CudaPackage): # Instrumentation args.extend(self.instrumentation_args()) + if 'instrumentation=apex' in spec: + args += ['-DAPEX_WITH_OTF2=ON' + '-DOTF2_ROOT={0}'.format(spec['otf2'].prefix)] + # Networking args.append('-DHPX_WITH_NETWORKING={0}'.format( 'OFF' if 'networking=none' in spec else 'ON' @@ -125,11 +132,21 @@ class Hpx(CMakePackage, CudaPackage): 'ON' if '+cuda' in spec else 'OFF' )) + # Tests + args.append('-DHPX_WITH_TESTS={0}'.format( + 'ON' if self.run_tests else 'OFF' + )) + # Tools args.append('-DHPX_WITH_TOOLS={0}'.format( 'ON' if '+tools' in spec else 'OFF' )) + # MAX_CPU_COUNT + args.append('-DHPX_WITH_MAX_CPU_COUNT={0}'.format( + spec.variants['max_cpu_count'].value + )) + # Examples args.append('-DHPX_WITH_EXAMPLES={0}'.format( 'ON' if '+examples' in spec else 'OFF' diff --git a/var/spack/repos/builtin/packages/hpx5/package.py b/var/spack/repos/builtin/packages/hpx5/package.py index 5ea3937c46..78dbf25ec7 100644 --- a/var/spack/repos/builtin/packages/hpx5/package.py +++ b/var/spack/repos/builtin/packages/hpx5/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hsakmt/package.py b/var/spack/repos/builtin/packages/hsakmt/package.py index 9e7064a90d..3af48b66cd 100644 --- a/var/spack/repos/builtin/packages/hsakmt/package.py +++ b/var/spack/repos/builtin/packages/hsakmt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hstr/package.py b/var/spack/repos/builtin/packages/hstr/package.py index 1a933f22fb..367d9d8d0b 100644 --- a/var/spack/repos/builtin/packages/hstr/package.py +++ b/var/spack/repos/builtin/packages/hstr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/htop/package.py b/var/spack/repos/builtin/packages/htop/package.py index f7da12491b..9de69ae0bf 100644 --- a/var/spack/repos/builtin/packages/htop/package.py +++ b/var/spack/repos/builtin/packages/htop/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py index cfad4c78ce..95c38d4a23 100644 --- a/var/spack/repos/builtin/packages/htslib/package.py +++ b/var/spack/repos/builtin/packages/htslib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,9 @@ class Htslib(AutotoolsPackage): """C library for high-throughput sequencing data formats.""" homepage = "https://github.com/samtools/htslib" + url = "https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz2" + version('1.10.2', sha256='e3b543de2f71723830a1e0472cf5489ec27d0fbeb46b1103e14a11b7177d1939') version('1.9', sha256='e04b877057e8b3b8425d957f057b42f0e8509173621d3eccaedd0da607d9929a') version('1.8', sha256='c0ef1eec954a98cc708e9f99f6037db85db45670b52b6ab37abcc89b6c057ca1') version('1.7', sha256='be3d4e25c256acdd41bebb8a7ad55e89bb18e2fc7fc336124b1e2c82ae8886c6') @@ -20,9 +22,15 @@ class Htslib(AutotoolsPackage): version('1.3.1', sha256='49d53a2395b8cef7d1d11270a09de888df8ba06f70fe68282e8235ee04124ae6') version('1.2', sha256='125c01421d5131afb4c3fd2bc9c7da6f4f1cd9ab5fc285c076080b9aca24bffc') + variant('libcurl', + default=True, + description='Enable libcurl-based support for http/https/etc URLs,' + ' for versions >= 1.3. This also enables S3 and GCS support.') + depends_on('zlib') - depends_on('bzip2', when="@1.4:") - depends_on('xz', when="@1.4:") + depends_on('bzip2', when='@1.4:') + depends_on('xz', when='@1.4:') + depends_on('curl', when='@1.3:+libcurl') depends_on('m4', when="@1.2") depends_on('autoconf', when="@1.2") @@ -37,3 +45,12 @@ class Htslib(AutotoolsPackage): else: url = "https://github.com/samtools/htslib/releases/download/{0}/htslib-{0}.tar.bz2" return url.format(version.dotted) + + def configure_args(self): + spec = self.spec + args = [] + + if spec.satisfies('@1.3:'): + args.extend(self.enable_or_disable('libcurl')) + + return args diff --git a/var/spack/repos/builtin/packages/httperf/package.py b/var/spack/repos/builtin/packages/httperf/package.py new file mode 100644 index 0000000000..4c33f98ed0 --- /dev/null +++ b/var/spack/repos/builtin/packages/httperf/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Httperf(AutotoolsPackage): + """Httperf is a tool for measuring web server performance. It provides + a flexible facility for generating various HTTP workloads and for + measuring server performance.""" + + homepage = "https://github.com/httperf" + git = "https://github.com/httperf/httperf.git" + + version('master', branch='master') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + + @run_before('autoreconf') + def e_autogen(self): + mkdirp('m4') diff --git a/var/spack/repos/builtin/packages/httpie/package.py b/var/spack/repos/builtin/packages/httpie/package.py index 70fc8d764f..53b95337b5 100644 --- a/var/spack/repos/builtin/packages/httpie/package.py +++ b/var/spack/repos/builtin/packages/httpie/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,4 +26,4 @@ class Httpie(PythonPackage): # https://github.com/spack/spack/issues/3628 # depends_on('py-argparse@1.2.1:', type=('build', 'run'), # when='^python@:2.6,3.0:3.1') - depends_on('py-argparse@1.2.1:', type=('build', 'run')) + depends_on('py-argparse@1.2.1:', type=('build', 'run'), when='^python@:2.6') diff --git a/var/spack/repos/builtin/packages/hub/package.py b/var/spack/repos/builtin/packages/hub/package.py index 068e7b4a35..7b342b234d 100644 --- a/var/spack/repos/builtin/packages/hub/package.py +++ b/var/spack/repos/builtin/packages/hub/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,10 +11,10 @@ class Hub(Package): """The github git wrapper""" homepage = "https://github.com/github/hub" - url = "https://github.com/github/hub/archive/v2.2.3.tar.gz" + url = "https://github.com/github/hub/archive/v2.2.2.tar.gz" git = "https://github.com/github/hub.git" - version('head', branch='master') + version('master', branch='master') version('2.2.2', sha256='610572ee903aea1fa8622c16ab7ddef2bd1bfec9f4854447ab8e0fbdbe6a0cae') version('2.2.1', sha256='9350aba6a8e3da9d26b7258a4020bf84491af69595f7484f922d75fc8b86dc10') version('2.2.0', sha256='2da1351197eb5696c207f22c69a5422af052d74277b73d0b8661efb9ec1d0eb1') diff --git a/var/spack/repos/builtin/packages/hugo/package.py b/var/spack/repos/builtin/packages/hugo/package.py index 9e35f37cf8..ea2891cfe4 100644 --- a/var/spack/repos/builtin/packages/hugo/package.py +++ b/var/spack/repos/builtin/packages/hugo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hunspell/package.py b/var/spack/repos/builtin/packages/hunspell/package.py index f127760dad..8eedf43539 100644 --- a/var/spack/repos/builtin/packages/hunspell/package.py +++ b/var/spack/repos/builtin/packages/hunspell/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,7 +12,7 @@ class Hunspell(AutotoolsPackage): homepage = "http://hunspell.github.io/" url = "https://github.com/hunspell/hunspell/archive/v1.6.0.tar.gz" - version('1.7.0', sha256='57be4e03ae9dd62c3471f667a0d81a14513e314d4d92081292b90435944ff951') + version('1.7.0', sha256='bb27b86eb910a8285407cf3ca33b62643a02798cf2eef468c0a74f6c3ee6bc8a') version('1.6.0', sha256='512e7d2ee69dad0b35ca011076405e56e0f10963a02d4859dbcc4faf53ca68e2') depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py index 79132f9807..2b7968a37a 100644 --- a/var/spack/repos/builtin/packages/hwloc/package.py +++ b/var/spack/repos/builtin/packages/hwloc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,6 +28,7 @@ class Hwloc(AutotoolsPackage): git = 'https://github.com/open-mpi/hwloc.git' version('master', branch='master') + version('2.1.0', sha256='1fb8cc1438de548e16ec3bb9e4b2abb9f7ce5656f71c0906583819fcfa8c2031') version('2.0.2', sha256='27dcfe42e3fb3422b72ce48b48bf601c0a3e46e850ee72d9bdd17b5863b6e42c') version('2.0.1', sha256='f1156df22fc2365a31a3dc5f752c53aad49e34a5e22d75ed231cd97eaa437f9d') version('2.0.0', sha256='a0d425a0fc7c7e3f2c92a272ffaffbd913005556b4443e1887d2e1718d902887') diff --git a/var/spack/repos/builtin/packages/hybpiper/package.py b/var/spack/repos/builtin/packages/hybpiper/package.py index 86bab5b86a..5c3f905167 100644 --- a/var/spack/repos/builtin/packages/hybpiper/package.py +++ b/var/spack/repos/builtin/packages/hybpiper/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,8 +31,8 @@ class Hybpiper(Package): depends_on('bwa') depends_on('samtools') - def setup_envionment(self, spack_env, run_env): - run_env.set('HYBPIPER_HOME', prefix) + def setup_run_environment(self, env): + env.set('HYBPIPER_HOME', self.prefix) def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/hydra/package.py b/var/spack/repos/builtin/packages/hydra/package.py index 4897f856ee..c5afe90b3e 100644 --- a/var/spack/repos/builtin/packages/hydra/package.py +++ b/var/spack/repos/builtin/packages/hydra/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hydrogen/package.py b/var/spack/repos/builtin/packages/hydrogen/package.py index 7dce9c0696..1607bc7319 100644 --- a/var/spack/repos/builtin/packages/hydrogen/package.py +++ b/var/spack/repos/builtin/packages/hydrogen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,15 @@ class Hydrogen(CMakePackage): url = "https://github.com/LLNL/Elemental/archive/v1.0.1.tar.gz" git = "https://github.com/LLNL/Elemental.git" + maintainers = ['bvanessen'] + version('develop', branch='hydrogen') + version('1.3.3', sha256='140112066b84d33ca4b75c8e520fb15748fa648c4d2b934c1eb5510173ede5f5') + version('1.3.2', sha256='50bc5e87955f8130003d04dfd9dcad63107e92b82704f8107baf95b0ccf98ed6') + version('1.3.1', sha256='a8b8521458e9e747f2b24af87c4c2749a06e500019c383e0cefb33e5df6aaa1d') + version('1.3.0', sha256='0f3006aa1d8235ecdd621e7344c99f56651c6836c2e1bc0cf006331b70126b36') + version('1.2.0', sha256='8545975139582ee7bfe5d00f8d83a8697afc285bf7026b0761e9943355974806') + version('1.1.0-1', sha256='73ce05e4166853a186469269cb00a454de71e126b2019f95bbae703b65606808') version('1.1.0', sha256='b4c12913acd01c72d31f4522266bfeb8df1d4d3b4aef02e07ccbc9a477894e71') version('1.0.1', sha256='27cf76e1ef1d58bd8f9b1e34081a14a682b7ff082fb5d1da56713e5e0040e528') version('1.0', sha256='d8a97de3133f2c6b6bb4b80d32b4a4cc25eb25e0df4f0cec0f8cb19bf34ece98') @@ -51,6 +59,8 @@ class Hydrogen(CMakePackage): description='Builds with Aluminum communication library') variant('omp_taskloops', default=False, description='Use OpenMP taskloops instead of parallel for loops.') + variant('half', default=True, + description='Builds with support for FP16 precision data types') # Note that #1712 forces us to enumerate the different blas variants depends_on('openblas', when='blas=openblas ~openmp_blas ~int64_blas') @@ -87,6 +97,7 @@ class Hydrogen(CMakePackage): depends_on('cuda', when='+cuda') depends_on('cub', when='+cuda') + depends_on('half', when='+half') conflicts('@0:0.98', msg="Hydrogen did not exist before v0.99. " + "Did you mean to use Elemental instead?") @@ -120,6 +131,7 @@ class Hydrogen(CMakePackage): '-DHydrogen_ENABLE_CUB=%s' % ('+cuda' in spec), '-DHydrogen_ENABLE_CUDA=%s' % ('+cuda' in spec), '-DHydrogen_ENABLE_TESTING=%s' % ('+test' in spec), + '-DHydrogen_ENABLE_HALF=%s' % ('+half' in spec), ] # Add support for OS X to find OpenMP diff --git a/var/spack/repos/builtin/packages/hyphy/package.py b/var/spack/repos/builtin/packages/hyphy/package.py index 8fb1bd0036..851c795b83 100644 --- a/var/spack/repos/builtin/packages/hyphy/package.py +++ b/var/spack/repos/builtin/packages/hyphy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 44ff3efc16..cf0ffb1896 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,6 +20,7 @@ class Hypre(Package): maintainers = ['ulrikeyang', 'osborn9', 'balay'] version('develop', branch='master') + version('2.18.2', sha256='28007b5b584eaf9397f933032d8367788707a2d356d78e47b99e551ab10cc76a') version('2.18.1', sha256='220f9c4ad024e815add8dad8950eaa2d8f4f231104788cf2a3c5d9da8f94ba6e') version('2.18.0', sha256='62591ac69f9cc9728bd6d952b65bcadd2dfe52b521081612609804a413f49b07') version('2.17.0', sha256='4674f938743aa29eb4d775211b13b089b9de84bfe5e9ea00c7d8782ed84a46d7') diff --git a/var/spack/repos/builtin/packages/i3/package.py b/var/spack/repos/builtin/packages/i3/package.py index 32cc318921..af598a051a 100644 --- a/var/spack/repos/builtin/packages/i3/package.py +++ b/var/spack/repos/builtin/packages/i3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ibm-java/package.py b/var/spack/repos/builtin/packages/ibm-java/package.py index 149a75aac4..df4b9d9c4e 100644 --- a/var/spack/repos/builtin/packages/ibm-java/package.py +++ b/var/spack/repos/builtin/packages/ibm-java/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,16 +14,23 @@ class IbmJava(Package): homepage = "https://developer.ibm.com/javasdk/" + # Note: IBM is fairly aggressive about taking down old versions, + # so we may need to update this frequently. Also, old revs may + # not be available for download. + + version_list = [ + ('8.0.6.0', 'ppc64', 'e142746a83e47ab91d71839d5776f112ed154ae180d0628e3f10886151dad710'), + ('8.0.6.0', 'ppc64le', '18c2eccf99225e6e7643141d8da4110cacc39f2fa00149fc26341d2272cc0102'), + ('8.0.5.30', 'ppc64', 'd39ce321bdadd2b2b829637cacf9c1c0d90235a83ff6e7dcfa7078faca2f212f'), + ('8.0.5.30', 'ppc64le', 'dec6434d926861366c135aac6234fc28b3e7685917015aa3a3089c06c3b3d8f0'), + ] + # There are separate tar files for big and little-endian machine - # types. When we add more versions, then turn this into a mapping - # from version and machine type to sha256sum. - mach = platform.machine() if platform.machine() == 'ppc64' else 'ppc64le' - if mach == 'ppc64le': - sha = 'dec6434d926861366c135aac6234fc28b3e7685917015aa3a3089c06c3b3d8f0' - else: - sha = 'd39ce321bdadd2b2b829637cacf9c1c0d90235a83ff6e7dcfa7078faca2f212f' + # types. And no, this won't work cross platform. - version('8.0.5.30', sha256=sha, expand=False) + for (ver, mach, sha) in version_list: + if mach == platform.machine(): + version(ver, sha256=sha, expand=False) provides('java@8') @@ -36,7 +43,7 @@ class IbmJava(Package): url = ('http://public.dhe.ibm.com/ibmdl/export/pub/systems/cloud' '/runtimes/java/{0}/linux/{1}/ibm-java-sdk-{2}-{1}' - '-archive.bin').format(version, self.mach, dash) + '-archive.bin').format(version, platform.machine(), dash) return url @@ -48,11 +55,11 @@ class IbmJava(Package): def libs(self): return find_libraries(['libjvm'], root=self.home, recursive=True) - def setup_environment(self, spack_env, run_env): - run_env.set('JAVA_HOME', self.home) + def setup_run_environment(self, env): + env.set('JAVA_HOME', self.home) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('JAVA_HOME', self.home) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('JAVA_HOME', self.home) def setup_dependent_package(self, module, dependent_spec): self.spec.home = self.home diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py index 1e901220a3..eabafb0a7e 100644 --- a/var/spack/repos/builtin/packages/ibmisc/package.py +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -40,7 +40,7 @@ class Ibmisc(CMakePackage): depends_on('proj@:4', when='+proj') depends_on('blitz', when='+blitz') depends_on('netcdf-cxx4', when='+netcdf') - depends_on('udunits2', when='+udunits2') + depends_on('udunits', when='+udunits2') depends_on('googletest', when='+googletest', type='build') depends_on('py-cython', when='+python', type=('build', 'run')) depends_on('py-numpy', when='+python', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/iceauth/package.py b/var/spack/repos/builtin/packages/iceauth/package.py index 2d16feb37c..fc55defa42 100644 --- a/var/spack/repos/builtin/packages/iceauth/package.py +++ b/var/spack/repos/builtin/packages/iceauth/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/icedtea/package.py b/var/spack/repos/builtin/packages/icedtea/package.py index a62550b2c1..415cd42723 100644 --- a/var/spack/repos/builtin/packages/icedtea/package.py +++ b/var/spack/repos/builtin/packages/icedtea/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -62,7 +62,6 @@ class Icedtea(AutotoolsPackage): depends_on('zlib') depends_on('alsa-lib') - provides('java') provides('java@8', when='@3.4.0:3.99.99') force_autoreconf = True @@ -153,18 +152,18 @@ class Icedtea(AutotoolsPackage): ] return args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set JAVA_HOME.""" - run_env.set('JAVA_HOME', self.home) + env.set('JAVA_HOME', self.home) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Set JAVA_HOME and CLASSPATH. CLASSPATH contains the installation prefix for the extension and any other Java extensions it depends on.""" - spack_env.set('JAVA_HOME', self.home) + env.set('JAVA_HOME', self.home) class_paths = [] for d in dependent_spec.traverse(deptype=('build', 'run', 'test')): @@ -172,14 +171,19 @@ class Icedtea(AutotoolsPackage): class_paths.extend(find(d.prefix, '*.jar')) classpath = os.pathsep.join(class_paths) - spack_env.set('CLASSPATH', classpath) + env.set('CLASSPATH', classpath) + def setup_dependent_run_environment(self, env, dependent_spec): + """Set CLASSPATH. + + CLASSPATH contains the installation prefix for the extension and any + other Java extensions it depends on.""" # For runtime environment set only the path for # dependent_spec and prepend it to CLASSPATH if dependent_spec.package.extends(self.spec): class_paths = find(dependent_spec.prefix, '*.jar') classpath = os.pathsep.join(class_paths) - run_env.prepend_path('CLASSPATH', classpath) + env.prepend_path('CLASSPATH', classpath) def setup_dependent_package(self, module, dependent_spec): """Allows spec['java'].home to work.""" diff --git a/var/spack/repos/builtin/packages/icet/package.py b/var/spack/repos/builtin/packages/icet/package.py index 6e708a7783..458777d3a3 100644 --- a/var/spack/repos/builtin/packages/icet/package.py +++ b/var/spack/repos/builtin/packages/icet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,6 +22,6 @@ class Icet(CMakePackage): def cmake_args(self): return ['-DICET_USE_OPENGL:BOOL=OFF'] - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Work-around for ill-placed CMake modules""" - spack_env.prepend_path('CMAKE_PREFIX_PATH', self.prefix.lib) + env.prepend_path('CMAKE_PREFIX_PATH', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/ico/package.py b/var/spack/repos/builtin/packages/ico/package.py index e79c8ba866..f5cfe58dae 100644 --- a/var/spack/repos/builtin/packages/ico/package.py +++ b/var/spack/repos/builtin/packages/ico/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/icu4c/package.py b/var/spack/repos/builtin/packages/icu4c/package.py index 9af9085ea6..29307a4522 100644 --- a/var/spack/repos/builtin/packages/icu4c/package.py +++ b/var/spack/repos/builtin/packages/icu4c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,10 +12,9 @@ class Icu4c(AutotoolsPackage): C/C++ interface.""" homepage = "http://site.icu-project.org/" - url = "http://download.icu-project.org/files/icu4c/57.1/icu4c-57_1-src.tgz" - list_url = "http://download.icu-project.org/files/icu4c" - list_depth = 2 + url = "https://github.com/unicode-org/icu/releases/download/release-65-1/icu4c-65_1-src.tgz" + version('65.1', sha256='53e37466b3d6d6d01ead029e3567d873a43a5d1c668ed2278e253b683136d948') version('64.1', sha256='92f1b7b9d51b396679c17f35a2112423361b8da3c1b9de00aa94fd768ae296e6') version('60.1', sha256='f8f5a6c8fbf32c015a467972bdb1477dc5f5d5dfea908b6ed218715eeb5ee225') version('58.2', sha256='2b0a4410153a9b20de0e20c7d8b66049a72aef244b53683d0d7521371683da0c') @@ -29,11 +28,18 @@ class Icu4c(AutotoolsPackage): depends_on('python', type='build', when='@64.1:') + conflicts('%intel@:16', when='@60.1:', + msg="Intel compilers have immature C++11 and multibyte support") + configure_directory = 'source' def url_for_version(self, version): - url = "http://download.icu-project.org/files/icu4c/{0}/icu4c-{1}-src.tgz" - return url.format(version.dotted, version.underscored) + if version >= Version('65'): + url = "https://github.com/unicode-org/icu/releases/download/release-{0}/icu4c-{1}-src.tgz" + return url.format(version.dashed, version.underscored) + else: + url = "http://download.icu-project.org/files/icu4c/{0}/icu4c-{1}-src.tgz" + return url.format(version.dotted, version.underscored) def flag_handler(self, name, flags): if name == 'cxxflags': @@ -44,6 +50,12 @@ class Icu4c(AutotoolsPackage): self.spec.variants['cxxstd'].value))) return (None, flags, None) + # Need to make sure that locale is UTF-8 in order to process source + # files in UTF-8. + @when('@59:') + def setup_build_environment(self, env): + env.set('LC_ALL', 'en_US.UTF-8') + def configure_args(self): args = [] diff --git a/var/spack/repos/builtin/packages/id3lib/package.py b/var/spack/repos/builtin/packages/id3lib/package.py index 066dee1466..2825b15152 100644 --- a/var/spack/repos/builtin/packages/id3lib/package.py +++ b/var/spack/repos/builtin/packages/id3lib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/idba/package.py b/var/spack/repos/builtin/packages/idba/package.py index 91bf23028f..5e4f6780dd 100644 --- a/var/spack/repos/builtin/packages/idba/package.py +++ b/var/spack/repos/builtin/packages/idba/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/iegenlib/package.py b/var/spack/repos/builtin/packages/iegenlib/package.py index 383bc6d5a4..be61f120c7 100644 --- a/var/spack/repos/builtin/packages/iegenlib/package.py +++ b/var/spack/repos/builtin/packages/iegenlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ignite/package.py b/var/spack/repos/builtin/packages/ignite/package.py new file mode 100644 index 0000000000..a5250fc7ef --- /dev/null +++ b/var/spack/repos/builtin/packages/ignite/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Ignite(Package): + """ + Apache Ignite is a memory-centric distributed database, caching, and + processing platform for transactional, analytical, and streaming + workloads delivering in-memory speeds at petabyte scale. + """ + + homepage = "https://ignite.apache.org/" + url = "https://archive.apache.org/dist/ignite/2.6.0/apache-ignite-hadoop-2.6.0-bin.zip" + + version('2.6.0', sha256='be40350f301a308a0ab09413a130d421730bf253d200e054b82a7d0c275c69f2') + version('2.5.0', sha256='00bd35b6c50754325b966d50c7eee7067e0558f3d52b3dee27aff981b6da38be') + version('2.4.0', sha256='3d4f44fbb1c46731cf6ad4acce26da72960b292b307221cec55057b4f305abd9') + version('2.3.0', sha256='aae162c3df243592f7baa0d63b9bf60a7bdb00c7198f43e75b0a777a6fe5b639') + version('2.2.0', sha256='e4c150f59b11e14fdf4f663cf6f2c433dd55c17720221c89f3c67b9868177bd3') + + depends_on('java', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/igraph/package.py b/var/spack/repos/builtin/packages/igraph/package.py index 67d3a0952f..57021a3e13 100644 --- a/var/spack/repos/builtin/packages/igraph/package.py +++ b/var/spack/repos/builtin/packages/igraph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/igvtools/package.py b/var/spack/repos/builtin/packages/igvtools/package.py index 15c81f42fb..98fb863f9e 100644 --- a/var/spack/repos/builtin/packages/igvtools/package.py +++ b/var/spack/repos/builtin/packages/igvtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ilmbase/package.py b/var/spack/repos/builtin/packages/ilmbase/package.py index 129c02f8d7..7aa9ff8337 100644 --- a/var/spack/repos/builtin/packages/ilmbase/package.py +++ b/var/spack/repos/builtin/packages/ilmbase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/image-magick/package.py b/var/spack/repos/builtin/packages/imagemagick/package.py index 2f9229c496..363c0c5fae 100644 --- a/var/spack/repos/builtin/packages/image-magick/package.py +++ b/var/spack/repos/builtin/packages/imagemagick/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class ImageMagick(AutotoolsPackage): +class Imagemagick(AutotoolsPackage): """ImageMagick is a software suite to create, edit, compose, or convert bitmap images.""" diff --git a/var/spack/repos/builtin/packages/imake/package.py b/var/spack/repos/builtin/packages/imake/package.py index 6f451fa45b..60f705e9aa 100644 --- a/var/spack/repos/builtin/packages/imake/package.py +++ b/var/spack/repos/builtin/packages/imake/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/imlib2/package.py b/var/spack/repos/builtin/packages/imlib2/package.py new file mode 100644 index 0000000000..8cb3dc59b0 --- /dev/null +++ b/var/spack/repos/builtin/packages/imlib2/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class Imlib2(AutotoolsPackage): + """ + Library that does image file loading and saving as well as rendering, + manipulation, arbitrary polygon support + """ + + homepage = "http://sourceforge.net/projects/enlightenment/" + url = "http://downloads.sourceforge.net/enlightenment/imlib2-1.5.1.tar.bz2" + + maintainers = ['TheQueasle'] + + version('1.6.1', sha256='4d393a77e13da883c8ee2da3b029da3570210fe37d000c9ac33d9fce751b166d') + version('1.6.0', sha256='cfc440ddfaed5fc85ba2572ad8d87a87cd77a5bffb33ebca882c42cefcd8691d') + version('1.5.1', sha256='fa4e57452b8843f4a70f70fd435c746ae2ace813250f8c65f977db5d7914baae') + + depends_on('libtiff') + depends_on('giflib') + depends_on('bzip2') + depends_on('freetype') + depends_on('libxext') + depends_on('libpng') + depends_on('libid3tag') + depends_on('libjpeg-turbo') diff --git a/var/spack/repos/builtin/packages/imp/package.py b/var/spack/repos/builtin/packages/imp/package.py index 93c16165db..fc9dd37990 100644 --- a/var/spack/repos/builtin/packages/imp/package.py +++ b/var/spack/repos/builtin/packages/imp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/impute2/package.py b/var/spack/repos/builtin/packages/impute2/package.py index 91046caf26..f4e040e67d 100644 --- a/var/spack/repos/builtin/packages/impute2/package.py +++ b/var/spack/repos/builtin/packages/impute2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/infernal/package.py b/var/spack/repos/builtin/packages/infernal/package.py index 39939ce098..d855013ec1 100644 --- a/var/spack/repos/builtin/packages/infernal/package.py +++ b/var/spack/repos/builtin/packages/infernal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/inputproto/package.py b/var/spack/repos/builtin/packages/inputproto/package.py index 935627e5be..f6db7868de 100644 --- a/var/spack/repos/builtin/packages/inputproto/package.py +++ b/var/spack/repos/builtin/packages/inputproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/intel-daal/package.py b/var/spack/repos/builtin/packages/intel-daal/package.py index 69b6f11a0e..9d5ab0f2ef 100644 --- a/var/spack/repos/builtin/packages/intel-daal/package.py +++ b/var/spack/repos/builtin/packages/intel-daal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,34 +11,41 @@ class IntelDaal(IntelPackage): homepage = "https://software.intel.com/en-us/daal" + version('2020.0.166', sha256='695166c9ab32ac5d3006d6d35162db3c98734210507144e315ed7c3b7dbca9c1', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16234/l_daal_2020.0.166.tgz') + version('2019.5.281', sha256='e92aaedbe35c9daf1c9483260cb2363da8a85fa1aa5566eb38cf4b1f410bc368', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15818/l_daal_2019.5.281.tgz') + version('2019.4.243', sha256='c74486a555ca5636c2ac1b060d5424726c022468f3ee0898bb46e333cda6f7b8', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15552/l_daal_2019.4.243.tgz') version('2019.3.199', sha256='1f7d9cdecc1091b03f1ee6303fc7566179d1e3f1813a98ef7a6239f7d456b8ef', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15277/l_daal_2019.3.199.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15277/l_daal_2019.3.199.tgz') + version('2019.2.187', sha256='2982886347e9376e892a5c4e22fa1d4b7b843e1ae988a107dd2d0a639f257765', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15097/l_daal_2019.2.187.tgz') version('2019.1.144', sha256='1672afac568c93e185283cf7e044d511381092ebc95d7204c4dccb83cc493197', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14869/l_daal_2019.1.144.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14869/l_daal_2019.1.144.tgz') version('2019.0.117', sha256='85ac8e983bc9b9cc635e87cb4ec775ffd3695e44275d20fdaf53c19ed280d69f', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13577/l_daal_2019.0.117.tgz") - # Doesn't appear to be a 2018.4 update yet + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13577/l_daal_2019.0.117.tgz') version('2018.3.222', sha256='378fec529a36508dd97529037e1164ff98e0e062a9a47ede99ccf9e91493d1e2', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13007/l_daal_2018.3.222.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13007/l_daal_2018.3.222.tgz') version('2018.2.199', sha256='cee30299b3ffaea515f5a9609f4df0f644579c8a1ba2b61747b390f6caf85b14', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12727/l_daal_2018.2.199.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12727/l_daal_2018.2.199.tgz') version('2018.1.163', sha256='ac96b5a6c137cda18817d9b3505975863f8f53347225ebb6ccdaaf4bdb8dc349', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_daal_2018.1.163.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_daal_2018.1.163.tgz') version('2018.0.128', sha256='d13a7cd1b6779971f2ba46797447de9409c98a4d2f0eb0dc9622d9d63ac8990f', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12072/l_daal_2018.0.128.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12072/l_daal_2018.0.128.tgz') version('2017.4.239', sha256='cc4b608f59f3b2fafee16389102a763d27c46f6d136a6cfa89847418a8ea7460', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12148/l_daal_2017.4.239.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12148/l_daal_2017.4.239.tgz') version('2017.3.196', sha256='cfa863f342dd1c5fe8f1c7b6fd69589140370fc92742a19d82c8594e4e1e46ce', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11546/l_daal_2017.3.196.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11546/l_daal_2017.3.196.tgz') version('2017.2.174', sha256='5ee838b08d4cda7fc3e006e1deeed41671cbd7cfd11b64ec3b762c94dfc2b660', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11308/l_daal_2017.2.174.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11308/l_daal_2017.2.174.tgz') version('2017.1.132', sha256='6281105d3947fc2860e67401ea0218198cc4753fd2d4b513528a89143248e4f3', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10983/l_daal_2017.1.132.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10983/l_daal_2017.1.132.tgz') version('2017.0.098', sha256='a7064425653b4f5f0fe51e25358d267d8ae023179eece61e08da891b67d79fe5', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9664/l_daal_2017.0.098.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9664/l_daal_2017.0.098.tgz') version('2016.3.210', sha256='367eaef21ea0143c11ae3fd56cd2a05315768c059e14caa15894bcf96853687c', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9099/l_daal_2016.3.210.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9099/l_daal_2016.3.210.tgz') version('2016.2.181', sha256='afdb65768957784d28ac537b4933a86eb4193c68a636157caed17b29ccdbfacb', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8687/l_daal_2016.2.181.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8687/l_daal_2016.2.181.tgz') provides('daal') diff --git a/var/spack/repos/builtin/packages/intel-gpu-tools/package.py b/var/spack/repos/builtin/packages/intel-gpu-tools/package.py index 7404e8de70..80abcc3938 100644 --- a/var/spack/repos/builtin/packages/intel-gpu-tools/package.py +++ b/var/spack/repos/builtin/packages/intel-gpu-tools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/intel-ipp/package.py b/var/spack/repos/builtin/packages/intel-ipp/package.py index cb9c0ccdb5..1727e488be 100644 --- a/var/spack/repos/builtin/packages/intel-ipp/package.py +++ b/var/spack/repos/builtin/packages/intel-ipp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,8 +11,16 @@ class IntelIpp(IntelPackage): homepage = "https://software.intel.com/en-us/intel-ipp" + version('2020.0.166', sha256='6844007892ba524e828f245355cee44e8149f4c233abbbea16f7bb55a7d6ecff', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16233/l_ipp_2020.0.166.tgz') + version('2019.5.281', sha256='61d1e1da1a4a50f1cf02a3ed44e87eed05e94d58b64ef1e67a3bdec363bee713', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15817/l_ipp_2019.5.281.tgz') + version('2019.4.243', sha256='d4f4232323e66b010d8440c75189aeb6a3249966e05035242b21982238a7a7f2', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15541/l_ipp_2019.4.243.tgz') version('2019.3.199', sha256='02545383206c1ae4dd66bfa6a38e2e14480ba11932eeed632df8ab798aa15ccd', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15276/l_ipp_2019.3.199.tgz') + version('2019.2.187', sha256='280e9081278a0db3892fe82474c1201ec780a6f7c8d1f896494867f4b3bd8421', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15096/l_ipp_2019.2.187.tgz') version('2019.1.144', sha256='1eb7cd0fba74615aeafa4e314c645414497eb73f1705200c524fe78f00620db3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14887/l_ipp_2019.1.144.tgz') version('2019.0.117', sha256='d552ba49fba58f0e94da2048176f21c5dfd490dca7c5ce666dfc2d18db7fd551', @@ -26,15 +34,15 @@ class IntelIpp(IntelPackage): version('2018.0.128', sha256='da568ceec1b7acbcc8f666b73d4092788b037b1b03c0436974b82155056ed166', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12071/l_ipp_2018.0.128.tgz') version('2017.3.196', sha256='50d49a1000a88a8a58bd610466e90ae28d07a70993a78cbbf85d44d27c4232b6', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11545/l_ipp_2017.3.196.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11545/l_ipp_2017.3.196.tgz') version('2017.2.174', sha256='92f866c9dce8503d7e04223ec35f281cfeb0b81cf94208c3becb11aacfda7b99', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11307/l_ipp_2017.2.174.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11307/l_ipp_2017.2.174.tgz') version('2017.1.132', sha256='2908bdeab3057d4ebcaa0b8ff5b00eb47425d35961a96f14780be68554d95376', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11031/l_ipp_2017.1.132.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11031/l_ipp_2017.1.132.tgz') version('2017.0.098', sha256='7633d16e2578be64533892336c8a15c905139147b0f74eaf9f281358ad7cdcba', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9663/l_ipp_2017.0.098.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9663/l_ipp_2017.0.098.tgz') # built from parallel_studio_xe_2016.3.067 version('9.0.3.210', sha256='8ce7bf17f4a0bbf8c441063de26be7f6e0f6179789e23f24eaa8b712632b3cdd', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9067/l_ipp_9.0.3.210.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9067/l_ipp_9.0.3.210.tgz') provides('ipp') diff --git a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py index ae5e10c2f0..ab3a7cde46 100644 --- a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py +++ b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,14 +10,58 @@ class IntelMklDnn(CMakePackage): """Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN).""" - homepage = "https://01.org/mkl-dnn" - url = "https://github.com/intel/mkl-dnn/archive/v0.19.tar.gz" + homepage = "https://intel.github.io/mkl-dnn/" + url = "https://github.com/intel/mkl-dnn/archive/v1.1.1.tar.gz" - version('1.0-pc2', sha256='fcc2d951f7170eade0cfdd0d8d1d58e3e7785bd326bca6555f3722f8cba71811') - version('0.19', sha256='ba39da6adb263df05c4ca2a120295641fc97be75b588922e4274cb628dbe1dcd', preferred=True) - version('0.18.1', sha256='fc7506701dfece9b03c0dc83d0cda9a44a5de17cdb54bc7e09168003f02dbb70') - version('0.11', sha256='4cb4a85b05fe42aa527fd70a048caddcba9361f6d3d7bea9f33d74524e206d7d') - version('0.10', sha256='59828764ae43f1151f77b8997012c52e0e757bc50af1196b86fce8934178c570') - version('0.9', sha256='8606a80851c45b0076f7d4047fbf774ce13d6b6d857cb2edf95c7e1fd4bca1c7') + maintainers = ['adamjstewart'] + version('1.2', sha256='30979a09753e8e35d942446c3778c9f0eba543acf2fb0282af8b9c89355d0ddf') + version('1.1.3', sha256='0e9bcbc86cc215a84a5455a395ce540c68e255eaa586e37222fff622b9b17df7') + version('1.1.2', sha256='284b20e0cab67025bb7d21317f805d6217ad77fb3a47ad84b3bacf37bde62da9') + version('1.1.1', sha256='a31b08a89473bfe3bd6ed542503336d21b4177ebe4ccb9a97810808f634db6b6') + version('1.1', sha256='c5aac67e5ed4d95fe9943f835df49bbe6d608507780787c64aa620bdbd2171ba') + version('1.0.4', sha256='2a3ca90a8b690e65ddd0ccc95a09818e6da439cc854d014367645fcfd58a9690') + version('1.0.3', sha256='e0de341bd0bbebde7637e69383899ba415ce67682ff2f0f3d5a0d268e1bea69b') + version('1.0.2', sha256='3164eb2914e2160ac6ffd345781cf7554ce410830398cc6b2761e8668faf5ca8') + version('1.0.1', sha256='91fb84601c18f8a5a87eccd7b63d61f03495f36c5c533bd7f59443e4f8bb2595') + version('1.0', sha256='27fd9da9720c452852f1226581e7914efcf74e1ff898468fdcbe1813528831ba') + version('0.21.3', sha256='31e78581e59d7e60d4becaba3834fc6a5bf2dccdae3e16b7f70d89ceab38423f') + version('0.21.2', sha256='ed56652dd237deb86ee9bf102c18de5f2625c059e5ab1d7512c8dc01e316b694') + version('0.21.1', sha256='766ecfa5ac68be8cf9eacd4c712935c0ed945e5e6fe51640f05ee735cff62a38') + version('0.21', sha256='eb0aff133134898cf173d582a90e39b90ea9ea59544de7914208c2392b51a15f') + version('0.20.6', sha256='74675e93eef339ff3d9a9be95c15d0c7ad8736a5356c23428ab2e33dcdb8e3e1') + version('0.20.5', sha256='081d9f853c00fe0b597c8f00f2f3ff8d79c2a9cb95f292ff2c90557709763021') + version('0.20.4', sha256='b6422a000a6754334bdae673c25f84efd95e6d3cd016b752145b9391dc13e729') + version('0.20.3', sha256='a198a9bd3c584607e6a467f780beca92c8411cd656fcc8ec6fa5abe73d4af823') + version('0.20.2', sha256='1ae0e8a1a3df58deadc08ca0a01f8d3720600b26ca9e53685493e8e8250243b2') + version('0.20.1', sha256='26f720ed912843ba293e8a1e0822fe5318e93c529d80c87af1cf555d68e642d0') + version('0.20', sha256='52e111fefbf5a38e36f7bae7646860f7cbc985eba0725768f3fee8cdb31a9977') + version('0.19', sha256='ba39da6adb263df05c4ca2a120295641fc97be75b588922e4274cb628dbe1dcd') + version('0.18.1', sha256='fc7506701dfece9b03c0dc83d0cda9a44a5de17cdb54bc7e09168003f02dbb70') + version('0.11', sha256='4cb4a85b05fe42aa527fd70a048caddcba9361f6d3d7bea9f33d74524e206d7d') + version('0.10', sha256='59828764ae43f1151f77b8997012c52e0e757bc50af1196b86fce8934178c570') + version('0.9', sha256='8606a80851c45b0076f7d4047fbf774ce13d6b6d857cb2edf95c7e1fd4bca1c7') + + depends_on('cmake@2.8.11:', type='build') depends_on('intel-mkl') + depends_on('llvm-openmp', when='%clang platform=darwin') + + def cmake_args(self): + args = [] + + # https://github.com/intel/mkl-dnn/issues/591 + if self.spec.satisfies('%clang platform=darwin'): + args.extend([ + '-DOpenMP_CXX_FLAGS={0}'.format(self.compiler.openmp_flag), + '-DOpenMP_C_FLAGS={0}'.format(self.compiler.openmp_flag), + '-DOpenMP_CXX_LIB_NAMES=libomp', + '-DOpenMP_C_LIB_NAMES=libomp', + '-DOpenMP_libomp_LIBRARY={0}'.format( + self.spec['llvm-openmp'].libs.libraries[0] + ), + '-DCMAKE_SHARED_LINKER_FLAGS={0}'.format( + self.spec['llvm-openmp'].libs.ld_flags + ), + ]) + + return args diff --git a/var/spack/repos/builtin/packages/intel-mkl/package.py b/var/spack/repos/builtin/packages/intel-mkl/package.py index c56873ea3e..b6d8c38dcb 100644 --- a/var/spack/repos/builtin/packages/intel-mkl/package.py +++ b/var/spack/repos/builtin/packages/intel-mkl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,38 +13,46 @@ class IntelMkl(IntelPackage): homepage = "https://software.intel.com/en-us/intel-mkl" + version('2020.0.166', sha256='f6d92deb3ff10b11ba3df26b2c62bb4f0f7ae43e21905a91d553e58f0f5a8ae0', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16232/l_mkl_2020.0.166.tgz') + version('2019.5.281', sha256='9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/l_mkl_2019.5.281.tgz') + version('2019.4.243', sha256='fcac7b0369665d93f0c4dd98afe2816aeba5410e2b760655fe55fc477f8f33d0', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15540/l_mkl_2019.4.243.tgz') version('2019.3.199', sha256='06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/l_mkl_2019.3.199.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/l_mkl_2019.3.199.tgz') + version('2019.2.187', sha256='2bf004e6b5adb4f956993d6c20ea6ce289bb630314dd501db7f2dd5b9978ed1d', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15095/l_mkl_2019.2.187.tgz') version('2019.1.144', sha256='5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/l_mkl_2019.1.144.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/l_mkl_2019.1.144.tgz') version('2019.0.117', sha256='4e1fe2c705cfc47050064c0d6c4dee1a8c6740ac1c4f64dde9c7511c4989c7ad', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/l_mkl_2019.0.117.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/l_mkl_2019.0.117.tgz') version('2018.4.274', sha256='18eb3cde3e6a61a88f25afff25df762a560013f650aaf363f7d3d516a0d04881', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13725/l_mkl_2018.4.274.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13725/l_mkl_2018.4.274.tgz') version('2018.3.222', sha256='108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/l_mkl_2018.3.222.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/l_mkl_2018.3.222.tgz') version('2018.2.199', sha256='e28d12173bef9e615b0ded2f95f59a42b3e9ad0afa713a79f8801da2bfb31936', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12725/l_mkl_2018.2.199.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12725/l_mkl_2018.2.199.tgz') version('2018.1.163', sha256='f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_mkl_2018.1.163.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_mkl_2018.1.163.tgz') version('2018.0.128', sha256='c368baa40ca88057292512534d7fad59fa24aef06da038ea0248e7cd1e280cec', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12070/l_mkl_2018.0.128.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12070/l_mkl_2018.0.128.tgz') version('2017.4.239', sha256='dcac591ed1e95bd72357fd778edba215a7eab9c6993236373231cc16c200c92a', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12147/l_mkl_2017.4.239.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12147/l_mkl_2017.4.239.tgz') version('2017.3.196', sha256='fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11544/l_mkl_2017.3.196.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11544/l_mkl_2017.3.196.tgz') version('2017.2.174', sha256='0b8a3fd6bc254c3c3d9d51acf047468c7f32bf0baff22aa1e064d16d9fea389f', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11306/l_mkl_2017.2.174.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11306/l_mkl_2017.2.174.tgz') version('2017.1.132', sha256='8c6bbeac99326d59ef3afdc2a95308c317067efdaae50240d2f4a61f37622e69', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11024/l_mkl_2017.1.132.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11024/l_mkl_2017.1.132.tgz') version('2017.0.098', sha256='f2233e8e011f461d9c15a853edf7ed0ae8849aa665a1ec765c1ff196fd70c4d9', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9662/l_mkl_2017.0.098.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9662/l_mkl_2017.0.098.tgz') # built from parallel_studio_xe_2016.3.x version('11.3.3.210', sha256='ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9068/l_mkl_11.3.3.210.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9068/l_mkl_11.3.3.210.tgz') # built from parallel_studio_xe_2016.2.062 version('11.3.2.181', sha256='bac04a07a1fe2ae4996a67d1439ee90c54f31305e8663d1ccfce043bed84fc27', - url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8711/l_mkl_11.3.2.181.tgz") + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8711/l_mkl_11.3.2.181.tgz') variant('shared', default=True, description='Builds shared library') variant('ilp64', default=False, description='64 bit integers') diff --git a/var/spack/repos/builtin/packages/intel-mpi/package.py b/var/spack/repos/builtin/packages/intel-mpi/package.py index 001e4be17f..27885ed1f2 100644 --- a/var/spack/repos/builtin/packages/intel-mpi/package.py +++ b/var/spack/repos/builtin/packages/intel-mpi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,10 +11,16 @@ class IntelMpi(IntelPackage): homepage = "https://software.intel.com/en-us/intel-mpi-library" + version('2019.6.166', sha256='119be69f1117c93a9e5e9b8b4643918e55d2a55a78ad9567f77d16cdaf18cd6e', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16120/l_mpi_2019.6.166.tgz') + version('2019.5.281', sha256='9c59da051f1325b221e5bc4d8b689152e85d019f143069fa39e17989306811f4', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15838/l_mpi_2019.5.281.tgz') version('2019.4.243', sha256='233a8660b92ecffd89fedd09f408da6ee140f97338c293146c9c080a154c5fcd', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15553/l_mpi_2019.4.243.tgz') version('2019.3.199', sha256='5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15260/l_mpi_2019.3.199.tgz') + version('2019.2.187', sha256='6a3305933b5ef9e3f7de969e394c91620f3fa4bb815a4f439577739d04778b20', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15040/l_mpi_2019.2.187.tgz') version('2019.1.144', sha256='dac86a5db6b86503313742b17535856a432955604f7103cb4549a9bfc256c3cd', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14879/l_mpi_2019.1.144.tgz') version('2019.0.117', sha256='dfb403f49c1af61b337aa952b71289c7548c3a79c32c57865eab0ea0f0e1bc08', @@ -43,7 +49,7 @@ class IntelMpi(IntelPackage): provides('mpi') - def setup_dependent_environment(self, *args): + def setup_dependent_build_environment(self, *args): # Handle in callback, conveying client's compilers in additional arg. # CAUTION - DUP code in: # ../intel-mpi/package.py diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py index cb3658020b..f1b453c257 100644 --- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py +++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,6 +20,9 @@ class IntelParallelStudio(IntelPackage): # in the 'intel' package. # Cluster Edition (top tier; all components included) + version('cluster.2020.0', sha256='573b1d20707d68ce85b70934cfad15b5ad9cc14124a261c17ddd7717ba842c64', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16225/parallel_studio_xe_2020_cluster_edition.tgz') + # + version('cluster.2019.5', sha256='c03421de616bd4e640ed25ce4103ec9c5c85768a940a5cb5bd1e97b45be33904', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15809/parallel_studio_xe_2019_update5_cluster_edition.tgz') version('cluster.2019.4', sha256='32aee12de3b5ca14caf7578313c06b205795c67620f4a9606ea45696ee3b3d9e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15533/parallel_studio_xe_2019_update4_cluster_edition.tgz') version('cluster.2019.3', sha256='b5b022366d6d1a98dbb63b60221c62bc951c9819653ad6f5142192e89f78cf63', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15268/parallel_studio_xe_2019_update3_cluster_edition.tgz') version('cluster.2019.2', sha256='8c526bdd95d1da454e5cada00f7a2353089b86d0c9df2088ca7f842fe3ff4cae', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15088/parallel_studio_xe_2019_update2_cluster_edition.tgz') @@ -55,8 +58,12 @@ class IntelParallelStudio(IntelPackage): # NB: Pre-2018 download packages for Professional are the same as for # Cluster; differences manifest only in the tokens present in the license # file delivered as part of the purchase. + version('professional.2020.0', sha256='e88cad18d28da50ed9cb87b12adccf13efd91bf94731dc33290481306c6f15ac', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16226/parallel_studio_xe_2020_professional_edition.tgz') + # + version('professional.2019.5', sha256='0ec638330214539361f8632e20759f385a5a78013dcc980ee93743d86d354452', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15810/parallel_studio_xe_2019_update5_professional_edition.tgz') version('professional.2019.4', sha256='9b2818ea5739ade100841e99ce79ef7f4049a2513beb2ce20fc94706f1ba0231', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15534/parallel_studio_xe_2019_update4_professional_edition.tgz') version('professional.2019.3', sha256='92a8879106d0bdf1ecf4670cd97fbcdc67d78b13bdf484f2c516a533aa7a27f9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15269/parallel_studio_xe_2019_update3_professional_edition.tgz') + version('professional.2019.2', sha256='cdb629d74612d135ca197f1f64e6a081e31df68cda92346a29e1223bb06e64ea', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15089/parallel_studio_xe_2019_update2_professional_edition.tgz') version('professional.2019.1', sha256='bc83ef5a728903359ae11a2b90ad7dae4ae61194afb28bb5bb419f6a6aea225d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14825/parallel_studio_xe_2019_update1_professional_edition.tgz') version('professional.2019.0', sha256='94b9714e353e5c4f58d38cb236e2f8911cbef31c4b42a148d60c988e926411e2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13578/parallel_studio_xe_2019_professional_edition.tgz') # @@ -85,8 +92,12 @@ class IntelParallelStudio(IntelPackage): version('professional.2015.1', sha256='84fdf48d1de20e1d580ba5d419a5bc1c55d217a4f5dc1807190ecffe0229a62b', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4992/parallel_studio_xe_2015_update1.tgz') # Composer Edition (basic tier; excluded: MPI/..., Advisor/Inspector/Vtune) + version('composer.2020.0', sha256='9168045466139b8e280f50f0606b9930ffc720bbc60bc76f5576829ac15757ae', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/parallel_studio_xe_2020_composer_edition.tgz') + # + version('composer.2019.5', sha256='e8c8e4b9b46826a02c49325c370c79f896858611bf33ddb7fb204614838ad56c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/parallel_studio_xe_2019_update5_composer_edition.tgz') version('composer.2019.4', sha256='1915993445323e1e78d6de73702a88fa3df2036109cde03d74ee38fef9f1abf2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/parallel_studio_xe_2019_update4_composer_edition.tgz') version('composer.2019.3', sha256='15373ac6df2a84e6dd9fa0eac8b5f07ab00cdbb67f494161fd0d4df7a71aff8e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15272/parallel_studio_xe_2019_update3_composer_edition.tgz') + version('composer.2019.2', sha256='1e0f400be1f458592a8c2e7d55c1b2a4506f68f22bacbf1175af947809a4cd87', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15092/parallel_studio_xe_2019_update2_composer_edition.tgz') version('composer.2019.1', sha256='db000cb2ebf411f6e91719db68a0c68b8d3f7d38ad7f2049ea5b2f1b5f006c25', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14832/parallel_studio_xe_2019_update1_composer_edition.tgz') version('composer.2019.0', sha256='e1a29463038b063e01f694e2817c0fcf1a8e824e24f15a26ce85f20afa3f963a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13581/parallel_studio_xe_2019_composer_edition.tgz') # @@ -199,7 +210,7 @@ class IntelParallelStudio(IntelPackage): conflicts('auto_dispatch=SSE3', 'platform=darwin target=x86_64:', msg='SSE3 is not supported on MacOS x86_64') - def setup_dependent_environment(self, *args): + def setup_dependent_build_environment(self, *args): # Handle in callback, conveying client's compilers in additional arg. # CAUTION - DUP code in: # ../intel-mpi/package.py diff --git a/var/spack/repos/builtin/packages/intel-pin/package.py b/var/spack/repos/builtin/packages/intel-pin/package.py index 4ad11b121f..ae0473734c 100644 --- a/var/spack/repos/builtin/packages/intel-pin/package.py +++ b/var/spack/repos/builtin/packages/intel-pin/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,7 +15,9 @@ class IntelPin(Package): homepage = "http://www.pintool.org" maintainers = ['matthiasdiener'] - version('3.7', sha256='4730328795be61f1addb0e505a3792a4b4ca80b1b9405acf217beec6b5b90fb8', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.7-97619-g0d0c92f4f-gcc-linux.tar.gz') + version('3.11', sha256='aa5abca475a6e106a75e6ed4ba518fb75a57549a59f00681e6bd6e3f221bd23a', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.11-97998-g7ecce2dac-gcc-linux.tar.gz') + version('3.10', sha256='7c8f14c3a0654bab662b58aba460403138fa44517bd40052501e8e0075b2702a', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.10-97971-gc5e41af74-gcc-linux.tar.gz') + version('3.7', sha256='4730328795be61f1addb0e505a3792a4b4ca80b1b9405acf217beec6b5b90fb8', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.7-97619-g0d0c92f4f-gcc-linux.tar.gz') def install(self, spec, prefix): install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/intel-tbb/makefile-debug.patch b/var/spack/repos/builtin/packages/intel-tbb/makefile-debug.patch new file mode 100644 index 0000000000..8db5e2b985 --- /dev/null +++ b/var/spack/repos/builtin/packages/intel-tbb/makefile-debug.patch @@ -0,0 +1,42 @@ +The debug targets were removed starting with rev 2020. +This patch restores them. + + +--- tbb-2020/Makefile.orig 2019-12-18 02:42:41.000000000 -0600 ++++ tbb-2020/Makefile 2020-02-09 00:27:17.058452442 -0600 +@@ -26,15 +26,19 @@ + all: tbb tbbmalloc tbbproxy test examples + + tbb: mkdir ++ $(MAKE) -C "$(work_dir)_debug" -r -f $(tbb_root)/build/Makefile.tbb cfg=debug + $(MAKE) -C "$(work_dir)_release" -r -f $(tbb_root)/build/Makefile.tbb cfg=release + + tbbmalloc: mkdir ++ $(MAKE) -C "$(work_dir)_debug" -r -f $(tbb_root)/build/Makefile.tbbmalloc cfg=debug malloc + $(MAKE) -C "$(work_dir)_release" -r -f $(tbb_root)/build/Makefile.tbbmalloc cfg=release malloc + + tbbproxy: mkdir ++ $(MAKE) -C "$(work_dir)_debug" -r -f $(tbb_root)/build/Makefile.tbbproxy cfg=debug tbbproxy + $(MAKE) -C "$(work_dir)_release" -r -f $(tbb_root)/build/Makefile.tbbproxy cfg=release tbbproxy + + tbbbind: mkdir ++ $(MAKE) -C "$(work_dir)_debug" -r -f $(tbb_root)/build/Makefile.tbbbind cfg=debug tbbbind + $(MAKE) -C "$(work_dir)_release" -r -f $(tbb_root)/build/Makefile.tbbbind cfg=release tbbbind + + test: tbb tbbmalloc $(if $(use_proxy),tbbproxy) +@@ -42,6 +46,7 @@ + -$(MAKE) -C "$(work_dir)_release" -r -f $(tbb_root)/build/Makefile.test cfg=release + + rml: mkdir ++ $(MAKE) -C "$(work_dir)_debug" -r -f $(tbb_root)/build/Makefile.rml cfg=debug + $(MAKE) -C "$(work_dir)_release" -r -f $(tbb_root)/build/Makefile.rml cfg=release + + examples: tbb tbbmalloc +@@ -64,6 +69,7 @@ + $(shell $(MAKE) -s -i -r -C examples -f Makefile tbb_root=.. clean >$(NUL) 2>$(NUL)) + + mkdir: ++ $(shell $(MD) "$(work_dir)_debug" >$(NUL) 2>$(NUL)) + $(shell $(MD) "$(work_dir)_release" >$(NUL) 2>$(NUL)) + @echo Created the $(work_dir)_release directory + diff --git a/var/spack/repos/builtin/packages/intel-tbb/package.py b/var/spack/repos/builtin/packages/intel-tbb/package.py index 4b64601261..4b68ae5b4e 100644 --- a/var/spack/repos/builtin/packages/intel-tbb/package.py +++ b/var/spack/repos/builtin/packages/intel-tbb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,6 +7,7 @@ from spack import * import glob import inspect import platform +import sys class IntelTbb(Package): @@ -17,7 +18,18 @@ class IntelTbb(Package): """ homepage = "http://www.threadingbuildingblocks.org/" + # Note: when adding new versions, please check and update the + # patches and filters below as needed. + # See url_for_version() below. + + version('2020.1', sha256='72cffaeac3b50b117c4e2279f9162308d35873b3e744aff5a088beff6f65c9af') + version('2020', sha256='db80f4f7abb95c2d08fe64abdc0a9250903e4c725f1c667ac517450de426023a') + version('2019.9', sha256='15652f5328cf00c576f065e5cd3eaf3317422fe82afb67a9bcec0dc065bd2abe') + version('2019.8', sha256='7b1fd8caea14be72ae4175896510bf99c809cd7031306a1917565e6de7382fba') + version('2019.7', sha256='4204a93f4c0fd989fb6f79acae74feb02ee39725c93968773d9b6efeb75c7a6a') + version('2019.6', sha256='2ba197b3964fce8a84429dd15b75eba7434cb89afc54f86d5ee6f726fdbe97fd') + version('2019.5', sha256='2ea82d74dec50e18075b4982b8d360f8bd2bf2950f38e2db483aef82e0047444') version('2019.4', sha256='342a0a2cd583879850658284b86e9351ea019b4f3fcd731f4c18456f0ce9f900') version('2019.3', sha256='b2244147bc8159cdd8f06a38afeb42f3237d3fc822555499d7ccfbd4b86f8ece') version('2019.2', sha256='1245aa394a92099e23ce2f60cdd50c90eb3ddcd61d86cae010ef2f1de61f32d9') @@ -49,6 +61,16 @@ class IntelTbb(Package): provides('tbb') + # Clang builds incorrectly determine GCC version which in turn incorrectly + # causes a mismatch in C++ features resulting in a link error. This also + # means that clang builds require a gcc compiler to work correctly (this + # has always been the case). + # + # See https://github.com/intel/tbb/pull/147 for details. + # + conflicts('%clang', when='@:2019.6', + msg='2019.7 or later required for clang') + conflicts('%gcc@6.1:', when='@:4.4.3', msg='4.4.4 or later required for GCC >= 6.1.') @@ -64,44 +86,24 @@ class IntelTbb(Package): variant('tm', default=True, description='Enable use of transactional memory on x86') + # Testing version ranges inside when clauses was fixed in e9ee9eaf. + # See: #8957 and #13989. + # Build and install CMake config files if we're new enough. - depends_on('cmake@3.0.0:', type='build', when='@2017.0:') - - # Note: see issues #11371 and #8957 to understand why 2019.x patches are - # specified one at a time. In a nutshell, it is currently impossible - # to patch `2019.1` without patching `2019`. When #8957 is fixed, this - # can be simplified. - - # Deactivate use of RTM with GCC when on an OS with an elderly assembler. - # one patch format for 2019.1 and after... - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.4 %gcc@4.8.0: os=rhel6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.4 %gcc@4.8.0: os=scientific6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.4 %gcc@4.8.0: os=centos6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.3 %gcc@4.8.0: os=rhel6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.3 %gcc@4.8.0: os=scientific6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.3 %gcc@4.8.0: os=centos6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.2 %gcc@4.8.0: os=rhel6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.2 %gcc@4.8.0: os=scientific6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.2 %gcc@4.8.0: os=centos6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.1 %gcc@4.8.0: os=rhel6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.1 %gcc@4.8.0: os=scientific6') - patch("tbb_gcc_rtm_key_2019U1.patch", level=0, when='@2019.1 %gcc@4.8.0: os=centos6') - # ...another patch file for 2019 and before - patch("tbb_gcc_rtm_key.patch", level=0, when='@:2019.0 %gcc@4.8.0: os=rhel6') - patch("tbb_gcc_rtm_key.patch", level=0, when='@:2019.0 %gcc@4.8.0: os=scientific6') - patch("tbb_gcc_rtm_key.patch", level=0, when='@:2019.0 %gcc@4.8.0: os=centos6') - - # patch for pedantic warnings (#10836) - # one patch file for 2019.1 and after... - patch("gcc_generic-pedantic-2019.patch", level=1, when='@2019.4') - patch("gcc_generic-pedantic-2019.patch", level=1, when='@2019.3') - patch("gcc_generic-pedantic-2019.patch", level=1, when='@2019.2') - patch("gcc_generic-pedantic-2019.patch", level=1, when='@2019.1') - # ...another patch file for 2019 and before - patch("gcc_generic-pedantic-4.4.patch", level=1, when='@:2019.0') + # CMake support started in 2017.7. + depends_on('cmake@3.0.0:', type='build', when='@2017.7:') + + # Patch for pedantic warnings (#10836). This was fixed in the TBB + # source tree in 2019.6. + patch("gcc_generic-pedantic-2019.patch", level=1, when='@2019.1:2019.5') + patch("gcc_generic-pedantic-4.4.patch", level=1, when='@:2019.0') # Patch cmakeConfig.cmake.in to find the libraries where we install them. - patch("tbb_cmakeConfig.patch", level=0, when='@2017.0:') + patch("tbb_cmakeConfig-2019.5.patch", level=0, when='@2019.5:') + patch("tbb_cmakeConfig.patch", level=0, when='@2017.7:2019.4') + + # Restore the debug targets. + patch("makefile-debug.patch", when="@2020:") # Some very old systems don't support transactional memory. patch("disable-tm.patch", when='~tm') @@ -131,6 +133,14 @@ class IntelTbb(Package): of.write(l) def install(self, spec, prefix): + # Deactivate use of RTM with GCC when on an OS with a very old + # assembler. + if (spec.satisfies('%gcc@4.8.0: os=rhel6') + or spec.satisfies('%gcc@4.8.0: os=centos6') + or spec.satisfies('%gcc@4.8.0: os=scientific6')): + filter_file(r'RTM_KEY.*=.*rtm.*', 'RTM_KEY =', + join_path('build', 'linux.gcc.inc')) + # We need to follow TBB's compiler selection logic to get the proper # build + link flags but we still need to use spack's compiler wrappers # to accomplish this, we do two things: @@ -190,7 +200,7 @@ class IntelTbb(Package): for f in fs: install(f, prefix.lib) - if self.spec.satisfies('@2017.0:'): + if spec.satisfies('@2017.8,2018.1:', strict=True): # Generate and install the CMake Config file. cmake_args = ('-DTBB_ROOT={0}'.format(prefix), '-DTBB_OS={0}'.format(platform.system()), @@ -198,3 +208,9 @@ class IntelTbb(Package): 'tbb_config_generator.cmake') with working_dir(join_path(self.stage.source_path, 'cmake')): inspect.getmodule(self).cmake(*cmake_args) + + @run_after('install') + def darwin_fix(self): + # Replace @rpath in ids with full path + if sys.platform == 'darwin': + fix_darwin_install_name(self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/intel-tbb/tbb_cmakeConfig-2019.5.patch b/var/spack/repos/builtin/packages/intel-tbb/tbb_cmakeConfig-2019.5.patch new file mode 100644 index 0000000000..f75fd6fa44 --- /dev/null +++ b/var/spack/repos/builtin/packages/intel-tbb/tbb_cmakeConfig-2019.5.patch @@ -0,0 +1,14 @@ +This patch adapts the tbb_cmakeConfig.patch for 2019.5 and later. +The file changed. + +--- cmake/TBBMakeConfig.cmake.orig 2019-03-21 10:28:21.000000000 -0500 ++++ cmake/TBBMakeConfig.cmake 2019-11-27 22:52:45.270824744 -0600 +@@ -175,7 +175,7 @@ + + ${TBB_CHOOSE_COMPILER_SUBDIR} + +-get_filename_component(_tbb_lib_path \"\${_tbb_root}/${TBB_SHARED_LIB_DIR}/\${_tbb_arch_subdir}/\${_tbb_compiler_subdir}\" ABSOLUTE) ++get_filename_component(_tbb_lib_path \"\${_tbb_root}/${TBB_SHARED_LIB_DIR}\" ABSOLUTE) + ") + + set(TBB_RELEASE_LIB_PATH "\${_tbb_lib_path}") diff --git a/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch b/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch deleted file mode 100644 index 29f040d4a8..0000000000 --- a/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- build/linux.gcc.inc~ 2016-09-15 07:00:44.000000000 -0500 -+++ build/linux.gcc.inc 2018-06-07 17:32:53.181194974 -0500 -@@ -46,7 +46,7 @@ - - # gcc 4.8 and later support RTM intrinsics, but require command line switch to enable them - ifneq (,$(shell gcc -dumpversion | egrep "^(4\.[8-9]|[5-9])")) -- RTM_KEY = -mrtm -+ RTM_KEY = # -mrtm - endif - - ifeq ($(cfg), release) diff --git a/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key_2019U1.patch b/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key_2019U1.patch deleted file mode 100644 index 5d4fe9aa89..0000000000 --- a/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key_2019U1.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- build/linux.gcc.inc~ 2016-09-15 07:00:44.000000000 -0500 -+++ build/linux.gcc.inc 2018-06-07 17:32:53.181194974 -0500 -@@ -46,7 +46,7 @@ - - # gcc 4.8 and later support RTM intrinsics, but require command line switch to enable them - ifneq (,$(shell $(CONLY) -dumpversion | egrep "^(4\.[8-9]|[5-9])")) -- RTM_KEY = -mrtm -+ RTM_KEY = # -mrtm - endif - - ifeq ($(cfg), release) diff --git a/var/spack/repos/builtin/packages/intel-xed/package.py b/var/spack/repos/builtin/packages/intel-xed/package.py index 9b95329a21..ac9a7a4b0c 100644 --- a/var/spack/repos/builtin/packages/intel-xed/package.py +++ b/var/spack/repos/builtin/packages/intel-xed/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -84,19 +84,23 @@ class IntelXed(Package): mkdirp(prefix.include) mkdirp(prefix.lib) + mkdirp(prefix.bin) libs = glob.glob(join_path('obj', 'lib*.a')) for lib in libs: install(lib, prefix.lib) - # Build and install shared libxed.so. + # Build and install shared libxed.so and examples (to get the CLI). mfile('--clean') - mfile('--shared', *args) + mfile('examples', '--shared', *args) libs = glob.glob(join_path('obj', 'lib*.so')) for lib in libs: install(lib, prefix.lib) + # Install the xed program + install(join_path('obj', 'examples', 'xed'), prefix.bin) + # Install header files. hdrs = glob.glob(join_path('include', 'public', 'xed', '*.h')) \ + glob.glob(join_path('obj', '*.h')) diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py index 7a207dccdb..5f3c19d578 100644 --- a/var/spack/repos/builtin/packages/intel/package.py +++ b/var/spack/repos/builtin/packages/intel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,8 @@ class Intel(IntelPackage): # Same as in ../intel-parallel-studio/package.py, Composer Edition, # but the version numbering in Spack differs. + version('19.1.0', sha256='9168045466139b8e280f50f0606b9930ffc720bbc60bc76f5576829ac15757ae', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/parallel_studio_xe_2020_composer_edition.tgz') + version('19.0.5', sha256='e8c8e4b9b46826a02c49325c370c79f896858611bf33ddb7fb204614838ad56c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/parallel_studio_xe_2019_update5_composer_edition.tgz') version('19.0.4', sha256='1915993445323e1e78d6de73702a88fa3df2036109cde03d74ee38fef9f1abf2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/parallel_studio_xe_2019_update4_composer_edition.tgz') version('19.0.3', sha256='15373ac6df2a84e6dd9fa0eac8b5f07ab00cdbb67f494161fd0d4df7a71aff8e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15272/parallel_studio_xe_2019_update3_composer_edition.tgz') version('19.0.1', sha256='db000cb2ebf411f6e91719db68a0c68b8d3f7d38ad7f2049ea5b2f1b5f006c25', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14832/parallel_studio_xe_2019_update1_composer_edition.tgz') diff --git a/var/spack/repos/builtin/packages/interproscan/package.py b/var/spack/repos/builtin/packages/interproscan/package.py index 981e85ccb5..7ffb7c1da8 100644 --- a/var/spack/repos/builtin/packages/interproscan/package.py +++ b/var/spack/repos/builtin/packages/interproscan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -42,6 +42,7 @@ class Interproscan(Package): patch('large-gid.patch', when='@5:') patch('non-interactive.patch', when='@:4.8') + patch('ps_scan.patch', when='@:4.8') def install(self, spec, prefix): with working_dir('core'): diff --git a/var/spack/repos/builtin/packages/interproscan/ps_scan.patch b/var/spack/repos/builtin/packages/interproscan/ps_scan.patch new file mode 100644 index 0000000000..f34aa2c432 --- /dev/null +++ b/var/spack/repos/builtin/packages/interproscan/ps_scan.patch @@ -0,0 +1,12 @@ +diff -ru a/bin/ps_scan.pl b/bin/ps_scan.pl +--- a/bin/ps_scan.pl 2020-01-01 14:07:54.243869822 -0600 ++++ b/bin/ps_scan.pl 2020-01-01 14:08:03.786850313 -0600 +@@ -8,7 +8,7 @@ + # Authors: + # Alexandre Gattiker + # Edouard de Castro; E-mail: ecastro@isb-sib.ch +-# Béatrice Cuche (evaluated_by post-processing) ++# Béatrice Cuche (evaluated_by post-processing) + # + # Contributions: + # Lorenza Bordoli (repeat method) diff --git a/var/spack/repos/builtin/packages/intltool/package.py b/var/spack/repos/builtin/packages/intltool/package.py index dd711f4bee..8225d465c5 100644 --- a/var/spack/repos/builtin/packages/intltool/package.py +++ b/var/spack/repos/builtin/packages/intltool/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ioapi/package.py b/var/spack/repos/builtin/packages/ioapi/package.py index 2081d70754..07f7220b4f 100644 --- a/var/spack/repos/builtin/packages/ioapi/package.py +++ b/var/spack/repos/builtin/packages/ioapi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,7 +15,7 @@ class Ioapi(MakefilePackage): homepage = "https://www.cmascenter.org/ioapi/" url = "https://www.cmascenter.org/ioapi/download/ioapi-3.2.tar.gz" version('3.2', sha256='56771ff0053d47f2445e00ff369bca7bfc484325a2816b2c648744e523134fe9') - depends_on('netcdf@4:') + depends_on('netcdf-c@4:') depends_on('netcdf-fortran@4:') depends_on('sed', type='build') diff --git a/var/spack/repos/builtin/packages/ior/package.py b/var/spack/repos/builtin/packages/ior/package.py index 023945979d..5a1d3f67dc 100644 --- a/var/spack/repos/builtin/packages/ior/package.py +++ b/var/spack/repos/builtin/packages/ior/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,9 +11,10 @@ class Ior(AutotoolsPackage): using POSIX, MPI-IO, or HDF5 interfaces.""" homepage = "https://github.com/hpc/ior" - url = "https://github.com/hpc/ior/archive/3.2.0.tar.gz" + url = "https://github.com/hpc/ior/archive/3.2.1.tar.gz" - version('3.2.0', sha256='91a766fb9c34b5780705d0997b71b236a1120da46652763ba11d9a8c44251852') + version('3.2.1', sha256='ebcf2495aecb357370a91a2d5852cfd83bba72765e586bcfaf15fb79ca46d00e') + version('3.2.0', sha256='91a766fb9c34b5780705d0997b71b236a1120da46652763ba11d9a8c44251852') version('3.0.1', sha256='0cbefbcdb02fb13ba364e102f9e7cc2dcf761698533dac25de446a3a3e81390d') variant('hdf5', default=False, description='support IO with HDF5 backend') diff --git a/var/spack/repos/builtin/packages/iozone/package.py b/var/spack/repos/builtin/packages/iozone/package.py index f25519fb69..b2a7d55286 100644 --- a/var/spack/repos/builtin/packages/iozone/package.py +++ b/var/spack/repos/builtin/packages/iozone/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/iperf2/package.py b/var/spack/repos/builtin/packages/iperf2/package.py index e35aa9fe60..6382010960 100644 --- a/var/spack/repos/builtin/packages/iperf2/package.py +++ b/var/spack/repos/builtin/packages/iperf2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/iperf3/package.py b/var/spack/repos/builtin/packages/iperf3/package.py index 5dee626d4e..9fbae17e2e 100644 --- a/var/spack/repos/builtin/packages/iperf3/package.py +++ b/var/spack/repos/builtin/packages/iperf3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ipopt/ipopt_aarch64_build.patch b/var/spack/repos/builtin/packages/ipopt/ipopt_aarch64_build.patch new file mode 100644 index 0000000000..18a653d2bd --- /dev/null +++ b/var/spack/repos/builtin/packages/ipopt/ipopt_aarch64_build.patch @@ -0,0 +1,12 @@ +--- spack-src/Ipopt/config.guess.org 2019-10-30 13:52:51.920159919 +0900 ++++ spack-src/Ipopt/config.guess 2019-10-30 13:55:27.956506585 +0900 +@@ -835,6 +835,9 @@ + arm*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; ++ aarch64:Linux:*:*) ++ echo ${UNAME_MACHINE}-unknown-linux-gnu ++ exit ;; + avr32*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py index fd9c87fba1..4a6f5fd167 100644 --- a/var/spack/repos/builtin/packages/ipopt/package.py +++ b/var/spack/repos/builtin/packages/ipopt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -39,6 +39,7 @@ class Ipopt(AutotoolsPackage): depends_on('metis@4.0:', when='+metis') patch('ipopt_ppc_build.patch', when='arch=ppc64le') + patch('ipopt_aarch64_build.patch', when='arch=aarch64') flag_handler = build_system_flags build_directory = 'spack-build' diff --git a/var/spack/repos/builtin/packages/isaac-server/package.py b/var/spack/repos/builtin/packages/isaac-server/package.py index df50148439..24fae8c32f 100644 --- a/var/spack/repos/builtin/packages/isaac-server/package.py +++ b/var/spack/repos/builtin/packages/isaac-server/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/isaac/package.py b/var/spack/repos/builtin/packages/isaac/package.py index 0477aabf8e..2c0badc88c 100644 --- a/var/spack/repos/builtin/packages/isaac/package.py +++ b/var/spack/repos/builtin/packages/isaac/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/isl/package.py b/var/spack/repos/builtin/packages/isl/package.py index eddb99a0f9..826f2c1969 100644 --- a/var/spack/repos/builtin/packages/isl/package.py +++ b/var/spack/repos/builtin/packages/isl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/iso-codes/package.py b/var/spack/repos/builtin/packages/iso-codes/package.py index d84da3924d..8023866c04 100644 --- a/var/spack/repos/builtin/packages/iso-codes/package.py +++ b/var/spack/repos/builtin/packages/iso-codes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/itstool/package.py b/var/spack/repos/builtin/packages/itstool/package.py index 18923479ff..967495a642 100644 --- a/var/spack/repos/builtin/packages/itstool/package.py +++ b/var/spack/repos/builtin/packages/itstool/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/itsx/package.py b/var/spack/repos/builtin/packages/itsx/package.py index fc31fee23c..08339c72a7 100644 --- a/var/spack/repos/builtin/packages/itsx/package.py +++ b/var/spack/repos/builtin/packages/itsx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jackcess/package.py b/var/spack/repos/builtin/packages/jackcess/package.py index 64486fd358..8d626cebe7 100644 --- a/var/spack/repos/builtin/packages/jackcess/package.py +++ b/var/spack/repos/builtin/packages/jackcess/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jafka/package.py b/var/spack/repos/builtin/packages/jafka/package.py new file mode 100644 index 0000000000..ab39d87b92 --- /dev/null +++ b/var/spack/repos/builtin/packages/jafka/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Jafka(Package): + """ + Jafka is a distributed publish-subscribe messaging system. + """ + + homepage = "https://github.com/adyliu/jafka" + url = "https://github.com/adyliu/jafka/releases/download/3.0.6/jafka-3.0.6.tgz" + + version('3.0.6', sha256='89c9456360ace5d43c3af52b5d2e712fc49be2f88b1b3dcfe0c8f195a3244e17') + version('3.0.5', sha256='43f1b4188a092c30f48f9cdd0bddd3074f331a9b916b6cb566da2e9e40bc09a7') + version('3.0.4', sha256='a5334fc9280764f9fd4b5eb156154c721f074c1bcc1e5496189af7c06cd16b45') + version('3.0.3', sha256='226e902af7754bb0df2cc0f30195e4f8f2512d9935265d40633293014582c7e2') + version('3.0.2', sha256='c7194476475a9c3cc09ed5a4e84eecf47a8d75011f413b26fd2c0b66c598f467') + version('3.0.1', sha256='3a75e7e5bb469b6d9061985a1ce3b5d0b622f44268da71cab4a854bce7150d41') + version('3.0.0', sha256='4c4bacdd5fba8096118f6e842b4731a3f7b3885514fe1c6b707ea45c86c7c409') + version('1.6.2', sha256='fbe5d6a3ce5e66282e27c7b71beaeeede948c598abb452abd2cae41149f44196') + + depends_on('java@7:', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/jags/package.py b/var/spack/repos/builtin/packages/jags/package.py index 1976806062..f816176827 100644 --- a/var/spack/repos/builtin/packages/jags/package.py +++ b/var/spack/repos/builtin/packages/jags/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jali/package.py b/var/spack/repos/builtin/packages/jali/package.py new file mode 100644 index 0000000000..cc2e025c88 --- /dev/null +++ b/var/spack/repos/builtin/packages/jali/package.py @@ -0,0 +1,56 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Jali(CMakePackage): + """Jali is a parallel, unstructured mesh infrastructure library designed + for use by multi-physics simulations. + """ + + homepage = "https://github.com/lanl/jali" + git = "https://github.com/lanl/jali" + url = "https://github.com/lanl/jali/archive/1.1.1.tar.gz" + + maintainers = ['raovgarimella'] + + version('master', branch='master') + version('1.1.1', sha256='c96c000b3893ea7f15bbc886524476dd466ae145e77deedc27e412fcc3541207') + version('1.1.0', sha256='783dfcd6a9284af83bb380ed257fa8b0757dc2f7f9196d935eb974fb6523c644') + version('1.0.5', sha256='979170615d33a7bf20c96bd4d0285e05a2bbd901164e377a8bccbd9af9463801') + + variant('mstk', default=True, description='Enable MSTK') + + # dependencies + depends_on('cmake@3.13:', type='build') + + depends_on('mpi') + + depends_on('boost') + + depends_on('mstk@3.3.0: +exodusii+parallel~use_markers partitioner=all', when='+mstk') + + depends_on('zoltan -fortran') + depends_on('metis') + depends_on('exodusii') + + # Unit testing variant + depends_on('unittest-cpp', type='test') + + def cmake_args(self): + options = [] + if '+with_mstk' in self.spec: + options.append('-DENABLE_MSTK_Mesh=ON') + else: + options.append('-DENABLE_MSTK_Mesh=OFF') + + # Unit test variant + if self.run_tests: + options.append('-DENABLE_Tests=ON') + else: + options.append('-DENABLE_Tests=OFF') + + return options diff --git a/var/spack/repos/builtin/packages/jansson/package.py b/var/spack/repos/builtin/packages/jansson/package.py index 5815d7aeba..6647b3d4e8 100644 --- a/var/spack/repos/builtin/packages/jansson/package.py +++ b/var/spack/repos/builtin/packages/jansson/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jasper/package.py b/var/spack/repos/builtin/packages/jasper/package.py index f3a5819bd8..f8351bbbc6 100644 --- a/var/spack/repos/builtin/packages/jasper/package.py +++ b/var/spack/repos/builtin/packages/jasper/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jbigkit/package.py b/var/spack/repos/builtin/packages/jbigkit/package.py index b829a54132..c5e4e26242 100644 --- a/var/spack/repos/builtin/packages/jbigkit/package.py +++ b/var/spack/repos/builtin/packages/jbigkit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jchronoss/package.py b/var/spack/repos/builtin/packages/jchronoss/package.py index ec631d52d3..d8ec01083e 100644 --- a/var/spack/repos/builtin/packages/jchronoss/package.py +++ b/var/spack/repos/builtin/packages/jchronoss/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py index d4b3371ff0..431943ac86 100644 --- a/var/spack/repos/builtin/packages/jdk/package.py +++ b/var/spack/repos/builtin/packages/jdk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -41,21 +41,26 @@ class Jdk(Package): version('12.0.1_12', sha256='9fd6dcdaf2cfca7da59e39b009a0f5bcd53bec2fb16105f7ca8d689cdab68d75', curl_options=curl_options, url='https://download.oracle.com/otn-pub/java/jdk/12.0.1+12/69cfe15208a647278a19ef0990eea691/jdk-12.0.1_linux-x64_bin.tar.gz') version('11.0.2_9', sha256='7b4fd8ffcf53e9ff699d964a80e4abf9706b5bdb5644a765c2b96f99e3a2cdc8', curl_options=curl_options, - url='http://download.oracle.com/otn-pub/java/jdk/11.0.2+9/f51449fcd52f4d52b93a989c5c56ed3c/jdk-11.0.2_linux-x64_bin.tar.gz') + url='https://download.oracle.com/otn-pub/java/jdk/11.0.2+9/f51449fcd52f4d52b93a989c5c56ed3c/jdk-11.0.2_linux-x64_bin.tar.gz') version('11.0.1_13', sha256='e7fd856bacad04b6dbf3606094b6a81fa9930d6dbb044bbd787be7ea93abc885', curl_options=curl_options, - url='http://download.oracle.com/otn-pub/java/jdk/11.0.1+13/90cf5d8f270a4347a95050320eef3fb7/jdk-11.0.1_linux-x64_bin.tar.gz') + url='https://download.oracle.com/otn-pub/java/jdk/11.0.1+13/90cf5d8f270a4347a95050320eef3fb7/jdk-11.0.1_linux-x64_bin.tar.gz') version('10.0.2_13', sha256='6633c20d53c50c20835364d0f3e172e0cbbce78fff81867488f22a6298fa372b', curl_options=curl_options, - url='http://download.oracle.com/otn-pub/java/jdk/10.0.2+13/19aef61b38124481863b1413dce1855f/jdk-10.0.2_linux-x64_bin.tar.gz') + url='https://download.oracle.com/otn-pub/java/jdk/10.0.2+13/19aef61b38124481863b1413dce1855f/jdk-10.0.2_linux-x64_bin.tar.gz') version('10.0.1_10', sha256='ae8ed645e6af38432a56a847597ac61d4283b7536688dbab44ab536199d1e5a4', curl_options=curl_options, - url='http://download.oracle.com/otn-pub/java/jdk/10.0.1+10/fb4372174a714e6b8c52526dc134031e/jdk-10.0.1_linux-x64_bin.tar.gz') - version('1.8.0_202', sha256='9a5c32411a6a06e22b69c495b7975034409fa1652d03aeb8eb5b6f59fd4594e0', curl_options=curl_options, + url='https://download.oracle.com/otn-pub/java/jdk/10.0.1+10/fb4372174a714e6b8c52526dc134031e/jdk-10.0.1_linux-x64_bin.tar.gz') + version('1.8.0_241-b07', sha256='419d32677855f676076a25aed58e79432969142bbd778ff8eb57cb618c69e8cb', curl_options=curl_options, + url='https://download.oracle.com/otn-pub/java/jdk/8u241-b07/1f5b5a70bf22433b84d0e960903adac8/jdk-8u241-linux-x64.tar.gz') + version('1.8.0_231-b11', sha256='a011584a2c9378bf70c6903ef5fbf101b30b08937441dc2ec67932fb3620b2cf', curl_options=curl_options, + url='https://download.oracle.com/otn-pub/java/jdk/8u231-b11/5b13a193868b4bf28bcb45c792fce896/jdk-8u231-linux-x64.tar.gz') + version('1.8.0_212-b10', sha256='3160c50aa8d8e081c8c7fe0f859ea452922eca5d2ae8f8ef22011ae87e6fedfb', curl_options=curl_options, + url='https://download.oracle.com/otn-pub/java/jdk/8u212-b10/59066701cf1a433da9770636fbc4c9aa/jdk-8u212-linux-x64.tar.gz') + version('1.8.0_202-b08', sha256='9a5c32411a6a06e22b69c495b7975034409fa1652d03aeb8eb5b6f59fd4594e0', curl_options=curl_options, url='https://download.oracle.com/otn-pub/java/jdk/8u202-b08/1961070e4c9b4e26a04e7f5a083f551e/jdk-8u202-linux-x64.tar.gz') version('1.8.0_141-b15', sha256='041d5218fbea6cd7e81c8c15e51d0d32911573af2ed69e066787a8dc8a39ba4f', curl_options=curl_options, - url='http://download.oracle.com/otn-pub/java/jdk/8u141-b15/336fa29ff2bb4ef291e347e091f7f4a7/jdk-8u141-linux-x64.tar.gz') + url='https://download.oracle.com/otn-pub/java/jdk/8u141-b15/336fa29ff2bb4ef291e347e091f7f4a7/jdk-8u141-linux-x64.tar.gz') version('1.8.0_131-b11', sha256='62b215bdfb48bace523723cdbb2157c665e6a25429c73828a32f00e587301236', curl_options=curl_options, - url='http://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.tar.gz') + url='https://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.tar.gz') - provides('java') provides('java@12', when='@12.0:12.999') provides('java@11', when='@11.0:11.999') provides('java@10', when='@10.0:10.999') @@ -148,18 +153,18 @@ and adding entries for each installation: def install(self, spec, prefix): install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set JAVA_HOME.""" - run_env.set('JAVA_HOME', self.home) + env.set('JAVA_HOME', self.home) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Set JAVA_HOME and CLASSPATH. CLASSPATH contains the installation prefix for the extension and any other Java extensions it depends on.""" - spack_env.set('JAVA_HOME', self.home) + env.set('JAVA_HOME', self.home) class_paths = [] for d in dependent_spec.traverse(deptype=('build', 'run', 'test')): @@ -167,14 +172,19 @@ and adding entries for each installation: class_paths.extend(find(d.prefix, '*.jar')) classpath = os.pathsep.join(class_paths) - spack_env.set('CLASSPATH', classpath) + env.set('CLASSPATH', classpath) + def setup_dependent_run_environment(self, env, dependent_spec): + """Set CLASSPATH. + + CLASSPATH contains the installation prefix for the extension and any + other Java extensions it depends on.""" # For runtime environment set only the path for # dependent_spec and prepend it to CLASSPATH if dependent_spec.package.extends(self.spec): class_paths = find(dependent_spec.prefix, '*.jar') classpath = os.pathsep.join(class_paths) - run_env.prepend_path('CLASSPATH', classpath) + env.prepend_path('CLASSPATH', classpath) def setup_dependent_package(self, module, dependent_spec): """Allows spec['java'].home to work.""" diff --git a/var/spack/repos/builtin/packages/jellyfish/package.py b/var/spack/repos/builtin/packages/jellyfish/package.py index 3063f45608..67092a81ad 100644 --- a/var/spack/repos/builtin/packages/jellyfish/package.py +++ b/var/spack/repos/builtin/packages/jellyfish/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py index febc529081..f87be56e69 100644 --- a/var/spack/repos/builtin/packages/jemalloc/package.py +++ b/var/spack/repos/builtin/packages/jemalloc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jmol/package.py b/var/spack/repos/builtin/packages/jmol/package.py index 421199f70f..6bbe7e28cd 100644 --- a/var/spack/repos/builtin/packages/jmol/package.py +++ b/var/spack/repos/builtin/packages/jmol/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,6 +20,6 @@ class Jmol(Package): def install(self, spec, prefix): install_tree('jmol-{0}'.format(self.version), prefix) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix) - run_env.set('JMOL_HOME', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix) + env.set('JMOL_HOME', self.prefix) diff --git a/var/spack/repos/builtin/packages/jq/input.json b/var/spack/repos/builtin/packages/jq/input.json new file mode 100644 index 0000000000..a7dc7fd6dd --- /dev/null +++ b/var/spack/repos/builtin/packages/jq/input.json @@ -0,0 +1,4 @@ +{ + "foo": 1, + "bar": 2 +} diff --git a/var/spack/repos/builtin/packages/jq/package.py b/var/spack/repos/builtin/packages/jq/package.py index a97c6c4b9e..13d3d939a2 100644 --- a/var/spack/repos/builtin/packages/jq/package.py +++ b/var/spack/repos/builtin/packages/jq/package.py @@ -1,18 +1,28 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import os.path class Jq(AutotoolsPackage): """jq is a lightweight and flexible command-line JSON processor.""" homepage = "https://stedolan.github.io/jq/" - url = "https://github.com/stedolan/jq/archive/jq-1.5.tar.gz" + url = "https://github.com/stedolan/jq/releases/download/jq-1.6/jq-1.6.tar.gz" - version('1.5', sha256='d5667641d28c27d0c1e70de83e7f9bd8b2fed7fbf6a1d68731177d400a533c65') + version('1.6', sha256='5de8c8e29aaa3fb9cc6b47bb27299f271354ebb72514e3accadc7d38b5bbaa72') + version('1.5', sha256='c4d2bfec6436341113419debf479d833692cc5cdab7eb0326b5a4d4fbe9f493c') depends_on('oniguruma') depends_on('bison@3.0:', type='build') + + @run_after('install') + @on_package_attributes(run_tests=True) + def installtest(self): + jq = self.spec['jq'].command + f = os.path.join(os.path.dirname(__file__), 'input.json') + + assert jq('.bar', input=f, output=str) == '2\n' diff --git a/var/spack/repos/builtin/packages/json-c/package.py b/var/spack/repos/builtin/packages/json-c/package.py index ff243c06c9..789cde7ed0 100644 --- a/var/spack/repos/builtin/packages/json-c/package.py +++ b/var/spack/repos/builtin/packages/json-c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,5 +22,6 @@ class JsonC(AutotoolsPackage): @when('@0.12.1 %gcc@7:') def patch(self): filter_file('-Wextra', - '-Wextra -Wno-error=implicit-fallthrough', + '-Wextra -Wno-error=implicit-fallthrough ' + '-Wno-error=unused-but-set-variable', 'Makefile.in') diff --git a/var/spack/repos/builtin/packages/json-cwx/package.py b/var/spack/repos/builtin/packages/json-cwx/package.py index db465dc507..d0d25816eb 100644 --- a/var/spack/repos/builtin/packages/json-cwx/package.py +++ b/var/spack/repos/builtin/packages/json-cwx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/json-fortran/package.py b/var/spack/repos/builtin/packages/json-fortran/package.py index 09ad99bfd8..2311bee898 100644 --- a/var/spack/repos/builtin/packages/json-fortran/package.py +++ b/var/spack/repos/builtin/packages/json-fortran/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,8 +15,16 @@ class JsonFortran(CMakePackage): version('7.1.0', sha256='e7aa1f6e09b25ebacb17188147380c3f8c0a254754cd24869c001745fcecc9e6') version('7.0.0', sha256='9b5b6235489b27d572bbc7620ed8e039fa9d4d14d41b1581b279be9db499f32c') + depends_on('cmake@2.8.8:', type='build') + def cmake_args(self): return [ '-DSKIP_DOC_GEN:BOOL=ON', '-DUSE_GNU_INSTALL_CONVENTION=ON', ] + + def check(self): + # `make check` works but `make test` doesn't: + # https://github.com/jacobwilliams/json-fortran/issues/154 + with working_dir(self.build_directory): + make('check') diff --git a/var/spack/repos/builtin/packages/json-glib/package.py b/var/spack/repos/builtin/packages/json-glib/package.py index 0647da6a9b..1a04cfe97b 100644 --- a/var/spack/repos/builtin/packages/json-glib/package.py +++ b/var/spack/repos/builtin/packages/json-glib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jsoncpp/package.py b/var/spack/repos/builtin/packages/jsoncpp/package.py index 2fc27ad974..546ea104f2 100644 --- a/var/spack/repos/builtin/packages/jsoncpp/package.py +++ b/var/spack/repos/builtin/packages/jsoncpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/jstorm/package.py b/var/spack/repos/builtin/packages/jstorm/package.py new file mode 100644 index 0000000000..0bc0be3d62 --- /dev/null +++ b/var/spack/repos/builtin/packages/jstorm/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Jstorm(Package): + """ + JStorm is an enterprise fast and stable streaming process engine. + """ + + homepage = "https://github.com/alibaba/jstorm" + url = "https://github.com/alibaba/jstorm/releases/download/2.4.0/jstorm-2.4.0.tgz" + + version('2.4.0', sha256='8a3965cb51ff95395a40e8d9fd83f12b0aad15c2726c74a796d8085cccc9d69f') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/jube/package.py b/var/spack/repos/builtin/packages/jube/package.py index 0eb96ffc12..dae9fc2932 100644 --- a/var/spack/repos/builtin/packages/jube/package.py +++ b/var/spack/repos/builtin/packages/jube/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -33,10 +33,8 @@ class Jube(PythonPackage): depends_on('py-setuptools', type='build') - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): if not self.spec.variants['resource_manager'].value == 'none': - run_env.prepend_path( - 'JUBE_INCLUDE_PATH', - prefix + "/platform/" + - self.spec.variants['resource_manager'].value - ) + env.prepend_path('JUBE_INCLUDE_PATH', join_path( + self.prefix.platform, + self.spec.variants['resource_manager'].value)) diff --git a/var/spack/repos/builtin/packages/judy/package.py b/var/spack/repos/builtin/packages/judy/package.py index bec338b95b..0c714c5b01 100644 --- a/var/spack/repos/builtin/packages/judy/package.py +++ b/var/spack/repos/builtin/packages/judy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 7191faf234..a056d40558 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -237,7 +237,7 @@ class Julia(Package): if "+plot" in spec: julia("-e", pkgstart + 'Pkg.add("PyPlot"); using PyPlot') julia("-e", pkgstart + 'Pkg.add("Colors"); using Colors') - # These require maybe gtk and image-magick + # These require maybe gtk and imagemagick julia("-e", pkgstart + 'Pkg.add("Plots"); using Plots') julia("-e", pkgstart + 'Pkg.add("PlotRecipes"); using PlotRecipes') julia( diff --git a/var/spack/repos/builtin/packages/k8/package.py b/var/spack/repos/builtin/packages/k8/package.py index d98c4eb858..d536e6e369 100644 --- a/var/spack/repos/builtin/packages/k8/package.py +++ b/var/spack/repos/builtin/packages/k8/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kafka/package.py b/var/spack/repos/builtin/packages/kafka/package.py new file mode 100644 index 0000000000..d37fd21276 --- /dev/null +++ b/var/spack/repos/builtin/packages/kafka/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Kafka(Package): + """ + Kafka is used for building real-time data pipelines and streaming apps. + It is horizontally scalable, fault-tolerant, wicked fast, and runs in + production in thousands of companies. + """ + + homepage = "https://www-eu.apache.org/dist/kafka" + url = "https://www-eu.apache.org/dist/kafka/2.3.1/kafka_2.12-2.3.1.tgz" + list_url = "https://www-eu.apache.org/dist/kafka/" + list_depth = 1 + + version('2.13-2.4.0', sha256='c1c5246c7075459687b3160b713a001f5cd1cc563b9a3db189868d2f22aa9110') + version('2.12-2.4.0', sha256='b9582bab0c3e8d131953b1afa72d6885ca1caae0061c2623071e7f396f2ccfee') + version('2.12-2.3.1', sha256='5a3ddd4148371284693370d56f6f66c7a86d86dd96c533447d2a94d176768d2e') + version('2.12-2.3.0', sha256='d86f5121a9f0c44477ae6b6f235daecc3f04ecb7bf98596fd91f402336eee3e7') + version('2.12-2.2.2', sha256='7a1713d2ee929e54b1c889a449d77006513e59afb3032366368b2ebccd9e9ec0') + + depends_on('java@8:', type='run') + + def url_for_version(self, version): + url = "https://www-eu.apache.org/dist/kafka/{0}/kafka_{1}.tgz" + parent_dir = str(version).split('-')[1] + return url.format(parent_dir, version) + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/kahip/package.py b/var/spack/repos/builtin/packages/kahip/package.py index 8ff5626945..7d12d36bc2 100644 --- a/var/spack/repos/builtin/packages/kahip/package.py +++ b/var/spack/repos/builtin/packages/kahip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kaiju/package.py b/var/spack/repos/builtin/packages/kaiju/package.py index f5c24daf07..784fcffee9 100644 --- a/var/spack/repos/builtin/packages/kaiju/package.py +++ b/var/spack/repos/builtin/packages/kaiju/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kaks-calculator/package.py b/var/spack/repos/builtin/packages/kaks-calculator/package.py index 0d29aeb5ed..f551728a22 100644 --- a/var/spack/repos/builtin/packages/kaks-calculator/package.py +++ b/var/spack/repos/builtin/packages/kaks-calculator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kaldi/fujitsu_fix_version_analysis.patch b/var/spack/repos/builtin/packages/kaldi/fujitsu_fix_version_analysis.patch new file mode 100644 index 0000000000..051e7a77a3 --- /dev/null +++ b/var/spack/repos/builtin/packages/kaldi/fujitsu_fix_version_analysis.patch @@ -0,0 +1,11 @@ +--- spack-src/src/configure.org 2019-12-03 10:51:10.415048439 +0900 ++++ spack-src/src/configure 2019-12-03 10:51:37.467877147 +0900 +@@ -214,7 +214,7 @@ + You need g++ >= 4.7, Apple clang >= 5.0 or LLVM clang >= 3.3." + fi + elif [[ $COMPILER_VER_INFO == *"LLVM"* ]]; then +- CLANG_VER=$(echo $COMPILER_VER_INFO | grep version | sed "s/.*version \([0-9\.]*\).*/\1/") ++ CLANG_VER=$(echo $COMPILER_VER_INFO | grep LLVM | sed "s/.*LLVM \([0-9\.]*\).*/\1/") + CLANG_VER_NUM=$(echo $CLANG_VER | sed 's/\./ /g' | xargs printf "%d%02d") + if [ $CLANG_VER_NUM -lt 303 ]; then + failure "$COMPILER (LLVM clang-$CLANG_VER) is not supported. diff --git a/var/spack/repos/builtin/packages/kaldi/package.py b/var/spack/repos/builtin/packages/kaldi/package.py index 8455763add..07d267c8af 100644 --- a/var/spack/repos/builtin/packages/kaldi/package.py +++ b/var/spack/repos/builtin/packages/kaldi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,6 +18,7 @@ class Kaldi(Package): # Does not use Autotools git = "https://github.com/kaldi-asr/kaldi.git" version('master') + version('2019-09-29', commit='6ffde4b41c58de778245149690927d592cd5956a') version('2019-07-29', commit='7637de77e0a77bf280bef9bf484e4f37c4eb9475') version('2018-07-11', commit='6f2140b032b0108bc313eefdca65151289642773') version('2015-10-07', commit='c024e8aa0a727bf76c91a318f76a1f8b0b59249e') @@ -37,11 +38,15 @@ class Kaldi(Package): # Does not use Autotools depends_on('openfst@1.4.1-patch', when='@2015-10-07') depends_on('openfst@1.6.0:', when='@2018-07-11') depends_on('openfst@1.6.0:', when='@2019-07-29') + depends_on('openfst@1.6.7:', when='@2019-09-29') depends_on('cub', when='@2019-07-29:') depends_on('openfst') patch('openfst-1.4.1.patch', when='@2015-10-07') + # Change process of version analysis when using Fujitsu compiler. + patch('fujitsu_fix_version_analysis.patch', when='@2018-07-11:%fj') + def install(self, spec, prefix): configure_args = ['--fst-root=' + spec['openfst'].prefix] configure_args.append('--fst-version=' + str(spec['openfst'].version)) diff --git a/var/spack/repos/builtin/packages/kallisto/package.py b/var/spack/repos/builtin/packages/kallisto/package.py index 9c13c773f3..337b50f188 100644 --- a/var/spack/repos/builtin/packages/kallisto/package.py +++ b/var/spack/repos/builtin/packages/kallisto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/karma/package.py b/var/spack/repos/builtin/packages/karma/package.py index 439369f697..f875f6d64f 100644 --- a/var/spack/repos/builtin/packages/karma/package.py +++ b/var/spack/repos/builtin/packages/karma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,15 +24,11 @@ class Karma(Package): phases = ['install'] resource( - name='karma-linux', - url='ftp://ftp.atnf.csiro.au/pub/software/karma/karma-1.7.25-amd64_Linux_libc6.3.tar.bz2', - sha256='effc3ed61c28b966b357147d90357d03c22d743c6af6edb49a863c6eb625a441', - destination='./' - ) - - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('LIBRARY_PATH', self.prefix.lib) - run_env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib) + name='karma-linux', + url='ftp://ftp.atnf.csiro.au/pub/software/karma/karma-1.7.25-amd64_Linux_libc6.3.tar.bz2', + sha256='effc3ed61c28b966b357147d90357d03c22d743c6af6edb49a863c6eb625a441', + destination='./' + ) def install(self, spec, prefix): install_tree('./karma-1.7.25/amd64_Linux_libc6.3/bin', prefix.bin) diff --git a/var/spack/repos/builtin/packages/kbproto/package.py b/var/spack/repos/builtin/packages/kbproto/package.py index aa20174720..8fa865bab2 100644 --- a/var/spack/repos/builtin/packages/kbproto/package.py +++ b/var/spack/repos/builtin/packages/kbproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kcov/package.py b/var/spack/repos/builtin/packages/kcov/package.py new file mode 100644 index 0000000000..8f01ffc985 --- /dev/null +++ b/var/spack/repos/builtin/packages/kcov/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Kcov(CMakePackage): + """Code coverage tool for compiled programs, Python and Bash which uses + debugging information to collect and report data without special + compilation options""" + + homepage = "http://simonkagstrom.github.io/kcov/index.html" + url = "https://github.com/SimonKagstrom/kcov/archive/38.tar.gz" + + version('38', sha256='b37af60d81a9b1e3b140f9473bdcb7975af12040feb24cc666f9bb2bb0be68b4') + + depends_on('cmake@2.8.4:', type='build') + depends_on('zlib') + depends_on('curl') + + def cmake_args(self): + # Necessary at least on macOS, fixes linking error to LLDB + # https://github.com/Homebrew/homebrew-core/blob/master/Formula/kcov.rb + return ['-DSPECIFY_RPATH=ON'] + + @run_after('install') + @on_package_attributes(run_tests=True) + def test(self): + # The help message exits with an exit code of 1 + kcov = Executable(self.prefix.bin.kcov) + kcov('-h', ignore_errors=1) diff --git a/var/spack/repos/builtin/packages/kdiff3/package.py b/var/spack/repos/builtin/packages/kdiff3/package.py index 1af0ea173b..483a0ffac9 100644 --- a/var/spack/repos/builtin/packages/kdiff3/package.py +++ b/var/spack/repos/builtin/packages/kdiff3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py index 8e0c964cbe..e164dac4b4 100644 --- a/var/spack/repos/builtin/packages/kealib/package.py +++ b/var/spack/repos/builtin/packages/kealib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/keepalived/package.py b/var/spack/repos/builtin/packages/keepalived/package.py new file mode 100644 index 0000000000..bb6cf01337 --- /dev/null +++ b/var/spack/repos/builtin/packages/keepalived/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Keepalived(AutotoolsPackage): + """ + Keepalived implements a set of checkers to dynamically and adaptively + maintain and manage loadbalanced server pool according their health + """ + + homepage = "http://www.keepalived.org" + url = "http://www.keepalived.org/software/keepalived-1.2.0.tar.gz" + + version('2.0.19', sha256='0e2f8454765bc6a5fa26758bd9cec18aae42882843cdd24848aff0ae65ce4ca7') + version('2.0.18', sha256='1423a2b1b8e541211029b9e1e1452e683bbe5f4b0b287eddd609aaf5ff024fd0') + version('2.0.17', sha256='8965ffa2ffe243014f9c0245daa65f00a9930cf746edf33525d28a86f97497b4') + version('2.0.16', sha256='f0c7dc86147a286913c1c2c918f557735016285d25779d4d2fce5732fcb888df') + version('2.0.15', sha256='933ee01bc6346aa573453b998f87510d3cce4aba4537c9642b24e6dbfba5c6f4') + version('2.0.14', sha256='1bf586e56ee38b47b82f2a27b27e04d0e5b23f1810db6a8e801bde9d3eb8617b') + version('2.0.13', sha256='c7fb38e8a322fb898fb9f6d5d566827a30aa5a4cd1774f474bb4041c85bcbc46') + version('2.0.12', sha256='fd50e433d784cfd948de5726752cf89ab7001f587fe10a5110c6c7cbda4b7b5e') + version('2.0.11', sha256='a298b0c02a20959cfc365b62c14f45abd50d5e0595b2869f5bce10ec2392fa48') + + depends_on('openssl', type='build') diff --git a/var/spack/repos/builtin/packages/kentutils/package.py b/var/spack/repos/builtin/packages/kentutils/package.py index 8ce948dce2..379d3486c0 100644 --- a/var/spack/repos/builtin/packages/kentutils/package.py +++ b/var/spack/repos/builtin/packages/kentutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kibana/package.py b/var/spack/repos/builtin/packages/kibana/package.py index 7d14be8cf1..6bf2562394 100644 --- a/var/spack/repos/builtin/packages/kibana/package.py +++ b/var/spack/repos/builtin/packages/kibana/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kim-api/package.py b/var/spack/repos/builtin/packages/kim-api/package.py index e7e2e6f431..8c2e13f994 100644 --- a/var/spack/repos/builtin/packages/kim-api/package.py +++ b/var/spack/repos/builtin/packages/kim-api/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kitty/package.py b/var/spack/repos/builtin/packages/kitty/package.py index 0a5e12df13..49fb0013cc 100644 --- a/var/spack/repos/builtin/packages/kitty/package.py +++ b/var/spack/repos/builtin/packages/kitty/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kmergenie/package.py b/var/spack/repos/builtin/packages/kmergenie/package.py index d242728ce4..0c7c5150c5 100644 --- a/var/spack/repos/builtin/packages/kmergenie/package.py +++ b/var/spack/repos/builtin/packages/kmergenie/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kokkos-kernels/package.py b/var/spack/repos/builtin/packages/kokkos-kernels/package.py index 7c3ea57047..614fa54196 100644 --- a/var/spack/repos/builtin/packages/kokkos-kernels/package.py +++ b/var/spack/repos/builtin/packages/kokkos-kernels/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py index dc97173755..4b8e02e495 100644 --- a/var/spack/repos/builtin/packages/kokkos/package.py +++ b/var/spack/repos/builtin/packages/kokkos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -67,6 +67,11 @@ class Kokkos(Package): variant('enable_lambda', default=False, description="set enable_lambda Kokkos CUDA option") + host_values = ('AMDAVX', 'ARMv80', 'ARMv81', 'ARMv8-ThunderX', + 'Power7', 'Power8', 'Power9', + 'WSM', 'SNB', 'HSW', 'BDW', 'SKX', + 'KNC', 'KNL') + gpu_values = ('Kepler30', 'Kepler32', 'Kepler35', 'Kepler37', 'Maxwell50', 'Maxwell52', 'Maxwell53', 'Pascal60', 'Pascal61', @@ -82,9 +87,7 @@ class Kokkos(Package): variant( 'host_arch', default='none', - values=('AMDAVX', 'ARMv80', 'ARMv81', 'ARMv8-ThunderX', - 'Power7', 'Power8', 'Power9', - 'WSM', 'SNB', 'HSW', 'BDW', 'SKX', 'KNC', 'KNL'), + values=host_values, description='Set the host architecture to use' ) diff --git a/var/spack/repos/builtin/packages/kraken/package.py b/var/spack/repos/builtin/packages/kraken/package.py index b9982ec585..e798e540cd 100644 --- a/var/spack/repos/builtin/packages/kraken/package.py +++ b/var/spack/repos/builtin/packages/kraken/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/krb5/package.py b/var/spack/repos/builtin/packages/krb5/package.py index 8e5e125691..24cf72f6d7 100644 --- a/var/spack/repos/builtin/packages/krb5/package.py +++ b/var/spack/repos/builtin/packages/krb5/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/krims/package.py b/var/spack/repos/builtin/packages/krims/package.py index 36887a3bdc..be3c7a3f16 100644 --- a/var/spack/repos/builtin/packages/krims/package.py +++ b/var/spack/repos/builtin/packages/krims/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kripke/package.py b/var/spack/repos/builtin/packages/kripke/package.py index 801fdecaf1..8a54f71d48 100644 --- a/var/spack/repos/builtin/packages/kripke/package.py +++ b/var/spack/repos/builtin/packages/kripke/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kvasir-mpl/package.py b/var/spack/repos/builtin/packages/kvasir-mpl/package.py index 82fc34019d..7d0b23fd8b 100644 --- a/var/spack/repos/builtin/packages/kvasir-mpl/package.py +++ b/var/spack/repos/builtin/packages/kvasir-mpl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/kvtree/package.py b/var/spack/repos/builtin/packages/kvtree/package.py index 6f164b12d6..be265f5ecd 100644 --- a/var/spack/repos/builtin/packages/kvtree/package.py +++ b/var/spack/repos/builtin/packages/kvtree/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class Kvtree(CMakePackage): hashes.""" homepage = "https://github.com/ECP-VeloC/KVTree" - url = "https://github.com/ECP-VeloC/KVTree/archive/v1.0.1.zip" + url = "https://github.com/ECP-VeloC/KVTree/archive/v1.0.2.zip" git = "https://github.com/ecp-veloc/kvtree.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/ladot/package.py b/var/spack/repos/builtin/packages/ladot/package.py index aa3f8f632e..b3c2922a91 100644 --- a/var/spack/repos/builtin/packages/ladot/package.py +++ b/var/spack/repos/builtin/packages/ladot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/laghos/package.py b/var/spack/repos/builtin/packages/laghos/package.py index 16b9934c0d..7edb886a83 100644 --- a/var/spack/repos/builtin/packages/laghos/package.py +++ b/var/spack/repos/builtin/packages/laghos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lame/package.py b/var/spack/repos/builtin/packages/lame/package.py index 0673ee2487..772fb4c01b 100644 --- a/var/spack/repos/builtin/packages/lame/package.py +++ b/var/spack/repos/builtin/packages/lame/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py index 1b9e4c1fd8..72a1a9246f 100644 --- a/var/spack/repos/builtin/packages/lammps/package.py +++ b/var/spack/repos/builtin/packages/lammps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,7 +7,7 @@ from spack import * import datetime as dt -class Lammps(CMakePackage): +class Lammps(CMakePackage, CudaPackage): """LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. @@ -48,10 +48,10 @@ class Lammps(CMakePackage): supported_packages = ['asphere', 'body', 'class2', 'colloid', 'compress', 'coreshell', 'dipole', 'granular', 'kspace', 'latte', 'manybody', 'mc', 'meam', 'misc', 'molecule', - 'mpiio', 'peri', 'poems', 'python', 'qeq', 'reax', - 'replica', 'rigid', 'shock', 'snap', 'srd', + 'mpiio', 'peri', 'poems', 'python', 'qeq', + 'replica', 'rigid', 'shock', 'snap', 'spin', 'srd', 'user-atc', 'user-h5md', 'user-lb', 'user-misc', - 'user-netcdf', 'user-omp', 'voronoi'] + 'user-netcdf', 'user-omp', 'user-reaxc', 'voronoi'] for pkg in supported_packages: variant(pkg, default=False, @@ -60,6 +60,8 @@ class Lammps(CMakePackage): description='Build the liblammps in addition to the executable') variant('mpi', default=True, description='Build with mpi') + variant('kokkos', default=False, + description='Build with Kokkos accelerated styles') variant('jpeg', default=True, description='Build with jpeg support') variant('png', default=True, @@ -67,18 +69,24 @@ class Lammps(CMakePackage): variant('ffmpeg', default=True, description='Build with ffmpeg support') variant('openmp', default=True, description='Build with OpenMP') + variant('opencl', default=False, description='Build with OpenCL') variant('exceptions', default=False, description='Build with lammps exceptions') + variant('cuda_mps', default=False, + description='(CUDA only) Enable tweaks for running ' + + 'with Nvidia CUDA Multi-process services daemon') depends_on('mpi', when='+mpi') depends_on('mpi', when='+mpiio') depends_on('fftw', when='+kspace') depends_on('voropp+pic', when='+voronoi') - depends_on('netcdf+mpi', when='+user-netcdf') + depends_on('netcdf-c+mpi', when='+user-netcdf') depends_on('blas', when='+user-atc') depends_on('lapack', when='+user-atc') depends_on('latte@1.0.1', when='@:20180222+latte') depends_on('latte@1.1.1:', when='@20180316:20180628+latte') + depends_on('opencl', when='+opencl') + depends_on('latte@1.2.1:', when='@20180629:+latte') depends_on('blas', when='+latte') depends_on('lapack', when='+latte') @@ -89,7 +97,9 @@ class Lammps(CMakePackage): depends_on('jpeg', when='+jpeg') depends_on('libpng', when='+png') depends_on('ffmpeg', when='+ffmpeg') + depends_on('kokkos', when='+kokkos') + conflicts('+cuda', when='+opencl') conflicts('+body', when='+poems@:20180628') conflicts('+latte', when='@:20170921') conflicts('+python', when='~lib') @@ -125,6 +135,19 @@ class Lammps(CMakePackage): '-DBUILD_OMP={0}'.format( 'ON' if '+openmp' in spec else 'OFF'), ] + if spec.satisfies('+cuda'): + args.append('-DPKG_GPU=ON') + args.append('-DGPU_API=cuda') + cuda_arch = spec.variants['cuda_arch'].value + if cuda_arch is not None: + args.append('-DGPU_ARCH=sm_{0}'.format(cuda_arch[0])) + args.append('-DCUDA_MPS_SUPPORT={0}'.format( + 'ON' if '+cuda_mps' in spec else 'OFF')) + elif spec.satisfies('+opencl'): + args.append('-DPKG_GPU=ON') + args.append('-DGPU_API=opencl') + else: + args.append('-DPKG_GPU=OFF') if spec.satisfies('@20180629:+lib'): args.append('-DBUILD_LIB=ON') diff --git a/var/spack/repos/builtin/packages/last/package.py b/var/spack/repos/builtin/packages/last/package.py index 47c4275432..9e6d1c49c3 100644 --- a/var/spack/repos/builtin/packages/last/package.py +++ b/var/spack/repos/builtin/packages/last/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lastz/package.py b/var/spack/repos/builtin/packages/lastz/package.py index 0b12265cc4..cbe4ee4e14 100644 --- a/var/spack/repos/builtin/packages/lastz/package.py +++ b/var/spack/repos/builtin/packages/lastz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/laszip/package.py b/var/spack/repos/builtin/packages/laszip/package.py index 3cb1c60167..57f349a2e1 100644 --- a/var/spack/repos/builtin/packages/laszip/package.py +++ b/var/spack/repos/builtin/packages/laszip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/latte/package.py b/var/spack/repos/builtin/packages/latte/package.py index 0656e6cc30..87d10fa152 100644 --- a/var/spack/repos/builtin/packages/latte/package.py +++ b/var/spack/repos/builtin/packages/latte/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/launchmon/package.py b/var/spack/repos/builtin/packages/launchmon/package.py index b223387b96..4b80687a27 100644 --- a/var/spack/repos/builtin/packages/launchmon/package.py +++ b/var/spack/repos/builtin/packages/launchmon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,9 +28,9 @@ class Launchmon(AutotoolsPackage): patch('launchmon-char-conv.patch', when='@1.0.2') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if self.spec.satisfies('@master'): # automake for launchmon requires the AM_PATH_LIBGCRYPT macro # which is defined in libgcrypt.m4 - spack_env.prepend_path('ACLOCAL_PATH', - self.spec['libgcrypt'].prefix.share.aclocal) + env.prepend_path('ACLOCAL_PATH', + self.spec['libgcrypt'].prefix.share.aclocal) diff --git a/var/spack/repos/builtin/packages/lazyten/package.py b/var/spack/repos/builtin/packages/lazyten/package.py index 8c782bedb0..b9a7b6cfa1 100644 --- a/var/spack/repos/builtin/packages/lazyten/package.py +++ b/var/spack/repos/builtin/packages/lazyten/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lbann/package.py b/var/spack/repos/builtin/packages/lbann/package.py index cf39b3e5c1..ca7d03703c 100644 --- a/var/spack/repos/builtin/packages/lbann/package.py +++ b/var/spack/repos/builtin/packages/lbann/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,8 @@ class Lbann(CMakePackage): url = "https://github.com/LLNL/lbann/archive/v0.91.tar.gz" git = "https://github.com/LLNL/lbann.git" + maintainers = ['bvanessen'] + version('develop', branch='develop') version('0.99', branch='develop') version('0.98.1', sha256='9a2da8f41cd8bf17d1845edf9de6d60f781204ebd37bffba96d8872036c10c66') @@ -46,6 +48,7 @@ class Lbann(CMakePackage): '(note that for v0.99 conduit is required)') variant('vtune', default=False, description='Builds with support for Intel VTune') variant('docs', default=False, description='Builds with support for building documentation') + variant('extras', default=False, description='Add python modules for LBANN related tools') conflicts('@:0.90,0.99:', when='~conduit') @@ -94,7 +97,6 @@ class Lbann(CMakePackage): '~pthreads_pf ~python ~qt ~stitching ~superres ~ts ~video' '~videostab ~videoio ~vtk', when='+opencv') - depends_on('protobuf@3.6.1: build_type=Release') depends_on('cnpy') depends_on('nccl', when='@0.94:0.98.2 +gpu +nccl') @@ -104,19 +106,23 @@ class Lbann(CMakePackage): depends_on('python@3: +shared', type=('build', 'run'), when='@:0.90,0.99:') extends("python") depends_on('py-setuptools', type='build') - depends_on('py-argparse', type='run', when='@:0.90,0.99:') - depends_on('py-configparser', type='run', when='@:0.90,0.99:') - depends_on('py-graphviz@0.10.1:', type='run', when='@:0.90,0.99:') - depends_on('py-matplotlib@3.0.0:', type='run', when='@:0.90,0.99:') - depends_on('py-numpy@1.16.0:', type=('build', 'run'), when='@:0.90,0.99:') - depends_on('py-onnx@1.3.0:', type='run', when='@:0.90,0.99:') - depends_on('py-pandas@0.24.1:', type='run', when='@:0.90,0.99:') - depends_on('py-texttable@1.4.0:', type='run', when='@:0.90,0.99:') + depends_on('py-argparse', type='run', when='@:0.90,0.99: ^python@:2.6') + depends_on('py-configparser', type='run', when='@:0.90,0.99: +extras') + depends_on('py-graphviz@0.10.1:', type='run', when='@:0.90,0.99: +extras') + depends_on('py-matplotlib@3.0.0:', type='run', when='@:0.90,0.99: +extras') + depends_on('py-numpy@1.16.0:', type=('build', 'run'), when='@:0.90,0.99: +extras') + depends_on('py-onnx@1.3.0:', type='run', when='@:0.90,0.99: +extras') + depends_on('py-pandas@0.24.1:', type='run', when='@:0.90,0.99: +extras') + depends_on('py-texttable@1.4.0:', type='run', when='@:0.90,0.99: +extras') + depends_on('py-pytest', type='test', when='@:0.90,0.99:') + depends_on('py-protobuf+cpp@3.6.1:', type=('build', 'run'), when='@:0.90,0.99:') depends_on('py-breathe', type='build', when='+docs') depends_on('py-m2r', type='build', when='+docs') depends_on('cereal') + depends_on('catch2', type='test') + depends_on('clara') generator = 'Ninja' depends_on('ninja', type='build') @@ -153,7 +159,10 @@ class Lbann(CMakePackage): '-DLBANN_WITH_TBINF=OFF', '-DLBANN_WITH_VTUNE:BOOL=%s' % ('+vtune' in spec), '-DLBANN_DATATYPE={0}'.format(spec.variants['dtype'].value), - '-DLBANN_VERBOSE=0']) + '-DLBANN_VERBOSE=0', + '-DCEREAL_DIR={0}'.format(spec['cereal'].prefix), + # protobuf is included by py-protobuf+cpp + '-DProtobuf_DIR={0}'.format(spec['protobuf'].prefix)]) if self.spec.satisfies('@:0.90') or self.spec.satisfies('@0.95:'): args.extend([ diff --git a/var/spack/repos/builtin/packages/lbxproxy/package.py b/var/spack/repos/builtin/packages/lbxproxy/package.py index bde29ec23a..3080e95b0b 100644 --- a/var/spack/repos/builtin/packages/lbxproxy/package.py +++ b/var/spack/repos/builtin/packages/lbxproxy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lbzip2/package.py b/var/spack/repos/builtin/packages/lbzip2/package.py index 74e818e65f..3a4f7577f4 100644 --- a/var/spack/repos/builtin/packages/lbzip2/package.py +++ b/var/spack/repos/builtin/packages/lbzip2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lcals/package.py b/var/spack/repos/builtin/packages/lcals/package.py index ccdc9da1d1..ebf5411d00 100644 --- a/var/spack/repos/builtin/packages/lcals/package.py +++ b/var/spack/repos/builtin/packages/lcals/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lcms/package.py b/var/spack/repos/builtin/packages/lcms/package.py index f420271710..2ad9137a2c 100644 --- a/var/spack/repos/builtin/packages/lcms/package.py +++ b/var/spack/repos/builtin/packages/lcms/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,3 +21,7 @@ class Lcms(AutotoolsPackage): depends_on('jpeg') depends_on('libtiff') depends_on('zlib') + + @property + def libs(self): + return find_libraries('liblcms2', root=self.prefix, recursive=True) diff --git a/var/spack/repos/builtin/packages/lcov/package.py b/var/spack/repos/builtin/packages/lcov/package.py new file mode 100644 index 0000000000..956d9abc0e --- /dev/null +++ b/var/spack/repos/builtin/packages/lcov/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class Lcov(MakefilePackage): + """LCOV is a graphical front-end for GCC's coverage testing tool gcov. + It collects gcov data for multiple source files and creates HTML pages + containing the source code annotated with coverage information. It also + adds overview pages for easy navigation within the file structure. LCOV + supports statement, function and branch coverage measurement.""" + + homepage = "http://ltp.sourceforge.net/coverage/lcov.php" + url = "https://github.com/linux-test-project/lcov/releases/download/v1.14/lcov-1.14.tar.gz" + + version('1.14', sha256='14995699187440e0ae4da57fe3a64adc0a3c5cf14feab971f8db38fb7d8f071a') + + def install(self, spec, prefix): + make("DESTDIR=", "PREFIX=%s" % prefix, "install") diff --git a/var/spack/repos/builtin/packages/ldc-bootstrap/package.py b/var/spack/repos/builtin/packages/ldc-bootstrap/package.py index 05291360f1..681d3d1811 100644 --- a/var/spack/repos/builtin/packages/ldc-bootstrap/package.py +++ b/var/spack/repos/builtin/packages/ldc-bootstrap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,14 +31,14 @@ class LdcBootstrap(CMakePackage): depends_on('libedit') depends_on('binutils') - def setup_dependent_environment(self, build_env, run_env, dep_spec): + def setup_dependent_build_environment(self, env, dep_spec): # The code below relies on this function being executed after the # environment has been sanitized (because LD_LIBRARY_PATH is among # the variables that get unset) # We need libphobos in LD_LIBRARY_PATH - build_env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib) + env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib) def cmake_args(self): return [ diff --git a/var/spack/repos/builtin/packages/ldc/package.py b/var/spack/repos/builtin/packages/ldc/package.py index 5a6cc8f0c6..0fc8025108 100644 --- a/var/spack/repos/builtin/packages/ldc/package.py +++ b/var/spack/repos/builtin/packages/ldc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/legion/package.py b/var/spack/repos/builtin/packages/legion/package.py index 055b954c46..5b8b761d49 100644 --- a/var/spack/repos/builtin/packages/legion/package.py +++ b/var/spack/repos/builtin/packages/legion/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,8 +25,11 @@ class Legion(CMakePackage): url = "https://github.com/StanfordLegion/legion/tarball/legion-17.02.0" git = "https://github.com/StanfordLegion/legion.git" - version('develop', branch='master') - version('ctrl-rep', commit='177584e77036c9913d8a62e33b55fa784748759c') + version('master', branch='master') + version('ctrl-rep', branch='control_replication') + version('ctrl-rep-2', commit='96682fd8aae071ecd30a3ed5f481a9d84457a4b6') + version('ctrl-rep-1', commit='a03671b21851d5f0d3f63210343cb61a630f4405') + version('ctrl-rep-0', commit='177584e77036c9913d8a62e33b55fa784748759c') version('19.06.0', sha256='31cd97e9264c510ab83b1f9e8e1e6bf72021a0c6ee4a028966fce08736e39fbf') version('19.04.0', sha256='279bbc8dcdab4c75be570318989a9fc9821178143e9db9c3f62e58bf9070b5ac') version('18.12.0', sha256='71f2c409722975c0ad92f2caffcc9eaa9260f7035e2b55b731d819eb6a94016c') diff --git a/var/spack/repos/builtin/packages/lemon/package.py b/var/spack/repos/builtin/packages/lemon/package.py index 6a978e524b..c87e60e677 100644 --- a/var/spack/repos/builtin/packages/lemon/package.py +++ b/var/spack/repos/builtin/packages/lemon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/leveldb/package.py b/var/spack/repos/builtin/packages/leveldb/package.py index c3aeefa8f2..f03da29be7 100644 --- a/var/spack/repos/builtin/packages/leveldb/package.py +++ b/var/spack/repos/builtin/packages/leveldb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lftp/package.py b/var/spack/repos/builtin/packages/lftp/package.py index d6f8296086..508dbdd586 100644 --- a/var/spack/repos/builtin/packages/lftp/package.py +++ b/var/spack/repos/builtin/packages/lftp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libaec/package.py b/var/spack/repos/builtin/packages/libaec/package.py index d79a6e8cec..5f12c653f1 100644 --- a/var/spack/repos/builtin/packages/libaec/package.py +++ b/var/spack/repos/builtin/packages/libaec/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libaio/package.py b/var/spack/repos/builtin/packages/libaio/package.py index 2e850e1cbc..ca857f2f16 100644 --- a/var/spack/repos/builtin/packages/libaio/package.py +++ b/var/spack/repos/builtin/packages/libaio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libapplewm/package.py b/var/spack/repos/builtin/packages/libapplewm/package.py index 23b0e7d324..b05d4c82fe 100644 --- a/var/spack/repos/builtin/packages/libapplewm/package.py +++ b/var/spack/repos/builtin/packages/libapplewm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libarchive/package.py b/var/spack/repos/builtin/packages/libarchive/package.py index 1529cda25b..1e0a09c959 100644 --- a/var/spack/repos/builtin/packages/libarchive/package.py +++ b/var/spack/repos/builtin/packages/libarchive/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ class Libarchive(AutotoolsPackage): homepage = "http://www.libarchive.org" url = "http://www.libarchive.org/downloads/libarchive-3.1.2.tar.gz" + version('3.4.1', sha256='fcf87f3ad8db2e4f74f32526dee62dd1fb9894782b0a503a89c9d7a70a235191') version('3.3.2', sha256='ed2dbd6954792b2c054ccf8ec4b330a54b85904a80cef477a1c74643ddafa0ce') version('3.2.1', sha256='72ee1a4e3fd534525f13a0ba1aa7b05b203d186e0c6072a8a4738649d0b3cfd2') version('3.1.2', sha256='eb87eacd8fe49e8d90c8fdc189813023ccc319c5e752b01fb6ad0cc7b2c53d5e') diff --git a/var/spack/repos/builtin/packages/libassuan/package.py b/var/spack/repos/builtin/packages/libassuan/package.py index 4f7ee1da19..e8ccc861c5 100644 --- a/var/spack/repos/builtin/packages/libassuan/package.py +++ b/var/spack/repos/builtin/packages/libassuan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libatomic-ops/package.py b/var/spack/repos/builtin/packages/libatomic-ops/package.py index bf88263e4c..9bcfe2d754 100644 --- a/var/spack/repos/builtin/packages/libatomic-ops/package.py +++ b/var/spack/repos/builtin/packages/libatomic-ops/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libbeagle/package.py b/var/spack/repos/builtin/packages/libbeagle/package.py index 0c21905a0a..968dcc00e4 100644 --- a/var/spack/repos/builtin/packages/libbeagle/package.py +++ b/var/spack/repos/builtin/packages/libbeagle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -44,15 +44,15 @@ class Libbeagle(AutotoolsPackage, CudaPackage): 'configure.ac', string=True) def configure_args(self): - args = [] + args = [ + # Since spack will inject architecture flags turn off -march=native + # when building libbeagle. + '--disable-march-native', + ] if '+cuda' in self.spec: - args.append('--with-cuda=%s' % spec['cuda'].prefix) + args.append('--with-cuda=%s' % self.spec['cuda'].prefix) else: args.append('--without-cuda') return args - - def setup_environment(self, spack_env, run_env): - prefix = self.prefix - run_env.prepend_path('BEAST_LIB', prefix.lib) diff --git a/var/spack/repos/builtin/packages/libbeato/package.py b/var/spack/repos/builtin/packages/libbeato/package.py index 58fde449ea..2f59240a09 100644 --- a/var/spack/repos/builtin/packages/libbeato/package.py +++ b/var/spack/repos/builtin/packages/libbeato/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libbsd/local-elf.h.patch b/var/spack/repos/builtin/packages/libbsd/local-elf.h.patch new file mode 100644 index 0000000000..697e75ed6d --- /dev/null +++ b/var/spack/repos/builtin/packages/libbsd/local-elf.h.patch @@ -0,0 +1,11 @@ +--- a/src/local-elf.h 2018-04-21 17:30:22.000000000 -0400 ++++ b/src/local-elf.h 2019-11-13 11:02:53.965684506 -0500 +@@ -43,7 +43,7 @@ + #define ELF_TARG_CLASS ELFCLASS64 + #define ELF_TARG_DATA ELFDATA2LSB + +-#elif defined(__amd64__) ++#elif defined(__amd64__) || defined(__x86_64__) + + #define ELF_TARG_MACH EM_X86_64 + #if defined(__ILP32__) diff --git a/var/spack/repos/builtin/packages/libbsd/package.py b/var/spack/repos/builtin/packages/libbsd/package.py index 987d90043e..ce99e98597 100644 --- a/var/spack/repos/builtin/packages/libbsd/package.py +++ b/var/spack/repos/builtin/packages/libbsd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,12 +16,14 @@ class Libbsd(AutotoolsPackage): homepage = "https://libbsd.freedesktop.org/wiki/" url = "https://libbsd.freedesktop.org/releases/libbsd-0.9.1.tar.xz" + version('0.10.0', sha256='34b8adc726883d0e85b3118fa13605e179a62b31ba51f676136ecb2d0bc1a887') version('0.9.1', sha256='56d835742327d69faccd16955a60b6dcf30684a8da518c4eca0ac713b9e0a7a4') version('0.9.0', sha256='8a469afd1bab340992cf99e1e6b7ae4f4c54882d663d8a2c5ea52250617afb01') version('0.8.7', sha256='f548f10e5af5a08b1e22889ce84315b1ebe41505b015c9596bad03fd13a12b31') version('0.8.6', sha256='467fbf9df1f49af11f7f686691057c8c0a7613ae5a870577bef9155de39f9687') patch('cdefs.h.patch', when='@0.8.6 %gcc@:4') + patch('local-elf.h.patch', when='%intel') # https://gitlab.freedesktop.org/libbsd/libbsd/issues/1 conflicts('platform=darwin') diff --git a/var/spack/repos/builtin/packages/libbson/package.py b/var/spack/repos/builtin/packages/libbson/package.py index ced955a5be..9f9a113884 100644 --- a/var/spack/repos/builtin/packages/libbson/package.py +++ b/var/spack/repos/builtin/packages/libbson/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libcanberra/package.py b/var/spack/repos/builtin/packages/libcanberra/package.py index 06c340b3ab..0d54ba178d 100644 --- a/var/spack/repos/builtin/packages/libcanberra/package.py +++ b/var/spack/repos/builtin/packages/libcanberra/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libcap/package.py b/var/spack/repos/builtin/packages/libcap/package.py index fedc9059ec..443cb0682b 100644 --- a/var/spack/repos/builtin/packages/libcap/package.py +++ b/var/spack/repos/builtin/packages/libcap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libceed/package.py b/var/spack/repos/builtin/packages/libceed/package.py index 2991b5bc8b..3b327a5058 100644 --- a/var/spack/repos/builtin/packages/libceed/package.py +++ b/var/spack/repos/builtin/packages/libceed/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libcerf/package.py b/var/spack/repos/builtin/packages/libcerf/package.py index 8dc336c38d..d9209bf57b 100644 --- a/var/spack/repos/builtin/packages/libcerf/package.py +++ b/var/spack/repos/builtin/packages/libcerf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libcheck/package.py b/var/spack/repos/builtin/packages/libcheck/package.py deleted file mode 100644 index 86886037f3..0000000000 --- a/var/spack/repos/builtin/packages/libcheck/package.py +++ /dev/null @@ -1,17 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Libcheck(CMakePackage): - """A unit testing framework for C.""" - - homepage = "https://libcheck.github.io/check/index.html" - url = "https://github.com/libcheck/check/releases/download/0.12.0/check-0.12.0.tar.gz" - - version('0.12.0', sha256='464201098bee00e90f5c4bdfa94a5d3ead8d641f9025b560a27755a83b824234') - version('0.11.0', sha256='24f7a48aae6b74755bcbe964ce8bc7240f6ced2141f8d9cf480bc3b3de0d5616') - version('0.10.0', sha256='f5f50766aa6f8fe5a2df752666ca01a950add45079aa06416b83765b1cf71052') diff --git a/var/spack/repos/builtin/packages/libcint/package.py b/var/spack/repos/builtin/packages/libcint/package.py index 3477b4fa92..9696947cdb 100644 --- a/var/spack/repos/builtin/packages/libcint/package.py +++ b/var/spack/repos/builtin/packages/libcint/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libcircle/package.py b/var/spack/repos/builtin/packages/libcircle/package.py index fa8b5a3376..f710d25f24 100644 --- a/var/spack/repos/builtin/packages/libcircle/package.py +++ b/var/spack/repos/builtin/packages/libcircle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,8 +11,18 @@ class Libcircle(AutotoolsPackage): using self-stabilizing work stealing.""" homepage = "https://github.com/hpc/libcircle" + git = "https://github.com/hpc/libcircle.git" + url = "https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz" - version('0.2.1-rc.1', sha256='5747f91cf4417023304dcc92fd07e3617ac712ca1eeb698880979bbca3f54865', - url='https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz') + version('master', branch='master') + version('0.3.0', sha256='5ce38eb5b3c2b394bca1316310758f276c893dd3f4c15d7bc14ea05d3110ce58', url='https://github.com/hpc/libcircle/releases/download/v0.3/libcircle-0.3.0.tar.gz') + version('0.2.1-rc.1', sha256='5747f91cf4417023304dcc92fd07e3617ac712ca1eeb698880979bbca3f54865') depends_on('mpi') + + @when('@master') + def autoreconf(self, spec, prefix): + with working_dir(self.configure_directory): + # Bootstrap with autotools + bash = which('bash') + bash('./autogen.sh') diff --git a/var/spack/repos/builtin/packages/libconfig/package.py b/var/spack/repos/builtin/packages/libconfig/package.py index c3b046b9a0..abed039400 100644 --- a/var/spack/repos/builtin/packages/libconfig/package.py +++ b/var/spack/repos/builtin/packages/libconfig/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,6 +14,7 @@ class Libconfig(AutotoolsPackage): force_autoreconf = True + version('1.7.2', sha256='f67ac44099916ae260a6c9e290a90809e7d782d96cdd462cac656ebc5b685726') version('1.7.1', sha256='d288e6ae817f4ef78df43cdb2647f768dc97899ee82fcc41f857e8eb9fd7fbdb') version('1.5', sha256='cae5c02361d8a9b2bb26946c64f089d2e5e599972f386203fbc48975c0d885c8') diff --git a/var/spack/repos/builtin/packages/libcroco/package.py b/var/spack/repos/builtin/packages/libcroco/package.py index d2cee04546..ef89961555 100644 --- a/var/spack/repos/builtin/packages/libcroco/package.py +++ b/var/spack/repos/builtin/packages/libcroco/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libctl/package.py b/var/spack/repos/builtin/packages/libctl/package.py index fba9e33f47..8ed0bf9c56 100644 --- a/var/spack/repos/builtin/packages/libctl/package.py +++ b/var/spack/repos/builtin/packages/libctl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libdap4/package.py b/var/spack/repos/builtin/packages/libdap4/package.py new file mode 100644 index 0000000000..f93c16cbbd --- /dev/null +++ b/var/spack/repos/builtin/packages/libdap4/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Libdap4(AutotoolsPackage): + """ + libdap4 is is a c++ library to serve as a client for the OPeNDAP framework + that simplifies all aspects of scientific data networking and provides + software which makes local data accessible to remote locations regardless + of local storage format. + """ + + homepage = "https://www.opendap.org/" + url = "https://github.com/OPENDAP/libdap4/archive/version-3.20.4.tar.gz" + + maintainers = ['tjhei'] + + version('3.20.4', sha256='c39fa310985cc8963029ad0d0aba784e7dbf1f70c566bd7ae58242f1bb06d24a') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('bison', type='build') + + depends_on('flex') + depends_on('curl') + depends_on('libxml2') + depends_on('libuuid') + + def configure_args(self): + # libxml2 exports ./include/libxml2/ instead of ./include/, which we + # need, so grab this path manually: + libxml2_include = self.spec['libxml2'].prefix.include + args = ['CPPFLAGS=-I{0}'.format(libxml2_include)] + return args diff --git a/var/spack/repos/builtin/packages/libdivsufsort/package.py b/var/spack/repos/builtin/packages/libdivsufsort/package.py index c06de91bfa..0dfdb9ea3f 100644 --- a/var/spack/repos/builtin/packages/libdivsufsort/package.py +++ b/var/spack/repos/builtin/packages/libdivsufsort/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libdmx/package.py b/var/spack/repos/builtin/packages/libdmx/package.py index 7c802a75f7..5986547c5d 100644 --- a/var/spack/repos/builtin/packages/libdmx/package.py +++ b/var/spack/repos/builtin/packages/libdmx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libdrm/package.py b/var/spack/repos/builtin/packages/libdrm/package.py index a765ba7ef9..c724f1cd4a 100644 --- a/var/spack/repos/builtin/packages/libdrm/package.py +++ b/var/spack/repos/builtin/packages/libdrm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libdwarf/package.py b/var/spack/repos/builtin/packages/libdwarf/package.py index f7667524d8..fa37f4e638 100644 --- a/var/spack/repos/builtin/packages/libdwarf/package.py +++ b/var/spack/repos/builtin/packages/libdwarf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libeatmydata/package.py b/var/spack/repos/builtin/packages/libeatmydata/package.py index b822cd00bb..c339d8b85f 100644 --- a/var/spack/repos/builtin/packages/libeatmydata/package.py +++ b/var/spack/repos/builtin/packages/libeatmydata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libedit/package.py b/var/spack/repos/builtin/packages/libedit/package.py index 7801643064..7e12182a85 100644 --- a/var/spack/repos/builtin/packages/libedit/package.py +++ b/var/spack/repos/builtin/packages/libedit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index cd3a659aac..9054753c48 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libemos/package.py b/var/spack/repos/builtin/packages/libemos/package.py index 40ae9ea67c..89779b32f6 100644 --- a/var/spack/repos/builtin/packages/libemos/package.py +++ b/var/spack/repos/builtin/packages/libemos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libepoxy/package.py b/var/spack/repos/builtin/packages/libepoxy/package.py index d3bc68d452..0f5fcf50d5 100644 --- a/var/spack/repos/builtin/packages/libepoxy/package.py +++ b/var/spack/repos/builtin/packages/libepoxy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libev/package.py b/var/spack/repos/builtin/packages/libev/package.py index dfdea69813..3cefa8f5ba 100644 --- a/var/spack/repos/builtin/packages/libev/package.py +++ b/var/spack/repos/builtin/packages/libev/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,9 +11,8 @@ class Libev(AutotoolsPackage): after libevent, but without its limitations and bugs.""" homepage = "http://software.schmorp.de/pkg/libev.html" - url = "http://dist.schmorp.de/libev/libev-4.24.tar.gz" + url = "http://dist.schmorp.de/libev/Attic/libev-4.24.tar.gz" git = "https://github.com/enki/libev.git" - list_url = "http://dist.schmorp.de/libev/Attic/" version('develop', branch='master') version('4.24', sha256='973593d3479abdf657674a55afe5f78624b0e440614e2b8cb3a07f16d4d7f821') diff --git a/var/spack/repos/builtin/packages/libevent/package.py b/var/spack/repos/builtin/packages/libevent/package.py index dc658bb1f3..07a873fc2f 100644 --- a/var/spack/repos/builtin/packages/libevent/package.py +++ b/var/spack/repos/builtin/packages/libevent/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libevpath/package.py b/var/spack/repos/builtin/packages/libevpath/package.py index c34936b66f..b9ab5129a4 100644 --- a/var/spack/repos/builtin/packages/libevpath/package.py +++ b/var/spack/repos/builtin/packages/libevpath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libexif/package.py b/var/spack/repos/builtin/packages/libexif/package.py new file mode 100644 index 0000000000..fe9110f62d --- /dev/null +++ b/var/spack/repos/builtin/packages/libexif/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class Libexif(AutotoolsPackage): + """A library to parse an EXIF file and read the data from those tags""" + + homepage = "https://sourceforge.net/projects/libexif" + url = "https://downloads.sourceforge.net/sourceforge/libexif/libexif-0.6.21.tar.bz2" + + maintainers = ['TheQueasle'] + + version('0.6.21', sha256='16cdaeb62eb3e6dfab2435f7d7bccd2f37438d21c5218ec4e58efa9157d4d41a') + depends_on('glib') diff --git a/var/spack/repos/builtin/packages/libfabric/package.py b/var/spack/repos/builtin/packages/libfabric/package.py index ede7f53f66..da5edc48f4 100644 --- a/var/spack/repos/builtin/packages/libfabric/package.py +++ b/var/spack/repos/builtin/packages/libfabric/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,8 @@ class Libfabric(AutotoolsPackage): git = "https://github.com/ofiwg/libfabric.git" version('develop', branch='master') + version('1.9.0', sha256='559bfb7376c38253c936d0b104591c3394880376d676894895706c4f5f88597c', + url='https://github.com/ofiwg/libfabric/releases/download/v1.9.0/libfabric-1.9.0.tar.bz2') version('1.8.1', sha256='3c560b997f9eafd89f961dd8e8a29a81aad3e39aee888e3f3822da419047dc88', url='https://github.com/ofiwg/libfabric/releases/download/v1.8.1/libfabric-1.8.1.tar.bz2') version('1.8.0', sha256='c4763383a96af4af52cd81b3b094227f5cf8e91662f861670965994539b7ee37', @@ -40,7 +42,9 @@ class Libfabric(AutotoolsPackage): 'rxd', 'mlx', 'tcp', - 'efa') + 'efa', + 'mrail', + 'shm') variant('fabrics', default='sockets', @@ -55,6 +59,12 @@ class Libfabric(AutotoolsPackage): variant('kdreg', default=False, description='Enable kdreg on supported Cray platforms') + # For version 1.9.0: + # headers: fix forward-declaration of enum fi_collective_op with C++ + patch('https://github.com/ofiwg/libfabric/commit/2e95b0efd85fa8a3d814128e34ec57ffd357460e.patch', + sha256='71f06e8bf0adeccd425b194ac524e4d596469e9dab9e7a4f8bb209e6b9a454f4', + when='@1.9.0') + depends_on('rdma-core', when='fabrics=verbs') depends_on('opa-psm2', when='fabrics=psm2') depends_on('psm', when='fabrics=psm') @@ -66,6 +76,10 @@ class Libfabric(AutotoolsPackage): depends_on('libtool', when='@develop', type='build') resource(name='fabtests', + url='https://github.com/ofiwg/libfabric/releases/download/v1.9.0/fabtests-1.9.0.tar.bz2', + sha256='60cc21db7092334904cbdafd142b2403572976018a22218e7c453195caef366e', + placement='fabtests', when='@1.9.0') + resource(name='fabtests', url='https://github.com/ofiwg/libfabric/releases/download/v1.7.0/fabtests-1.7.0.tar.gz', sha256='ebb4129dc69dc0e1f48310ce1abb96673d8ddb18166bc595312ebcb96e803de9', placement='fabtests', when='@1.7.0') @@ -90,9 +104,9 @@ class Libfabric(AutotoolsPackage): sha256='3b78d0ca1b223ff21b7f5b3627e67e358e3c18b700f86b017e2233fee7e88c2e', placement='fabtests', when='@1.5.0') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if self.run_tests: - spack_env.prepend_path('PATH', self.prefix.bin) + env.prepend_path('PATH', self.prefix.bin) @when('@develop') def autoreconf(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/libfastcommon/package.py b/var/spack/repos/builtin/packages/libfastcommon/package.py new file mode 100644 index 0000000000..fbd3518b58 --- /dev/null +++ b/var/spack/repos/builtin/packages/libfastcommon/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Libfastcommon(Package): + """ + Libfastcommon is a c common functions library extracted from my open + source project FastDFS. this library is very simple and stable. + functions including: string, logger, chain, hash, socket, ini file + reader, base64 encode / decode, url encode / decode, fast timer, + skiplist, object pool etc. detail info please see the c header files. + """ + + homepage = "https://github.com/happyfish100/libfastcommon" + url = "https://github.com/happyfish100/libfastcommon/archive/V1.0.43.tar.gz" + + version('1.0.43', sha256='05425aed8e6bc7ba283abba4e1bb500cc7f8c873c35bb86712d7123144a37b4c') + version('1.0.42', sha256='653c781b8e19a53f69aa8b1d823a832270e310438385f4c176a337304c03bc52') + version('1.0.41', sha256='23cc5900bdf82fe907084deaf4e36a4f1857ac2a7378a2999a6c806bd3b22562') + version('1.0.40', sha256='ebb89a1bfeb5b140f596fd3e2a0ff202420be05a4d80ef67ddcfdbb248b9fef8') + version('1.0.39', sha256='72ca36f83f3453564ca09d2d0c31354b868cf52ef5a24cfb15e66d0e505c90ac') + + def install(self, spec, prefix): + sh = which('sh') + sh('make.sh') + sh('make.sh', 'install') + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py index 825d52b7e2..e5bf7b1df6 100644 --- a/var/spack/repos/builtin/packages/libffi/package.py +++ b/var/spack/repos/builtin/packages/libffi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,7 +14,7 @@ class Libffi(AutotoolsPackage): homepage = "https://sourceware.org/libffi/" version('3.2.1', sha256='d06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37', - url="https://www.mirrorservice.org/sites/sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") + url="https://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") @property def headers(self): diff --git a/var/spack/repos/builtin/packages/libffs/package.py b/var/spack/repos/builtin/packages/libffs/package.py index 9958c4c080..8c7637a7a5 100644 --- a/var/spack/repos/builtin/packages/libffs/package.py +++ b/var/spack/repos/builtin/packages/libffs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libfive/package.py b/var/spack/repos/builtin/packages/libfive/package.py index 7e9f577fee..e2a9b65d13 100644 --- a/var/spack/repos/builtin/packages/libfive/package.py +++ b/var/spack/repos/builtin/packages/libfive/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libflame/package.py b/var/spack/repos/builtin/packages/libflame/package.py index 9ed5baec59..1a8de4b47a 100644 --- a/var/spack/repos/builtin/packages/libflame/package.py +++ b/var/spack/repos/builtin/packages/libflame/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libfontenc/package.py b/var/spack/repos/builtin/packages/libfontenc/package.py index 9c841abe50..0f4f6a87a8 100644 --- a/var/spack/repos/builtin/packages/libfontenc/package.py +++ b/var/spack/repos/builtin/packages/libfontenc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libfs/package.py b/var/spack/repos/builtin/packages/libfs/package.py index 681fe929d2..b250ab7353 100644 --- a/var/spack/repos/builtin/packages/libfs/package.py +++ b/var/spack/repos/builtin/packages/libfs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libgcrypt/package.py b/var/spack/repos/builtin/packages/libgcrypt/package.py index 0edc1a0d20..496bfc3465 100644 --- a/var/spack/repos/builtin/packages/libgcrypt/package.py +++ b/var/spack/repos/builtin/packages/libgcrypt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py index 8c77d01e4a..232b826bbf 100644 --- a/var/spack/repos/builtin/packages/libgd/package.py +++ b/var/spack/repos/builtin/packages/libgd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libgeotiff/package.py b/var/spack/repos/builtin/packages/libgeotiff/package.py index c3a2e1913c..cf221fa6fe 100644 --- a/var/spack/repos/builtin/packages/libgeotiff/package.py +++ b/var/spack/repos/builtin/packages/libgeotiff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libgit2/package.py b/var/spack/repos/builtin/packages/libgit2/package.py index 5ada427806..b896675ece 100644 --- a/var/spack/repos/builtin/packages/libgit2/package.py +++ b/var/spack/repos/builtin/packages/libgit2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,7 +14,7 @@ class Libgit2(CMakePackage): """ homepage = "https://libgit2.github.com/" - url = "https://github.com/libgit2/libgit2/archive/v0.24.2.tar.gz" + url = "https://github.com/libgit2/libgit2/archive/v0.26.0.tar.gz" version('0.26.0', sha256='6a62393e0ceb37d02fe0d5707713f504e7acac9006ef33da1e88960bd78b6eac') diff --git a/var/spack/repos/builtin/packages/libglvnd/package.py b/var/spack/repos/builtin/packages/libglvnd/package.py index 4f6fb0b938..84f5440f27 100644 --- a/var/spack/repos/builtin/packages/libglvnd/package.py +++ b/var/spack/repos/builtin/packages/libglvnd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libgpg-error/awk-5.patch b/var/spack/repos/builtin/packages/libgpg-error/awk-5.patch new file mode 100644 index 0000000000..1ccd61e61d --- /dev/null +++ b/var/spack/repos/builtin/packages/libgpg-error/awk-5.patch @@ -0,0 +1,196 @@ +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -1615,7 +1615,7 @@ + + errnos-sym.h: Makefile mkstrtable.awk errnos.in + $(AWK) -f $(srcdir)/mkstrtable.awk -v textidx=2 -v nogettext=1 \ +- -v prefix=GPG_ERR_ -v namespace=errnos_ \ ++ -v prefix=GPG_ERR_ -v pkg_namespace=errnos_ \ + $(srcdir)/errnos.in >$@ + + mkheader$(EXEEXT_FOR_BUILD): mkheader.c Makefile + +diff --git a/NEWS b/NEWS +index 75b8a99..ef29558 100644 +--- a/NEWS ++++ b/NEWS +@@ -1,3 +1,7 @@ ++Noteworthy changes in version 1.37 (unreleased) [C27/A27/R_] ++----------------------------------------------- ++ ++ + Noteworthy changes in version 1.36 (2019-03-19) [C27/A27/R0] + ----------------------------------------------- + +diff --git a/configure.ac b/configure.ac +index e46b240..a6526a9 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -29,7 +29,7 @@ min_automake_version="1.14" + # See below for the LT versions. + m4_define([mym4_package],[libgpg-error]) + m4_define([mym4_major], [1]) +-m4_define([mym4_minor], [36]) ++m4_define([mym4_minor], [37]) + + # Below is m4 magic to extract and compute the revision number, the + # decimalized short revision number, a beta version string, and a flag +diff --git a/doc/yat2m.c b/doc/yat2m.c +index 3c7b363..a6a74c9 100644 +--- a/doc/yat2m.c ++++ b/doc/yat2m.c +@@ -49,7 +49,7 @@ + .B whateever you want + @end ifset + +- alternativly a special comment may be used: ++ alternatively a special comment may be used: + + @c man:.B whatever you want + +@@ -705,7 +705,7 @@ write_th (FILE *fp) + + + /* Process the texinfo command COMMAND (without the leading @) and +- write output if needed to FP. REST is the remainer of the line ++ write output if needed to FP. REST is the remainder of the line + which should either point to an opening brace or to a white space. + The function returns the number of characters already processed + from REST. LEN is the usable length of REST. TABLE_LEVEL is used to +@@ -725,7 +725,8 @@ proc_texi_cmd (FILE *fp, const char *command, const char *rest, size_t len, + { "url", 0, "\\fB", "\\fR" }, + { "sc", 0, "\\fB", "\\fR" }, + { "var", 0, "\\fI", "\\fR" }, +- { "samp", 0, "\\(aq", "\\(aq" }, ++ { "samp", 0, "\\(oq", "\\(cq" }, ++ { "kbd", 0, "\\(oq", "\\(cq" }, + { "file", 0, "\\(oq\\fI","\\fR\\(cq" }, + { "env", 0, "\\(oq\\fI","\\fR\\(cq" }, + { "acronym", 0 }, +diff --git a/lang/cl/mkerrcodes.awk b/lang/cl/mkerrcodes.awk +index ae29043..9a1fc18 100644 +--- a/lang/cl/mkerrcodes.awk ++++ b/lang/cl/mkerrcodes.awk +@@ -122,7 +122,7 @@ header { + } + + !header { +- sub (/\#.+/, ""); ++ sub (/#.+/, ""); + sub (/[ ]+$/, ""); # Strip trailing space and tab characters. + + if (/^$/) +diff --git a/src/Makefile.am b/src/Makefile.am +index ce1b882..f2590cb 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -293,7 +293,7 @@ code-from-errno.h: mkerrcodes$(EXEEXT_FOR_BUILD) Makefile + + errnos-sym.h: Makefile mkstrtable.awk errnos.in + $(AWK) -f $(srcdir)/mkstrtable.awk -v textidx=2 -v nogettext=1 \ +- -v prefix=GPG_ERR_ -v namespace=errnos_ \ ++ -v prefix=GPG_ERR_ -v pkg_namespace=errnos_ \ + $(srcdir)/errnos.in >$@ + + +diff --git a/src/mkerrcodes.awk b/src/mkerrcodes.awk +index 46d436c..e9c857c 100644 +--- a/src/mkerrcodes.awk ++++ b/src/mkerrcodes.awk +@@ -85,7 +85,7 @@ header { + } + + !header { +- sub (/\#.+/, ""); ++ sub (/#.+/, ""); + sub (/[ ]+$/, ""); # Strip trailing space and tab characters. + + if (/^$/) +diff --git a/src/mkerrcodes1.awk b/src/mkerrcodes1.awk +index a771a73..4578e29 100644 +--- a/src/mkerrcodes1.awk ++++ b/src/mkerrcodes1.awk +@@ -81,7 +81,7 @@ header { + } + + !header { +- sub (/\#.+/, ""); ++ sub (/#.+/, ""); + sub (/[ ]+$/, ""); # Strip trailing space and tab characters. + + if (/^$/) +diff --git a/src/mkerrcodes2.awk b/src/mkerrcodes2.awk +index ea58503..188f7a4 100644 +--- a/src/mkerrcodes2.awk ++++ b/src/mkerrcodes2.awk +@@ -91,7 +91,7 @@ header { + } + + !header { +- sub (/\#.+/, ""); ++ sub (/#.+/, ""); + sub (/[ ]+$/, ""); # Strip trailing space and tab characters. + + if (/^$/) +diff --git a/src/mkerrnos.awk b/src/mkerrnos.awk +index f79df66..15b1aad 100644 +--- a/src/mkerrnos.awk ++++ b/src/mkerrnos.awk +@@ -83,7 +83,7 @@ header { + } + + !header { +- sub (/\#.+/, ""); ++ sub (/#.+/, ""); + sub (/[ ]+$/, ""); # Strip trailing space and tab characters. + + if (/^$/) +diff --git a/src/mkstrtable.awk b/src/mkstrtable.awk +index c9de9c1..285e45f 100644 +--- a/src/mkstrtable.awk ++++ b/src/mkstrtable.awk +@@ -77,7 +77,7 @@ + # + # The variable prefix can be used to prepend a string to each message. + # +-# The variable namespace can be used to prepend a string to each ++# The variable pkg_namespace can be used to prepend a string to each + # variable and macro name. + + BEGIN { +@@ -102,7 +102,7 @@ header { + print "/* The purpose of this complex string table is to produce"; + print " optimal code with a minimum of relocations. */"; + print ""; +- print "static const char " namespace "msgstr[] = "; ++ print "static const char " pkg_namespace "msgstr[] = "; + header = 0; + } + else +@@ -110,7 +110,7 @@ header { + } + + !header { +- sub (/\#.+/, ""); ++ sub (/#.+/, ""); + sub (/[ ]+$/, ""); # Strip trailing space and tab characters. + + if (/^$/) +@@ -150,7 +150,7 @@ END { + else + print " gettext_noop (\"" last_msgstr "\");"; + print ""; +- print "static const int " namespace "msgidx[] ="; ++ print "static const int " pkg_namespace "msgidx[] ="; + print " {"; + for (i = 0; i < coded_msgs; i++) + print " " pos[i] ","; +@@ -158,7 +158,7 @@ END { + print " };"; + print ""; + print "static GPG_ERR_INLINE int"; +- print namespace "msgidxof (int code)"; ++ print pkg_namespace "msgidxof (int code)"; + print "{"; + print " return (0 ? 0"; + diff --git a/var/spack/repos/builtin/packages/libgpg-error/package.py b/var/spack/repos/builtin/packages/libgpg-error/package.py index 848f4760f4..6e61bf1403 100644 --- a/var/spack/repos/builtin/packages/libgpg-error/package.py +++ b/var/spack/repos/builtin/packages/libgpg-error/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,3 +19,7 @@ class LibgpgError(AutotoolsPackage): version('1.27', sha256='4f93aac6fecb7da2b92871bb9ee33032be6a87b174f54abf8ddf0911a22d29d2') version('1.21', sha256='b7dbdb3cad63a740e9f0c632a1da32d4afdb694ec86c8625c98ea0691713b84d') version('1.18', sha256='9ff1d6e61d4cef7c1d0607ceef6d40dc33f3da7a3094170c3718c00153d80810') + + depends_on('awk', type=('build')) + # Patch for using gawk@5, c.f. https://dev.gnupg.org/T4459 + patch('awk-5.patch', when='@1.36^gawk@5:') diff --git a/var/spack/repos/builtin/packages/libgpuarray/package.py b/var/spack/repos/builtin/packages/libgpuarray/package.py index 1f26b75628..edaebac7af 100644 --- a/var/spack/repos/builtin/packages/libgpuarray/package.py +++ b/var/spack/repos/builtin/packages/libgpuarray/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,4 +25,4 @@ class Libgpuarray(CMakePackage): depends_on('cuda') depends_on('cmake@3:', type='build') - depends_on('libcheck') + depends_on('check') diff --git a/var/spack/repos/builtin/packages/libgridxc/package.py b/var/spack/repos/builtin/packages/libgridxc/package.py index 3de369473e..96c7918d95 100644 --- a/var/spack/repos/builtin/packages/libgridxc/package.py +++ b/var/spack/repos/builtin/packages/libgridxc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libgtextutils/package.py b/var/spack/repos/builtin/packages/libgtextutils/package.py index 2d8fdb0c34..4c9820f5d2 100644 --- a/var/spack/repos/builtin/packages/libgtextutils/package.py +++ b/var/spack/repos/builtin/packages/libgtextutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libharu/package.py b/var/spack/repos/builtin/packages/libharu/package.py index e2ccc19902..dc308bb06f 100644 --- a/var/spack/repos/builtin/packages/libharu/package.py +++ b/var/spack/repos/builtin/packages/libharu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libhio/package.py b/var/spack/repos/builtin/packages/libhio/package.py index f06939398d..42ef377a5a 100644 --- a/var/spack/repos/builtin/packages/libhio/package.py +++ b/var/spack/repos/builtin/packages/libhio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -49,10 +49,6 @@ class Libhio(AutotoolsPackage): patch('0001-hdf5-make-docs-optional.patch', when="@1.4.1.0") patch('0001-spack-fix-for-spack-to-work-on-non-cray-systems.patch', when="@1.4.1.2") - def autoreconf(self, spec, prefix): - autoreconf = which('autoreconf') - autoreconf('-ifv') - def configure_args(self): spec = self.spec args = [] diff --git a/var/spack/repos/builtin/packages/libiberty/package.py b/var/spack/repos/builtin/packages/libiberty/package.py index cd4895db6d..fd3c6d6ea9 100644 --- a/var/spack/repos/builtin/packages/libiberty/package.py +++ b/var/spack/repos/builtin/packages/libiberty/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,13 +11,16 @@ from spack import * # is useful for other packages that want the demangling functions # without the rest of binutils. -class Libiberty(AutotoolsPackage): +class Libiberty(AutotoolsPackage, GNUMirrorPackage): """The libiberty.a library from GNU binutils. Libiberty provides demangling and support functions for the GNU toolchain.""" homepage = "https://www.gnu.org/software/binutils/" - url = "https://ftpmirror.gnu.org/binutils/binutils-2.31.1.tar.xz" + gnu_mirror_path = "binutils/binutils-2.31.1.tar.xz" + maintainers = ['mwkrentel'] + version('2.33.1', sha256='ab66fc2d1c3ec0359b8e08843c9f33b63e8707efdff5e4cc5c200eae24722cbf') + version('2.32', sha256='0ab6c55dd86a92ed561972ba15b9b70a8b9f75557f896446c82e8b36e473ee04') version('2.31.1', sha256='5d20086ecf5752cc7d9134246e9588fa201740d540f7eb84d795b1f7a93bca86') version('2.30', sha256='6e46b8aeae2f727a36f0bd9505e405768a72218f1796f0d09757d45209871ae6') version('2.29.1', sha256='e7010a46969f9d3e53b650a518663f98a5dde3c3ae21b7d71e5e6803bc36b577') diff --git a/var/spack/repos/builtin/packages/libibumad/package.py b/var/spack/repos/builtin/packages/libibumad/package.py index 4d5a683677..e401073519 100644 --- a/var/spack/repos/builtin/packages/libibumad/package.py +++ b/var/spack/repos/builtin/packages/libibumad/package.py @@ -1,5 +1,5 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libice/package.py b/var/spack/repos/builtin/packages/libice/package.py index 3f18de3153..2dedf163cb 100644 --- a/var/spack/repos/builtin/packages/libice/package.py +++ b/var/spack/repos/builtin/packages/libice/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libiconv/package.py b/var/spack/repos/builtin/packages/libiconv/package.py index a1e76e4894..642ad289fd 100644 --- a/var/spack/repos/builtin/packages/libiconv/package.py +++ b/var/spack/repos/builtin/packages/libiconv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Libiconv(AutotoolsPackage): +class Libiconv(AutotoolsPackage, GNUMirrorPackage): """GNU libiconv provides an implementation of the iconv() function and the iconv program for character set conversion.""" homepage = "https://www.gnu.org/software/libiconv/" - url = "https://ftpmirror.gnu.org/libiconv/libiconv-1.16.tar.gz" + gnu_mirror_path = "libiconv/libiconv-1.16.tar.gz" version('1.16', sha256='e6a1b1b589654277ee790cce3734f07876ac4ccfaecbee8afa0b649cf529cc04') version('1.15', sha256='ccf536620a45458d26ba83887a983b96827001e92a13847b45e4925cc8913178') diff --git a/var/spack/repos/builtin/packages/libid3tag/10_utf16.diff b/var/spack/repos/builtin/packages/libid3tag/10_utf16.diff new file mode 100644 index 0000000000..a3218d26d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/libid3tag/10_utf16.diff @@ -0,0 +1,48 @@ +#! /bin/sh -e +## 10_utf16.dpatch by <kurt@roeckx.be> +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: Handle bogus UTF16 sequences that have a length that is not +## DP: an even number of 8 bit characters. + +if [ $# -lt 1 ]; then + echo "`basename $0`: script expects -patch|-unpatch as argument" >&2 + exit 1 +fi + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch} ${2:+-d $2}" + +case "$1" in + -patch) patch -p1 ${patch_opts} < $0;; + -unpatch) patch -R -p1 ${patch_opts} < $0;; + *) + echo "`basename $0`: script expects -patch|-unpatch as argument" >&2 + exit 1;; +esac + +exit 0 + +@DPATCH@ +diff -urNad libid3tag-0.15.1b/utf16.c /tmp/dpep.tKvO7a/libid3tag-0.15.1b/utf16.c +--- libid3tag-0.15.1b/utf16.c 2006-01-13 15:26:29.000000000 +0100 ++++ /tmp/dpep.tKvO7a/libid3tag-0.15.1b/utf16.c 2006-01-13 15:27:19.000000000 +0100 +@@ -282,5 +282,18 @@ + + free(utf16); + ++ if (end == *ptr && length % 2 != 0) ++ { ++ /* We were called with a bogus length. It should always ++ * be an even number. We can deal with this in a few ways: ++ * - Always give an error. ++ * - Try and parse as much as we can and ++ * - return an error if we're called again when we ++ * already tried to parse everything we can. ++ * - tell that we parsed it, which is what we do here. ++ */ ++ (*ptr)++; ++ } ++ + return ucs4; + } diff --git a/var/spack/repos/builtin/packages/libid3tag/11_unknown_encoding.dif b/var/spack/repos/builtin/packages/libid3tag/11_unknown_encoding.dif new file mode 100644 index 0000000000..7387f2f7d4 --- /dev/null +++ b/var/spack/repos/builtin/packages/libid3tag/11_unknown_encoding.dif @@ -0,0 +1,37 @@ +#! /bin/sh /usr/share/dpatch/dpatch-run +## 11_unknown_encoding.dpatch by Andreas Henriksson <andreas@fatal.se> +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: In case of an unknown/invalid encoding, id3_parse_string() will +## DP: return NULL, but the return value wasn't checked resulting +## DP: in segfault in id3_ucs4_length(). This is the only place +## DP: the return value wasn't checked. + +@DPATCH@ +diff -urNad libid3tag-0.15.1b~/compat.gperf libid3tag-0.15.1b/compat.gperf +--- libid3tag-0.15.1b~/compat.gperf 2004-01-23 09:41:32.000000000 +0000 ++++ libid3tag-0.15.1b/compat.gperf 2007-01-14 14:36:53.000000000 +0000 +@@ -236,6 +236,10 @@ + + encoding = id3_parse_uint(&data, 1); + string = id3_parse_string(&data, end - data, encoding, 0); ++ if (!string) ++ { ++ continue; ++ } + + if (id3_ucs4_length(string) < 4) { + free(string); +diff -urNad libid3tag-0.15.1b~/parse.c libid3tag-0.15.1b/parse.c +--- libid3tag-0.15.1b~/parse.c 2004-01-23 09:41:32.000000000 +0000 ++++ libid3tag-0.15.1b/parse.c 2007-01-14 14:37:34.000000000 +0000 +@@ -165,6 +165,9 @@ + case ID3_FIELD_TEXTENCODING_UTF_8: + ucs4 = id3_utf8_deserialize(ptr, length); + break; ++ default: ++ /* FIXME: Unknown encoding! Print warning? */ ++ return NULL; + } + + if (ucs4 && !full) { diff --git a/var/spack/repos/builtin/packages/libid3tag/CVE-2008-2109.patch b/var/spack/repos/builtin/packages/libid3tag/CVE-2008-2109.patch new file mode 100644 index 0000000000..26c54c5d2c --- /dev/null +++ b/var/spack/repos/builtin/packages/libid3tag/CVE-2008-2109.patch @@ -0,0 +1,11 @@ +--- field.c.orig 2008-05-05 09:49:15.000000000 -0400 ++++ field.c 2008-05-05 09:49:25.000000000 -0400 +@@ -291,7 +291,7 @@ + + end = *ptr + length; + +- while (end - *ptr > 0) { ++ while (end - *ptr > 0 && **ptr != '\0') { + ucs4 = id3_parse_string(ptr, end - *ptr, *encoding, 0); + if (ucs4 == 0) + goto fail; diff --git a/var/spack/repos/builtin/packages/libid3tag/libid3tag-gperf.patch b/var/spack/repos/builtin/packages/libid3tag/libid3tag-gperf.patch new file mode 100644 index 0000000000..9dfad6c723 --- /dev/null +++ b/var/spack/repos/builtin/packages/libid3tag/libid3tag-gperf.patch @@ -0,0 +1,26 @@ +Index: libid3tag-0.15.1b/frametype.h +=================================================================== +--- libid3tag-0.15.1b.orig/frametype.h ++++ libid3tag-0.15.1b/frametype.h +@@ -37,6 +37,6 @@ extern struct id3_frametype const id3_fr + extern struct id3_frametype const id3_frametype_obsolete; + + struct id3_frametype const *id3_frametype_lookup(register char const *, +- register unsigned int); ++ register size_t); + + # endif +Index: libid3tag-0.15.1b/compat.h +=================================================================== +--- libid3tag-0.15.1b.orig/compat.h ++++ libid3tag-0.15.1b/compat.h +@@ -34,7 +34,7 @@ struct id3_compat { + }; + + struct id3_compat const *id3_compat_lookup(register char const *, +- register unsigned int); ++ register size_t); + + int id3_compat_fixup(struct id3_tag *); + + diff --git a/var/spack/repos/builtin/packages/libid3tag/package.py b/var/spack/repos/builtin/packages/libid3tag/package.py new file mode 100644 index 0000000000..6a9880b00c --- /dev/null +++ b/var/spack/repos/builtin/packages/libid3tag/package.py @@ -0,0 +1,39 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + +import os + + +class Libid3tag(AutotoolsPackage): + """library for id3 tagging""" + + homepage = "https://www.underbit.com/products/mad/" + url = "ftp://ftp.mars.org/pub/mpeg/libid3tag-0.15.1b.tar.gz" + + maintainers = ['TheQueasle'] + + version('0.15.1b', '63da4f6e7997278f8a3fef4c6a372d342f705051d1eeb6a46a86b03610e26151') + + depends_on('zlib') + depends_on('gperf') + + # source: https://git.archlinux.org/svntogit/packages.git/tree/trunk/10_utf16.diff?h=packages/libid3tag + patch('10_utf16.diff') + # source: https://git.archlinux.org/svntogit/packages.git/tree/trunk/11_unknown_encoding.diff?h=packages/libid3tag + patch('11_unknown_encoding.dif') + # source: https://git.archlinux.org/svntogit/packages.git/tree/trunk/CVE-2008-2109.patch?h=packages/libid3tag + patch('CVE-2008-2109.patch', level=0) + # source: https://git.archlinux.org/svntogit/packages.git/tree/trunk/libid3tag-gperf.patch?h=packages/libid3tag + patch('libid3tag-gperf.patch', when="^gperf@3.1:") + + @run_before('configure') + def preclean(self): + """ + Remove compat.c and frametype.c in order to regenerate from gperf + sources + """ + os.remove('compat.c') + os.remove('frametype.c') diff --git a/var/spack/repos/builtin/packages/libidn2/package.py b/var/spack/repos/builtin/packages/libidn2/package.py index f6bf213297..14986165e4 100644 --- a/var/spack/repos/builtin/packages/libidn2/package.py +++ b/var/spack/repos/builtin/packages/libidn2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libint/package.py b/var/spack/repos/builtin/packages/libint/package.py index d58e4fec1d..27fdc3b41d 100644 --- a/var/spack/repos/builtin/packages/libint/package.py +++ b/var/spack/repos/builtin/packages/libint/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -81,15 +81,15 @@ class Libint(AutotoolsPackage): return flags - def setup_environment(self, build_env, run_env): + def setup_build_environment(self, env): # Set optimization flags - build_env.set('CFLAGS', self.optflags) - build_env.set('CXXFLAGS', self.optflags) + env.set('CFLAGS', self.optflags) + env.set('CXXFLAGS', self.optflags) # Change AR to xiar if we compile with Intel and we # find the executable if '%intel' in self.spec and which('xiar'): - build_env.set('AR', 'xiar') + env.set('AR', 'xiar') def configure_args(self): diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py index 6c0f544380..10bddc37e0 100644 --- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py +++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libjpeg/package.py b/var/spack/repos/builtin/packages/libjpeg/package.py index c457bcb7ba..a4d52cca26 100644 --- a/var/spack/repos/builtin/packages/libjpeg/package.py +++ b/var/spack/repos/builtin/packages/libjpeg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libkml/package.py b/var/spack/repos/builtin/packages/libkml/package.py index acf3174728..c3e7d7619b 100644 --- a/var/spack/repos/builtin/packages/libkml/package.py +++ b/var/spack/repos/builtin/packages/libkml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libksba/package.py b/var/spack/repos/builtin/packages/libksba/package.py index 70da99d682..1d90c71502 100644 --- a/var/spack/repos/builtin/packages/libksba/package.py +++ b/var/spack/repos/builtin/packages/libksba/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/liblas/package.py b/var/spack/repos/builtin/packages/liblas/package.py index 380d27f710..efdd0b542f 100644 --- a/var/spack/repos/builtin/packages/liblas/package.py +++ b/var/spack/repos/builtin/packages/liblas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/liblbxutil/package.py b/var/spack/repos/builtin/packages/liblbxutil/package.py index 9b6d9f71c9..6a8f48dbfd 100644 --- a/var/spack/repos/builtin/packages/liblbxutil/package.py +++ b/var/spack/repos/builtin/packages/liblbxutil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/liblockfile/package.py b/var/spack/repos/builtin/packages/liblockfile/package.py index e25d335ef2..500b3c80eb 100644 --- a/var/spack/repos/builtin/packages/liblockfile/package.py +++ b/var/spack/repos/builtin/packages/liblockfile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libmad/package.py b/var/spack/repos/builtin/packages/libmad/package.py index 42fa7341b2..2af11c4f94 100644 --- a/var/spack/repos/builtin/packages/libmad/package.py +++ b/var/spack/repos/builtin/packages/libmad/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libmatheval/package.py b/var/spack/repos/builtin/packages/libmatheval/package.py index 5cfab6000d..b50c4906f7 100644 --- a/var/spack/repos/builtin/packages/libmatheval/package.py +++ b/var/spack/repos/builtin/packages/libmatheval/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Libmatheval(AutotoolsPackage): +class Libmatheval(AutotoolsPackage, GNUMirrorPackage): """GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. It supports expressions in any number of variables of arbitrary names, decimal and symbolic @@ -15,7 +15,7 @@ class Libmatheval(AutotoolsPackage): compute symbolic derivatives and output expressions to strings.""" homepage = "https://www.gnu.org/software/libmatheval/" - url = "https://ftpmirror.gnu.org/libmatheval/libmatheval-1.1.11.tar.gz" + gnu_mirror_path = "libmatheval/libmatheval-1.1.11.tar.gz" version('1.1.11', sha256='474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab') diff --git a/var/spack/repos/builtin/packages/libmaxminddb/package.py b/var/spack/repos/builtin/packages/libmaxminddb/package.py index 8c34e62281..db1590444a 100644 --- a/var/spack/repos/builtin/packages/libmaxminddb/package.py +++ b/var/spack/repos/builtin/packages/libmaxminddb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libmesh/package.py b/var/spack/repos/builtin/packages/libmesh/package.py index 0990d25a2f..541e98a0d4 100644 --- a/var/spack/repos/builtin/packages/libmesh/package.py +++ b/var/spack/repos/builtin/packages/libmesh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -245,5 +245,5 @@ class Libmesh(AutotoolsPackage): return options - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.append_flags('PERL', self.spec['perl'].command.path) + def setup_dependent_build_environment(self, env, dependent_spec): + env.append_flags('PERL', self.spec['perl'].command.path) diff --git a/var/spack/repos/builtin/packages/libmmtf-cpp/package.py b/var/spack/repos/builtin/packages/libmmtf-cpp/package.py new file mode 100644 index 0000000000..3b2f58882f --- /dev/null +++ b/var/spack/repos/builtin/packages/libmmtf-cpp/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class LibmmtfCpp(CMakePackage): + """The macromolecular transmission format (MMTF) is a binary encoding of + biological structures. This repository holds the C++-03 compatible API, + encoding and decoding libraries.""" + + homepage = "https://github.com/rcsb/mmtf-cpp" + url = "https://github.com/rcsb/mmtf-cpp/archive/v1.0.0.tar.gz" + + version('1.0.0', sha256='881f69c4bb56605fa63fd5ca50842facc4947f686cbf678ad04930674d714f40') + + depends_on('msgpack-c') diff --git a/var/spack/repos/builtin/packages/libmng/package.py b/var/spack/repos/builtin/packages/libmng/package.py index 6b35fd4449..29d70379bc 100644 --- a/var/spack/repos/builtin/packages/libmng/package.py +++ b/var/spack/repos/builtin/packages/libmng/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,16 +6,17 @@ from spack import * -class Libmng(AutotoolsPackage): - """libmng -THE reference library for reading, displaying, writing +class Libmng(CMakePackage): + """THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation - extension to the popular PNG image-format.""" + extension to the popular PNG image format.""" homepage = "http://sourceforge.net/projects/libmng/" url = "http://downloads.sourceforge.net/project/libmng/libmng-devel/2.0.3/libmng-2.0.3.tar.gz" version('2.0.3', sha256='cf112a1fb02f5b1c0fce5cab11ea8243852c139e669c44014125874b14b7dfaa') version('2.0.2', sha256='4908797bb3541fb5cd8fffbe0b1513ed163509f2a4d57a78b26a96f8d1dd05a2') + depends_on("gzip") depends_on("jpeg") depends_on("zlib") depends_on("lcms") @@ -25,11 +26,6 @@ class Libmng(AutotoolsPackage): filter_file(r'^(\#include \<jpeglib\.h\>)', '#include<stdio.h>\n\\1', 'libmng_types.h') - @run_before('configure') - def clean_configure_directory(self): - """Without this, configure crashes with: - - configure: error: source directory already configured; - run "make distclean" there first - """ - make('distclean') + def cmake_args(self): + return ['-DWITH_LCMS2:BOOL=ON', + '-DWITH_LCMS1:BOOL=OFF'] diff --git a/var/spack/repos/builtin/packages/libmo-unpack/package.py b/var/spack/repos/builtin/packages/libmo-unpack/package.py index af76b682cb..a188f95652 100644 --- a/var/spack/repos/builtin/packages/libmo-unpack/package.py +++ b/var/spack/repos/builtin/packages/libmo-unpack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libmonitor/package.py b/var/spack/repos/builtin/packages/libmonitor/package.py index d4a1a2d60b..49509fbe36 100644 --- a/var/spack/repos/builtin/packages/libmonitor/package.py +++ b/var/spack/repos/builtin/packages/libmonitor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libnbc/package.py b/var/spack/repos/builtin/packages/libnbc/package.py index 1f9f6183dd..b3c4795206 100644 --- a/var/spack/repos/builtin/packages/libnbc/package.py +++ b/var/spack/repos/builtin/packages/libnbc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libnl/package.py b/var/spack/repos/builtin/packages/libnl/package.py index bd4a9e4cdf..4a2c1daa73 100644 --- a/var/spack/repos/builtin/packages/libnl/package.py +++ b/var/spack/repos/builtin/packages/libnl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libnova/package.py b/var/spack/repos/builtin/packages/libnova/package.py index e28014c49c..179c7aa9d1 100644 --- a/var/spack/repos/builtin/packages/libnova/package.py +++ b/var/spack/repos/builtin/packages/libnova/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libnrm/package.py b/var/spack/repos/builtin/packages/libnrm/package.py index ad79170f9e..ea4d151f7e 100644 --- a/var/spack/repos/builtin/packages/libnrm/package.py +++ b/var/spack/repos/builtin/packages/libnrm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,5 +19,5 @@ class Libnrm(AutotoolsPackage): depends_on('automake', type='build') depends_on('libtool', type='build') - depends_on('zeromq') + depends_on('libzmq') depends_on('mpich') diff --git a/var/spack/repos/builtin/packages/libnsl/package.py b/var/spack/repos/builtin/packages/libnsl/package.py index 1a1f9ab837..8be6d48f71 100644 --- a/var/spack/repos/builtin/packages/libnsl/package.py +++ b/var/spack/repos/builtin/packages/libnsl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libogg/package.py b/var/spack/repos/builtin/packages/libogg/package.py index f4d463993b..71d0d90c98 100644 --- a/var/spack/repos/builtin/packages/libogg/package.py +++ b/var/spack/repos/builtin/packages/libogg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/liboldx/package.py b/var/spack/repos/builtin/packages/liboldx/package.py index a7b1a16941..264a8546d7 100644 --- a/var/spack/repos/builtin/packages/liboldx/package.py +++ b/var/spack/repos/builtin/packages/liboldx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libpaper/package.py b/var/spack/repos/builtin/packages/libpaper/package.py new file mode 100644 index 0000000000..ac474b7036 --- /dev/null +++ b/var/spack/repos/builtin/packages/libpaper/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Libpaper(AutotoolsPackage): + """The paper library and accompanying files are intended to provide a + simple way for applications to take actions based on a system- or + user-specified paper size.""" + + homepage = "https://packages.debian.org/unstable/source/libpaper" + url = "http://deb.debian.org/debian/pool/main/libp/libpaper/libpaper_1.1.28.tar.gz" + + version('1.1.28', sha256='c8bb946ec93d3c2c72bbb1d7257e90172a22a44a07a07fb6b802a5bb2c95fddc') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') diff --git a/var/spack/repos/builtin/packages/libpcap/package.py b/var/spack/repos/builtin/packages/libpcap/package.py index 37a5b1f7fd..6c7614b901 100644 --- a/var/spack/repos/builtin/packages/libpcap/package.py +++ b/var/spack/repos/builtin/packages/libpcap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libpciaccess/package.py b/var/spack/repos/builtin/packages/libpciaccess/package.py index 14ee76f0b9..874db15721 100644 --- a/var/spack/repos/builtin/packages/libpciaccess/package.py +++ b/var/spack/repos/builtin/packages/libpciaccess/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,3 +18,12 @@ class Libpciaccess(AutotoolsPackage): depends_on('libtool', type='build') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') + + # A known issue exists when building with PGI as documented here: + # https://bugs.freedesktop.org/show_bug.cgi?id=94398 + # https://www.pgroup.com/userforum/viewtopic.php?f=4&t=5126 + # https://gitlab.freedesktop.org/xorg/lib/libpciaccess/issues/7 + # + # When the ability to use dependencies built by another compiler, using a + # libpciaccess built by gcc should be usable by PGI builds. + conflicts('%pgi') diff --git a/var/spack/repos/builtin/packages/libpeas/package.py b/var/spack/repos/builtin/packages/libpeas/package.py index 01aef48f15..ef96d9d91f 100644 --- a/var/spack/repos/builtin/packages/libpeas/package.py +++ b/var/spack/repos/builtin/packages/libpeas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,7 +23,7 @@ class Libpeas(AutotoolsPackage): depends_on('automake', type='build') depends_on('libtool', type='build') depends_on('gettext', type='build') - depends_on('pkg-config', type='build') + depends_on('pkgconfig', type='build') depends_on('atk') depends_on('intltool@0.40.0:') depends_on('xmlto', type='build') @@ -44,11 +44,13 @@ class Libpeas(AutotoolsPackage): url += '{0}/libpeas-{1}.tar.xz' return url.format(version.up_to(2), version) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) - def setup_environment(self, spack_env, run_env): + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) + + def setup_build_environment(self, env): # Let # # python = self.spec['python'] @@ -76,10 +78,11 @@ class Libpeas(AutotoolsPackage): python_pc_file = os.path.join(python_prefix, 'python3.pc') python_ldflags = pkg_config('--libs', python_pc_file, output=str) - spack_env.append_path('LDFLAGS', - python_ldflags) - spack_env.prepend_path('XDG_DATA_DIRS', self.prefix.share) - run_env.prepend_path('XDG_DATA_DIRS', self.prefix.share) + env.append_path('LDFLAGS', python_ldflags) + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) + + def setup_run_environment(self, env): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) def autoreconf(self, spec, prefix): autoreconf_args = ['-ivf'] diff --git a/var/spack/repos/builtin/packages/libpfm4/package.py b/var/spack/repos/builtin/packages/libpfm4/package.py index a4ff0358e2..2d4028855e 100644 --- a/var/spack/repos/builtin/packages/libpfm4/package.py +++ b/var/spack/repos/builtin/packages/libpfm4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libpipeline/package.py b/var/spack/repos/builtin/packages/libpipeline/package.py index 35e90956fa..e5314da745 100644 --- a/var/spack/repos/builtin/packages/libpipeline/package.py +++ b/var/spack/repos/builtin/packages/libpipeline/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libplist/package.py b/var/spack/repos/builtin/packages/libplist/package.py index ea183f2020..8b102b66fd 100644 --- a/var/spack/repos/builtin/packages/libplist/package.py +++ b/var/spack/repos/builtin/packages/libplist/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libpmemobj-cpp/package.py b/var/spack/repos/builtin/packages/libpmemobj-cpp/package.py index 9800feb3d7..60ee417714 100644 --- a/var/spack/repos/builtin/packages/libpmemobj-cpp/package.py +++ b/var/spack/repos/builtin/packages/libpmemobj-cpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py index 1b699fff01..8d615ef890 100644 --- a/var/spack/repos/builtin/packages/libpng/package.py +++ b/var/spack/repos/builtin/packages/libpng/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libpsl/package.py b/var/spack/repos/builtin/packages/libpsl/package.py index a8c430a3dd..8deec5bd41 100644 --- a/var/spack/repos/builtin/packages/libpsl/package.py +++ b/var/spack/repos/builtin/packages/libpsl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libpthread-stubs/package.py b/var/spack/repos/builtin/packages/libpthread-stubs/package.py index 3bc0471622..528372f24a 100644 --- a/var/spack/repos/builtin/packages/libpthread-stubs/package.py +++ b/var/spack/repos/builtin/packages/libpthread-stubs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libquo/package.py b/var/spack/repos/builtin/packages/libquo/package.py index 770bf2329f..808eb4e0fe 100644 --- a/var/spack/repos/builtin/packages/libquo/package.py +++ b/var/spack/repos/builtin/packages/libquo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,10 +13,11 @@ class Libquo(AutotoolsPackage): single- and multi-threaded libraries.""" homepage = "https://github.com/lanl/libquo" - url = "http://lanl.github.io/libquo/dists/libquo-1.3.tar.gz" + url = "http://lanl.github.io/libquo/dists/libquo-1.3.1.tar.gz" git = "https://github.com/lanl/libquo.git" version('develop', branch='master') + version('1.3.1', sha256='407f7c61cc80aa934cf6086f3516a31dee3b803047713c297102452c3d7d6ed1') version('1.3', sha256='61b0beff15eae4be94b5d3cbcbf7bf757659604465709ed01827cbba45efcf90') version('1.2.9', sha256='0a64bea8f52f9eecd89e4ab82fde1c5bd271f3866c612da0ce7f38049409429b') diff --git a/var/spack/repos/builtin/packages/librom/package.py b/var/spack/repos/builtin/packages/librom/package.py index 14f7a8491c..9840e1dfc1 100644 --- a/var/spack/repos/builtin/packages/librom/package.py +++ b/var/spack/repos/builtin/packages/librom/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/librsb/package.py b/var/spack/repos/builtin/packages/librsb/package.py new file mode 100644 index 0000000000..90cc5b67a8 --- /dev/null +++ b/var/spack/repos/builtin/packages/librsb/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Librsb(AutotoolsPackage): + """librsb : A shared memory parallel sparse matrix computations + library for the Recursive Sparse Blocks format""" + + homepage = "http://librsb.sourceforge.net/" + url = "http://download.sourceforge.net/librsb/librsb-1.2.0.8.tar.gz" + list_url = "https://sourceforge.net/projects/librsb/files/" + + version('1.2.0.8', '8bebd19a1866d80ade13eabfdd0f07ae7e8a485c0b975b5d15f531ac204d80cb') + + depends_on('zlib') + conflicts('%clang') + + def configure_args(self): + args = [ + '--enable-openmp', + '--with-zlib', + '--enable-fortran-module-install', + 'CPPFLAGS={0}'.format(self.spec['zlib'].headers.include_flags), + 'CFLAGS=-O3', + 'LDFLAGS={0}'.format(self.spec['zlib'].libs.search_flags) + ] + return args diff --git a/var/spack/repos/builtin/packages/librsvg/package.py b/var/spack/repos/builtin/packages/librsvg/package.py index 99131420de..c35225540c 100644 --- a/var/spack/repos/builtin/packages/librsvg/package.py +++ b/var/spack/repos/builtin/packages/librsvg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,10 +30,14 @@ class Librsvg(AutotoolsPackage): url += "{0}/librsvg-{1}.tar.xz" return url.format(version.up_to(2), version) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) - def setup_environment(self, spack_env, run_env): - spack_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", self.prefix.share) + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) + + def setup_build_environment(self, env): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) + + def setup_run_environment(self, env): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) diff --git a/var/spack/repos/builtin/packages/libseccomp/package.py b/var/spack/repos/builtin/packages/libseccomp/package.py index e049be698d..e1c1374964 100644 --- a/var/spack/repos/builtin/packages/libseccomp/package.py +++ b/var/spack/repos/builtin/packages/libseccomp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libsecret/package.py b/var/spack/repos/builtin/packages/libsecret/package.py index d7ee09cfaa..8c41caf1c3 100644 --- a/var/spack/repos/builtin/packages/libsecret/package.py +++ b/var/spack/repos/builtin/packages/libsecret/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libsharp/package.py b/var/spack/repos/builtin/packages/libsharp/package.py index 332d2b0e5f..c78534c6c4 100644 --- a/var/spack/repos/builtin/packages/libsharp/package.py +++ b/var/spack/repos/builtin/packages/libsharp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libshm/package.py b/var/spack/repos/builtin/packages/libshm/package.py index 4f386beb10..9938493cc4 100644 --- a/var/spack/repos/builtin/packages/libshm/package.py +++ b/var/spack/repos/builtin/packages/libshm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libsigcpp/package.py b/var/spack/repos/builtin/packages/libsigcpp/package.py index 500fba16d2..bb62980d73 100644 --- a/var/spack/repos/builtin/packages/libsigcpp/package.py +++ b/var/spack/repos/builtin/packages/libsigcpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py index f8afacc8a3..7aab695b76 100644 --- a/var/spack/repos/builtin/packages/libsigsegv/package.py +++ b/var/spack/repos/builtin/packages/libsigsegv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,11 @@ from spack import * -class Libsigsegv(AutotoolsPackage): +class Libsigsegv(AutotoolsPackage, GNUMirrorPackage): """GNU libsigsegv is a library for handling page faults in user mode.""" homepage = "https://www.gnu.org/software/libsigsegv/" - url = "https://ftpmirror.gnu.org/libsigsegv/libsigsegv-2.12.tar.gz" + gnu_mirror_path = "libsigsegv/libsigsegv-2.12.tar.gz" version('2.12', sha256='3ae1af359eebaa4ffc5896a1aee3568c052c99879316a1ab57f8fe1789c390b6') version('2.11', sha256='dd7c2eb2ef6c47189406d562c1dc0f96f2fc808036834d596075d58377e37a18') diff --git a/var/spack/repos/builtin/packages/libsm/package.py b/var/spack/repos/builtin/packages/libsm/package.py index 7ab37b7e51..3856c526c7 100644 --- a/var/spack/repos/builtin/packages/libsm/package.py +++ b/var/spack/repos/builtin/packages/libsm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libsodium/package.py b/var/spack/repos/builtin/packages/libsodium/package.py index 5f5d283223..b14e633ed2 100644 --- a/var/spack/repos/builtin/packages/libsodium/package.py +++ b/var/spack/repos/builtin/packages/libsodium/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libspatialindex/package.py b/var/spack/repos/builtin/packages/libspatialindex/package.py index 110f6d52e3..8ffd6d4cf5 100644 --- a/var/spack/repos/builtin/packages/libspatialindex/package.py +++ b/var/spack/repos/builtin/packages/libspatialindex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libspatialite/package.py b/var/spack/repos/builtin/packages/libspatialite/package.py index abf40719fa..e725fdfe0f 100644 --- a/var/spack/repos/builtin/packages/libspatialite/package.py +++ b/var/spack/repos/builtin/packages/libspatialite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ class Libspatialite(AutotoolsPackage): version('4.3.0a', sha256='88900030a4762904a7880273f292e5e8ca6b15b7c6c3fb88ffa9e67ee8a5a499') version('3.0.1', sha256='4983d6584069fd5ff0cfcccccee1015088dab2db177c0dc7050ce8306b68f8e6') - depends_on('pkg-config', type='build') + depends_on('pkgconfig', type='build') depends_on('sqlite+rtree') depends_on('proj@:5') depends_on('geos') diff --git a/var/spack/repos/builtin/packages/libsplash/package.py b/var/spack/repos/builtin/packages/libsplash/package.py index 1db0534b0a..c45deeae40 100644 --- a/var/spack/repos/builtin/packages/libsplash/package.py +++ b/var/spack/repos/builtin/packages/libsplash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libssh/package.py b/var/spack/repos/builtin/packages/libssh/package.py index 597b528975..c56d545cf3 100644 --- a/var/spack/repos/builtin/packages/libssh/package.py +++ b/var/spack/repos/builtin/packages/libssh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libssh2/package.py b/var/spack/repos/builtin/packages/libssh2/package.py index 9f198d3cf6..3cada3de90 100644 --- a/var/spack/repos/builtin/packages/libssh2/package.py +++ b/var/spack/repos/builtin/packages/libssh2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libsvm/package.py b/var/spack/repos/builtin/packages/libsvm/package.py index ee49566e9f..bb9a651a71 100644 --- a/var/spack/repos/builtin/packages/libsvm/package.py +++ b/var/spack/repos/builtin/packages/libsvm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libszip/package.py b/var/spack/repos/builtin/packages/libszip/package.py index 2c9bcc639a..00a2b9b5bc 100644 --- a/var/spack/repos/builtin/packages/libszip/package.py +++ b/var/spack/repos/builtin/packages/libszip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libtasn1/package.py b/var/spack/repos/builtin/packages/libtasn1/package.py index fb0e711b8d..97324b8394 100644 --- a/var/spack/repos/builtin/packages/libtasn1/package.py +++ b/var/spack/repos/builtin/packages/libtasn1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libtermkey/package.py b/var/spack/repos/builtin/packages/libtermkey/package.py index 173edc8f11..90617e7014 100644 --- a/var/spack/repos/builtin/packages/libtermkey/package.py +++ b/var/spack/repos/builtin/packages/libtermkey/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libtiff/package.py b/var/spack/repos/builtin/packages/libtiff/package.py index f24cd86844..06f3d43da4 100644 --- a/var/spack/repos/builtin/packages/libtiff/package.py +++ b/var/spack/repos/builtin/packages/libtiff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libtirpc/package.py b/var/spack/repos/builtin/packages/libtirpc/package.py index eb56c34627..e6ce06e0ea 100644 --- a/var/spack/repos/builtin/packages/libtirpc/package.py +++ b/var/spack/repos/builtin/packages/libtirpc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libtomlc99/package.py b/var/spack/repos/builtin/packages/libtomlc99/package.py index bc7459fba7..dde282be28 100644 --- a/var/spack/repos/builtin/packages/libtomlc99/package.py +++ b/var/spack/repos/builtin/packages/libtomlc99/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py index bbad95e573..decc4b114e 100644 --- a/var/spack/repos/builtin/packages/libtool/package.py +++ b/var/spack/repos/builtin/packages/libtool/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,11 @@ from spack import * -class Libtool(AutotoolsPackage): +class Libtool(AutotoolsPackage, GNUMirrorPackage): """libtool -- library building part of autotools.""" homepage = 'https://www.gnu.org/software/libtool/' - url = 'https://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz' + gnu_mirror_path = "libtool/libtool-2.4.2.tar.gz" version('develop', git='https://git.savannah.gnu.org/git/libtool.git', branch='master', submodules=True) @@ -37,9 +37,8 @@ class Libtool(AutotoolsPackage): def _make_executable(self, name): return Executable(join_path(self.prefix.bin, name)) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.append_path('ACLOCAL_PATH', - join_path(self.prefix.share, 'aclocal')) + def setup_dependent_build_environment(self, env, dependent_spec): + env.append_path('ACLOCAL_PATH', self.prefix.share.aclocal) def setup_dependent_package(self, module, dependent_spec): # Automake is very likely to be a build dependency, so we add diff --git a/var/spack/repos/builtin/packages/libunistring/package.py b/var/spack/repos/builtin/packages/libunistring/package.py index 86f03a10a6..94b1c24b98 100644 --- a/var/spack/repos/builtin/packages/libunistring/package.py +++ b/var/spack/repos/builtin/packages/libunistring/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Libunistring(AutotoolsPackage): +class Libunistring(AutotoolsPackage, GNUMirrorPackage): """This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.""" homepage = "https://www.gnu.org/software/libunistring/" - url = "https://ftpmirror.gnu.org/libunistring/libunistring-0.9.10.tar.xz" + gnu_mirror_path = "libunistring/libunistring-0.9.10.tar.xz" version('0.9.10', sha256='eb8fb2c3e4b6e2d336608377050892b54c3c983b646c561836550863003c05d7') version('0.9.9', sha256='a4d993ecfce16cf503ff7579f5da64619cee66226fb3b998dafb706190d9a833') diff --git a/var/spack/repos/builtin/packages/libunwind/package.py b/var/spack/repos/builtin/packages/libunwind/package.py index e729b7c20d..727cac44bb 100644 --- a/var/spack/repos/builtin/packages/libunwind/package.py +++ b/var/spack/repos/builtin/packages/libunwind/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libusb/package.py b/var/spack/repos/builtin/packages/libusb/package.py index 51bd4dc780..ee5612c9db 100644 --- a/var/spack/repos/builtin/packages/libusb/package.py +++ b/var/spack/repos/builtin/packages/libusb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libusbmuxd/package.py b/var/spack/repos/builtin/packages/libusbmuxd/package.py index 0de782c204..999636b785 100644 --- a/var/spack/repos/builtin/packages/libusbmuxd/package.py +++ b/var/spack/repos/builtin/packages/libusbmuxd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libuuid/package.py b/var/spack/repos/builtin/packages/libuuid/package.py index 140cd7f93f..3ec15ceb6b 100644 --- a/var/spack/repos/builtin/packages/libuuid/package.py +++ b/var/spack/repos/builtin/packages/libuuid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py index 57662913e5..55d7dcebba 100644 --- a/var/spack/repos/builtin/packages/libuv/package.py +++ b/var/spack/repos/builtin/packages/libuv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libvdwxc/package.py b/var/spack/repos/builtin/packages/libvdwxc/package.py index cec8e06002..786561ce42 100644 --- a/var/spack/repos/builtin/packages/libvdwxc/package.py +++ b/var/spack/repos/builtin/packages/libvdwxc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libvorbis/package.py b/var/spack/repos/builtin/packages/libvorbis/package.py index 6f6de52b46..372a93efef 100644 --- a/var/spack/repos/builtin/packages/libvorbis/package.py +++ b/var/spack/repos/builtin/packages/libvorbis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libvterm/package.py b/var/spack/repos/builtin/packages/libvterm/package.py index 95c5b819ed..a3ca1ced15 100644 --- a/var/spack/repos/builtin/packages/libvterm/package.py +++ b/var/spack/repos/builtin/packages/libvterm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libwebp/package.py b/var/spack/repos/builtin/packages/libwebp/package.py index f07620be51..9c5f56a804 100644 --- a/var/spack/repos/builtin/packages/libwebp/package.py +++ b/var/spack/repos/builtin/packages/libwebp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,14 +6,56 @@ from spack import * -class Libwebp(CMakePackage): - """ - WebP is a modern image format that provides superior lossless and lossy +class Libwebp(AutotoolsPackage): + """WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web - developers can create smaller, richer images that make the web faster. - """ + developers can create smaller, richer images that make the web faster.""" homepage = "https://developers.google.com/speed/webp/" - url = "https://github.com/webmproject/libwebp/archive/v1.0.3.tar.gz" + url = "https://storage.googleapis.com/downloads.webmproject.org/releases/webp/libwebp-1.0.3.tar.gz" - version('1.0.3', sha256='082d114bcb18a0e2aafc3148d43367c39304f86bf18ba0b2e766447e111a4a91') + version('1.0.3', sha256='082d114bcb18a0e2aafc3148d43367c39304f86bf18ba0b2e766447e111a4a91') + + variant('libwebpmux', default=False, description='Build libwebpmux') + variant('libwebpdemux', default=False, description='Build libwebpdemux') + variant('libwebpdecoder', default=False, description='Build libwebpdecoder') + variant('libwebpextras', default=False, description='Build libwebpextras') + + depends_on('automake', type='build') + depends_on('autoconf', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + + def configure_args(self): + # TODO: add variants and dependencies for these + args = [ + '--disable-gl', + '--disable-sdl', + '--disable-png', + '--disable-jpeg', + '--disable-tiff', + '--disable-gif', + '--disable-wic', + ] + + if '+libwebpmux' in self.spec: + args.append('--enable-libwebpmux') + else: + args.append('--disable-libwebpmux') + + if '+libwebpdemux' in self.spec: + args.append('--enable-libwebpdemux') + else: + args.append('--disable-libwebpdemux') + + if '+libwebpdecoder' in self.spec: + args.append('--enable-libwebpdecoder') + else: + args.append('--disable-libwebpdecoder') + + if '+libwebpextras' in self.spec: + args.append('--enable-libwebpextras') + else: + args.append('--disable-libwebpextras') + + return args diff --git a/var/spack/repos/builtin/packages/libwebsockets/package.py b/var/spack/repos/builtin/packages/libwebsockets/package.py index b49aea6f03..a00f841a7c 100644 --- a/var/spack/repos/builtin/packages/libwebsockets/package.py +++ b/var/spack/repos/builtin/packages/libwebsockets/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libwindowswm/package.py b/var/spack/repos/builtin/packages/libwindowswm/package.py index 3d38b28095..543cdad3ec 100644 --- a/var/spack/repos/builtin/packages/libwindowswm/package.py +++ b/var/spack/repos/builtin/packages/libwindowswm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libx11/package.py b/var/spack/repos/builtin/packages/libx11/package.py index 5c1a7f21f3..0668ba7fad 100644 --- a/var/spack/repos/builtin/packages/libx11/package.py +++ b/var/spack/repos/builtin/packages/libx11/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,9 +27,11 @@ class Libx11(AutotoolsPackage): depends_on('util-macros', type='build') depends_on('perl', type='build') - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path('XLOCALEDIR', self.prefix.share.X11.locale) - run_env.prepend_path('XLOCALEDIR', self.prefix.share.X11.locale) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path('XLOCALEDIR', self.prefix.share.X11.locale) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path('XLOCALEDIR', self.prefix.share.X11.locale) @property def libs(self): diff --git a/var/spack/repos/builtin/packages/libxau/package.py b/var/spack/repos/builtin/packages/libxau/package.py index a9ffe42930..72650a35aa 100644 --- a/var/spack/repos/builtin/packages/libxau/package.py +++ b/var/spack/repos/builtin/packages/libxau/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxaw/package.py b/var/spack/repos/builtin/packages/libxaw/package.py index 068e9ec795..9a6dc204c1 100644 --- a/var/spack/repos/builtin/packages/libxaw/package.py +++ b/var/spack/repos/builtin/packages/libxaw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxaw3d/package.py b/var/spack/repos/builtin/packages/libxaw3d/package.py index 61bba5ca6d..2d3e028e93 100644 --- a/var/spack/repos/builtin/packages/libxaw3d/package.py +++ b/var/spack/repos/builtin/packages/libxaw3d/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxc/configure_add_fj.patch b/var/spack/repos/builtin/packages/libxc/configure_add_fj.patch deleted file mode 100644 index e5c2b36ea0..0000000000 --- a/var/spack/repos/builtin/packages/libxc/configure_add_fj.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- libxc-4.3.2/configure 2019-02-08 17:40:50.000000000 +0900 -+++ libxc-4.3.2/configure_b 2019-07-25 14:48:51.825394300 +0900 -@@ -14405,6 +14405,18 @@ - lt_prog_compiler_pic_FC='-qpic' - lt_prog_compiler_static_FC='-qstaticlink' - ;; -+ fcc* | FCC* ) -+ # Fujitsu C/C++ compiler -+ lt_prog_compiler_wl_FC='-Wl,' -+ lt_prog_compiler_pic_FC='-KPIC' -+ lt_prog_compiler_static_FC='-Bstatic' -+ ;; -+ frt* ) -+ # Fujitsu Fortran compiler -+ lt_prog_compiler_wl_FC='-Wl,' -+ lt_prog_compiler_pic_FC='-KPIC' -+ lt_prog_compiler_static_FC='-Kstatic_fjlib' -+ ;; - *) - case `$CC -V 2>&1 | sed 5q` in - *Sun\ Ceres\ Fortran* | *Sun*Fortran*\ [1-7].* | *Sun*Fortran*\ 8.[0-3]*) diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py index 82bac01673..6803488e48 100644 --- a/var/spack/repos/builtin/packages/libxc/package.py +++ b/var/spack/repos/builtin/packages/libxc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,8 +10,8 @@ class Libxc(AutotoolsPackage): """Libxc is a library of exchange-correlation functionals for density-functional theory.""" - homepage = "http://www.tddft.org/programs/octopus/wiki/index.php/Libxc" - url = "http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz" + homepage = "https://tddft.org/programs/libxc/" + url = "https://www.tddft.org/programs/libxc/down.php?file=2.2.2/libxc-2.2.2.tar.gz" version('4.3.2', sha256='bc159aea2537521998c7fb1199789e1be71e04c4b7758d58282622e347603a6f') version('4.2.3', sha256='02e49e9ba7d21d18df17e9e57eae861e6ce05e65e966e1e832475aa09e344256') @@ -19,18 +19,6 @@ class Libxc(AutotoolsPackage): version('2.2.2', sha256='6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642') version('2.2.1', sha256='ade61c1fa4ed238edd56408fd8ee6c2e305a3d5753e160017e2a71817c98fd00') - patch('configure_add_fj.patch') - - def url_for_version(self, version): - if version < Version('3.0.0'): - return ("http://www.tddft.org/programs/octopus/" - "down.php?file=libxc/libxc-{0}.tar.gz" - .format(version)) - - return ("http://www.tddft.org/programs/octopus/" - "down.php?file=libxc/{0}/libxc-{0}.tar.gz" - .format(version)) - @property def libs(self): """Libxc can be queried for the following parameters: @@ -61,7 +49,7 @@ class Libxc(AutotoolsPackage): libraries, root=self.prefix, shared=shared, recursive=True ) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): optflags = '-O2' if self.compiler.name == 'intel': # Optimizations for the Intel compiler, suggested by CP2K @@ -88,10 +76,10 @@ class Libxc(AutotoolsPackage): # optflags += ' -xSSE4.2 -axAVX,CORE-AVX2 -ipo' if which('xiar'): - spack_env.set('AR', 'xiar') + env.set('AR', 'xiar') - spack_env.append_flags('CFLAGS', optflags) - spack_env.append_flags('FCFLAGS', optflags) + env.append_flags('CFLAGS', optflags) + env.append_flags('FCFLAGS', optflags) def configure_args(self): args = ['--enable-shared'] diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py index b1e4eea2a6..4116b6a059 100644 --- a/var/spack/repos/builtin/packages/libxcb/package.py +++ b/var/spack/repos/builtin/packages/libxcb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxcomposite/package.py b/var/spack/repos/builtin/packages/libxcomposite/package.py index b9ce5083db..0f990ca424 100644 --- a/var/spack/repos/builtin/packages/libxcomposite/package.py +++ b/var/spack/repos/builtin/packages/libxcomposite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxcursor/package.py b/var/spack/repos/builtin/packages/libxcursor/package.py index 6b906ad051..6ff52d9e1d 100644 --- a/var/spack/repos/builtin/packages/libxcursor/package.py +++ b/var/spack/repos/builtin/packages/libxcursor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxdamage/package.py b/var/spack/repos/builtin/packages/libxdamage/package.py index fedfee9efb..dd722cb70a 100644 --- a/var/spack/repos/builtin/packages/libxdamage/package.py +++ b/var/spack/repos/builtin/packages/libxdamage/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxdmcp/package.py b/var/spack/repos/builtin/packages/libxdmcp/package.py index bf9a0c8993..0a6af544fc 100644 --- a/var/spack/repos/builtin/packages/libxdmcp/package.py +++ b/var/spack/repos/builtin/packages/libxdmcp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxevie/package.py b/var/spack/repos/builtin/packages/libxevie/package.py index c8e86f558a..4fc3187a1f 100644 --- a/var/spack/repos/builtin/packages/libxevie/package.py +++ b/var/spack/repos/builtin/packages/libxevie/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxext/package.py b/var/spack/repos/builtin/packages/libxext/package.py index 03986f088e..73f1ce77de 100644 --- a/var/spack/repos/builtin/packages/libxext/package.py +++ b/var/spack/repos/builtin/packages/libxext/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxfixes/package.py b/var/spack/repos/builtin/packages/libxfixes/package.py index 93671b41e8..84b4caad8f 100644 --- a/var/spack/repos/builtin/packages/libxfixes/package.py +++ b/var/spack/repos/builtin/packages/libxfixes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxfont/package.py b/var/spack/repos/builtin/packages/libxfont/package.py index 0a3c9e4882..561371d523 100644 --- a/var/spack/repos/builtin/packages/libxfont/package.py +++ b/var/spack/repos/builtin/packages/libxfont/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxfont2/package.py b/var/spack/repos/builtin/packages/libxfont2/package.py index 4678212baa..7c2de91db4 100644 --- a/var/spack/repos/builtin/packages/libxfont2/package.py +++ b/var/spack/repos/builtin/packages/libxfont2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxfontcache/package.py b/var/spack/repos/builtin/packages/libxfontcache/package.py index 1d8c14d900..f764df19b1 100644 --- a/var/spack/repos/builtin/packages/libxfontcache/package.py +++ b/var/spack/repos/builtin/packages/libxfontcache/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxft/package.py b/var/spack/repos/builtin/packages/libxft/package.py index 9ab8687de5..144450e2ba 100644 --- a/var/spack/repos/builtin/packages/libxft/package.py +++ b/var/spack/repos/builtin/packages/libxft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxi/package.py b/var/spack/repos/builtin/packages/libxi/package.py index 037a0e36a2..e1cbac1433 100644 --- a/var/spack/repos/builtin/packages/libxi/package.py +++ b/var/spack/repos/builtin/packages/libxi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxinerama/package.py b/var/spack/repos/builtin/packages/libxinerama/package.py index bfc12e8136..374b151d17 100644 --- a/var/spack/repos/builtin/packages/libxinerama/package.py +++ b/var/spack/repos/builtin/packages/libxinerama/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxkbcommon/package.py b/var/spack/repos/builtin/packages/libxkbcommon/package.py index 4756f450ea..657d3b4dae 100644 --- a/var/spack/repos/builtin/packages/libxkbcommon/package.py +++ b/var/spack/repos/builtin/packages/libxkbcommon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxkbfile/package.py b/var/spack/repos/builtin/packages/libxkbfile/package.py index a91198e05a..ac28aeb1b4 100644 --- a/var/spack/repos/builtin/packages/libxkbfile/package.py +++ b/var/spack/repos/builtin/packages/libxkbfile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxkbui/package.py b/var/spack/repos/builtin/packages/libxkbui/package.py index 7fd81908a0..3e0c734425 100644 --- a/var/spack/repos/builtin/packages/libxkbui/package.py +++ b/var/spack/repos/builtin/packages/libxkbui/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py index b7a6381f30..8c91852ae3 100644 --- a/var/spack/repos/builtin/packages/libxml2/package.py +++ b/var/spack/repos/builtin/packages/libxml2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,14 +27,15 @@ class Libxml2(AutotoolsPackage): depends_on('zlib') depends_on('xz') - depends_on('python+shared', when='+python') + # avoid cycle dependency for concretizer + depends_on('python+shared~libxml2', when='+python') extends('python', when='+python', ignore=r'(bin.*$)|(include.*$)|(share.*$)|(lib/libxml2.*$)|' '(lib/xml2.*$)|(lib/cmake.*$)') # XML Conformance Test Suites # See http://www.w3.org/XML/Test/ for information - resource(name='xmlts', url='http://www.w3.org/XML/Test/xmlts20080827.tar.gz', + resource(name='xmlts', url='https://www.w3.org/XML/Test/xmlts20080827.tar.gz', sha256='96151685cec997e1f9f3387e3626d61e6284d4d6e66e0e440c209286c03e9cc7') @property diff --git a/var/spack/repos/builtin/packages/libxmu/package.py b/var/spack/repos/builtin/packages/libxmu/package.py index cf825ec74a..9f7904404d 100644 --- a/var/spack/repos/builtin/packages/libxmu/package.py +++ b/var/spack/repos/builtin/packages/libxmu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxp/package.py b/var/spack/repos/builtin/packages/libxp/package.py index 7a4d194a95..ff590a14cf 100644 --- a/var/spack/repos/builtin/packages/libxp/package.py +++ b/var/spack/repos/builtin/packages/libxp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxpm/package.py b/var/spack/repos/builtin/packages/libxpm/package.py index 542052d4dd..0e73980d19 100644 --- a/var/spack/repos/builtin/packages/libxpm/package.py +++ b/var/spack/repos/builtin/packages/libxpm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,10 +26,10 @@ class Libxpm(AutotoolsPackage): depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # If libxpm is installed as an external package, gettext won't # be available in the spec. See # https://github.com/spack/spack/issues/9149 for details. if 'gettext' in self.spec: - spack_env.append_flags('LDFLAGS', '-L{0} -lintl'.format( + env.append_flags('LDFLAGS', '-L{0} -lintl'.format( self.spec['gettext'].prefix.lib)) diff --git a/var/spack/repos/builtin/packages/libxpresent/package.py b/var/spack/repos/builtin/packages/libxpresent/package.py index 0acfcd44de..0fddba389a 100644 --- a/var/spack/repos/builtin/packages/libxpresent/package.py +++ b/var/spack/repos/builtin/packages/libxpresent/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxprintapputil/package.py b/var/spack/repos/builtin/packages/libxprintapputil/package.py index 5d145ee024..888861bca9 100644 --- a/var/spack/repos/builtin/packages/libxprintapputil/package.py +++ b/var/spack/repos/builtin/packages/libxprintapputil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxprintutil/package.py b/var/spack/repos/builtin/packages/libxprintutil/package.py index 2f13cc0964..5e28a23109 100644 --- a/var/spack/repos/builtin/packages/libxprintutil/package.py +++ b/var/spack/repos/builtin/packages/libxprintutil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxrandr/package.py b/var/spack/repos/builtin/packages/libxrandr/package.py index 85fdb0ab94..bb49275643 100644 --- a/var/spack/repos/builtin/packages/libxrandr/package.py +++ b/var/spack/repos/builtin/packages/libxrandr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxrender/package.py b/var/spack/repos/builtin/packages/libxrender/package.py index db2da986c6..d5284fa222 100644 --- a/var/spack/repos/builtin/packages/libxrender/package.py +++ b/var/spack/repos/builtin/packages/libxrender/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxres/package.py b/var/spack/repos/builtin/packages/libxres/package.py index d90d81b615..73690b53b3 100644 --- a/var/spack/repos/builtin/packages/libxres/package.py +++ b/var/spack/repos/builtin/packages/libxres/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxscrnsaver/package.py b/var/spack/repos/builtin/packages/libxscrnsaver/package.py index 176b0186d8..c8a659b872 100644 --- a/var/spack/repos/builtin/packages/libxscrnsaver/package.py +++ b/var/spack/repos/builtin/packages/libxscrnsaver/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxshmfence/package.py b/var/spack/repos/builtin/packages/libxshmfence/package.py index a81380ac29..df437baf14 100644 --- a/var/spack/repos/builtin/packages/libxshmfence/package.py +++ b/var/spack/repos/builtin/packages/libxshmfence/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxslt/package.py b/var/spack/repos/builtin/packages/libxslt/package.py index e68fab7e55..7cdb0e41b2 100644 --- a/var/spack/repos/builtin/packages/libxslt/package.py +++ b/var/spack/repos/builtin/packages/libxslt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py index fd0c78afd9..070b24396f 100644 --- a/var/spack/repos/builtin/packages/libxsmm/package.py +++ b/var/spack/repos/builtin/packages/libxsmm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxstream/package.py b/var/spack/repos/builtin/packages/libxstream/package.py index 7ab9e5e674..af28a10736 100644 --- a/var/spack/repos/builtin/packages/libxstream/package.py +++ b/var/spack/repos/builtin/packages/libxstream/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxt/package.py b/var/spack/repos/builtin/packages/libxt/package.py index 88d579c608..2cb198b7f5 100644 --- a/var/spack/repos/builtin/packages/libxt/package.py +++ b/var/spack/repos/builtin/packages/libxt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxtrap/package.py b/var/spack/repos/builtin/packages/libxtrap/package.py index 320b674d91..efb44c34eb 100644 --- a/var/spack/repos/builtin/packages/libxtrap/package.py +++ b/var/spack/repos/builtin/packages/libxtrap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxtst/package.py b/var/spack/repos/builtin/packages/libxtst/package.py index 6ba8cc824f..e2f82f909a 100644 --- a/var/spack/repos/builtin/packages/libxtst/package.py +++ b/var/spack/repos/builtin/packages/libxtst/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxv/package.py b/var/spack/repos/builtin/packages/libxv/package.py index b0d5209b8b..da2a97713a 100644 --- a/var/spack/repos/builtin/packages/libxv/package.py +++ b/var/spack/repos/builtin/packages/libxv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxvmc/package.py b/var/spack/repos/builtin/packages/libxvmc/package.py index 4d2fa16704..7987677f8f 100644 --- a/var/spack/repos/builtin/packages/libxvmc/package.py +++ b/var/spack/repos/builtin/packages/libxvmc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxxf86dga/package.py b/var/spack/repos/builtin/packages/libxxf86dga/package.py index 6160033167..8a6645d729 100644 --- a/var/spack/repos/builtin/packages/libxxf86dga/package.py +++ b/var/spack/repos/builtin/packages/libxxf86dga/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxxf86misc/package.py b/var/spack/repos/builtin/packages/libxxf86misc/package.py index 64ccd738ec..5c22536c0e 100644 --- a/var/spack/repos/builtin/packages/libxxf86misc/package.py +++ b/var/spack/repos/builtin/packages/libxxf86misc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libxxf86vm/package.py b/var/spack/repos/builtin/packages/libxxf86vm/package.py index 1a332f3153..b13234b768 100644 --- a/var/spack/repos/builtin/packages/libxxf86vm/package.py +++ b/var/spack/repos/builtin/packages/libxxf86vm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libyaml/package.py b/var/spack/repos/builtin/packages/libyaml/package.py index 4289751cc1..d795b2f8a6 100644 --- a/var/spack/repos/builtin/packages/libyaml/package.py +++ b/var/spack/repos/builtin/packages/libyaml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libyogrt/package.py b/var/spack/repos/builtin/packages/libyogrt/package.py index c7445c0499..3590193516 100644 --- a/var/spack/repos/builtin/packages/libyogrt/package.py +++ b/var/spack/repos/builtin/packages/libyogrt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libzip/package.py b/var/spack/repos/builtin/packages/libzip/package.py index 16a9bf3976..b218d18e59 100644 --- a/var/spack/repos/builtin/packages/libzip/package.py +++ b/var/spack/repos/builtin/packages/libzip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/zeromq/package.py b/var/spack/repos/builtin/packages/libzmq/package.py index 7612bf5695..6dce35c18a 100644 --- a/var/spack/repos/builtin/packages/zeromq/package.py +++ b/var/spack/repos/builtin/packages/libzmq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Zeromq(AutotoolsPackage): +class Libzmq(AutotoolsPackage): """The ZMQ networking/concurrency library and core API""" homepage = "http://zguide.zeromq.org/" diff --git a/var/spack/repos/builtin/packages/liggghts/package.py b/var/spack/repos/builtin/packages/liggghts/package.py index 324439c05f..54fab4a056 100644 --- a/var/spack/repos/builtin/packages/liggghts/package.py +++ b/var/spack/repos/builtin/packages/liggghts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lighttpd/package.py b/var/spack/repos/builtin/packages/lighttpd/package.py index d2b384ff00..70e3a7a8b8 100644 --- a/var/spack/repos/builtin/packages/lighttpd/package.py +++ b/var/spack/repos/builtin/packages/lighttpd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,11 @@ class Lighttpd(CMakePackage): homepage = "https://www.lighttpd.net" url = "https://download.lighttpd.net/lighttpd/releases-1.4.x/lighttpd-1.4.50.tar.gz" + version('1.4.55', sha256='065259fb618774df516add13df22a52cac76a8f59e4561f143fe3ec810f4a03a') + version('1.4.54', sha256='5151d38cb7c4c40effa13710e77ebdbef899f945b062cf32befc02d128ac424c') + version('1.4.53', sha256='423b3951f212e3a30511eb86f4662a1848c6e857074289ff23fc310eef520266') + version('1.4.52', sha256='0f9de0227681c078f6b8c6154b581ced5fe7bcb5ff428ccf292581764b771145') + version('1.4.51', sha256='4301fe64136c7030d63cccc96996c6603dcbe82cca9a72e0aca29ce88284c978') version('1.4.50', sha256='c9a9f175aca6db22ebebbc47de52c54a99bbd1dce8d61bb75103609a3d798235') version('1.4.49', sha256='8b744baf9f29c386fff1a6d2e435491e726cb8d29cfdb1fe20ab782ee2fc2ac7') diff --git a/var/spack/repos/builtin/packages/likwid/package.py b/var/spack/repos/builtin/packages/likwid/package.py index 411a6f8fe6..c24d5e720a 100644 --- a/var/spack/repos/builtin/packages/likwid/package.py +++ b/var/spack/repos/builtin/packages/likwid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,8 +17,10 @@ class Likwid(Package): for information.""" homepage = "https://github.com/RRZE-HPC/likwid" - url = "https://github.com/RRZE-HPC/likwid/archive/4.1.2.tar.gz" + url = "https://github.com/RRZE-HPC/likwid/archive/v5.0.0.tar.gz" + git = "https://github.com/RRZE-HPC/likwid.git" + version('5.0.0', sha256='26623f5a1a5fec19d798f0114774a5293d1c93a148538b9591a13e50930fa41e') version('4.3.4', sha256='5c0d1c66b25dac8292a02232f06454067f031a238f010c62f40ef913c6609a83') version('4.3.3', sha256='a681378cd66c1679ca840fb5fac3136bfec93c01b3d78cc1d00a641db325a9a3') version('4.3.2', sha256='fd39529854b8952e7530da1684835aa43ac6ce2169f5ebd1fb2a481f6fb288ac') diff --git a/var/spack/repos/builtin/packages/linkphase3/package.py b/var/spack/repos/builtin/packages/linkphase3/package.py index 285afdccf9..417518bc18 100644 --- a/var/spack/repos/builtin/packages/linkphase3/package.py +++ b/var/spack/repos/builtin/packages/linkphase3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/linux-headers/package.py b/var/spack/repos/builtin/packages/linux-headers/package.py index 6b0133dd75..8e33f63471 100644 --- a/var/spack/repos/builtin/packages/linux-headers/package.py +++ b/var/spack/repos/builtin/packages/linux-headers/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,11 +16,11 @@ class LinuxHeaders(Package): version('4.9.10', sha256='bd6e05476fd8d9ea4945e11598d87bc97806bbc8d03556abbaaf809707661525') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # This variable is used in the Makefile. If it is defined on the # system, it can break the build if there is no build recipe for # that specific ARCH - spack_env.unset('ARCH') + env.unset('ARCH') def install(self, spec, prefix): make('headers_install', 'INSTALL_HDR_PATH={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/listres/package.py b/var/spack/repos/builtin/packages/listres/package.py index 25742deaab..3adbe696a3 100644 --- a/var/spack/repos/builtin/packages/listres/package.py +++ b/var/spack/repos/builtin/packages/listres/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lizard/fix-install-decompress.patch b/var/spack/repos/builtin/packages/lizard/fix-install-decompress.patch new file mode 100644 index 0000000000..d5a8242a23 --- /dev/null +++ b/var/spack/repos/builtin/packages/lizard/fix-install-decompress.patch @@ -0,0 +1,76 @@ +From 02c35c25e565a090ec6b49fbc6210f6593519b44 Mon Sep 17 00:00:00 2001 +From: Przemyslaw Skibinski <przemyslaw.skibinski@percona.com> +Date: Fri, 25 Oct 2019 10:03:39 +0200 +Subject: [PATCH] Fix missing `lizard_decompress.h` after `make install`. + +--- + lib/Makefile | 2 ++ + lib/lizard_common.h | 7 +++++++ + lib/lizard_decompress.h | 9 +-------- + 3 files changed, 10 insertions(+), 8 deletions(-) + +diff --git a/lib/Makefile b/lib/Makefile +index 64c07dd..9484056 100644 +--- a/lib/Makefile ++++ b/lib/Makefile +@@ -143,6 +143,7 @@ endif + @ln -sf liblizard.$(SHARED_EXT_VER) $(DESTDIR)$(LIBDIR)/liblizard.$(SHARED_EXT) + @echo Installing includes + @$(INSTALL_DATA) lizard_compress.h $(DESTDIR)$(INCLUDEDIR)/lizard_compress.h ++ @$(INSTALL_DATA) lizard_decompress.h $(DESTDIR)$(INCLUDEDIR)/lizard_decompress.h + @$(INSTALL_DATA) lizard_common.h $(DESTDIR)$(INCLUDEDIR)/lizard_common.h + @$(INSTALL_DATA) lizard_frame.h $(DESTDIR)$(INCLUDEDIR)/lizard_frame.h + @echo lizard static and shared libraries installed +@@ -154,6 +155,7 @@ uninstall: + @$(RM) $(DESTDIR)$(LIBDIR)/liblizard.$(SHARED_EXT_VER) + @$(RM) $(DESTDIR)$(LIBDIR)/liblizard.a + @$(RM) $(DESTDIR)$(INCLUDEDIR)/lizard_compress.h ++ @$(RM) $(DESTDIR)$(INCLUDEDIR)/lizard_decompress.h + @$(RM) $(DESTDIR)$(INCLUDEDIR)/lizard_common.h + @$(RM) $(DESTDIR)$(INCLUDEDIR)/lizard_frame.h + @echo lizard libraries successfully uninstalled +diff --git a/lib/lizard_common.h b/lib/lizard_common.h +index 1677abb..45730cf 100644 +--- a/lib/lizard_common.h ++++ b/lib/lizard_common.h +@@ -192,6 +192,13 @@ struct Lizard_stream_s + const BYTE* destBase; + }; + ++struct Lizard_streamDecode_s { ++ const BYTE* externalDict; ++ size_t extDictSize; ++ const BYTE* prefixEnd; ++ size_t prefixSize; ++}; ++ + struct Lizard_dstream_s + { + const BYTE* offset16Ptr; +diff --git a/lib/lizard_decompress.h b/lib/lizard_decompress.h +index 5453b4d..ad9fc8e 100644 +--- a/lib/lizard_decompress.h ++++ b/lib/lizard_decompress.h +@@ -39,8 +39,6 @@ + extern "C" { + #endif + +-#include "entropy/mem.h" /* U32 */ +- + + /*^*************************************************************** + * Export parameters +@@ -95,12 +93,7 @@ LIZARDDLIB_API int Lizard_decompress_safe_partial (const char* source, char* des + /*-********************************************** + * Streaming Decompression Functions + ************************************************/ +-typedef struct { +- const BYTE* externalDict; +- size_t extDictSize; +- const BYTE* prefixEnd; +- size_t prefixSize; +-} Lizard_streamDecode_t; ++typedef struct Lizard_streamDecode_s Lizard_streamDecode_t; + + /* + * Lizard_streamDecode_t diff --git a/var/spack/repos/builtin/packages/lizard/package.py b/var/spack/repos/builtin/packages/lizard/package.py new file mode 100644 index 0000000000..d0b165e750 --- /dev/null +++ b/var/spack/repos/builtin/packages/lizard/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Lizard(MakefilePackage): + """Lizard (formerly LZ5) is an efficient compressor with very + fast decompression. It achieves compression ratio that is + comparable to zip/zlib and zstd/brotli (at low and medium + compression levels) at decompression speed of 1000 MB/s and + faster.""" + + homepage = "https://github.com/inikep/lizard" + url = "https://github.com/inikep/lizard/archive/v1.0.tar.gz" + git = "https://github.com/inikep/lizard.git" + + version('develop', branch='lizard') + version('1.0', + sha256='6f666ed699fc15dc7fdaabfaa55787b40ac251681b50c0d8df017c671a9457e6') + + patch('fix-install-decompress.patch', when='@1.0') + + def install(self, spec, prefix): + make("PREFIX=%s" % prefix, "install") diff --git a/var/spack/repos/builtin/packages/llvm-flang/package.py b/var/spack/repos/builtin/packages/llvm-flang/package.py new file mode 100644 index 0000000000..4c19e7b54b --- /dev/null +++ b/var/spack/repos/builtin/packages/llvm-flang/package.py @@ -0,0 +1,168 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class LlvmFlang(CMakePackage): + """LLVM-Flang is the Flang fork of LLVM needed by the Flang package.""" + + homepage = "https://github.com/flang-compiler" + + git = "https://github.com/flang-compiler/llvm.git" + + maintainer = ['naromero77'] + + version('master', branch='master') + version('release_70', branch='release_70') + version('release_60', branch='release_60') + version('20190329', tag='flang_20190329') + version('20181226_70', tag='20181226_70') + version('20181226_60', tag='20181226_60') + version('20180921', tag='20180921') + version('20180319', tag='20180319') + version('20180328', tag='20180308') + + # Variants + variant('all_targets', default=False, + description='Build all supported targets') + + # Build dependency + depends_on('cmake@3.8:', type='build') + depends_on('python@2.7:', type='build') + + # LLVM-Flang Componentes: Driver, OpenMP + resource(name='flang-driver', + git='https://github.com/flang-compiler/flang-driver.git', + branch='master', + destination='tools', + placement='clang', + when='@master') + + resource(name='flang-driver', + git='https://github.com/flang-compiler/flang-driver.git', + branch='release_70', + destination='tools', + placement='clang', + when='@release_70') + + resource(name='flang-driver', + git='https://github.com/flang-compiler/flang-driver.git', + branch='release_60', + destination='tools', + placement='clang', + when='@release_60') + + resource(name='flang-driver', + git='https://github.com/flang-compiler/flang-driver.git', + tag='flang_20190329', + destination='tools', + placement='clang', + when='@20190329') + + resource(name='flang-driver', + git='https://github.com/flang-compiler/flang-driver.git', + tag='flang_20181226_70', + destination='tools', + placement='clang', + when='@20181226_70') + + resource(name='flang-driver', + git='https://github.com/flang-compiler/flang-driver.git', + tag='flang_20181226_60', + destination='tools', + placement='clang', + when='@20181226_60') + + resource(name='flang-driver', + git='https://github.com/flang-compiler/flang-driver.git', + tag='flang_20180921', + destination='tools', + placement='clang', + when='@20180921') + + resource(name='flang-driver', + git='https://github.com/flang-compiler/flang-driver.git', + tag='flang_20180921', + destination='tools', + placement='clang', + when='@20180308') + + resource(name='openmp', + git='https://github.com/flang-compiler/openmp.git', + branch='master', + destination='projects', + placement='openmp', + when='@master') + + resource(name='openmp', + git='https://github.com/flang-compiler/openmp.git', + branch='release_70', + destination='projects', + placement='openmp', + when='@release_70') + + resource(name='openmp', + git='https://github.com/flang-compiler/openmp.git', + branch='release_60', + destination='projects', + placement='openmp', + when='@release_60') + + resource(name='openmp', + git='https://github.com/flang-compiler/openmp.git', + tag='flang_20190329', + destination='projects', + placement='openmp', + when='@20190329') + + resource(name='openmp', + git='https://github.com/flang-compiler/openmp.git', + tag='flang_20181226_70', + destination='projects', + placement='openmp', + when='@20181226_70') + + resource(name='openmp', + git='https://github.com/flang-compiler/openmp.git', + tag='flang_20181226_60', + destination='projects', + placement='openmp', + when='@20181226_60') + + resource(name='openmp', + git='https://github.com/flang-compiler/openmp.git', + tag='flang_20180921', + destination='projects', + placement='openmp', + when='@20180921') + + def cmake_args(self): + spec = self.spec + args = [] + args.append('-DPYTHON_EXECUTABLE={0}'.format( + spec['python'].command.path)) + + if '+all_targets' not in spec: # all is default in cmake + if spec.target.family == 'x86' or spec.target.family == 'x86_64': + target = 'X86' + elif spec.target.family == 'arm': + target = 'ARM' + elif spec.target.family == 'aarch64': + target = 'AArch64' + elif (spec.target.family == 'ppc64' or + spec.target.family == 'ppc64le' or + spec.target.family == 'ppc' or + spec.target.family == 'ppcle'): + target = 'PowerPC' + else: + raise InstallError( + 'Unsupported architecture: ' + spec.target.family) + + args.append( + '-DLLVM_TARGETS_TO_BUILD:STRING=' + target) + + return args diff --git a/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py b/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py index 3969da869d..40babc8243 100644 --- a/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py +++ b/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/llvm-openmp/package.py b/var/spack/repos/builtin/packages/llvm-openmp/package.py index 356b0c93f5..166b0c7a6e 100644 --- a/var/spack/repos/builtin/packages/llvm-openmp/package.py +++ b/var/spack/repos/builtin/packages/llvm-openmp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/llvm/constexpr_longdouble.patch b/var/spack/repos/builtin/packages/llvm/constexpr_longdouble.patch index 337b068d4b..f825b14210 100644 --- a/var/spack/repos/builtin/packages/llvm/constexpr_longdouble.patch +++ b/var/spack/repos/builtin/packages/llvm/constexpr_longdouble.patch @@ -1,5 +1,5 @@ ---- a/projects/libcxx/include/thread -+++ b/projects/libcxx/include/thread +--- a/libcxx/include/thread ++++ b/libcxx/include/thread @@ -435,7 +435,12 @@ sleep_for(const chrono::duration<_Rep, _Period>& __d) using namespace chrono; if (__d > duration<_Rep, _Period>::zero()) diff --git a/var/spack/repos/builtin/packages/llvm/constexpr_longdouble_9.0.patch b/var/spack/repos/builtin/packages/llvm/constexpr_longdouble_9.0.patch new file mode 100644 index 0000000000..bbc5ab7385 --- /dev/null +++ b/var/spack/repos/builtin/packages/llvm/constexpr_longdouble_9.0.patch @@ -0,0 +1,12 @@ +-- a/libcxx/include/thread ++++ b/libcxx/include/thread +@@ -370,7 +370,7 @@ sleep_for(const chrono::duration<_Rep, _Period>& __d) + using namespace chrono; + if (__d > duration<_Rep, _Period>::zero()) + { +-#if defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__) ++#if ! (defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__)) + // GCC's long double const folding is incomplete for IBM128 long doubles. + _LIBCPP_CONSTEXPR duration<long double> _Max = nanoseconds::max(); + #else + diff --git a/var/spack/repos/builtin/packages/llvm/llvm_gcc7.patch b/var/spack/repos/builtin/packages/llvm/llvm_gcc7.patch index e3bb8a14ad..c6d9d33a08 100644 --- a/var/spack/repos/builtin/packages/llvm/llvm_gcc7.patch +++ b/var/spack/repos/builtin/packages/llvm/llvm_gcc7.patch @@ -1,5 +1,5 @@ ---- a/tools/lldb/include/lldb/Utility/TaskPool.h 2016-09-06 16:57:50.000000000 -0400 -+++ b/tools/lldb/include/lldb/Utility/TaskPool.h 2017-08-29 16:29:41.448584015 -0400 +--- a/lldb/include/lldb/Utility/TaskPool.h 2016-09-06 16:57:50.000000000 -0400 ++++ b/lldb/include/lldb/Utility/TaskPool.h 2017-08-29 16:29:41.448584015 -0400 @@ -28,6 +28,7 @@ #include <cassert> diff --git a/var/spack/repos/builtin/packages/llvm/llvm_py37.patch b/var/spack/repos/builtin/packages/llvm/llvm_py37.patch new file mode 100644 index 0000000000..478be87994 --- /dev/null +++ b/var/spack/repos/builtin/packages/llvm/llvm_py37.patch @@ -0,0 +1,37 @@ +From ecdefed7f6ba11421fe1ecc6c13a135ab7bcda73 Mon Sep 17 00:00:00 2001 +From: Pavel Labath <labath@google.com> +Date: Mon, 23 Jul 2018 11:37:36 +0100 +Subject: [PATCH] Fix PythonString::GetString for >=python-3.7 + +The return value of PyUnicode_AsUTF8AndSize is now "const char *". +--- + .../Plugins/ScriptInterpreter/Python/PythonDataObjects.cpp | 6 ++++-- + 1 file changed, 4 insertions(+), 2 deletions(-) + +diff --git a/tools/lldb/source/Plugins/ScriptInterpreter/Python/PythonDataObjects.cpp b/tools/lldb/source/Plugins/ScriptInterpreter/Python/PythonDataObjects.cpp +index 6a9d57d5a..94f16b2c7 100644 +--- a/lldb/source/Plugins/ScriptInterpreter/Python/PythonDataObjects.cpp ++++ b/lldb/source/Plugins/ScriptInterpreter/Python/PythonDataObjects.cpp +@@ -404,14 +404,16 @@ llvm::StringRef PythonString::GetString() const { + return llvm::StringRef(); + + Py_ssize_t size; +- char *c; ++ const char *data; + + #if PY_MAJOR_VERSION >= 3 +- c = PyUnicode_AsUTF8AndSize(m_py_obj, &size); ++ data = PyUnicode_AsUTF8AndSize(m_py_obj, &size); + #else ++ char *c; + PyString_AsStringAndSize(m_py_obj, &c, &size); ++ data = c; + #endif +- return llvm::StringRef(c, size); ++ return llvm::StringRef(data, size); + } + + size_t PythonString::GetSize() const { +-- +2.18.0.233.g985f88cf7e-goog + diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index b79798eb53..05e9404592 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,14 +15,33 @@ class Llvm(CMakePackage): """ homepage = 'http://llvm.org/' - url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz' + url = "https://github.com/llvm/llvm-project/archive/llvmorg-7.1.0.tar.gz" list_url = 'http://releases.llvm.org/download.html' + git = 'https://github.com/llvm/llvm-project' family = 'compiler' # Used by lmod - # currently required by mesa package - version('3.0', sha256='519eb11d3499ce99c6ffdb8718651fc91425ed7690eac91c8d6853474f7c0477', - url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') + version('master', branch='master') + version('9.0.1', sha256='be7b034641a5fda51ffca7f5d840b1a768737779f75f7c4fd18fe2d37820289a') + version('9.0.0', sha256='7807fac25330e24e9955ca46cd855dd34bbc9cc4fdba8322366206654d1036f2') + version('8.0.0', sha256='d81238b4a69e93e29f74ce56f8107cbfcf0c7d7b40510b7879e98cc031e25167') + version('7.1.0', sha256='71c93979f20e01f1a1cc839a247945f556fa5e63abf2084e8468b238080fd839') + version('7.0.1', sha256='f17a6cd401e8fd8f811fbfbb36dcb4f455f898c9d03af4044807ad005df9f3c0') + version('6.0.1', sha256='aefadceb231f4c195fe6d6cd3b1a010b269c8a22410f339b5a089c2e902aa177') + version('6.0.0', sha256='1946ec629c88d30122afa072d3c6a89cc5d5e4e2bb28dc63b2f9ebcc7917ee64') + version('5.0.2', sha256='fe87aa11558c08856739bfd9bd971263a28657663cb0c3a0af01b94f03b0b795') + version('5.0.1', sha256='84ca454abf262579814a2a2b846569f6e0cb3e16dc33ca3642b4f1dff6fbafd3') + version('5.0.0', sha256='1f1843315657a4371d8ca37f01265fa9aae17dbcf46d2d0a95c1fdb3c6a4bab6') + version('4.0.1', sha256='cd664fb3eec3208c08fb61189c00c9118c290b3be5adb3215a97b24255618be5') + version('4.0.0', sha256='28ca4b2fc434cb1f558e8865386c233c2a6134437249b8b3765ae745ffa56a34') + version('3.9.1', sha256='f5b6922a5c65f9232f83d89831191f2c3ccf4f41fdd8c63e6645bbf578c4ab92') + version('3.9.0', sha256='9c6563a72c8b5b79941c773937d997dd2b1b5b3f640136d02719ec19f35e0333') + version('3.8.1', sha256='69360f0648fde0dc3d3c4b339624613f3bc2a89c4858933bc3871a250ad02826') + version('3.8.0', sha256='b5cc5974cc2fd4e9e49e1bbd0700f872501a8678bd9694fa2b36c65c026df1d1') + version('3.7.1', sha256='d2cb0eb9b8eb21e07605bfe5e7a5c6c5f5f8c2efdac01ec1da6ffacaabe4195a') + version('3.7.0', sha256='dc00bc230be2006fb87b84f6fe4800ca28bc98e6692811a98195da53c9cb28c6') + version('3.6.2', sha256='f75d703a388ba01d607f9cf96180863a5e4a106827ade17b221d43e6db20778a') + version('3.5.1', sha256='5d739684170d5b2b304e4fb521532d5c8281492f71e1a8568187bfa38eb5909d') # NOTE: The debug version of LLVM is an order of magnitude larger than # the release version, and may take up 20-30 GB of space. If you want @@ -69,6 +88,7 @@ class Llvm(CMakePackage): variant('omp_tsan', default=False, description="Build with OpenMP capable thread sanitizer") variant('python', default=False, description="Install python bindings") + extends('python', when='+python') # Build dependency @@ -83,8 +103,10 @@ class Llvm(CMakePackage): # openmp dependencies depends_on('perl-data-dumper', type=('build')) + # ncurses dependency + depends_on('ncurses+termlib') + # lldb dependencies - depends_on('ncurses', when='+lldb') depends_on('swig', when='+lldb') depends_on('libedit', when='+lldb') depends_on('py-six', when='@5.0.0: +lldb +python') @@ -96,499 +118,11 @@ class Llvm(CMakePackage): depends_on('gmp', when='@:3.6.999 +polly') depends_on('isl', when='@:3.6.999 +polly') - base_url = 'http://llvm.org/releases/%%(version)s/%(pkg)s-%%(version)s.src.tar.xz' - llvm_url = base_url % {'pkg': 'llvm'} - # Flang uses its own fork of llvm. - flang_llvm_url = 'https://github.com/flang-compiler/llvm.git' - - resources = { - 'compiler-rt': { - 'url': base_url % {'pkg': 'compiler-rt'}, - 'destination': 'projects', - 'placement': 'compiler-rt', - 'variant': '+compiler-rt', - }, - 'openmp': { - 'url': base_url % {'pkg': 'openmp'}, - 'destination': 'projects', - 'placement': 'openmp', - 'variant': '+clang', - }, - 'libcxx': { - 'url': base_url % {'pkg': 'libcxx'}, - 'destination': 'projects', - 'placement': 'libcxx', - 'variant': '+libcxx', - }, - 'libcxxabi': { - 'url': base_url % {'pkg': 'libcxxabi'}, - 'destination': 'projects', - 'placement': 'libcxxabi', - 'variant': '+libcxx', - }, - 'cfe': { - 'url': base_url % {'pkg': 'cfe'}, - 'destination': 'tools', - 'placement': 'clang', - 'variant': '+clang', - }, - 'clang-tools-extra': { - 'url': base_url % {'pkg': 'clang-tools-extra'}, - 'destination': 'tools/clang/tools', - 'placement': 'extra', - 'variant': '+clang', - }, - 'lldb': { - 'url': base_url % {'pkg': 'lldb'}, - 'destination': 'tools', - 'placement': 'lldb', - 'variant': '+lldb', - }, - 'lld': { - 'url': base_url % {'pkg': 'lld'}, - 'destination': 'tools', - 'placement': 'lld', - 'variant': '+lld', - }, - 'polly': { - 'url': base_url % {'pkg': 'polly'}, - 'destination': 'tools', - 'placement': 'polly', - 'variant': '+polly', - }, - 'libunwind': { - 'url': base_url % {'pkg': 'libunwind'}, - 'destination': 'projects', - 'placement': 'libunwind', - 'variant': '+internal_unwind', - }, - } - releases = [ - { - 'version': 'develop', - 'repo': 'http://llvm.org/svn/llvm-project/llvm/trunk', - 'resources': { - 'compiler-rt': 'http://llvm.org/svn/llvm-project/compiler-rt/trunk', - 'openmp': 'http://llvm.org/svn/llvm-project/openmp/trunk', - 'polly': 'http://llvm.org/svn/llvm-project/polly/trunk', - 'libcxx': 'http://llvm.org/svn/llvm-project/libcxx/trunk', - 'libcxxabi': 'http://llvm.org/svn/llvm-project/libcxxabi/trunk', - 'cfe': 'http://llvm.org/svn/llvm-project/cfe/trunk', - 'clang-tools-extra': 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk', - 'lldb': 'http://llvm.org/svn/llvm-project/lldb/trunk', - 'lld': 'http://llvm.org/svn/llvm-project/lld/trunk', - 'libunwind': 'http://llvm.org/svn/llvm-project/libunwind/trunk', - } - }, - { - 'version': '9.0.0', - 'sha256': 'd6a0565cf21f22e9b4353b2eb92622e8365000a9e90a16b09b56f8157eabfe84', - 'resources': { - 'compiler-rt': '56e4cd96dd1d8c346b07b4d6b255f976570c6f2389697347a6c3dcb9e820d10e', - 'openmp': '9979eb1133066376cc0be29d1682bc0b0e7fb541075b391061679111ae4d3b5b', - 'polly': 'a4fa92283de725399323d07f18995911158c1c5838703f37862db815f513d433', - 'libcxx': '3c4162972b5d3204ba47ac384aa456855a17b5e97422723d4758251acf1ed28c', - 'libcxxabi': '675041783565c906ac2f7f8b2bc5c40f14d871ecfa8ade34855aa18de95530e9', - 'cfe': '7ba81eef7c22ca5da688fdf9d88c20934d2d6b40bfe150ffd338900890aa4610', - 'clang-tools-extra': 'ea1c86ce352992d7b6f6649bc622f6a2707b9f8b7153e9f9181a35c76aa3ac10', - 'lldb': '1e4c2f6a1f153f4b8afa2470d2e99dab493034c1ba8b7ffbbd7600de016d0794', - 'lld': '31c6748b235d09723fb73fea0c816ed5a3fab0f96b66f8fbc546a0fcc8688f91', - 'libunwind': '976a8d09e1424fb843210eecec00a506b956e6c31adda3b0d199e945be0d0db2' - } - }, - { - 'version': '8.0.0', - 'sha256': '8872be1b12c61450cacc82b3d153eab02be2546ef34fa3580ed14137bb26224c', - 'resources': { - 'compiler-rt': 'b435c7474f459e71b2831f1a4e3f1d21203cb9c0172e94e9d9b69f50354f21b1', - 'openmp': 'f7b1705d2f16c4fc23d6531f67d2dd6fb78a077dd346b02fed64f4b8df65c9d5', - 'polly': 'e3f5a3d6794ef8233af302c45ceb464b74cdc369c1ac735b6b381b21e4d89df4', - 'libcxx': 'c2902675e7c84324fb2c1e45489220f250ede016cc3117186785d9dc291f9de2', - 'libcxxabi': 'c2d6de9629f7c072ac20ada776374e9e3168142f20a46cdb9d6df973922b07cd', - 'cfe': '084c115aab0084e63b23eee8c233abb6739c399e29966eaeccfc6e088e0b736b', - 'clang-tools-extra': '4f00122be408a7482f2004bcf215720d2b88cf8dc78b824abb225da8ad359d4b', - 'lldb': '49918b9f09816554a20ac44c5f85a32dc0a7a00759b3259e78064d674eac0373', - 'lld': '9caec8ec922e32ffa130f0fb08e4c5a242d7e68ce757631e425e9eba2e1a6e37', - 'libunwind': 'ff243a669c9cef2e2537e4f697d6fb47764ea91949016f2d643cb5d8286df660' - } - }, - { - 'version': '7.0.1', - 'sha256': 'a38dfc4db47102ec79dcc2aa61e93722c5f6f06f0a961073bd84b78fb949419b', - 'resources': { - 'compiler-rt': '782edfc119ee172f169c91dd79f2c964fb6b248bd9b73523149030ed505bbe18', - 'openmp': 'bf16b78a678da67d68405214ec7ee59d86a15f599855806192a75dcfca9b0d0c', - 'polly': '1bf146842a09336b9c88d2d76c2d117484e5fad78786821718653d1a9d57fb71', - 'libcxx': '020002618b319dc2a8ba1f2cba88b8cc6a209005ed8ad29f9de0c562c6ebb9f1', - 'libcxxabi': '8168903a157ca7ab8423d3b974eaa497230b1564ceb57260be2bd14412e8ded8', - 'cfe': 'a45b62dde5d7d5fdcdfa876b0af92f164d434b06e9e89b5d0b1cbc65dfe3f418', - 'clang-tools-extra': '4c93c7d2bb07923a8b272da3ef7914438080aeb693725f4fc5c19cd0e2613bed', - 'lldb': '76b46be75b412a3d22f0d26279306ae7e274fe4d7988a2184c529c38a6a76982', - 'lld': '8869aab2dd2d8e00d69943352d3166d159d7eae2615f66a684f4a0999fc74031', - 'libunwind': '89c852991dfd9279dbca9d5ac10b53c67ad7d0f54bbab7156e9f057a978b5912' - } - }, - { - 'version': '7.0.0', - 'sha256': '8bc1f844e6cbde1b652c19c1edebc1864456fd9c78b8c1bea038e51b363fe222', - 'resources': { - 'compiler-rt': 'bdec7fe3cf2c85f55656c07dfb0bd93ae46f2b3dd8f33ff3ad6e7586f4c670d6', - 'openmp': '30662b632f5556c59ee9215c1309f61de50b3ea8e89dcc28ba9a9494bba238ff', - 'polly': '919810d3249f4ae79d084746b9527367df18412f30fe039addbf941861c8534b', - 'libcxx': '9b342625ba2f4e65b52764ab2061e116c0337db2179c6bce7f9a0d70c52134f0', - 'libcxxabi': '9b45c759ff397512eae4d938ff82827b1bd7ccba49920777e5b5e460baeb245f', - 'cfe': '550212711c752697d2f82c648714a7221b1207fd9441543ff4aa9e3be45bba55', - 'clang-tools-extra': '937c5a8c8c43bc185e4805144744799e524059cac877a44d9063926cd7a19dbe', - 'lldb': '7ff6d8fee49977d25b3b69be7d22937b92592c7609cf283ed0dcf9e5cd80aa32', - 'lld': 'fbcf47c5e543f4cdac6bb9bbbc6327ff24217cd7eafc5571549ad6d237287f9c', - 'libunwind': '50aee87717421e70450f1e093c6cd9a27f2b111025e1e08d64d5ace36e338a9c' - } - }, - { - 'version': '6.0.1', - 'sha256': 'b6d6c324f9c71494c0ccaf3dac1f16236d970002b42bb24a6c9e1634f7d0f4e2', - 'resources': { - 'compiler-rt': 'f4cd1e15e7d5cb708f9931d4844524e4904867240c306b06a4287b22ac1c99b9', - 'openmp': '66afca2b308351b180136cf899a3b22865af1a775efaf74dc8a10c96d4721c5a', - 'polly': 'e7765fdf6c8c102b9996dbb46e8b3abc41396032ae2315550610cf5a1ecf4ecc', - 'libcxx': '7654fbc810a03860e6f01a54c2297a0b9efb04c0b9aa0409251d9bdb3726fc67', - 'libcxxabi': '209f2ec244a8945c891f722e9eda7c54a5a7048401abd62c62199f3064db385f', - 'cfe': '7c243f1485bddfdfedada3cd402ff4792ea82362ff91fbdac2dae67c6026b667', - 'clang-tools-extra': '0d2e3727786437574835b75135f9e36f861932a958d8547ced7e13ebdda115f1', - 'lldb': '6b8573841f2f7b60ffab9715c55dceff4f2a44e5a6d590ac189d20e8e7472714', - 'lld': 'e706745806921cea5c45700e13ebe16d834b5e3c0b7ad83bf6da1f28b0634e11', - 'libunwind': 'a8186c76a16298a0b7b051004d0162032b9b111b857fbd939d71b0930fd91b96' - } - }, - { - 'version': '6.0.0', - 'sha256': '1ff53c915b4e761ef400b803f07261ade637b0c269d99569f18040f3dcee4408', - 'resources': { - 'compiler-rt': 'd0cc1342cf57e9a8d52f5498da47a3b28d24ac0d39cbc92308781b3ee0cea79a', - 'openmp': '7c0e050d5f7da3b057579fb3ea79ed7dc657c765011b402eb5bbe5663a7c38fc', - 'polly': '47e493a799dca35bc68ca2ceaeed27c5ca09b12241f87f7220b5f5882194f59c', - 'libcxx': '70931a87bde9d358af6cb7869e7535ec6b015f7e6df64def6d2ecdd954040dd9', - 'libcxxabi': '91c6d9c5426306ce28d0627d6a4448e7d164d6a3f64b01cb1d196003b16d641b', - 'cfe': 'e07d6dd8d9ef196cfc8e8bb131cbd6a2ed0b1caf1715f9d05b0f0eeaddb6df32', - 'clang-tools-extra': '053b424a4cd34c9335d8918734dd802a8da612d13a26bbb88fcdf524b2d989d2', - 'lldb': '46f54c1d7adcd047d87c0179f7b6fa751614f339f4f87e60abceaa45f414d454', - 'lld': '6b8c4a833cf30230c0213d78dbac01af21387b298225de90ab56032ca79c0e0b', - 'libunwind': '256c4ed971191bde42208386c8d39e5143fa4afd098e03bd2c140c878c63f1d6' - } - }, - { - 'version': '5.0.2', - 'sha256': 'd522eda97835a9c75f0b88ddc81437e5edbb87dc2740686cb8647763855c2b3c', - 'resources': { - 'compiler-rt': '3efe9ddf3f69e0c0a45cde57ee93911f36f3ab5f2a7f6ab8c8efb3db9b24ed46', - 'openmp': '39ca542c540608d95d3299a474836a7b5f8377bcc5a68493379872738c28565c', - 'polly': 'dda84e48b2195768c4ef25893edd5eeca731bed7e80a2376119dfbc3350e91b8', - 'libcxx': '6edf88e913175536e1182058753fff2365e388e017a9ec7427feb9929c52e298', - 'libcxxabi': '1bbf9bf2c92a4d627dd7bb7a15166acecae924b19898dc0573244f9d533a978a', - 'cfe': 'fa9ce9724abdb68f166deea0af1f71ca0dfa9af8f7e1261f2cae63c280282800', - 'clang-tools-extra': 'a3362a854ba4a60336b21a95612f647f4b6de0afd88858f2420e41c5a31b0b05', - 'lldb': '78ba05326249b4d7577db56d16b2a7ffea43fc51e8592b0a1ac4d2ef87514216', - 'lld': '46456d72ec411c6d5327ad3fea1358296f0dfe508caf1fa63ce4184f652e07aa', - 'libunwind': '706e43c69c7be0fdeb55ebdf653cf47ca77e471d1584f1dbf12a568a93df9928', - } - }, - { - 'version': '5.0.1', - 'sha256': '5fa7489fc0225b11821cab0362f5813a05f2bcf2533e8a4ea9c9c860168807b0', - 'resources': { - 'compiler-rt': '4edd1417f457a9b3f0eb88082530490edf3cf6a7335cdce8ecbc5d3e16a895da', - 'openmp': 'adb635cdd2f9f828351b1e13d892480c657fb12500e69c70e007bddf0fca2653', - 'polly': '9dd52b17c07054aa8998fc6667d41ae921430ef63fa20ae130037136fdacf36e', - 'libcxx': 'fa8f99dd2bde109daa3276d529851a3bce5718d46ce1c5d0806f46caa3e57c00', - 'libcxxabi': '5a25152cb7f21e3c223ad36a1022faeb8a5ac27c9e75936a5ae2d3ac48f6e854', - 'cfe': '135f6c9b0cd2da1aff2250e065946258eb699777888df39ca5a5b4fe5e23d0ff', - 'clang-tools-extra': '9aada1f9d673226846c3399d13fab6bba4bfd38bcfe8def5ee7b0ec24f8cd225', - 'lldb': 'b7c1c9e67975ca219089a3a6a9c77c2d102cead2dc38264f2524aa3326da376a', - 'lld': 'd5b36c0005824f07ab093616bdff247f3da817cae2c51371e1d1473af717d895', - 'libunwind': '6bbfbf6679435b858bd74bdf080386d084a76dfbf233fb6e47b2c28e0872d0fe', - } - }, - { - 'version': '5.0.0', - 'sha256': 'e35dcbae6084adcf4abb32514127c5eabd7d63b733852ccdb31e06f1373136da', - 'resources': { - 'compiler-rt': 'd5ad5266462134a482b381f1f8115b6cad3473741b3bb7d1acc7f69fd0f0c0b3', - 'openmp': 'c0ef081b05e0725a04e8711d9ecea2e90d6c3fbb1622845336d3d095d0a3f7c5', - 'polly': '44694254a2b105cec13ce0560f207e8552e6116c181b8d21bda728559cf67042', - 'libcxx': 'eae5981e9a21ef0decfcac80a1af584ddb064a32805f95a57c7c83a5eb28c9b1', - 'libcxxabi': '176918c7eb22245c3a5c56ef055e4d69f5345b4a98833e0e8cb1a19cab6b8911', - 'cfe': '019f23c2192df793ac746595e94a403908749f8e0c484b403476d2611dd20970', - 'clang-tools-extra': '87d078b959c4a6e5ff9fd137c2f477cadb1245f93812512996f73986a6d973c6', - 'lldb': 'c0a0ca32105e9881d86b7ca886220147e686edc97fdb9f3657c6659dc6568b7d', - 'lld': '399a7920a5278d42c46a7bf7e4191820ec2301457a7d0d4fcc9a4ac05dd53897', - 'libunwind': '9a70e2333d54f97760623d89512c4831d6af29e78b77a33d824413ce98587f6f', - } - }, - { - 'version': '4.0.1', - 'sha256': 'da783db1f82d516791179fe103c71706046561f7972b18f0049242dee6712b51', - 'resources': { - 'compiler-rt': 'a3c87794334887b93b7a766c507244a7cdcce1d48b2e9249fc9a94f2c3beb440', - 'openmp': 'ec693b170e0600daa7b372240a06e66341ace790d89eaf4a843e8d56d5f4ada4', - 'polly': 'b443bb9617d776a7d05970e5818aa49aa2adfb2670047be8e9f242f58e84f01a', - 'libcxx': '520a1171f272c9ff82f324d5d89accadcec9bc9f3c78de11f5575cdb99accc4c', - 'libcxxabi': '8f08178989a06c66cd19e771ff9d8ca526dd4a23d1382d63e416c04ea9fa1b33', - 'cfe': '61738a735852c23c3bdbe52d035488cdb2083013f384d67c1ba36fabebd8769b', - 'clang-tools-extra': '35d1e64efc108076acbe7392566a52c35df9ec19778eb9eb12245fc7d8b915b6', - 'lldb': '8432d2dfd86044a0fc21713e0b5c1d98e1d8aad863cf67562879f47f841ac47b', - 'lld': '63ce10e533276ca353941ce5ab5cc8e8dcd99dbdd9c4fa49f344a212f29d36ed', - 'libunwind': '3b072e33b764b4f9b5172698e080886d1f4d606531ab227772a7fc08d6a92555', - } - }, - { - 'version': '4.0.0', - 'sha256': '8d10511df96e73b8ff9e7abbfb4d4d432edbdbe965f1f4f07afaf370b8a533be', - 'resources': { - 'compiler-rt': 'd3f25b23bef24c305137e6b44f7e81c51bbec764c119e01512a9bd2330be3115', - 'openmp': 'db55d85a7bb289804dc42fc5c8e35ca24dfc3885782261b675a194fd7e206e26', - 'polly': '27a5dbf95e8aa9e0bbe3d6c5d1e83c92414d734357aa0d6c16020a65dc4dcd97', - 'libcxx': '4f4d33c4ad69bf9e360eebe6b29b7b19486948b1a41decf89d4adec12473cf96', - 'libcxxabi': 'dca9cb619662ad2d3a0d685c4366078345247218c3702dd35bcaaa23f63481d8', - 'cfe': 'cea5f88ebddb30e296ca89130c83b9d46c2d833685e2912303c828054c4dc98a', - 'clang-tools-extra': '41b7d37eb128fd362ab3431be5244cf50325bb3bb153895735c5bacede647c99', - 'lldb': '2dbd8f05c662c1c9f11270fc9d0c63b419ddc988095e0ad107ed911cf882033d', - 'lld': '33e06457b9ce0563c89b11ccc7ccabf9cff71b83571985a5bf8684c9150e7502', - 'libunwind': '0755efa9f969373d4d543123bbed4b3f9a835f6302875c1379c5745857725973', - } - }, - { - 'version': '3.9.1', - 'sha256': '1fd90354b9cf19232e8f168faf2220e79be555df3aa743242700879e8fd329ee', - 'resources': { - 'compiler-rt': 'd30967b1a5fa51a2503474aacc913e69fd05ae862d37bf310088955bdb13ec99', - 'openmp': 'd23b324e422c0d5f3d64bae5f550ff1132c37a070e43c7ca93991676c86c7766', - 'polly': '9ba5e61fc7bf8c7435f64e2629e0810c9b1d1b03aa5b5605b780d0e177b4cb46', - 'libcxx': '25e615e428f60e651ed09ffd79e563864e3f4bc69a9e93ee41505c419d1a7461', - 'libcxxabi': '920d8be32e6f5574a3fb293f93a31225eeba15086820fcb942155bf50dc029e2', - 'cfe': 'e6c4cebb96dee827fa0470af313dff265af391cb6da8d429842ef208c8f25e63', - 'clang-tools-extra': '29a5b65bdeff7767782d4427c7c64d54c3a8684bc6b217b74a70e575e4813635', - 'lldb': '7e3311b2a1f80f4d3426e09f9459d079cab4d698258667e50a46dccbaaa460fc', - 'lld': '48e128fabb2ddaee64ecb8935f7ac315b6e68106bc48aeaf655d179c65d87f34', - 'libunwind': '0b0bc73264d7ab77d384f8a7498729e3c4da8ffee00e1c85ad02a2f85e91f0e6', - } - }, - { - 'version': '3.9.0', - 'sha256': '66c73179da42cee1386371641241f79ded250e117a79f571bbd69e56daa48948', - 'resources': { - 'compiler-rt': 'e0e5224fcd5740b61e416c549dd3dcda92f10c524216c1edb5e979e42078a59a', - 'openmp': 'df88f90d7e5b5e9525a35fa2e2b93cbbb83c4882f91df494e87ee3ceddacac91', - 'polly': 'ef0dd25010099baad84597cf150b543c84feac2574d055d6780463d5de8cd97e', - 'libcxx': 'd0b38d51365c6322f5666a2a8105785f2e114430858de4c25a86b49f227f5b06', - 'libcxxabi': 'b037a92717856882e05df57221e087d7d595a2ae9f170f7bc1a23ec7a92c8019', - 'cfe': '7596a7c7d9376d0c89e60028fe1ceb4d3e535e8ea8b89e0eb094e0dcb3183d28', - 'clang-tools-extra': '5b7aec46ec8e999ec683c87ad744082e1133781ee4b01905b4bdae5d20785f14', - 'lldb': '61280e07411e3f2b4cca0067412b39c16b0a9edd19d304d3fc90249899d12384', - 'lld': '986e8150ec5f457469a20666628bf634a5ca992a53e157f3b69dbc35056b32d9', - 'libunwind': '66675ddec5ba0d36689757da6008cb2596ee1a9067f4f598d89ce5a3b43f4c2b', - } - }, - { - 'version': '3.8.1', - 'sha256': '6e82ce4adb54ff3afc18053d6981b6aed1406751b8742582ed50f04b5ab475f9', - 'resources': { - 'compiler-rt': '0df011dae14d8700499dfc961602ee0a9572fef926202ade5dcdfe7858411e5c', - 'openmp': '68fcde6ef34e0275884a2de3450a31e931caf1d6fda8606ef14f89c4123617dc', - 'polly': '453c27e1581614bb3b6351bf5a2da2939563ea9d1de99c420f85ca8d87b928a2', - 'libcxx': '77d7f3784c88096d785bd705fa1bab7031ce184cd91ba8a7008abf55264eeecc', - 'libcxxabi': 'e1b55f7be3fad746bdd3025f43e42d429fb6194aac5919c2be17c4a06314dae1', - 'cfe': '4cd3836dfb4b88b597e075341cae86d61c63ce3963e45c7fe6a8bf59bb382cdf', - 'clang-tools-extra': '664a5c60220de9c290bf2a5b03d902ab731a4f95fe73a00856175ead494ec396', - 'lldb': '349148116a47e39dcb5d5042f10d8a6357d2c865034563283ca512f81cdce8a3', - 'lld': '2bd9be8bb18d82f7f59e31ea33b4e58387dbdef0bc11d5c9fcd5ce9a4b16dc00', - 'libunwind': '21e58ce09a5982255ecf86b86359179ddb0be4f8f284a95be14201df90e48453', - } - }, - { - 'version': '3.8.0', - 'sha256': '555b028e9ee0f6445ff8f949ea10e9cd8be0d084840e21fbbe1d31d51fc06e46', - 'resources': { - 'compiler-rt': 'c8d3387e55f229543dac1941769120f24dc50183150bf19d1b070d53d29d56b0', - 'openmp': '92510e3f62e3de955e3a0b6708cebee1ca344d92fb02369cba5fdd5c68f773a0', - 'polly': '84cbabc0b6a10a664797907d291b6955d5ea61aef04e3f3bb464e42374d1d1f2', - 'libcxx': '36804511b940bc8a7cefc7cb391a6b28f5e3f53f6372965642020db91174237b', - 'libcxxabi': 'c5ee0871aff6ec741380c4899007a7d97f0b791c81df69d25b744eebc5cee504', - 'cfe': '04149236de03cf05232d68eb7cb9c50f03062e339b68f4f8a03b650a11536cf9', - 'clang-tools-extra': 'afbda810106a6e64444bc164b921be928af46829117c95b996f2678ce4cb1ec4', - 'lldb': 'e3f68f44147df0433e7989bf6ed1c58ff28d7c68b9c47553cb9915f744785a35', - 'lld': '94704dda228c9f75f4403051085001440b458501ec97192eee06e8e67f7f9f0c', - 'libunwind': 'af3eaf39ecdc3b9e89863fb62e1aa3c135cfde7e9415424e4e396d7486a9422b', - } - }, - { - 'version': '3.7.1', - 'sha256': 'be7794ed0cec42d6c682ca8e3517535b54555a3defabec83554dbc74db545ad5', - 'resources': { - 'compiler-rt': '9d4769e4a927d3824bcb7a9c82b01e307c68588e6de4e7f04ab82d82c5af8181', - 'openmp': '9a702e20c247014f6de8c45b738c6ea586eca0559304520f565ac9a7cba4bf9a', - 'polly': 'ce9273ad315e1904fd35dc64ac4375fd592f3c296252ab1d163b9ff593ec3542', - 'libcxx': '357fbd4288ce99733ba06ae2bec6f503413d258aeebaab8b6a791201e6f7f144', - 'libcxxabi': 'a47faaed90f577da8ca3b5f044be9458d354a53fab03003a44085a912b73ab2a', - 'cfe': '56e2164c7c2a1772d5ed2a3e57485ff73ff06c97dff12edbeea1acc4412b0674', - 'clang-tools-extra': '4a91edaccad1ce984c7c49a4a87db186b7f7b21267b2b03bcf4bd7820715bc6b', - 'lldb': '9a0bc315ef55f44c98cdf92d064df0847f453ed156dd0ef6a87e04f5fd6a0e01', - 'lld': 'a929cb44b45e3181a0ad02d8c9df1d3fc71e001139455c6805f3abf2835ef3ac', - 'libunwind': 'b69f445253c2e5d3c8be6abe379372a52d223e0e5a5520b79983866c03f949fb', - } - }, - { - 'version': '3.7.0', - 'sha256': 'ab45895f9dcdad1e140a3a79fd709f64b05ad7364e308c0e582c5b02e9cc3153', - 'resources': { - 'compiler-rt': '227fa998520bc94974a428dc8e7654d9bdf277e5bc70d4064ebc05691bd62b0b', - 'openmp': '8d8a224e5689596a35652fda87e4be29853c4b85fbc7a6562019badfad779f2a', - 'polly': '3e5f3f4dc141c7d25b36b910d48c7da74ecc92f10cea5b568c909623d6067edf', - 'libcxx': 'c18f3c8333cd7e678c1424a57fe5e25efe740ca7caf62ac67152b4723f3ad08e', - 'libcxxabi': '48b074fd334958b2d8bab893c897a0c8258328782cdec2d229c7bce432b49beb', - 'cfe': '4ed740c5a91df1c90a4118c5154851d6a475f39a91346bdf268c1c29c13aa1cc', - 'clang-tools-extra': '8ae8a0a3a96b7a700412d67df0af172cb2fc1326beec575fcc0f71d2e72709cd', - 'lldb': 'f4d7505bc111044eaa4033af012221e492938405b62522b8e3e354c20c4b71e9', - 'lld': 'ddb658b789c501efbe4f54ff8ced2c07cd9ff686c92445d8a1ab2cd5dbd837ed', - 'libunwind': '6a600f30b9f3a54a1faf8c2dfd12522a0c90eb65f1aad63fec540aa27bcaca5b', - } - }, - { - 'version': '3.6.2', - 'sha256': 'f60dc158bfda6822de167e87275848969f0558b3134892ff54fced87e4667b94', - 'resources': { - 'compiler-rt': '0f2ff37d80a64575fecd8cf0d5c50f7ac1f837ddf700d1855412bb7547431d87', - 'openmp': '9d9640e7fc76ef531b5e919d79ee241cb35aa599fd1cac97c52ca49c97778f8e', - 'libcxx': '52f3d452f48209c9df1792158fdbd7f3e98ed9bca8ebb51fcd524f67437c8b81', - 'libcxxabi': '6fb48ce5a514686b9b75e73e59869f782ed374a86d71be8423372e4b3329b09b', - 'cfe': 'ae9180466a23acb426d12444d866b266ff2289b266064d362462e44f8d4699f3', - 'clang-tools-extra': '6a0ec627d398f501ddf347060f7a2ccea4802b2494f1d4fd7bda3e0442d04feb', - 'lldb': '940dc96b64919b7dbf32c37e0e1d1fc88cc18e1d4b3acf1e7dfe5a46eb6523a9', - 'lld': '43f553c115563600577764262f1f2fac3740f0c639750f81e125963c90030b33', - } - }, - { - 'version': '3.5.1', - 'sha256': 'bf3275d2d7890015c8d8f5e6f4f882f8cf3bf51967297ebe74111d6d8b53be15', - 'resources': { - 'compiler-rt': 'adf4b526f33e681aff5961f0821f5b514d3fc375410008842640b56a2e6a837a', - 'openmp': '43ea73eeac3045127cf01b496d714b559e42311043480682049e8fea243eac55', - 'libcxx': 'a16d0ae0c0cf2c8cebb94fafcb907022cd4f8579ebac99a4c9919990a37ad475', - 'libcxxabi': '7ff14fdce0ed7bfcc532c627c7a2dc7876dd8a3d788b2aa201d3bbdc443d06a3', - 'cfe': '6773f3f9cf815631cc7e779ec134ddd228dc8e9a250e1ea3a910610c59eb8f5c', - 'clang-tools-extra': 'e8d011250389cfc36eb51557ca25ae66ab08173e8d53536a0747356105d72906', - 'lldb': 'e8b948c6c85cd61bd9a48361959401b9c631fa257c0118db26697c5d57460e13', - 'lld': 'f29f684723effd204b6fe96edb1bf2f66f0f81297230bc92b8cc514f7a24236f', - } - }, - ] - - # Flang uses its own fork of clang (renamed flang-driver). - flang_resources = { - 'flang-driver': { - 'git': 'https://github.com/flang-compiler/flang-driver.git', - 'destination': 'tools', - 'placement': 'clang' - }, - 'openmp': { - 'git': 'https://github.com/llvm-mirror/openmp.git', - 'destination': 'projects', - 'placement': 'openmp' - } - } - - flang_releases = [ - { - 'version': 'develop', - 'branch': 'release_60', - 'resources': { - 'flang-driver': 'release_60', - 'openmp': 'release_60', - } - }, - { - 'version': '20180921', - 'commit': 'd8b30082648dc869eba68f9e539605f437d7760c', - 'resources': { - 'flang-driver': 'dd7587310ae498c22514a33e1a2546b86af9cf25', - 'openmp': 'd5aa29cb3bcf51289d326b4e565613db8aff65ef' - } - }, - { - 'version': 'ppc64le-20180921', - 'commit': 'd8b30082648dc869eba68f9e539605f437d7760c', - 'resources': { - 'flang-driver': 'dd7587310ae498c22514a33e1a2546b86af9cf25', - 'openmp': '29b515e1e6d26b5b0d32d47d28dcdb4b8a11470d' - } - }, - { - 'version': '20180612', - 'commit': 'f26a3ece4ccd68a52f5aa970ec42837ee0743296', - 'resources': { - 'flang-driver': 'e079fa68cb35a53c88c41a1939f90b94d539e984', - 'openmp': 'd5aa29cb3bcf51289d326b4e565613db8aff65ef' - } - }, - { - 'version': 'ppc64le-20180612', - 'commit': '4158932a46eb2f06a166f22a4a52ae48c7d2949e', - 'resources': { - 'flang-driver': '50c1828a134d5a0f1553b355bf0946db48b0aa6d', - 'openmp': '29b515e1e6d26b5b0d32d47d28dcdb4b8a11470d' - } - } - ] - - for release in releases: - if release['version'] == 'develop': - version(release['version'], svn=release['repo']) - - for rname, repo in release['resources'].items(): - resource(name=rname, - svn=repo, - destination=resources[rname]['destination'], - when='@%s%s' % (release['version'], - resources[rname].get('variant', "")), - placement=resources[rname].get('placement', None)) - else: - version(release['version'], release['sha256'], url=llvm_url % release) - - for rname, sha256 in release['resources'].items(): - resource(name=rname, - url=resources[rname]['url'] % release, - sha256=sha256, - destination=resources[rname]['destination'], - when='@%s%s' % (release['version'], - resources[rname].get('variant', "")), - placement=resources[rname].get('placement', None)) - - for release in flang_releases: - if release['version'] == 'develop': - version('flang-' + release['version'], git=flang_llvm_url, branch=release['branch']) - - for rname, branch in release['resources'].items(): - flang_resource = flang_resources[rname] - resource(name=rname, - git=flang_resource['git'], - branch=branch, - destination=flang_resource['destination'], - placement=flang_resource['placement'], - when='@flang-' + release['version']) - - else: - version('flang-' + release['version'], git=flang_llvm_url, commit=release['commit']) - - for rname, commit in release['resources'].items(): - flang_resource = flang_resources[rname] - resource(name=rname, - git=flang_resource['git'], - commit=commit, - destination=flang_resource['destination'], - placement=flang_resource['placement'], - when='@flang-' + release['version']) - - conflicts('+clang_extra', when='~clang') - conflicts('+lldb', when='~clang') + conflicts('+clang_extra', when='~clang') + conflicts('+lldb', when='~clang') + conflicts('+libcxx', when='~clang') + conflicts('+internal_unwind', when='~clang') + conflicts('+compiler-rt', when='~clang') # LLVM 4 and 5 does not build with GCC 8 conflicts('%gcc@8:', when='@:5') @@ -602,7 +136,16 @@ class Llvm(CMakePackage): # Backport from llvm master + additional fix # see https://bugs.llvm.org/show_bug.cgi?id=39696 # for a bug report about this problem in llvm master. - patch('constexpr_longdouble.patch', when='@7:8+libcxx') + patch('constexpr_longdouble.patch', when='@6:8+libcxx') + patch('constexpr_longdouble_9.0.patch', when='@9+libcxx') + + # Backport from llvm master; see + # https://bugs.llvm.org/show_bug.cgi?id=38233 + # for a bug report about this problem in llvm master. + patch('llvm_py37.patch', when='@4:6 ^python@3.7:') + + # https://bugs.llvm.org/show_bug.cgi?id=39696 + patch('thread-p9.patch', when='@develop+libcxx') @run_before('cmake') def check_darwin_lldb_codesign_requirement(self): @@ -619,17 +162,20 @@ class Llvm(CMakePackage): except ProcessError: explanation = ('The "lldb_codesign" identity must be available' - ' to build LLVM with LLDB. See https://github.com/' - 'jevinskie/llvm-lldb/blob/master/docs/code-signing' - '.txt for details on how to create this identity.') + ' to build LLVM with LLDB. See https://lldb.llvm' + '.org/resources/build.html#code-signing-on-macos' + 'for details on how to create this identity.') raise RuntimeError(explanation) - def setup_environment(self, spack_env, run_env): - spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag) + def setup_build_environment(self, env): + env.append_flags('CXXFLAGS', self.compiler.cxx11_flag) + def setup_run_environment(self, env): if '+clang' in self.spec: - run_env.set('CC', join_path(self.spec.prefix.bin, 'clang')) - run_env.set('CXX', join_path(self.spec.prefix.bin, 'clang++')) + env.set('CC', join_path(self.spec.prefix.bin, 'clang')) + env.set('CXX', join_path(self.spec.prefix.bin, 'clang++')) + + root_cmakelists_dir = 'llvm' def cmake_args(self): spec = self.spec @@ -641,6 +187,8 @@ class Llvm(CMakePackage): '-DPYTHON_EXECUTABLE:PATH={0}'.format(spec['python'].command.path), ] + projects = [] + # TODO: Instead of unconditionally disabling CUDA, add a "cuda" variant # (see TODO above), and set the paths if enabled. cmake_args.extend([ @@ -649,36 +197,36 @@ class Llvm(CMakePackage): '-DCUDA_NVCC_EXECUTABLE:FILEPATH=IGNORE', '-DLIBOMPTARGET_DEP_CUDA_DRIVER_LIBRARIES:STRING=IGNORE']) + if '+python' in spec and '+lldb' in spec and spec.satisfies('@5.0.0:'): + cmake_args.append('-DLLDB_USE_SYSTEM_SIX:Bool=TRUE') + + if '~python' in spec and '+lldb' in spec: + cmake_args.append('-DLLDB_DISABLE_PYTHON:Bool=TRUE') + if '+gold' in spec: cmake_args.append('-DLLVM_BINUTILS_INCDIR=' + spec['binutils'].prefix.include) - if '+polly' in spec: - cmake_args.append('-DLINK_POLLY_INTO_TOOLS:Bool=ON') - else: - cmake_args.extend(['-DLLVM_EXTERNAL_POLLY_BUILD:Bool=OFF', - '-DLLVM_TOOL_POLLY_BUILD:Bool=OFF', - '-DLLVM_POLLY_BUILD:Bool=OFF', - '-DLLVM_POLLY_LINK_INTO_TOOLS:Bool=OFF']) - if '+python' in spec and '+lldb' in spec and spec.satisfies('@5.0.0:'): - cmake_args.append('-DLLDB_USE_SYSTEM_SIX:Bool=TRUE') - if '+clang' not in spec: - cmake_args.append('-DLLVM_EXTERNAL_CLANG_BUILD:Bool=OFF') - if '+lldb' not in spec: - cmake_args.extend(['-DLLVM_EXTERNAL_LLDB_BUILD:Bool=OFF', - '-DLLVM_TOOL_LLDB_BUILD:Bool=OFF']) - if '+lld' not in spec: - cmake_args.append('-DLLVM_TOOL_LLD_BUILD:Bool=OFF') - if '+internal_unwind' not in spec: - cmake_args.append('-DLLVM_EXTERNAL_LIBUNWIND_BUILD:Bool=OFF') + if '+clang' in spec: + projects.append('clang') + projects.append('clang-tools-extra') + projects.append('openmp') + if '+lldb' in spec: + projects.append('lldb') + if '+lld' in spec: + projects.append('lld') + if '+compiler-rt' in spec: + projects.append('compiler-rt') if '+libcxx' in spec: + projects.append('libcxx') + projects.append('libcxxabi') if spec.satisfies('@3.9.0:'): cmake_args.append('-DCLANG_DEFAULT_CXX_STDLIB=libc++') - else: - cmake_args.append('-DLLVM_EXTERNAL_LIBCXX_BUILD:Bool=OFF') - cmake_args.append('-DLLVM_EXTERNAL_LIBCXXABI_BUILD:Bool=OFF') - if '+compiler-rt' not in spec: - cmake_args.append('-DLLVM_EXTERNAL_COMPILER_RT_BUILD:Bool=OFF') + if '+internal_unwind' in spec: + projects.append('libunwind') + if '+polly' in spec: + projects.append('polly') + cmake_args.append('-DLINK_POLLY_INTO_TOOLS:Bool=ON') if '+shared_libs' in spec: cmake_args.append('-DBUILD_SHARED_LIBS:Bool=ON') @@ -689,14 +237,10 @@ class Llvm(CMakePackage): if '+all_targets' not in spec: # all is default on cmake targets = ['NVPTX', 'AMDGPU'] - if (spec.version < Version('3.9.0') - and spec.version[0] != 'flang'): + if (spec.version < Version('3.9.0')): # Starting in 3.9.0 CppBackend is no longer a target (see # LLVM_ALL_TARGETS in llvm's top-level CMakeLists.txt for # the complete list of targets) - - # This also applies to the version of llvm used by flang - # hence the test to see if the version starts with "flang". targets.append('CppBackend') if spec.target.family == 'x86' or spec.target.family == 'x86_64': @@ -724,8 +268,15 @@ class Llvm(CMakePackage): gcc_prefix = ancestor(self.compiler.cc, 2) cmake_args.append('-DGCC_INSTALL_PREFIX=' + gcc_prefix) - if spec.satisfies('@4.0.0:') and spec.satisfies('platform=linux'): - cmake_args.append('-DCMAKE_BUILD_WITH_INSTALL_RPATH=1') + if spec.satisfies('@4.0.0:'): + if spec.satisfies('platform=cray') or \ + spec.satisfies('platform=linux'): + cmake_args.append('-DCMAKE_BUILD_WITH_INSTALL_RPATH=1') + + # Semicolon seperated list of projects to enable + cmake_args.append( + '-DLLVM_ENABLE_PROJECTS:STRING={0}'.format(';'.join(projects))) + return cmake_args @run_before('build') @@ -740,10 +291,11 @@ class Llvm(CMakePackage): @run_after('install') def post_install(self): - if '+clang' in self.spec and '+python' in self.spec: - install_tree( - 'tools/clang/bindings/python/clang', - join_path(site_packages_dir, 'clang')) + if '+python' in self.spec: + install_tree('llvm/bindings/python', site_packages_dir) + + if '+clang' in self.spec: + install_tree('clang/bindings/python', site_packages_dir) with working_dir(self.build_directory): install_tree('bin', join_path(self.prefix, 'libexec', 'llvm')) diff --git a/var/spack/repos/builtin/packages/llvm/thread-p9.patch b/var/spack/repos/builtin/packages/llvm/thread-p9.patch new file mode 100644 index 0000000000..140473a850 --- /dev/null +++ b/var/spack/repos/builtin/packages/llvm/thread-p9.patch @@ -0,0 +1,16 @@ +diff --git a/libcxx/include/thread b/libcxx/include/thread +index 02da703..d1677a1 100644 +--- a/projects/libcxx/include/thread ++++ b/projects/libcxx/include/thread +@@ -368,9 +368,9 @@ sleep_for(const chrono::duration<_Rep, _Period>& __d) + { + #if defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__) + // GCC's long double const folding is incomplete for IBM128 long doubles. +- _LIBCPP_CONSTEXPR duration<long double> _Max = nanoseconds::max(); +-#else + _LIBCPP_CONSTEXPR duration<long double> _Max = duration<long double>(ULLONG_MAX/1000000000ULL) ; ++#else ++ _LIBCPP_CONSTEXPR duration<long double> _Max = nanoseconds::max(); + #endif + nanoseconds __ns; + if (__d < _Max) diff --git a/var/spack/repos/builtin/packages/lm-sensors/package.py b/var/spack/repos/builtin/packages/lm-sensors/package.py index 39e2f2b75d..ac9ad2c236 100644 --- a/var/spack/repos/builtin/packages/lm-sensors/package.py +++ b/var/spack/repos/builtin/packages/lm-sensors/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,6 +14,8 @@ class LmSensors(MakefilePackage): url = "https://github.com/groeck/lm-sensors/archive/V3-4-0.tar.gz" maintainers = ['G-Ragghianti'] + version('3-6-0', sha256='0591f9fa0339f0d15e75326d0365871c2d4e2ed8aa1ff759b3a55d3734b7d197') + version('3-5-0', sha256='f671c1d63a4cd8581b3a4a775fd7864a740b15ad046fe92038bcff5c5134d7e0') version('3-4-0', sha256='e334c1c2b06f7290e3e66bdae330a5d36054701ffd47a5dde7a06f9a7402cb4e') version('3-3-5', sha256='e3802f80785c54822027a8c187b10066ba685ec5e997fd02c1d29761ea9c83d4') version('3-3-4', sha256='1c586684b39292b5fabaf5a2701241885ea6483e5e15265e1f501e1b639fdd86') @@ -32,3 +34,8 @@ class LmSensors(MakefilePackage): def install(self, spec, prefix): make('install', 'PREFIX={0}'.format(prefix), 'ETCDIR={0}/etc'.format(prefix)) + + @property + def libs(self): + return find_libraries( + 'libsensors', root=self.prefix, shared=True, recursive=True) diff --git a/var/spack/repos/builtin/packages/lmdb/package.py b/var/spack/repos/builtin/packages/lmdb/package.py index 34dd4cbd20..9b45303766 100644 --- a/var/spack/repos/builtin/packages/lmdb/package.py +++ b/var/spack/repos/builtin/packages/lmdb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py index 697eb9c1bc..146ef9e3b4 100644 --- a/var/spack/repos/builtin/packages/lmod/package.py +++ b/var/spack/repos/builtin/packages/lmod/package.py @@ -1,24 +1,26 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * from glob import glob class Lmod(AutotoolsPackage): """Lmod is a Lua based module system that easily handles the MODULEPATH - Hierarchical problem. Environment Modules provide a convenient way to - dynamically change the users' environment through modulefiles. This - includes easily adding or removing directories to the PATH environment - variable. Modulefiles for Library packages provide environment variables - that specify where the library and header files can be found. + Hierarchical problem. + + Environment Modules provide a convenient way to dynamically change the + users' environment through modulefiles. This includes easily adding or + removing directories to the PATH environment variable. Modulefiles for + Library packages provide environment variables that specify where the + library and header files can be found. """ homepage = 'https://www.tacc.utexas.edu/research-development/tacc-projects/lmod' url = 'https://github.com/TACC/Lmod/archive/7.4.11.tar.gz' + version('8.3', sha256='c2c2e9e6b387b011ee617cb009a2199caac8bf200330cb8a065ceedee09e664a') + version('8.2.10', sha256='15676d82235faf5c755a747f0e318badb1a5c3ff1552fa8022c67ff083ee9e2f') version('8.1.5', sha256='3e5846d3d8e593cbcdfa0aed1474569bf5b5cfd19fd288de22051823d449d344') version('8.0.9', sha256='9813c22ae4dd21eb3dc480f6ce307156512092b4bca954bf8aacc15944f23673') version('7.8.15', sha256='00a257f5073d656adc73045997c28f323b7a4f6d901f1c57b7db2b0cd6bee6e6') @@ -48,10 +50,10 @@ class Lmod(AutotoolsPackage): parallel = False - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): stage_lua_path = join_path( self.stage.source_path, 'src', '?.lua') - spack_env.append_path('LUA_PATH', stage_lua_path.format( + env.append_path('LUA_PATH', stage_lua_path.format( version=self.version), separator=';') def patch(self): diff --git a/var/spack/repos/builtin/packages/lndir/package.py b/var/spack/repos/builtin/packages/lndir/package.py index 41184c46a7..cbef2fc769 100644 --- a/var/spack/repos/builtin/packages/lndir/package.py +++ b/var/spack/repos/builtin/packages/lndir/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/log4cplus/package.py b/var/spack/repos/builtin/packages/log4cplus/package.py index 5ea94a877e..12e766aa7c 100644 --- a/var/spack/repos/builtin/packages/log4cplus/package.py +++ b/var/spack/repos/builtin/packages/log4cplus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/log4cxx/package.py b/var/spack/repos/builtin/packages/log4cxx/package.py index a8507a7c41..090376fe9d 100644 --- a/var/spack/repos/builtin/packages/log4cxx/package.py +++ b/var/spack/repos/builtin/packages/log4cxx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/logstash/package.py b/var/spack/repos/builtin/packages/logstash/package.py new file mode 100644 index 0000000000..a348f42f8f --- /dev/null +++ b/var/spack/repos/builtin/packages/logstash/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Logstash(Package): + """ + Logstash is part of the Elastic Stack along with Beats, Elasticsearch + and Kibana. Logstash is a server-side data processing pipeline that + ingests data from a multitude of sources simultaneously, transforms it, + and then sends it to your favorite "stash. + """ + + homepage = "https://artifacts.elastic.co" + url = "https://artifacts.elastic.co/downloads/logstash/logstash-6.6.0.tar.gz" + + version('6.6.0', sha256='5a9a8b9942631e9d4c3dfb8d47075276e8c2cff343841145550cc0c1cfe7bba7') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/loki/package.py b/var/spack/repos/builtin/packages/loki/package.py index f88eeb1db5..7c16974345 100644 --- a/var/spack/repos/builtin/packages/loki/package.py +++ b/var/spack/repos/builtin/packages/loki/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lordec/package.py b/var/spack/repos/builtin/packages/lordec/package.py index 012a01fde7..e222aff6f6 100644 --- a/var/spack/repos/builtin/packages/lordec/package.py +++ b/var/spack/repos/builtin/packages/lordec/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lrslib/fix-return-value.patch b/var/spack/repos/builtin/packages/lrslib/fix-return-value.patch new file mode 100644 index 0000000000..ab18cb8cac --- /dev/null +++ b/var/spack/repos/builtin/packages/lrslib/fix-return-value.patch @@ -0,0 +1,38 @@ +--- spack-src/lrsnashlib.c.org 2020-01-08 13:22:31.512928411 +0900 ++++ spack-src/lrsnashlib.c 2020-01-08 13:24:51.047429971 +0900 +@@ -52,7 +52,7 @@ + + Q1 = lrs_alloc_dat("LRS globals"); /* allocate and init structure for static problem data */ + if (Q1 == NULL) { +- return; ++ return 1; + } + + Q1->nash = TRUE; +@@ -64,7 +64,7 @@ + + P1 = lrs_alloc_dic(Q1); /* allocate and initialize lrs_dic */ + if (P1 == NULL) { +- return; ++ return 1; + } + + BuildRep(P1, Q1, g, 1, 0); +@@ -74,7 +74,7 @@ + /* allocate and init structure for player 2's problem data */ + Q2 = lrs_alloc_dat("LRS globals"); + if (Q2 == NULL) { +- return; ++ return 1; + } + + Q2->debug = Debug_flag; +@@ -86,7 +86,7 @@ + + P2orig = lrs_alloc_dic(Q2); /* allocate and initialize lrs_dic */ + if (P2orig == NULL) { +- return; ++ return 1; + } + BuildRep(P2orig, Q2, g, 0, 1); + A2orig = P2orig->A; diff --git a/var/spack/repos/builtin/packages/lrslib/package.py b/var/spack/repos/builtin/packages/lrslib/package.py index a27b74f769..a1ec47d3df 100644 --- a/var/spack/repos/builtin/packages/lrslib/package.py +++ b/var/spack/repos/builtin/packages/lrslib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,6 +27,8 @@ class Lrslib(Package): depends_on("libtool", type="build") patch("Makefile.spack.patch") + # Ref: https://github.com/mkoeppe/lrslib/commit/2e8c5bd6c06430151faea5910f44aa032c4178a9 + patch('fix-return-value.patch') def url_for_version(self, version): url = "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/lrslib-0{0}.tar.gz" diff --git a/var/spack/repos/builtin/packages/lrzip/package.py b/var/spack/repos/builtin/packages/lrzip/package.py index de2375622a..d264d6da48 100644 --- a/var/spack/repos/builtin/packages/lrzip/package.py +++ b/var/spack/repos/builtin/packages/lrzip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lsf/package.py b/var/spack/repos/builtin/packages/lsf/package.py index 7c8827c0bf..ccb04d01ac 100644 --- a/var/spack/repos/builtin/packages/lsf/package.py +++ b/var/spack/repos/builtin/packages/lsf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,6 @@ class Lsf(Package): """IBM Platform LSF is a batch scheduler for HPC environments""" homepage = "https://www.ibm.com/marketplace/hpc-workload-management" - url = "https://www.ibm.com/marketplace/hpc-workload-management" # LSF needs to be added as an external package to SPACK. For this, the # config file packages.yaml needs to be adjusted: diff --git a/var/spack/repos/builtin/packages/lshw/package.py b/var/spack/repos/builtin/packages/lshw/package.py new file mode 100644 index 0000000000..99c5d30767 --- /dev/null +++ b/var/spack/repos/builtin/packages/lshw/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Lshw(MakefilePackage): + """ + lshw is a small tool to provide detailed information on the + hardware configuration of the machine. It can report exact memory + configuration, firmware version, mainboard configuration, CPU version + and speed, cache configuration, bus speed, etc. on DMI-capable x86 or + EFI (IA-64) systems and on some ARM and PowerPC machines. + """ + + homepage = "https://github.com/lyonel/lshw" + url = "https://github.com/lyonel/lshw/archive/B.02.18.tar.gz" + + version('02.18', sha256='aa8cb2eebf36e9e46dfc227f24784aa8c87181ec96e57ee6c455da8a0ce4fa77') + version('02.17', sha256='0bb76c7df7733dc9b80d5d35f9d9752409ddb506e190453a2cc960461de5ddeb') + version('02.16', sha256='58a7731d204791dd33db5eb3fde9808d1235283e069e6c33a193637ccec27b3e') + version('02.15', sha256='33c51ba0554d4bcd8ff9a67e5971a63b9ddd58213e2901a09000815376bc61b9') + + def install(self, spec, prefix): + make('install') + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/lsof/package.py b/var/spack/repos/builtin/packages/lsof/package.py index 8bc2c8897a..d66a45a5ea 100644 --- a/var/spack/repos/builtin/packages/lsof/package.py +++ b/var/spack/repos/builtin/packages/lsof/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,9 +10,12 @@ class Lsof(Package): """Lsof displays information about files open to Unix processes.""" homepage = "https://people.freebsd.org/~abe/" - url = "https://www.mirrorservice.org/sites/lsof.itap.purdue.edu/pub/tools/unix/lsof/lsof_4.89.tar.gz" + url = "https://www.mirrorservice.org/sites/lsof.itap.purdue.edu/pub/tools/unix/lsof/lsof_4.91.tar.gz" + list_url = "https://www.mirrorservice.org/sites/lsof.itap.purdue.edu/pub/tools/unix/lsof/OLD/" - version('4.89', sha256='ff4ac555966b587f06338475c8fcc0f41402b4c8e970e730f6f83b62be8b5c0d') + version('4.91', sha256='3ca57887470fdf223a8e8aae4559cd3a26787bea93b94336c90ee8062e29e352') + version('4.90', sha256='27794d3d6499fd5f0f08710b4518b33aed8a4580951d1adf27f6c25898685c9e') + version('4.89', sha256='5d08da7ebe049c9d9a6472d6afb81aa5af54c4733a3f8822cbc22b57867633c9') def install(self, spec, prefix): tar = which('tar') diff --git a/var/spack/repos/builtin/packages/ltp/package.py b/var/spack/repos/builtin/packages/ltp/package.py new file mode 100644 index 0000000000..ff02c7dd80 --- /dev/null +++ b/var/spack/repos/builtin/packages/ltp/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Ltp(AutotoolsPackage): + """Ltp is a joint project started by SGI, developed and maintained by IBM, + Cisco, Fujitsu, SUSE, Red Hat and others, that has a goal to deliver + test suites to the open source community that validate the reliability, + robustness,and stability of Linux. The LTP testsuite contains a collection + of tools for testing the Linux kernel and related features.""" + + homepage = "https://github.com/linux-test-project/ltp" + url = "https://github.com/linux-test-project/ltp/archive/20190517.tar.gz" + + version('20190930', sha256='eca11dbe11a61f3035561a2aa272d578ca9380563440f9ba876c0c4755a42533') + version('20190517', sha256='538175fff2d6c9d69748b2d4afcf5ac43f7300456f839fa7b5b101c7ad447af7') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') diff --git a/var/spack/repos/builtin/packages/ltrace/package.py b/var/spack/repos/builtin/packages/ltrace/package.py index bad6faa5c8..01f0e4fd86 100644 --- a/var/spack/repos/builtin/packages/ltrace/package.py +++ b/var/spack/repos/builtin/packages/ltrace/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lua-bitlib/package.py b/var/spack/repos/builtin/packages/lua-bitlib/package.py index ca5d20764f..dec5e59f58 100644 --- a/var/spack/repos/builtin/packages/lua-bitlib/package.py +++ b/var/spack/repos/builtin/packages/lua-bitlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,8 +14,7 @@ class LuaBitlib(Package): homepage = "http://luaforge.net/projects/bitlib" url = "https://luarocks.org/bitlib-23-2.src.rock" - version('23', sha256='fe226edc2808162e67418e6b2c98befc0ed25a489ecffc6974fa153f951c0c34', - url="https://luarocks.org/bitlib-23-2.src.rock", + version('23-2', sha256='fe226edc2808162e67418e6b2c98befc0ed25a489ecffc6974fa153f951c0c34', expand=False) extends('lua') diff --git a/var/spack/repos/builtin/packages/lua-lpeg/package.py b/var/spack/repos/builtin/packages/lua-lpeg/package.py index 8d6d35d1ff..eb4c8de77b 100644 --- a/var/spack/repos/builtin/packages/lua-lpeg/package.py +++ b/var/spack/repos/builtin/packages/lua-lpeg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,8 +13,7 @@ class LuaLpeg(Package): homepage = "http://www.inf.puc-rio.br/~roberto/lpeg/" url = "https://luarocks.org/manifests/luarocks/lpeg-0.12-1.src.rock" - version('0.12.1', sha256='3962e8d695d0f9095c9453f2a42f9f1a89fb94db9b0c3bf22934c1e8a3b0ef5a', - url='https://luarocks.org/manifests/luarocks/lpeg-0.12-1.src.rock', + version('0.12-1', sha256='3962e8d695d0f9095c9453f2a42f9f1a89fb94db9b0c3bf22934c1e8a3b0ef5a', expand=False) extends("lua") diff --git a/var/spack/repos/builtin/packages/lua-luafilesystem/package.py b/var/spack/repos/builtin/packages/lua-luafilesystem/package.py index b549486b3b..7e526d6e7c 100644 --- a/var/spack/repos/builtin/packages/lua-luafilesystem/package.py +++ b/var/spack/repos/builtin/packages/lua-luafilesystem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lua-jit/package.py b/var/spack/repos/builtin/packages/lua-luajit/package.py index a0f8e2b88d..46ebb01349 100644 --- a/var/spack/repos/builtin/packages/lua-jit/package.py +++ b/var/spack/repos/builtin/packages/lua-luajit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,7 +7,7 @@ import os from spack import * -class LuaJit(Package): +class LuaLuajit(Package): """Flast flexible JITed lua""" homepage = "http://www.luajit.org" url = "http://luajit.org/download/LuaJIT-2.0.4.tar.gz" diff --git a/var/spack/repos/builtin/packages/lua-luaposix/package.py b/var/spack/repos/builtin/packages/lua-luaposix/package.py index 08c64b189c..f69c2a3682 100644 --- a/var/spack/repos/builtin/packages/lua-luaposix/package.py +++ b/var/spack/repos/builtin/packages/lua-luaposix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lua-mpack/package.py b/var/spack/repos/builtin/packages/lua-mpack/package.py index 777ff19e18..c03b6418ba 100644 --- a/var/spack/repos/builtin/packages/lua-mpack/package.py +++ b/var/spack/repos/builtin/packages/lua-mpack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,8 +15,7 @@ class LuaMpack(Package): depends_on('msgpack-c') - version('1.0.0-0', sha256='9068d9d3f407c72a7ea18bc270b0fa90aad60a2f3099fa23d5902dd71ea4cd5f', - url='https://luarocks.org/manifests/tarruda/mpack-1.0.6-0.src.rock', + version('1.0.6-0', sha256='9068d9d3f407c72a7ea18bc270b0fa90aad60a2f3099fa23d5902dd71ea4cd5f', expand=False) extends('lua') diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py index 91528a6e2a..ea6265e28a 100644 --- a/var/spack/repos/builtin/packages/lua/package.py +++ b/var/spack/repos/builtin/packages/lua/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -94,7 +94,7 @@ class Lua(Package): paths.append(os.path.join(path, '?', 'init.lua')) cpaths.append(os.path.join(path, '?.so')) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def _setup_dependent_env_helper(self, env, dependent_spec): lua_paths = [] for d in dependent_spec.traverse( deptypes=('build', 'run'), deptype_query='run'): @@ -115,38 +115,44 @@ class Lua(Package): os.path.join(self.spec.prefix, self.lua_share_dir)): self.append_paths(lua_patterns, lua_cpatterns, p) - spack_env.set('LUA_PATH', ';'.join(lua_patterns), separator=';') - spack_env.set('LUA_CPATH', ';'.join(lua_cpatterns), separator=';') + return lua_patterns, lua_cpatterns - # Add LUA to PATH for dependent packages - spack_env.prepend_path('PATH', self.prefix.bin) + def setup_dependent_build_environment(self, env, dependent_spec): + lua_patterns, lua_cpatterns = self._setup_dependent_env_helper( + env, dependent_spec) + env.set('LUA_PATH', ';'.join(lua_patterns), separator=';') + env.set('LUA_CPATH', ';'.join(lua_cpatterns), separator=';') + + def setup_dependent_run_environment(self, env, dependent_spec): # For run time environment set only the path for dependent_spec and # prepend it to LUAPATH + lua_patterns, lua_cpatterns = self._setup_dependent_env_helper( + env, dependent_spec) + if dependent_spec.package.extends(self.spec): - run_env.prepend_path('LUA_PATH', ';'.join(lua_patterns), - separator=';') - run_env.prepend_path('LUA_CPATH', ';'.join(lua_cpatterns), - separator=';') + env.prepend_path('LUA_PATH', ';'.join(lua_patterns), separator=';') + env.prepend_path('LUA_CPATH', ';'.join(lua_cpatterns), + separator=';') - def setup_environment(self, spack_env, run_env): - run_env.prepend_path( + def setup_run_environment(self, env): + env.prepend_path( 'LUA_PATH', os.path.join(self.spec.prefix, self.lua_share_dir, '?.lua'), separator=';') - run_env.prepend_path( + env.prepend_path( 'LUA_PATH', os.path.join(self.spec.prefix, self.lua_share_dir, '?', 'init.lua'), separator=';') - run_env.prepend_path( + env.prepend_path( 'LUA_PATH', os.path.join(self.spec.prefix, self.lua_lib_dir, '?.lua'), separator=';') - run_env.prepend_path( + env.prepend_path( 'LUA_PATH', os.path.join(self.spec.prefix, self.lua_lib_dir, '?', 'init.lua'), separator=';') - run_env.prepend_path( + env.prepend_path( 'LUA_CPATH', os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'), separator=';') diff --git a/var/spack/repos/builtin/packages/lucene/package.py b/var/spack/repos/builtin/packages/lucene/package.py new file mode 100644 index 0000000000..692a681337 --- /dev/null +++ b/var/spack/repos/builtin/packages/lucene/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Lucene(Package): + """ + Apache Lucene is a high-performance, full featured text search engine + library written in Java. + """ + + homepage = "https://lucene.apache.org/" + url = "http://archive.apache.org/dist/lucene/java/8.3.1/lucene-8.3.1.tgz" + list_url = "http://archive.apache.org/dist/lucene/java/" + list_depth = 1 + + version('8.3.1', sha256='acd61ad458d16f3c98b9dd4653c6a34dd666a965842e461f7cdf8947fa041e1a') + version('8.3.0', sha256='67c4f8081f24ff9f4eb4f2b999ac19f7a639b416e5b6f1c1c74e0524a481fc7e') + version('8.2.0', sha256='505cad34698b217fd6ceee581a8215223a47df5af820c94ca70a6bdbba9d5d7c') + version('8.1.1', sha256='d62b0acdf2b1ed7a25ccdb593ad8584caeaa20cc9870e22790d3ec7fa6240a8c') + + depends_on('java', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/luit/package.py b/var/spack/repos/builtin/packages/luit/package.py index 6770ed8153..3cafde98ba 100644 --- a/var/spack/repos/builtin/packages/luit/package.py +++ b/var/spack/repos/builtin/packages/luit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lulesh/package.py b/var/spack/repos/builtin/packages/lulesh/package.py index c6e7e3d7a6..26772b6bcb 100644 --- a/var/spack/repos/builtin/packages/lulesh/package.py +++ b/var/spack/repos/builtin/packages/lulesh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lumpy-sv/package.py b/var/spack/repos/builtin/packages/lumpy-sv/package.py index 442fe91553..ded7a89e2c 100644 --- a/var/spack/repos/builtin/packages/lumpy-sv/package.py +++ b/var/spack/repos/builtin/packages/lumpy-sv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lvm2/package.py b/var/spack/repos/builtin/packages/lvm2/package.py index f49c8371a2..c552fe3ef5 100644 --- a/var/spack/repos/builtin/packages/lvm2/package.py +++ b/var/spack/repos/builtin/packages/lvm2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lwgrp/package.py b/var/spack/repos/builtin/packages/lwgrp/package.py index 72ee0a0e6a..4356f211a8 100644 --- a/var/spack/repos/builtin/packages/lwgrp/package.py +++ b/var/spack/repos/builtin/packages/lwgrp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lwm2/package.py b/var/spack/repos/builtin/packages/lwm2/package.py index 6dd281d189..023c2ef771 100644 --- a/var/spack/repos/builtin/packages/lwm2/package.py +++ b/var/spack/repos/builtin/packages/lwm2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lz4/package.py b/var/spack/repos/builtin/packages/lz4/package.py index b062c25b26..86b5d112bc 100644 --- a/var/spack/repos/builtin/packages/lz4/package.py +++ b/var/spack/repos/builtin/packages/lz4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lzma/package.py b/var/spack/repos/builtin/packages/lzma/package.py index 7cc8b376b3..1bea0dcb1b 100644 --- a/var/spack/repos/builtin/packages/lzma/package.py +++ b/var/spack/repos/builtin/packages/lzma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/lzo/package.py b/var/spack/repos/builtin/packages/lzo/package.py index 0d2c1e7856..f5c12c6159 100644 --- a/var/spack/repos/builtin/packages/lzo/package.py +++ b/var/spack/repos/builtin/packages/lzo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py index 7b440e845e..7b649656d0 100644 --- a/var/spack/repos/builtin/packages/m4/package.py +++ b/var/spack/repos/builtin/packages/m4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,11 @@ from spack import * -class M4(AutotoolsPackage): +class M4(AutotoolsPackage, GNUMirrorPackage): """GNU M4 is an implementation of the traditional Unix macro processor.""" homepage = "https://www.gnu.org/software/m4/m4.html" - url = "https://ftpmirror.gnu.org/m4/m4-1.4.18.tar.gz" + gnu_mirror_path = "m4/m4-1.4.18.tar.gz" version('1.4.18', sha256='ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab') version('1.4.17', sha256='3ce725133ee552b8b4baca7837fb772940b25e81b2a9dc92537aeaf733538c9e') @@ -19,7 +19,9 @@ class M4(AutotoolsPackage): patch('pgi.patch', when='@1.4.17') # from: https://github.com/Homebrew/homebrew-core/blob/master/Formula/m4.rb # Patch credit to Jeremy Huddleston Sequoia <jeremyhu@apple.com> - patch('secure_snprintf.patch', when='platform_os = highsierra') + patch('secure_snprintf.patch', when='os = highsierra') + patch('secure_snprintf.patch', when='os = mojave') + patch('secure_snprintf.patch', when='os = catalina') # https://bugzilla.redhat.com/show_bug.cgi?id=1573342 patch('https://src.fedoraproject.org/rpms/m4/raw/5d147168d4b93f38a4833f5dd1d650ad88af5a8a/f/m4-1.4.18-glibc-change-work-around.patch', sha256='fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8', when='@1.4.18') diff --git a/var/spack/repos/builtin/packages/macsio/package.py b/var/spack/repos/builtin/packages/macsio/package.py index d90aad340d..579fabda7e 100644 --- a/var/spack/repos/builtin/packages/macsio/package.py +++ b/var/spack/repos/builtin/packages/macsio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -93,6 +93,6 @@ class Macsio(CMakePackage): .format(spec['exodusii'].prefix)) # exodus requires netcdf cmake_args.append("-DWITH_NETCDF_PREFIX={0}" - .format(spec['netcdf'].prefix)) + .format(spec['netcdf-c'].prefix)) return cmake_args diff --git a/var/spack/repos/builtin/packages/mad-numdiff/package.py b/var/spack/repos/builtin/packages/mad-numdiff/package.py index afa13c5cd0..3eedcd3707 100644 --- a/var/spack/repos/builtin/packages/mad-numdiff/package.py +++ b/var/spack/repos/builtin/packages/mad-numdiff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mafft/package.py b/var/spack/repos/builtin/packages/mafft/package.py index 886e491d0b..ab14e529e3 100644 --- a/var/spack/repos/builtin/packages/mafft/package.py +++ b/var/spack/repos/builtin/packages/mafft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py index b281df021b..627454af75 100644 --- a/var/spack/repos/builtin/packages/magics/package.py +++ b/var/spack/repos/builtin/packages/magics/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/magma/package.py b/var/spack/repos/builtin/packages/magma/package.py index e15635e399..27f2f438e9 100644 --- a/var/spack/repos/builtin/packages/magma/package.py +++ b/var/spack/repos/builtin/packages/magma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,7 @@ class Magma(CMakePackage): url = "http://icl.cs.utk.edu/projectsfiles/magma/downloads/magma-2.2.0.tar.gz" maintainers = ['luszczek'] + version('2.5.2', sha256='065feb85558f9dd6f4cc4db36ac633a3f787827fc832d0b578a049a43a195620') version('2.5.1', sha256='ce32c199131515336b30c92a907effe0c441ebc5c5bdb255e4b06b2508de109f') version('2.5.0', sha256='4fd45c7e46bd9d9124253e7838bbfb9e6003c64c2c67ffcff02e6c36d2bcfa33') version('2.4.0', sha256='4eb839b1295405fd29c8a6f5b4ed578476010bf976af46573f80d1169f1f9a4f') diff --git a/var/spack/repos/builtin/packages/makedepend/package.py b/var/spack/repos/builtin/packages/makedepend/package.py index 42c38a0dee..43c523e1a4 100644 --- a/var/spack/repos/builtin/packages/makedepend/package.py +++ b/var/spack/repos/builtin/packages/makedepend/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/maker/package.py b/var/spack/repos/builtin/packages/maker/package.py index 41363ec0a1..c481697041 100644 --- a/var/spack/repos/builtin/packages/maker/package.py +++ b/var/spack/repos/builtin/packages/maker/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -55,7 +55,7 @@ class Maker(Package): depends_on('perl-inline-c', type=('build', 'run')) depends_on('perl-io-all', type=('build', 'run')) depends_on('perl-io-prompt', type=('build', 'run')) - depends_on('perl-bio-perl', type=('build', 'run')) + depends_on('perl-bioperl', type=('build', 'run')) depends_on('blast-plus') depends_on('snap-korf') depends_on('repeatmasker') diff --git a/var/spack/repos/builtin/packages/mallocmc/package.py b/var/spack/repos/builtin/packages/mallocmc/package.py index 667267a969..2dd30bea6b 100644 --- a/var/spack/repos/builtin/packages/mallocmc/package.py +++ b/var/spack/repos/builtin/packages/mallocmc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/man-db/package.py b/var/spack/repos/builtin/packages/man-db/package.py index 44e75d7eda..18007cc9cd 100644 --- a/var/spack/repos/builtin/packages/man-db/package.py +++ b/var/spack/repos/builtin/packages/man-db/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/manta/package.py b/var/spack/repos/builtin/packages/manta/package.py index 52dc3b2e9b..77961bb84a 100644 --- a/var/spack/repos/builtin/packages/manta/package.py +++ b/var/spack/repos/builtin/packages/manta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mapnik/package.py b/var/spack/repos/builtin/packages/mapnik/package.py index de3e1ffb90..2fc61f568d 100644 --- a/var/spack/repos/builtin/packages/mapnik/package.py +++ b/var/spack/repos/builtin/packages/mapnik/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -29,7 +29,7 @@ class Mapnik(AutotoolsPackage): depends_on('libjpeg') depends_on('libtiff') depends_on('proj') - depends_on('cairo') + depends_on('cairo+pdf') # +pdf needed for mapnik.printing depends_on('postgresql', type=('build', 'link', 'run')) depends_on('gdal', type=('build', 'link', 'run')) depends_on('sqlite+rtree', type=('build', 'link', 'run')) @@ -37,9 +37,9 @@ class Mapnik(AutotoolsPackage): conflicts('%gcc@9.0.0:') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('GDAL_DATA', spec['gdal'].prefix.share.gdal) + env.set('GDAL_DATA', spec['gdal'].prefix.share.gdal) def configure_args(self): return [ diff --git a/var/spack/repos/builtin/packages/mapserver/package.py b/var/spack/repos/builtin/packages/mapserver/package.py index 245ea1c714..e4b7eda157 100644 --- a/var/spack/repos/builtin/packages/mapserver/package.py +++ b/var/spack/repos/builtin/packages/mapserver/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/maq/package.py b/var/spack/repos/builtin/packages/maq/package.py index fbb5b3feaa..2fda250658 100644 --- a/var/spack/repos/builtin/packages/maq/package.py +++ b/var/spack/repos/builtin/packages/maq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/margo/package.py b/var/spack/repos/builtin/packages/margo/package.py index 928066d1a0..c6f932e1bb 100644 --- a/var/spack/repos/builtin/packages/margo/package.py +++ b/var/spack/repos/builtin/packages/margo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mariadb-c-client/package.py b/var/spack/repos/builtin/packages/mariadb-c-client/package.py index e64a34303a..5a31cdfc60 100644 --- a/var/spack/repos/builtin/packages/mariadb-c-client/package.py +++ b/var/spack/repos/builtin/packages/mariadb-c-client/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,6 +22,9 @@ class MariadbCClient(CMakePackage): list_url = "https://downloads.mariadb.com/Connectors/c/" list_depth = 1 + version('3.1.6', sha256='d266bb67df83c088c4fb05392713d2504c67be620894cedaf758a9561c116720') + version('3.1.5', sha256='a9de5fedd1a7805c86e23be49b9ceb79a86b090ad560d51495d7ba5952a9d9d5') + version('3.1.4', sha256='7a1a72fee00e4c28060f96c3efbbf38aabcbbab17903e82fce85a85002565316') version('3.0.9', sha256='7277c0caba6f50b1d07e1d682baf0b962a63e2e6af9e00e09b8dcf36a7858641') version('3.0.8', sha256='2ca368fd79e87e80497a5c9fd18922d8316af8584d87cecb35bd5897cb1efd05') version('3.0.7', sha256='f63883c9360675d111646fba5c97feb0d08e0def5873dd189d78bafbb75fa004') diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py index 42019809c7..c89c4c44e6 100644 --- a/var/spack/repos/builtin/packages/mariadb/package.py +++ b/var/spack/repos/builtin/packages/mariadb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,6 +20,7 @@ class Mariadb(CMakePackage): homepage = "https://mariadb.org/about/" url = "http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-10.2.8/source/mariadb-10.2.8.tar.gz" + version('10.4.8', sha256='10cc2c3bdb76733c9c6fd1e3c6c860d8b4282c85926da7d472d2a0e00fffca9b') version('10.4.7', sha256='c8e6a6d0bb4f22c416ed675d24682a3ecfa383c5283efee70c8edf131374d817') version('10.2.8', sha256='8dd250fe79f085e26f52ac448fbdb7af2a161f735fae3aed210680b9f2492393') version('10.1.23', sha256='54d8114e24bfa5e3ebdc7d69e071ad1471912847ea481b227d204f9d644300bf') @@ -45,7 +46,16 @@ class Mariadb(CMakePackage): depends_on('curl') depends_on('libxml2') depends_on('lz4') - depends_on('zeromq') + depends_on('libzmq') depends_on('msgpack-c') + depends_on('openssl') + depends_on('openssl@:1.0', when='@:10.1') conflicts('%gcc@9.1.0:', when='@:5.5') + + def cmake_args(self): + args = [] + + args.append('-DENABLE_DTRACE:BOOL=OFF') + + return args diff --git a/var/spack/repos/builtin/packages/masa/package.py b/var/spack/repos/builtin/packages/masa/package.py index ebeb7a997e..06bcefb4d3 100644 --- a/var/spack/repos/builtin/packages/masa/package.py +++ b/var/spack/repos/builtin/packages/masa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/masurca/package.py b/var/spack/repos/builtin/packages/masurca/package.py index 28e657d8d5..1e0f74e3bb 100644 --- a/var/spack/repos/builtin/packages/masurca/package.py +++ b/var/spack/repos/builtin/packages/masurca/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mathematica/package.py b/var/spack/repos/builtin/packages/mathematica/package.py index c86d98fa75..f7171c6081 100644 --- a/var/spack/repos/builtin/packages/mathematica/package.py +++ b/var/spack/repos/builtin/packages/mathematica/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,12 +20,26 @@ class Mathematica(Package): homepage = "https://www.wolfram.com/mathematica/" url = 'file://{0}/Mathematica_12.0.0_LINUX.sh'.format(os.getcwd()) - version('12.0.0', sha256='b9fb71e1afcc1d72c200196ffa434512d208fa2920e207878433f504e58ae9d7', + version('12.0.0', + sha256='b9fb71e1afcc1d72c200196ffa434512d208fa2920e207878433f504e58ae9d7', expand=False) + # Licensing + license_required = True + license_comment = '#' + license_files = ['Configuration/Licensing/mathpass'] + license_url = 'https://reference.wolfram.com/language/tutorial/RegistrationAndPasswords.html#857035062' + def install(self, spec, prefix): sh = which('sh') sh(self.stage.archive_file, '--', '-auto', '-verbose', '-targetdir={0}'.format(prefix), '-execdir={0}'.format(prefix.bin), '-selinux=y') + # This is what most people would use on a cluster but the installer + # does not symlink it + ws_link_path = os.path.join(prefix.bin, 'wolframscript') + if not os.path.exists(ws_link_path): + ln = which('ln') + ws_path = os.path.join(prefix, 'Executables', 'wolframscript') + ln('-s', ws_path, ws_link_path) diff --git a/var/spack/repos/builtin/packages/matio/package.py b/var/spack/repos/builtin/packages/matio/package.py index 972eb167a6..69732a333b 100644 --- a/var/spack/repos/builtin/packages/matio/package.py +++ b/var/spack/repos/builtin/packages/matio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/matlab/package.py b/var/spack/repos/builtin/packages/matlab/package.py index 65d4792bb8..ae9c95c241 100644 --- a/var/spack/repos/builtin/packages/matlab/package.py +++ b/var/spack/repos/builtin/packages/matlab/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/maven/package.py b/var/spack/repos/builtin/packages/maven/package.py index c4108c6e2f..832104fd78 100644 --- a/var/spack/repos/builtin/packages/maven/package.py +++ b/var/spack/repos/builtin/packages/maven/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,10 @@ class Maven(Package): homepage = "https://maven.apache.org/index.html" url = "https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.3.9/apache-maven-3.3.9-bin.tar.gz" + version('3.6.3', sha256='26ad91d751b3a9a53087aefa743f4e16a17741d3915b219cf74112bf87a438c5') + version('3.6.2', sha256='3fbc92d1961482d6fbd57fbf3dd6d27a4de70778528ee3fb44aa7d27eb32dfdc') + version('3.6.1', sha256='2528c35a99c30f8940cc599ba15d34359d58bec57af58c1075519b8cd33b69e7') + version('3.6.0', sha256='6a1b346af36a1f1a491c1c1a141667c5de69b42e6611d3687df26868bc0f4637') version('3.5.0', sha256='beb91419245395bd69a4a6edad5ca3ec1a8b64e41457672dc687c173a495f034') version('3.3.9', sha256='6e3e9c949ab4695a204f74038717aa7b2689b1be94875899ac1b3fe42800ff82') diff --git a/var/spack/repos/builtin/packages/maverick/package.py b/var/spack/repos/builtin/packages/maverick/package.py index 539dc1a411..6c560bb202 100644 --- a/var/spack/repos/builtin/packages/maverick/package.py +++ b/var/spack/repos/builtin/packages/maverick/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mawk/package.py b/var/spack/repos/builtin/packages/mawk/package.py index 24a79c0214..89c8f9e3ac 100644 --- a/var/spack/repos/builtin/packages/mawk/package.py +++ b/var/spack/repos/builtin/packages/mawk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mbdyn/package.py b/var/spack/repos/builtin/packages/mbdyn/package.py new file mode 100644 index 0000000000..ccaf44a262 --- /dev/null +++ b/var/spack/repos/builtin/packages/mbdyn/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Mbdyn(AutotoolsPackage): + """MBDyn is the first and possibly the only free general purpose + multibody dynamics analysis software.""" + + homepage = "https://www.mbdyn.org/" + url = "https://www.mbdyn.org/userfiles/downloads/mbdyn-1.7.3.tar.gz" + + version('1.7.3', sha256='3cf05cd1cb14c1af3d987aac119b6ecf0d835bc1aee06bc4cf7cc5a245c1f36d') + + # Failed to build mbdyn with gcc@4.8.5 and gcc@9.2.0 + conflicts('%gcc@:5.0,9.0:') diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py index e5104eeb24..73247217e4 100644 --- a/var/spack/repos/builtin/packages/mbedtls/package.py +++ b/var/spack/repos/builtin/packages/mbedtls/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mc/package.py b/var/spack/repos/builtin/packages/mc/package.py index e67d10069d..611a104e11 100644 --- a/var/spack/repos/builtin/packages/mc/package.py +++ b/var/spack/repos/builtin/packages/mc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,11 +21,11 @@ class Mc(AutotoolsPackage): depends_on('glib@2.14:') depends_on('libssh2@1.2.5:') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Fix compilation bug on macOS by pretending we don't have utimensat() # https://github.com/MidnightCommander/mc/pull/130 if 'darwin' in self.spec.architecture: - env['ac_cv_func_utimensat'] = 'no' + env.set('ac_cv_func_utimensat', 'no') def configure_args(self): args = [ diff --git a/var/spack/repos/builtin/packages/mcl/package.py b/var/spack/repos/builtin/packages/mcl/package.py index 29372c73f4..9b60faadce 100644 --- a/var/spack/repos/builtin/packages/mcl/package.py +++ b/var/spack/repos/builtin/packages/mcl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mdtest/package.py b/var/spack/repos/builtin/packages/mdtest/package.py index 137c3c3432..6e18ef3b41 100644 --- a/var/spack/repos/builtin/packages/mdtest/package.py +++ b/var/spack/repos/builtin/packages/mdtest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/med/add_space.patch b/var/spack/repos/builtin/packages/med/add_space.patch new file mode 100644 index 0000000000..e757742529 --- /dev/null +++ b/var/spack/repos/builtin/packages/med/add_space.patch @@ -0,0 +1,20 @@ +--- spack-src/tools/medimport/2.3.1/MED231champRefInfoEtRenMaabuilt.cxx.org 2020-01-28 16:02:49.656440054 +0900 ++++ spack-src/tools/medimport/2.3.1/MED231champRefInfoEtRenMaabuilt.cxx 2020-01-28 16:03:45.222261190 +0900 +@@ -95,7 +95,7 @@ + SSCRUTE(maai); goto ERROR; + } + if ( MAJ_231_232_chaine(maai,maaf) ) { +- fprintf(stdout," >>> Normalisation du nom de maillage par défaut [%s] associé au champ [%s] pour (n°dt,n°it) ("IFORMAT","IFORMAT")\n",maai,champ,numdt,numo); ++ fprintf(stdout," >>> Normalisation du nom de maillage par défaut [%s] associé au champ [%s] pour (n°dt,n°it) (" IFORMAT "," IFORMAT ")\n",maai,champ,numdt,numo); + ret = _MEDattrStringEcrire(datagroup2,MED_NOM_MAI,MED_TAILLE_NOM,maaf); + EXIT_IF(ret < 0,"Renommage du maillage en",maaf); + fprintf(stdout," >>> Normalisation du nom du maillage par défaut [%s] ... OK ... \n",maaf); +@@ -120,7 +120,7 @@ + + if ( MAJ_231_232_chaine(maa,maaf) ) { + +- fprintf(stdout," >>> Normalisation du nom de maillage [%s] associé au champ [%s] pour (n°dt,n°it) ("IFORMAT","IFORMAT")\n",maa,champ,numdt,numo); ++ fprintf(stdout," >>> Normalisation du nom de maillage [%s] associé au champ [%s] pour (n°dt,n°it) (" IFORMAT "," IFORMAT ")\n",maa,champ,numdt,numo); + /* on accede au maillage */ + strcpy(chemini,chemin); + strcat(chemini,maa); diff --git a/var/spack/repos/builtin/packages/med/package.py b/var/spack/repos/builtin/packages/med/package.py index 55d6be7b03..3b416c0274 100644 --- a/var/spack/repos/builtin/packages/med/package.py +++ b/var/spack/repos/builtin/packages/med/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,6 +22,9 @@ class Med(CMakePackage): depends_on('mpi') depends_on('hdf5@:1.8.19+mpi') + # C++11 requires a space between literal and identifier + patch('add_space.patch') + # FIXME This is minimal installation. def cmake_args(self): diff --git a/var/spack/repos/builtin/packages/meep/package.py b/var/spack/repos/builtin/packages/meep/package.py index 2620b62f48..a5ffb30290 100644 --- a/var/spack/repos/builtin/packages/meep/package.py +++ b/var/spack/repos/builtin/packages/meep/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mefit/package.py b/var/spack/repos/builtin/packages/mefit/package.py index 6eed07134b..bd24a324cf 100644 --- a/var/spack/repos/builtin/packages/mefit/package.py +++ b/var/spack/repos/builtin/packages/mefit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,5 +23,5 @@ class Mefit(Package): def install(self, spec, prefix): install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/megadock/package.py b/var/spack/repos/builtin/packages/megadock/package.py index 488ec3424d..f8131784c6 100644 --- a/var/spack/repos/builtin/packages/megadock/package.py +++ b/var/spack/repos/builtin/packages/megadock/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/megahit/package.py b/var/spack/repos/builtin/packages/megahit/package.py index cc69790f65..863a684505 100644 --- a/var/spack/repos/builtin/packages/megahit/package.py +++ b/var/spack/repos/builtin/packages/megahit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/memaxes/package.py b/var/spack/repos/builtin/packages/memaxes/package.py index 1fa7011339..f7f1da41a1 100644 --- a/var/spack/repos/builtin/packages/memaxes/package.py +++ b/var/spack/repos/builtin/packages/memaxes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/memcached/package.py b/var/spack/repos/builtin/packages/memcached/package.py new file mode 100644 index 0000000000..e082c6b04c --- /dev/null +++ b/var/spack/repos/builtin/packages/memcached/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Memcached(AutotoolsPackage): + """ + Memcached is a high performance multithreaded event-based key/value + cache store intended to be used in a distributed system. + """ + + homepage = "https://github.com/memcached/memcached" + url = "https://github.com/memcached/memcached/archive/1.5.20.tar.gz" + + version('1.5.20', sha256='ee93aff47123e0b464e9f007b651b14c89c19e0c20352d8d1c399febbb038cb6') + version('1.5.19', sha256='7af7a2e9b1f468d7f6056f23ce21c04936ce6891f8cb8cd54e133f489a8226e8') + version('1.5.18', sha256='0bf8154f53d2781164421acd195a1665ac2f77316263c3526206c38e402c4b0d') + version('1.5.17', sha256='cb30ad851e95c0190e6b7e59695f1ed2e51d65a9e6c82c893e043dc066053377') + version('1.5.16', sha256='a0c1a7e72186722d7c0e9d5527a63beb339b933d768687f183e163adf935c662') + version('1.5.15', sha256='4ef8627308e99bdd4200ef4f260fbcdd65a4ba634bd593ca02dbbfd71222e9f7') + version('1.5.14', sha256='ae8ed2ed853b840a8430d8575d4e91b87c550b111874b416c551001403ac6a74') + version('1.5.13', sha256='ae59a8b49be17afb344e57c8a8d64f9ae38b6efbc3f9115a422dbcb2b23795fc') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('libevent', type='build') + + def autoreconf(self, spec, prefix): + sh = which('sh') + sh('./autogen.sh') + autoreconf('--install', '--verbose', '--force') + + def configure_args(self): + args = ['--with-libevent={0}'.format(self.spec['libevent'].prefix)] + return args diff --git a/var/spack/repos/builtin/packages/meme/package.py b/var/spack/repos/builtin/packages/meme/package.py index a045e6d1ee..b4bb90bb39 100644 --- a/var/spack/repos/builtin/packages/meme/package.py +++ b/var/spack/repos/builtin/packages/meme/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,7 +25,7 @@ class Meme(AutotoolsPackage): depends_on('perl', type=('build', 'run')) depends_on('python@2.7:', type=('build', 'run')) depends_on('mpi', when='+mpi') - depends_on('image-magick', type=('build', 'run'), when='+image-magick') + depends_on('imagemagick', type=('build', 'run'), when='+image-magick') depends_on('perl-xml-parser', type=('build', 'run')) def configure_args(self): diff --git a/var/spack/repos/builtin/packages/memkind/package.py b/var/spack/repos/builtin/packages/memkind/package.py index 95b0714a7a..37175646c6 100644 --- a/var/spack/repos/builtin/packages/memkind/package.py +++ b/var/spack/repos/builtin/packages/memkind/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/memsurfer/package.py b/var/spack/repos/builtin/packages/memsurfer/package.py index 6c28f3b293..8dab3f0356 100644 --- a/var/spack/repos/builtin/packages/memsurfer/package.py +++ b/var/spack/repos/builtin/packages/memsurfer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -41,8 +41,8 @@ class Memsurfer(PythonPackage): depends_on('hdf5 +hl') # memsurfer's setup needs path to these deps to build extension modules - def setup_environment(self, spack_env, run_env): - spack_env.set('VTK_ROOT', self.spec['vtk'].prefix) - spack_env.set('CGAL_ROOT', self.spec['cgal'].prefix) - spack_env.set('BOOST_ROOT', self.spec['boost'].prefix) - spack_env.set('EIGEN_ROOT', self.spec['eigen'].prefix) + def setup_build_environment(self, env): + env.set('VTK_ROOT', self.spec['vtk'].prefix) + env.set('CGAL_ROOT', self.spec['cgal'].prefix) + env.set('BOOST_ROOT', self.spec['boost'].prefix) + env.set('EIGEN_ROOT', self.spec['eigen'].prefix) diff --git a/var/spack/repos/builtin/packages/meraculous/package.py b/var/spack/repos/builtin/packages/meraculous/package.py index 271e8756ad..46a1de77ea 100644 --- a/var/spack/repos/builtin/packages/meraculous/package.py +++ b/var/spack/repos/builtin/packages/meraculous/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,6 +28,6 @@ class Meraculous(CMakePackage): edit = FileFilter('CMakeLists.txt') edit.filter(r"-static-libstdc\+\+", "") - def setup_environment(self, spack_env, run_env): - run_env.set('MERACULOUS_ROOT', self.prefix) - run_env.prepend_path('PERL5LIB', self.prefix.lib) + def setup_run_environment(self, env): + env.set('MERACULOUS_ROOT', self.prefix) + env.prepend_path('PERL5LIB', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/mercurial/package.py b/var/spack/repos/builtin/packages/mercurial/package.py index f099bb1774..f2f398f176 100644 --- a/var/spack/repos/builtin/packages/mercurial/package.py +++ b/var/spack/repos/builtin/packages/mercurial/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -39,12 +39,12 @@ class Mercurial(PythonPackage): depends_on('py-pygments', type=('build', 'run')) depends_on('py-certifi', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Python 3 support is still experimental, explicitly allow - spack_env.set('HGALLOWPYTHON3', True) - spack_env.set('HGPYTHON3', True) + env.set('HGALLOWPYTHON3', True) + env.set('HGPYTHON3', True) # Setuptools is still opt-in, explicitly enable - spack_env.set('FORCE_SETUPTOOLS', True) + env.set('FORCE_SETUPTOOLS', True) @run_after('install') def post_install(self): diff --git a/var/spack/repos/builtin/packages/mercury/package.py b/var/spack/repos/builtin/packages/mercury/package.py index d6eb21cb40..b09256b7ad 100644 --- a/var/spack/repos/builtin/packages/mercury/package.py +++ b/var/spack/repos/builtin/packages/mercury/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -39,6 +39,8 @@ class Mercury(CMakePackage): # Cray-MPICH if libfabric and MPI are used at the same time variant('udreg', default=False, description='Enable udreg on supported Cray platforms') + variant('verbose', default=True, + description='Enable Mercury to print errors on stderr') depends_on('cmake@2.8.12.2:', type='build') # depends_on('cci', when='+cci') # TODO: add CCI package @@ -77,6 +79,7 @@ class Mercury(CMakePackage): '-DNA_USE_CCI:BOOL=%s' % variant_bool('+cci'), '-DNA_USE_MPI:BOOL=%s' % variant_bool('+mpi'), '-DNA_USE_SM:BOOL=%s' % variant_bool('+sm'), + '-DMERCURY_ENABLE_VERBOSE_ERROR=%s' % variant_bool('+verbose'), ] if '@1.0.0:' in spec: diff --git a/var/spack/repos/builtin/packages/mesa-glu/package.py b/var/spack/repos/builtin/packages/mesa-glu/package.py index 9e8412414a..9593c56271 100644 --- a/var/spack/repos/builtin/packages/mesa-glu/package.py +++ b/var/spack/repos/builtin/packages/mesa-glu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mesa/package.py b/var/spack/repos/builtin/packages/mesa/package.py index 918ae841d0..d46c75796e 100644 --- a/var/spack/repos/builtin/packages/mesa/package.py +++ b/var/spack/repos/builtin/packages/mesa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -101,7 +101,7 @@ class Mesa(AutotoolsPackage): args_gallium_drivers = ['swrast'] args_dri_drivers = [] - if spec.target.family == 'arm': + if spec.target.family == 'arm' or spec.target.family == 'aarch64': args.append('--disable-libunwind') num_frontends = 0 diff --git a/var/spack/repos/builtin/packages/meshkit/package.py b/var/spack/repos/builtin/packages/meshkit/package.py index 5229105653..a103db11c9 100644 --- a/var/spack/repos/builtin/packages/meshkit/package.py +++ b/var/spack/repos/builtin/packages/meshkit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/meson/package.py b/var/spack/repos/builtin/packages/meson/package.py index 9e0da3b9f0..2878c712fc 100644 --- a/var/spack/repos/builtin/packages/meson/package.py +++ b/var/spack/repos/builtin/packages/meson/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mesquite/package.py b/var/spack/repos/builtin/packages/mesquite/package.py index 199065e585..d5f3516652 100644 --- a/var/spack/repos/builtin/packages/mesquite/package.py +++ b/var/spack/repos/builtin/packages/mesquite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,10 +28,15 @@ class Mesquite(AutotoolsPackage): def configure_args(self): args = [ - 'CC=%s' % self.spec['mpi'].mpicc, - 'CXX=%s' % self.spec['mpi'].mpicxx, - '--with-mpi=%s' % self.spec['mpi'].prefix, '--enable-release', '--enable-shared', ] + + if '+mpi' in self.spec: + args.append('CC=%s' % self.spec['mpi'].mpicc) + args.append('CXX=%s' % self.spec['mpi'].mpicxx) + args.append('--with-mpi=%s' % self.spec['mpi'].prefix) + else: + args.append('--without-mpi') + return args diff --git a/var/spack/repos/builtin/packages/metabat/package.py b/var/spack/repos/builtin/packages/metabat/package.py index fc9f22d225..fa5a424396 100644 --- a/var/spack/repos/builtin/packages/metabat/package.py +++ b/var/spack/repos/builtin/packages/metabat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,8 @@ class Metabat(SConsPackage): homepage = "https://bitbucket.org/berkeleylab/metabat" url = "https://bitbucket.org/berkeleylab/metabat/get/v2.12.1.tar.gz" + version('2.14', sha256='d43d5e91afa8f2d211a913739127884669516bfbed870760597fcee2b513abe2') + version('2.13', sha256='aa75a2b62ec9588add4c288993821bab5312a83b1259ff0d508c215133492d74') version('2.12.1', sha256='e3aca0656f56f815135521360dc56667ec26af25143c3a31d645fef1a96abbc2') version('2.11.2', sha256='9baf81b385e503e71792706237c308a21ff9177a3211c79057dcecf8434e9a67') @@ -21,8 +23,8 @@ class Metabat(SConsPackage): depends_on('zlib', type='link') depends_on('ncurses', type='link') - def setup_environment(self, spack_env, run_env): - spack_env.set('BOOST_ROOT', self.spec['boost'].prefix) + def setup_build_environment(self, env): + env.set('BOOST_ROOT', self.spec['boost'].prefix) def install_args(self, spec, prefix): return ["PREFIX={0}".format(prefix)] diff --git a/var/spack/repos/builtin/packages/metaphysicl/package.py b/var/spack/repos/builtin/packages/metaphysicl/package.py index 91e62331ca..e281f40fe5 100644 --- a/var/spack/repos/builtin/packages/metaphysicl/package.py +++ b/var/spack/repos/builtin/packages/metaphysicl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index 4e64f43b40..f9371c4b2d 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,13 +17,15 @@ class Metis(Package): multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" - homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview" - url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz" - list_url = "http://glaros.dtc.umn.edu/gkhome/fsroot/sw/metis/OLD" + # + # the previous metis website http://glaros.dtc.umn.edu/gkhome/metis/metis + # no longer exists. This is a github mirror that provides metis 5.1.0 + # + + homepage = "https://github.com/scivision/METIS/" + url = "https://github.com/scivision/METIS/raw/master/metis-5.1.0.tar.gz" version('5.1.0', sha256='76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2') - version('5.0.2', sha256='f79790676ca2ce3dfa9d5e2d74801e91d92415664ede2c2fc18fc49d4a161981') - version('4.0.3', sha256='5efa35de80703c1b2c4d0de080fafbcf4e0d363a21149a1ad2f96e0144841a55') variant('shared', default=True, description='Enables the build of shared libraries.') variant('gdb', default=False, description='Enables gdb support (version 5+).') @@ -50,13 +52,6 @@ class Metis(Package): patch('install_gklib_defs_rename.patch', when='@5:') patch('gklib_nomisleadingindentation_warning.patch', when='@5: %gcc@6:') - def url_for_version(self, version): - url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis" - if version < Version('4.0.3'): - url += "/OLD" - url += "/metis-{0}.tar.gz".format(version) - return url - @when('@5:') def patch(self): source_path = self.stage.source_path diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index d8ff47d0b4..08a4790f68 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -189,7 +189,7 @@ class Mfem(Package): # depends_on('petsc@3.8:+mpi+double+hypre+suite-sparse+mumps', # when='+petsc') depends_on('mpfr', when='+mpfr') - depends_on('netcdf@4.1.3:', when='+netcdf') + depends_on('netcdf-c@4.1.3:', when='+netcdf') depends_on('unwind', when='+libunwind') depends_on('zlib', when='+gzstream') depends_on('gnutls', when='+gnutls') @@ -368,9 +368,9 @@ class Mfem(Package): if '+netcdf' in spec: options += [ - 'NETCDF_OPT=-I%s' % spec['netcdf'].prefix.include, + 'NETCDF_OPT=-I%s' % spec['netcdf-c'].prefix.include, 'NETCDF_LIB=%s' % - ld_flags_from_dirs([spec['netcdf'].prefix.lib], ['netcdf'])] + ld_flags_from_dirs([spec['netcdf-c'].prefix.lib], ['netcdf'])] if '+gzstream' in spec: if "@:3.3.2" in spec: @@ -439,8 +439,35 @@ class Mfem(Package): hdf5 = conduit['hdf5'] headers += find_headers('hdf5', hdf5.prefix.include) libs += hdf5.libs + + ################## + # cyrush note: + ################## + # spack's HeaderList is applying too much magic, undermining us: + # + # It applies a regex to strip back to the last "include" dir + # in the path. In our case we need to pass the following + # as part of the CONDUIT_OPT flags: + # + # -I<install_path>/include/conduit + # + # I tried several ways to present this path to the HeaderList, + # but the regex always kills the trailing conduit dir + # breaking build. + # + # To resolve the issue, we simply join our own string with + # the headers results (which are important b/c they handle + # hdf5 paths when enabled). + ################## + + # construct proper include path + conduit_include_path = conduit.prefix.include.conduit + # add this path to the found flags + conduit_opt_flags = "-I{0} {1}".format(conduit_include_path, + headers.cpp_flags) + options += [ - 'CONDUIT_OPT=%s' % headers.cpp_flags, + 'CONDUIT_OPT=%s' % conduit_opt_flags, 'CONDUIT_LIB=%s' % ld_flags_from_library_list(libs)] make('config', *options, parallel=False) diff --git a/var/spack/repos/builtin/packages/mg/package.py b/var/spack/repos/builtin/packages/mg/package.py new file mode 100644 index 0000000000..b2059c5182 --- /dev/null +++ b/var/spack/repos/builtin/packages/mg/package.py @@ -0,0 +1,37 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Mg(Package): + """Mg is intended to be a small, fast, and portable editor for people + who can't (or don't want to) run emacs for one reason or another, + or are not familiar with the vi editor. It is compatible with + emacs because there shouldn't be any reason to learn more editor + types than emacs or vi.""" + + homepage = "https://github.com/ibara/mg" + url = "https://github.com/ibara/mg/archive/mg-6.6.tar.gz" + + version('6.6', sha256='e8440353da1a52ec7d40fb88d4f145da49c320b5ba31daf895b0b0db5ccd0632') + + depends_on('ncurses') + + phases = ['configure', 'build', 'install'] + + def configure(self, spec, prefix): + configure = Executable('./configure') + args = [ + '--mandir={0}'.format(self.prefix.man), + '--prefix={0}'.format(self.prefix), + ] + configure(*args) + + def build(self, spec, prefix): + make() + + def install(self, spec, prefix): + make('install') diff --git a/var/spack/repos/builtin/packages/mgis/package.py b/var/spack/repos/builtin/packages/mgis/package.py index d51327c3c0..c03680a7d6 100644 --- a/var/spack/repos/builtin/packages/mgis/package.py +++ b/var/spack/repos/builtin/packages/mgis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,15 +18,17 @@ class Mgis(CMakePackage): """ homepage = "https://thelfer.github.io/mgis/web/index.html" - url = "https://github.com/thelfer/MFrontGenericInterfaceSupport/archive/MFrontGenericInterfaceSupport-1.0.tar.gz" + url = "https://github.com/thelfer/MFrontGenericInterfaceSupport/archive/MFrontGenericInterfaceSupport-1.1.tar.gz" git = "https://github.com/thelfer/MFrontGenericInterfaceSupport.git" maintainers = ['thelfer'] # development branches version("master", branch="master") + version("rliv-1.1", branch="rliv-1.1") version("rliv-1.0", branch="rliv-1.0") # released version + version('1.1', sha256='06593d7a052678deaee87ef60b2213db7545c5be9823f261d3388b3978a0b7a5') version('1.0.1', sha256='6102621455bc5d9b1591cd33e93b2e15a9572d2ce59ca6dfa30ba57ae1265c08') version('1.0', sha256='279c98da00fa6855edf29c2b8f8bad6e7732298dc62ef67d028d6bbeaac043b3') @@ -42,11 +44,13 @@ class Mgis(CMakePackage): values=('Debug', 'Release')) # dependencies - depends_on('tfel@3.2.0', when="@1.0") + depends_on('tfel@3.3.0', when="@1.1") depends_on('tfel@3.2.1', when="@1.0.1") + depends_on('tfel@3.2.0', when="@1.0") + depends_on('tfel@rliv-3.3', when="@rliv-1.1") depends_on('tfel@rliv-3.2', when="@rliv-1.0") depends_on('tfel@master', when="@master") - depends_on('boost+python', when='+python') + depends_on('boost+python+numpy', when='+python') extends('python', when='+python') def cmake_args(self): diff --git a/var/spack/repos/builtin/packages/microbiomeutil/package.py b/var/spack/repos/builtin/packages/microbiomeutil/package.py index d536c13989..2155e877d9 100644 --- a/var/spack/repos/builtin/packages/microbiomeutil/package.py +++ b/var/spack/repos/builtin/packages/microbiomeutil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,8 +27,8 @@ class Microbiomeutil(MakefilePackage): install_tree('RESOURCES', prefix.resources) install_tree('AmosCmp16Spipeline', prefix.AmosCmp16Spipeline) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix.ChimeraSlayer) - run_env.prepend_path('PATH', join_path(self.prefix, 'NAST-iEr')) - run_env.prepend_path('PATH', self.prefix.TreeChopper) - run_env.prepend_path('PATH', self.prefix.WigeoN) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix.ChimeraSlayer) + env.prepend_path('PATH', join_path(self.prefix, 'NAST-iEr')) + env.prepend_path('PATH', self.prefix.TreeChopper) + env.prepend_path('PATH', self.prefix.WigeoN) diff --git a/var/spack/repos/builtin/packages/migrate/package.py b/var/spack/repos/builtin/packages/migrate/package.py index 90ccd1abd5..61602546a1 100644 --- a/var/spack/repos/builtin/packages/migrate/package.py +++ b/var/spack/repos/builtin/packages/migrate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mii/package.py b/var/spack/repos/builtin/packages/mii/package.py index 063ec4072d..15e9dad660 100644 --- a/var/spack/repos/builtin/packages/mii/package.py +++ b/var/spack/repos/builtin/packages/mii/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,5 +21,5 @@ class Mii(MakefilePackage): version('1.0.3', sha256='9b5a0e4e0961cf848677ed61b4f6c03e6a443f8592ed668d1afea302314b47a8') version('1.0.2', sha256='1c2c86ec37779ecd3821c30ce5b6dd19be4ec1813da41832d49ff3dcf615e22d') - def setup_environment(self, spack_env, run_env): - spack_env.set('PREFIX', self.prefix) + def setup_build_environment(self, env): + env.set('PREFIX', self.prefix) diff --git a/var/spack/repos/builtin/packages/minced/package.py b/var/spack/repos/builtin/packages/minced/package.py index 18418b15eb..06f1ff457f 100644 --- a/var/spack/repos/builtin/packages/minced/package.py +++ b/var/spack/repos/builtin/packages/minced/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mindthegap/package.py b/var/spack/repos/builtin/packages/mindthegap/package.py index 34a56d11cb..d3e847a129 100644 --- a/var/spack/repos/builtin/packages/mindthegap/package.py +++ b/var/spack/repos/builtin/packages/mindthegap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/miniaero/package.py b/var/spack/repos/builtin/packages/miniaero/package.py index 58d89dde4c..f467947719 100644 --- a/var/spack/repos/builtin/packages/miniaero/package.py +++ b/var/spack/repos/builtin/packages/miniaero/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/miniamr/package.py b/var/spack/repos/builtin/packages/miniamr/package.py index d0d2d445f4..b2166618c7 100644 --- a/var/spack/repos/builtin/packages/miniamr/package.py +++ b/var/spack/repos/builtin/packages/miniamr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,6 +19,7 @@ class Miniamr(MakefilePackage): tags = ['proxy-app', 'ecp-proxy-app'] version('develop', branch='master') + version('1.4.4', sha256='b83f438ff351481b4310c46ddf63b9fffc7f29f916a5717377e72919a5b788b6') version('1.4.3', sha256='4c3fbc1662ae3e139669fb3844134486a7488a0b6e085c3b24bebcc8d12d3ac6') version('1.4.2', sha256='d2347e0e22a8e79aa0dc3316b67dd7c40dded39d82f6e068e6fb8c9f0766566b') version('1.4.1', sha256='dd8e8d9fd0768cb4f2c5d7fe6989dfa6bb95a8461f04deaccdbb50b0dd51e97a') diff --git a/var/spack/repos/builtin/packages/miniasm/package.py b/var/spack/repos/builtin/packages/miniasm/package.py index 1d017d5c55..3ab3832b7e 100644 --- a/var/spack/repos/builtin/packages/miniasm/package.py +++ b/var/spack/repos/builtin/packages/miniasm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/miniconda2/package.py b/var/spack/repos/builtin/packages/miniconda2/package.py index e79d94528f..1173011a0e 100644 --- a/var/spack/repos/builtin/packages/miniconda2/package.py +++ b/var/spack/repos/builtin/packages/miniconda2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ class Miniconda2(Package): homepage = "https://conda.io/miniconda.html" url = "https://repo.continuum.io/miniconda/Miniconda2-4.6.14-Linux-x86_64.sh" + version('4.7.12.1', sha256='383fe7b6c2574e425eee3c65533a5101e68a2d525e66356844a80aa02a556695', expand=False) version('4.6.14', sha256='3e20425afa1a2a4c45ee30bd168b90ca30a3fdf8598b61cb68432886aadc6f4d', expand=False) version('4.5.11', sha256='0e23e8d0a1a14445f78960a66b363b464b889ee3b0e3f275b7ffb836df1cb0c6', expand=False) version('4.5.4', sha256='77d95c99996495b9e44db3c3b7d7981143d32d5e9a58709c51d35bf695fda67d', expand=False) diff --git a/var/spack/repos/builtin/packages/miniconda3/package.py b/var/spack/repos/builtin/packages/miniconda3/package.py index 3ad1f81b63..f75ce7420c 100644 --- a/var/spack/repos/builtin/packages/miniconda3/package.py +++ b/var/spack/repos/builtin/packages/miniconda3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ class Miniconda3(Package): homepage = "https://conda.io/miniconda.html" url = "https://repo.continuum.io/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh" + version('4.7.12.1', sha256='bfe34e1fa28d6d75a7ad05fd02fa5472275673d5f5621b77380898dee1be15d2', expand=False) version('4.6.14', sha256='0d6b23895a91294a4924bd685a3a1f48e35a17970a073cd2f684ffe2c31fc4be', expand=False) version('4.5.11', sha256='ea4594241e13a2671c5b158b3b813f0794fe58d514795fbf72a1aad24db918cf', expand=False) version('4.5.4', sha256='80ecc86f8c2f131c5170e43df489514f80e3971dd105c075935470bbf2476dea', expand=False) diff --git a/var/spack/repos/builtin/packages/minife/package.py b/var/spack/repos/builtin/packages/minife/package.py index c72b8cce48..034b9f9569 100644 --- a/var/spack/repos/builtin/packages/minife/package.py +++ b/var/spack/repos/builtin/packages/minife/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/minighost/package.py b/var/spack/repos/builtin/packages/minighost/package.py index 3af09fa8de..f39655baf0 100644 --- a/var/spack/repos/builtin/packages/minighost/package.py +++ b/var/spack/repos/builtin/packages/minighost/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ class Minighost(MakefilePackage): """ homepage = "http://mantevo.org" - url = "http://mantevo.org/downloads/releaseTarballs/miniapps/MiniGhost/miniGhost_1.0.1.tar.gz" + url = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/miniGhost_1.0.1.tar.gz" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/minigmg/package.py b/var/spack/repos/builtin/packages/minigmg/package.py index c1e4eece40..5087ff094e 100644 --- a/var/spack/repos/builtin/packages/minigmg/package.py +++ b/var/spack/repos/builtin/packages/minigmg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/minimap2/package.py b/var/spack/repos/builtin/packages/minimap2/package.py index 0159123cb5..16f7f7aec1 100644 --- a/var/spack/repos/builtin/packages/minimap2/package.py +++ b/var/spack/repos/builtin/packages/minimap2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/minimd/package.py b/var/spack/repos/builtin/packages/minimd/package.py index 4ecaf1412d..d505015fb5 100644 --- a/var/spack/repos/builtin/packages/minimd/package.py +++ b/var/spack/repos/builtin/packages/minimd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ class Minimd(MakefilePackage): """ homepage = "http://mantevo.org" - url = "http://mantevo.org/downloads/releaseTarballs/miniapps/MiniMD/miniMD_1.2.tgz" + url = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/miniMD_1.2.tgz" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/miniqmc/package.py b/var/spack/repos/builtin/packages/miniqmc/package.py index 0da43dbfbf..b98545f284 100644 --- a/var/spack/repos/builtin/packages/miniqmc/package.py +++ b/var/spack/repos/builtin/packages/miniqmc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/minisign/package.py b/var/spack/repos/builtin/packages/minisign/package.py index 34d07d075e..7bb02eb453 100644 --- a/var/spack/repos/builtin/packages/minisign/package.py +++ b/var/spack/repos/builtin/packages/minisign/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/minismac2d/package.py b/var/spack/repos/builtin/packages/minismac2d/package.py index ded2ad08f2..545176aa77 100644 --- a/var/spack/repos/builtin/packages/minismac2d/package.py +++ b/var/spack/repos/builtin/packages/minismac2d/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,7 +14,7 @@ class Minismac2d(MakefilePackage): """ homepage = "http://mantevo.org" - url = "http://mantevo.org/downloads/releaseTarballs/miniapps/MiniSMAC2D/miniSMAC2D-2.0.tgz" + url = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/miniSMAC2D-2.0.tgz" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/minitri/package.py b/var/spack/repos/builtin/packages/minitri/package.py index fb2e5cb176..ec7aff1530 100644 --- a/var/spack/repos/builtin/packages/minitri/package.py +++ b/var/spack/repos/builtin/packages/minitri/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/minivite/package.py b/var/spack/repos/builtin/packages/minivite/package.py index 726299f081..6fb46e80c4 100644 --- a/var/spack/repos/builtin/packages/minivite/package.py +++ b/var/spack/repos/builtin/packages/minivite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/minixyce/package.py b/var/spack/repos/builtin/packages/minixyce/package.py index b45761d1fa..ee8fe84c86 100644 --- a/var/spack/repos/builtin/packages/minixyce/package.py +++ b/var/spack/repos/builtin/packages/minixyce/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,7 @@ class Minixyce(MakefilePackage): """ homepage = "https://mantevo.org" - url = "http://mantevo.org/downloads/releaseTarballs/miniapps/MiniXyce/miniXyce_1.0.tar.gz" + url = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/miniXyce_1.0.tar.gz" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/minizip/package.py b/var/spack/repos/builtin/packages/minizip/package.py index f7f564f9f9..0042bce589 100644 --- a/var/spack/repos/builtin/packages/minizip/package.py +++ b/var/spack/repos/builtin/packages/minizip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/minuit/package.py b/var/spack/repos/builtin/packages/minuit/package.py index 7f38a88cb9..d385fe5f7d 100644 --- a/var/spack/repos/builtin/packages/minuit/package.py +++ b/var/spack/repos/builtin/packages/minuit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mira/package.py b/var/spack/repos/builtin/packages/mira/package.py index a4c9b7d4a7..beee0a4906 100644 --- a/var/spack/repos/builtin/packages/mira/package.py +++ b/var/spack/repos/builtin/packages/mira/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/miranda/package.py b/var/spack/repos/builtin/packages/miranda/package.py new file mode 100644 index 0000000000..7f17619f4b --- /dev/null +++ b/var/spack/repos/builtin/packages/miranda/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Miranda(AutotoolsPackage): + """miRanda is an algorithm for finding genomic targets for microRNAs.""" + + homepage = "http://www.microrna.org/microrna/getDownloads.do" + url = "http://cbio.mskcc.org/microrna_data/miRanda-aug2010.tar.gz" + + version('3.3a', sha256='a671da562cf4636ef5085b27349df2df2f335774663fd423deb08f31212ec778', + url='http://cbio.mskcc.org/microrna_data/miRanda-aug2010.tar.gz') diff --git a/var/spack/repos/builtin/packages/mirdeep2/package.py b/var/spack/repos/builtin/packages/mirdeep2/package.py index 3de2fccf6b..b2c4cd60eb 100644 --- a/var/spack/repos/builtin/packages/mirdeep2/package.py +++ b/var/spack/repos/builtin/packages/mirdeep2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mitofates/package.py b/var/spack/repos/builtin/packages/mitofates/package.py index e6140808b2..0fb356637e 100644 --- a/var/spack/repos/builtin/packages/mitofates/package.py +++ b/var/spack/repos/builtin/packages/mitofates/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -44,6 +44,6 @@ class Mitofates(Package): chmod = which('chmod') chmod('+x', join_path(prefix, 'MitoFates.pl')) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # We want the main MitoFates.pl script in the path - run_env.prepend_path('PATH', self.prefix) + env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/mitos/package.py b/var/spack/repos/builtin/packages/mitos/package.py index 414a074f47..080b6cd742 100644 --- a/var/spack/repos/builtin/packages/mitos/package.py +++ b/var/spack/repos/builtin/packages/mitos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mixcr/package.py b/var/spack/repos/builtin/packages/mixcr/package.py index f201eae25c..1b0e781b45 100644 --- a/var/spack/repos/builtin/packages/mixcr/package.py +++ b/var/spack/repos/builtin/packages/mixcr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,5 +25,5 @@ class Mixcr(Package): def install(self, spec, prefix): install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/mkfontdir/package.py b/var/spack/repos/builtin/packages/mkfontdir/package.py index fcf0b08e93..2f4d8801b9 100644 --- a/var/spack/repos/builtin/packages/mkfontdir/package.py +++ b/var/spack/repos/builtin/packages/mkfontdir/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mkfontscale/package.py b/var/spack/repos/builtin/packages/mkfontscale/package.py index 3a78857e0b..53613b290a 100644 --- a/var/spack/repos/builtin/packages/mkfontscale/package.py +++ b/var/spack/repos/builtin/packages/mkfontscale/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mlhka/package.py b/var/spack/repos/builtin/packages/mlhka/package.py index 7328530563..32d259139c 100644 --- a/var/spack/repos/builtin/packages/mlhka/package.py +++ b/var/spack/repos/builtin/packages/mlhka/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mmg/package.py b/var/spack/repos/builtin/packages/mmg/package.py index 16c41550c5..b48f969bc8 100644 --- a/var/spack/repos/builtin/packages/mmg/package.py +++ b/var/spack/repos/builtin/packages/mmg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/moab/package.py b/var/spack/repos/builtin/packages/moab/package.py index 6ab1311309..b1b4d79b3f 100644 --- a/var/spack/repos/builtin/packages/moab/package.py +++ b/var/spack/repos/builtin/packages/moab/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -39,8 +39,6 @@ class Moab(AutotoolsPackage): description='Required to enable the ExodusII reader/writer.') variant('pnetcdf', default=False, description='Enable pnetcdf (AKA parallel-netcdf) support') - variant('netcdf', default=False, - description='Required to enable the ExodusII reader/writer.') variant('zoltan', default=False, description='Enable zoltan support') variant('cgm', default=False, description='Enable common geometric module') variant('metis', default=True, description='Enable metis link') @@ -77,7 +75,7 @@ class Moab(AutotoolsPackage): depends_on('mpi', when='+mpi') depends_on('hdf5', when='+hdf5') depends_on('hdf5+mpi', when='+hdf5+mpi') - depends_on('netcdf', when='+netcdf') + depends_on('netcdf-c', when='+netcdf') depends_on('parallel-netcdf', when='+pnetcdf') depends_on('cgm', when='+cgm') depends_on('metis', when='+metis') @@ -129,7 +127,7 @@ class Moab(AutotoolsPackage): options.append('--without-hdf5') if '+netcdf' in spec: - options.append('--with-netcdf=%s' % spec['netcdf'].prefix) + options.append('--with-netcdf=%s' % spec['netcdf-c'].prefix) else: options.append('--without-netcdf') diff --git a/var/spack/repos/builtin/packages/modern-wheel/package.py b/var/spack/repos/builtin/packages/modern-wheel/package.py index 03e70290d8..e6c76bdc47 100644 --- a/var/spack/repos/builtin/packages/modern-wheel/package.py +++ b/var/spack/repos/builtin/packages/modern-wheel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mofem-cephas/package.py b/var/spack/repos/builtin/packages/mofem-cephas/package.py index 034f70e292..28e00565d2 100644 --- a/var/spack/repos/builtin/packages/mofem-cephas/package.py +++ b/var/spack/repos/builtin/packages/mofem-cephas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mofem-fracture-module/package.py b/var/spack/repos/builtin/packages/mofem-fracture-module/package.py index 00c7aad6d8..784bb9931c 100644 --- a/var/spack/repos/builtin/packages/mofem-fracture-module/package.py +++ b/var/spack/repos/builtin/packages/mofem-fracture-module/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py b/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py index 38613f334d..58e0342080 100644 --- a/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py +++ b/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mofem-users-modules/package.py b/var/spack/repos/builtin/packages/mofem-users-modules/package.py index f1f4afd938..f0acc98d94 100644 --- a/var/spack/repos/builtin/packages/mofem-users-modules/package.py +++ b/var/spack/repos/builtin/packages/mofem-users-modules/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/molcas/package.py b/var/spack/repos/builtin/packages/molcas/package.py index 9b0d4424d8..bbe92073ad 100644 --- a/var/spack/repos/builtin/packages/molcas/package.py +++ b/var/spack/repos/builtin/packages/molcas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/libmongoc/package.py b/var/spack/repos/builtin/packages/mongo-c-driver/package.py index 0d3110a803..27008d7561 100644 --- a/var/spack/repos/builtin/packages/libmongoc/package.py +++ b/var/spack/repos/builtin/packages/mongo-c-driver/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Libmongoc(AutotoolsPackage): +class MongoCDriver(AutotoolsPackage): """libmongoc is a client library written in C for MongoDB.""" homepage = "https://github.com/mongodb/mongo-c-driver" diff --git a/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py b/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py index 0f36e6174e..7184995b5b 100644 --- a/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py +++ b/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,4 +15,4 @@ class MongoCxxDriver(CMakePackage): version('3.2.0', sha256='e26edd44cf20bd6be91907403b6d63a065ce95df4c61565770147a46716aad8c') - depends_on('libmongoc@1.9.2:') + depends_on('mongo-c-driver@1.9.2:') diff --git a/var/spack/repos/builtin/packages/mono/package.py b/var/spack/repos/builtin/packages/mono/package.py index 69f0542deb..40a6a25fe9 100644 --- a/var/spack/repos/builtin/packages/mono/package.py +++ b/var/spack/repos/builtin/packages/mono/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/montage/package.py b/var/spack/repos/builtin/packages/montage/package.py index 30fb6a65e1..e663fb418c 100644 --- a/var/spack/repos/builtin/packages/montage/package.py +++ b/var/spack/repos/builtin/packages/montage/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/moosefs/package.py b/var/spack/repos/builtin/packages/moosefs/package.py new file mode 100644 index 0000000000..c74de5a723 --- /dev/null +++ b/var/spack/repos/builtin/packages/moosefs/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Moosefs(AutotoolsPackage): + """ + MooseFS is a Petabyte Open Source Network Distributed File System. It + is easy to deploy and maintain, fault tolerant, highly performing, + easily scalable, POSIX compliant. + """ + + homepage = "https://github.com/moosefs/moosefs" + url = "https://github.com/moosefs/moosefs/archive/v3.0.109.tar.gz" + + version('3.0.109', sha256='413349d254f75ea9b9c974a12f67225c7cbec389f8a39a68db569c0d0f6f4ef3') + version('3.0.108', sha256='344c4b7875603fc0b091e5c80f4a5b2eda780a3d050de2ef38232e55e56b054a') + version('3.0.107', sha256='192dca0c04f61334846e00c1193952bb0f69f3960f223a8d55016b74d72cfdb6') + version('3.0.105', sha256='12a5bb265d774da8fc6f051c51de08105ddeaa162b2d972d491caa542e01164f') + version('3.0.104', sha256='b3209ecd8366038ba898c4642dd6fdf2fa5d50a37345f01ed209e078700db5bb') + version('3.0.103', sha256='c5f1f6f78c2b7d8d6563000deed704ead3deac77279cb13f9f16d7ee56ee7ff7') diff --git a/var/spack/repos/builtin/packages/moreutils/package.py b/var/spack/repos/builtin/packages/moreutils/package.py new file mode 100644 index 0000000000..96e081c92a --- /dev/null +++ b/var/spack/repos/builtin/packages/moreutils/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Moreutils(MakefilePackage): + """Additional Unix utilities. This is a growing collection of the Unix + tools that nobody thought to write long ago, when Unix was young.""" + + homepage = "https://joeyh.name/code/moreutils" + url = "https://deb.debian.org/debian/pool/main/m/moreutils/moreutils_0.63.orig.tar.xz" + + maintainers = ['matthiasdiener'] + + version('0.63', sha256='01f0b331e07e62c70d58c2dabbb68f5c4ddae4ee6f2d8f070fd1e316108af72c') + + depends_on('perl', type='build') + depends_on('docbook-xsl', type='build') + depends_on('libxml2', type='build') + + def edit(self, spec, prefix): + isutf8_makefile = FileFilter('is_utf8/Makefile') + isutf8_makefile.filter('CC = .*', '') + + env['DOCBOOKXSL'] = spec['docbook-xsl'].prefix + env['PREFIX'] = self.prefix diff --git a/var/spack/repos/builtin/packages/mosh/package.py b/var/spack/repos/builtin/packages/mosh/package.py index 69ce155c8a..f741279159 100644 --- a/var/spack/repos/builtin/packages/mosh/package.py +++ b/var/spack/repos/builtin/packages/mosh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mothur/package.py b/var/spack/repos/builtin/packages/mothur/package.py index 26235cb9a0..3f2283191a 100644 --- a/var/spack/repos/builtin/packages/mothur/package.py +++ b/var/spack/repos/builtin/packages/mothur/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,11 +14,16 @@ class Mothur(MakefilePackage): homepage = "https://github.com/mothur/mothur" url = "https://github.com/mothur/mothur/archive/v1.39.5.tar.gz" + version('1.43.0', sha256='12ccd95a85bec3bb1564b8feabd244ea85413973740754803d01fc71ecb0a2c1') + version('1.42.1', sha256='6b61591dda289ac2d8361f9c1547ffbeeba3b9fbdff877dd286bad850bbd5539') version('1.40.5', sha256='a0fbdfa68b966d7adc4560e3787506a0dad8b47b4b996c2663cd6c0b416d101a') version('1.39.5', sha256='9f1cd691e9631a2ab7647b19eb59cd21ea643f29b22cde73d7f343372dfee342') + variant('vsearch', default=False, description='Use vsearch') + depends_on('boost') depends_on('readline') + depends_on('vsearch', when='+vsearch', type='run') def edit(self, spec, prefix): makefile = FileFilter('Makefile') diff --git a/var/spack/repos/builtin/packages/motif/add_xbitmaps_dependency.patch b/var/spack/repos/builtin/packages/motif/add_xbitmaps_dependency.patch new file mode 100644 index 0000000000..993b5108f3 --- /dev/null +++ b/var/spack/repos/builtin/packages/motif/add_xbitmaps_dependency.patch @@ -0,0 +1,36 @@ +diff -Naur motif-2.3.8/ac_find_xbitmaps.m4 motif-2.3.8_patched/ac_find_xbitmaps.m4 +--- motif-2.3.8/ac_find_xbitmaps.m4 1970-01-01 01:00:00.000000000 +0100 ++++ motif-2.3.8_patched/ac_find_xbitmaps.m4 2019-12-11 16:01:58.463883900 +0100 +@@ -0,0 +1,10 @@ ++AC_DEFUN([AC_FIND_XBITMAPS], ++[ ++ ++AC_CHECK_HEADERS(X11/bitmaps/gray) ++ ++CFLAGS="$CFLAGS `pkg-config xbitmaps --cflags`" ++AC_SUBST(CFLAGS) ++LIBS="$LIBS `pkg-config xbitmaps --libs`" ++AC_SUBST(LIBS) ++]) +diff -Naur motif-2.3.8/AUTHORS motif-2.3.8_patched/AUTHORS +--- motif-2.3.8/AUTHORS 1970-01-01 01:00:00.000000000 +0100 ++++ motif-2.3.8_patched/AUTHORS 2019-12-12 08:40:39.947561253 +0100 +@@ -0,0 +1 @@ ++Dummy AUTHORS file: upstream Motif did not supply this and autoreconf needs it. +\ No newline at end of file +diff -Naur motif-2.3.8/configure.ac motif-2.3.8_patched/configure.ac +--- motif-2.3.8/configure.ac 2017-12-05 13:43:54.000000000 +0100 ++++ motif-2.3.8_patched/configure.ac 2019-12-11 16:01:58.467217264 +0100 +@@ -274,6 +274,7 @@ + AC_SUBST(LIB_XP) + + AC_FIND_XFT ++AC_FIND_XBITMAPS + AC_IMAGE_SUPPORT + + +diff -Naur motif-2.3.8/NEWS motif-2.3.8_patched/NEWS +--- motif-2.3.8/NEWS 1970-01-01 01:00:00.000000000 +0100 ++++ motif-2.3.8_patched/NEWS 2019-12-12 08:40:59.010963846 +0100 +@@ -0,0 +1 @@ ++Dummy NEWS file: upstream motif did not supply this but autoreconf needs it. diff --git a/var/spack/repos/builtin/packages/motif/package.py b/var/spack/repos/builtin/packages/motif/package.py index b15302c64c..7a6bc0de8f 100644 --- a/var/spack/repos/builtin/packages/motif/package.py +++ b/var/spack/repos/builtin/packages/motif/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,6 +11,8 @@ class Motif(AutotoolsPackage): Motif - Graphical user interface (GUI) specification and the widget toolkit """ + force_autoreconf = True + homepage = "http://motif.ics.com/" url = "http://cfhcable.dl.sourceforge.net/project/motif/Motif%202.3.8%20Source%20Code/motif-2.3.8.tar.gz" @@ -25,3 +27,16 @@ class Motif(AutotoolsPackage): depends_on("libxfixes") depends_on("xbitmaps") depends_on("jpeg") + + # we need the following for autoreconf + depends_on("automake", type="build") + depends_on("autoconf", type="build") + depends_on("m4", type="build") + depends_on("libtool", type="build") + + patch('add_xbitmaps_dependency.patch') + + def autoreconf(self, spec, prefix): + autoreconf = which('autoreconf') + with working_dir(self.configure_directory): + autoreconf('-ivf') diff --git a/var/spack/repos/builtin/packages/motioncor2/package.py b/var/spack/repos/builtin/packages/motioncor2/package.py index 219a468bb2..b7b114d27f 100644 --- a/var/spack/repos/builtin/packages/motioncor2/package.py +++ b/var/spack/repos/builtin/packages/motioncor2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mount-point-attributes/package.py b/var/spack/repos/builtin/packages/mount-point-attributes/package.py index 990cdd1b46..3ab6808c3e 100644 --- a/var/spack/repos/builtin/packages/mount-point-attributes/package.py +++ b/var/spack/repos/builtin/packages/mount-point-attributes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mozjs/package.py b/var/spack/repos/builtin/packages/mozjs/package.py index bff5708a0f..664ba0a08a 100644 --- a/var/spack/repos/builtin/packages/mozjs/package.py +++ b/var/spack/repos/builtin/packages/mozjs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mpark-variant/nvcc.patch b/var/spack/repos/builtin/packages/mpark-variant/nvcc.patch new file mode 100644 index 0000000000..9bd7e60d5b --- /dev/null +++ b/var/spack/repos/builtin/packages/mpark-variant/nvcc.patch @@ -0,0 +1,40 @@ +From d7fb6201cbe830c2aef35b3fd0df040f9eae6d4d Mon Sep 17 00:00:00 2001 +From: Gavin Ridley <gavin.keith.ridley@gmail.com> +Date: Tue, 31 Dec 2019 14:42:14 -0500 +Subject: [PATCH] now compiles in nvcc 10.2 + +--- + include/mpark/variant.hpp | 10 +++++----- + 1 file changed, 5 insertions(+), 5 deletions(-) + +diff --git a/include/mpark/variant.hpp b/include/mpark/variant.hpp +index ef496619b..f4848db88 100644 +--- a/include/mpark/variant.hpp ++++ b/include/mpark/variant.hpp +@@ -2001,20 +2001,20 @@ namespace mpark { + #ifdef MPARK_CPP14_CONSTEXPR + namespace detail { + +- inline constexpr bool all(std::initializer_list<bool> bs) { ++ inline constexpr bool any(std::initializer_list<bool> bs) { + for (bool b : bs) { +- if (!b) { +- return false; ++ if (b) { ++ return true; + } + } +- return true; ++ return false; + } + + } // namespace detail + + template <typename Visitor, typename... Vs> + inline constexpr decltype(auto) visit(Visitor &&visitor, Vs &&... vs) { +- return (detail::all({!vs.valueless_by_exception()...}) ++ return (!detail::any({vs.valueless_by_exception()...}) + ? (void)0 + : throw_bad_variant_access()), + detail::visitation::variant::visit_value( + diff --git a/var/spack/repos/builtin/packages/mpark-variant/package.py b/var/spack/repos/builtin/packages/mpark-variant/package.py index afeb4bd7e5..85b9bfb82d 100644 --- a/var/spack/repos/builtin/packages/mpark-variant/package.py +++ b/var/spack/repos/builtin/packages/mpark-variant/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,5 +16,8 @@ class MparkVariant(CMakePackage): version('1.4.0', sha256='8f6b28ab3640b5d76d5b6664dda7257a4405ce59179220431b8fd196c79b2ecb') version('1.3.0', sha256='d0f7e41f818fcc839797a8017e76b8b66b323651c304cff641a83a56ae9943c6') + # Ref.: https://github.com/mpark/variant/pull/73 + patch('nvcc.patch', when='@:1.4.0') + conflicts('%gcc@:4.7') conflicts('%clang@:3.5') diff --git a/var/spack/repos/builtin/packages/mpc/package.py b/var/spack/repos/builtin/packages/mpc/package.py index a8d3a30ab9..adca4e3fcf 100644 --- a/var/spack/repos/builtin/packages/mpc/package.py +++ b/var/spack/repos/builtin/packages/mpc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,13 +6,13 @@ from spack import * -class Mpc(AutotoolsPackage): +class Mpc(AutotoolsPackage, GNUMirrorPackage): """Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result.""" homepage = "http://www.multiprecision.org" - url = "https://ftpmirror.gnu.org/mpc/mpc-1.1.0.tar.gz" + gnu_mirror_path = "mpc/mpc-1.1.0.tar.gz" list_url = "http://www.multiprecision.org/mpc/download.html" version('1.1.0', sha256='6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e') @@ -25,14 +25,6 @@ class Mpc(AutotoolsPackage): depends_on('mpfr@2.4.2:') depends_on('mpfr@3.0.0:', when='@1.1.0:') - def url_for_version(self, version): - if version < Version("1.0.1"): - url = "http://www.multiprecision.org/mpc/download/mpc-{0}.tar.gz" - else: - url = "https://ftpmirror.gnu.org/mpc/mpc-{0}.tar.gz" - - return url.format(version) - def configure_args(self): spec = self.spec return [ diff --git a/var/spack/repos/builtin/packages/mpdecimal/package.py b/var/spack/repos/builtin/packages/mpdecimal/package.py index 3353041931..a8ae10d5ff 100644 --- a/var/spack/repos/builtin/packages/mpdecimal/package.py +++ b/var/spack/repos/builtin/packages/mpdecimal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mpe2/package.py b/var/spack/repos/builtin/packages/mpe2/package.py index e185e42c0b..236b2550cc 100644 --- a/var/spack/repos/builtin/packages/mpe2/package.py +++ b/var/spack/repos/builtin/packages/mpe2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mpest/package.py b/var/spack/repos/builtin/packages/mpest/package.py index e1ecca84f9..17787761fb 100644 --- a/var/spack/repos/builtin/packages/mpest/package.py +++ b/var/spack/repos/builtin/packages/mpest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,8 +24,8 @@ class Mpest(MakefilePackage): mkdirp(prefix.bin) install('mpest', prefix.bin) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if self.spec.satisfies('platform=darwin'): - spack_env.set('ARCHITECTURE', 'mac') + env.set('ARCHITECTURE', 'mac') else: - spack_env.set('ARCHITECTURE', 'unix') + env.set('ARCHITECTURE', 'unix') diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py index 97d0f090b2..b0aaafb892 100644 --- a/var/spack/repos/builtin/packages/mpfr/package.py +++ b/var/spack/repos/builtin/packages/mpfr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Mpfr(AutotoolsPackage): +class Mpfr(AutotoolsPackage, GNUMirrorPackage): """The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.""" homepage = "https://www.mpfr.org/" - url = "https://ftpmirror.gnu.org/mpfr/mpfr-4.0.2.tar.bz2" + gnu_mirror_path = "mpfr/mpfr-4.0.2.tar.bz2" version('4.0.2', sha256='c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc') version('4.0.1', sha256='a4d97610ba8579d380b384b225187c250ef88cfe1d5e7226b89519374209b86b') diff --git a/var/spack/repos/builtin/packages/mpibash/mpibash-4.3.patch b/var/spack/repos/builtin/packages/mpi-bash/mpibash-4.3.patch index 17e285b0bf..17e285b0bf 100644 --- a/var/spack/repos/builtin/packages/mpibash/mpibash-4.3.patch +++ b/var/spack/repos/builtin/packages/mpi-bash/mpibash-4.3.patch diff --git a/var/spack/repos/builtin/packages/mpibash/package.py b/var/spack/repos/builtin/packages/mpi-bash/package.py index 174109f6d9..0a3d9eb30a 100644 --- a/var/spack/repos/builtin/packages/mpibash/package.py +++ b/var/spack/repos/builtin/packages/mpi-bash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Mpibash(AutotoolsPackage): +class MpiBash(AutotoolsPackage): """Parallel scripting right from the Bourne-Again Shell (Bash)""" homepage = "https://github.com/lanl/MPI-Bash" diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 5d7a74cb59..0980c66818 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,6 +19,7 @@ class Mpich(AutotoolsPackage): list_depth = 1 version('develop', submodules=True) + version('3.3.2', sha256='4bfaf8837a54771d3e4922c84071ef80ffebddbb6971a006038d91ee7ef959b9') version('3.3.1', sha256='fe551ef29c8eea8978f679484441ed8bb1d943f6ad25b63c235d4b9243d551e5') version('3.3', sha256='329ee02fe6c3d101b6b30a7b6fb97ddf6e82b28844306771fa9dd8845108fa0b') version('3.2.1', sha256='5db53bf2edfaa2238eb6a0a5bc3d2c2ccbfbb1badd79b664a1a919d2ce2330f1') @@ -93,6 +94,8 @@ spack package at this time.''', # See https://github.com/pmodels/mpich/issues/3665 depends_on('libfabric@:1.6', when='device=ch3 netmod=ofi') + depends_on('ucx', when='netmod=ucx') + depends_on('libpciaccess', when="+pci") depends_on('libxml2') @@ -101,6 +104,12 @@ spack package at this time.''', depends_on('pmix', when='pmi=pmix') + # building from git requires regenerating autotools files + depends_on('automake@1.15:', when='@develop', type=("build")) + depends_on('libtool@2.4.4:', when='@develop', type=("build")) + depends_on("m4", when="@develop", type=("build")), + depends_on("autoconf@2.67:", when='@develop', type=("build")) + conflicts('device=ch4', when='@:3.2') conflicts('netmod=ofi', when='@:3.1.4') conflicts('netmod=ucx', when='device=ch3') @@ -166,7 +175,7 @@ spack package at this time.''', # avoid delayed build errors in dependents. if (self.compiler.f77 is None) or (self.compiler.fc is None): raise InstallError( - 'Mpich requires both C and Fortran compilers!' + 'MPICH requires both C and Fortran compilers!' ) def configure_args(self): @@ -180,6 +189,15 @@ spack package at this time.''', spec else 'yes') ] + if '+slurm' in spec: + config_args.append('--with-slurm=yes') + config_args.append('--with-slurm-include={0}'.format( + spec['slurm'].prefix.include)) + config_args.append('--with-slurm-lib={0}'.format( + spec['slurm'].prefix.lib)) + else: + config_args.append('--with-slurm=no') + if 'pmi=off' in spec: config_args.append('--with-pmi=no') elif 'pmi=pmi' in spec: @@ -207,10 +225,13 @@ spack package at this time.''', config_args.append(device_config) - # Specify libfabric's path explicitly, otherwise configure might fall - # back to an embedded version of libfabric. + # Specify libfabric or ucx path explicitly, otherwise + # configure might fall back to an embedded version. if 'netmod=ofi' in spec: config_args.append('--with-libfabric={0}'.format( spec['libfabric'].prefix)) + if 'netmod=ucx' in spec: + config_args.append('--with-ucx={0}'.format( + spec['ucx'].prefix)) return config_args diff --git a/var/spack/repos/builtin/packages/mpifileutils/package.py b/var/spack/repos/builtin/packages/mpifileutils/package.py index 6bcdd02ce2..30fc982505 100644 --- a/var/spack/repos/builtin/packages/mpifileutils/package.py +++ b/var/spack/repos/builtin/packages/mpifileutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,13 +21,14 @@ class Mpifileutils(Package): git = "https://github.com/hpc/mpifileutils.git" version('develop', branch='master') + version('0.10', sha256='5a71a9acd9841c3c258fc0eaea942f18abcb40098714cc90462b57696c07e3c5') version('0.9.1', sha256='15a22450f86b15e7dc4730950b880fda3ef6f59ac82af0b268674d272aa61c69') - version('0.9', sha256='1b8250af01aae91c985ca5d61521bfaa4564e46efa15cee65cd0f82cf5a2bcfb') + version('0.9', sha256='1b8250af01aae91c985ca5d61521bfaa4564e46efa15cee65cd0f82cf5a2bcfb') conflicts('platform=darwin') depends_on('mpi') - depends_on('libcircle') + depends_on('libcircle@0.3:') # need precise version of dtcmp, since DTCMP_Segmented_exscan added # in v1.0.3 but renamed in v1.1.0 and later @@ -44,14 +45,14 @@ class Mpifileutils(Package): variant('lustre', default=False, description="Enable optimizations and features for Lustre") - variant('experimental', default=False, - description="Install experimental tools") - conflicts('+experimental', when='@:0.6') - variant('gpfs', default=False, description="Enable optimizations and features for GPFS") conflicts('+gpfs', when='@:0.8.1') + variant('experimental', default=False, + description="Install experimental tools") + conflicts('+experimental', when='@:0.6') + def cmake_args(self): args = std_cmake_args args.append('-DCMAKE_INSTALL_PREFIX=%s' % self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/mpilander/package.py b/var/spack/repos/builtin/packages/mpilander/package.py index 54c246699f..276f380a86 100644 --- a/var/spack/repos/builtin/packages/mpilander/package.py +++ b/var/spack/repos/builtin/packages/mpilander/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mpileaks/package.py b/var/spack/repos/builtin/packages/mpileaks/package.py index b4dfd551f8..e30a1d62fb 100644 --- a/var/spack/repos/builtin/packages/mpileaks/package.py +++ b/var/spack/repos/builtin/packages/mpileaks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mpip/package.py b/var/spack/repos/builtin/packages/mpip/package.py index 4f4d5c006d..36fe6e31a7 100644 --- a/var/spack/repos/builtin/packages/mpip/package.py +++ b/var/spack/repos/builtin/packages/mpip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,9 @@ class Mpip(AutotoolsPackage): """mpiP: Lightweight, Scalable MPI Profiling""" homepage = "http://mpip.sourceforge.net/" url = "http://downloads.sourceforge.net/project/mpip/mpiP/mpiP-3.4.1/mpiP-3.4.1.tar.gz" + git = "https://github.com/llnl/mpip.git" + version('master', branch='master') version("3.4.1", sha256="688bf37d73211e6a915f9fc59c358282a266d166c0a10af07a38a01a473296f0") depends_on("elf") diff --git a/var/spack/repos/builtin/packages/mpir/package.py b/var/spack/repos/builtin/packages/mpir/package.py index 06b6db7e27..b2ec566f49 100644 --- a/var/spack/repos/builtin/packages/mpir/package.py +++ b/var/spack/repos/builtin/packages/mpir/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mpix-launch-swift/package.py b/var/spack/repos/builtin/packages/mpix-launch-swift/package.py index 55a829467b..801d298110 100644 --- a/var/spack/repos/builtin/packages/mpix-launch-swift/package.py +++ b/var/spack/repos/builtin/packages/mpix-launch-swift/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mpt/package.py b/var/spack/repos/builtin/packages/mpt/package.py new file mode 100644 index 0000000000..12f7202ebc --- /dev/null +++ b/var/spack/repos/builtin/packages/mpt/package.py @@ -0,0 +1,77 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Mpt(Package): + """HPE MPI is HPE's implementation of + the Message Passing Interface (MPI) standard. + + Note: HPE MPI is proprietry software. Spack will search your + current directory for the download file. Alternatively, add this file to a + mirror so that Spack can find it. For instructions on how to set up a + mirror, see http://spack.readthedocs.io/en/latest/mirrors.html""" + + homepage = "https://buy.hpe.com/us/en/software/high-performance-computing-software/hpe-message-passing-interface-mpi/p/1010144155" + + provides('mpi') + provides('mpi@:3.1', when='@3:') + provides('mpi@:1.3', when='@1:') + + filter_compiler_wrappers( + 'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpif08', + relative_root='bin' + ) + + @property + def libs(self): + query_parameters = self.spec.last_query.extra_parameters + libraries = ['libmpi'] + + if 'cxx' in query_parameters: + libraries = ['libmpicxx'] + libraries + + return find_libraries( + libraries, root=self.prefix, shared=True, recursive=True + ) + + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('MPICC', self.prefix.bin.mpicc) + env.set('MPICXX', self.prefix.bin.mpicxx) + env.set('MPIF77', self.prefix.bin.mpif77) + env.set('MPIF90', self.prefix.bin.mpif90) + env.set('MPICC_CC', spack_cc) + env.set('MPICXX_CXX', spack_cxx) + env.set('MPIF90_F90', spack_fc) + + def setup_dependent_package(self, module, dependent_spec): + if 'platform=cray' in self.spec: + self.spec.mpicc = spack_cc + self.spec.mpicxx = spack_cxx + self.spec.mpifc = spack_fc + self.spec.mpif77 = spack_f77 + else: + self.spec.mpicc = self.prefix.bin.mpicc + self.spec.mpicxx = self.prefix.bin.mpicxx + self.spec.mpifc = self.prefix.bin.mpif90 + self.spec.mpif77 = self.prefix.bin.mpif77 + + @property + def fetcher(self): + msg = """This package is a placeholder for HPE MPI, a + system-provided, proprietary MPI implementation. + + Add to your packages.yaml (changing the /opt/ path to match + where HPE MPI is actually installed): + + packages: + mpt: + paths: + mpt@2.20: /opt/ + buildable: False + + """ + raise InstallError(msg) diff --git a/var/spack/repos/builtin/packages/mrbayes/package.py b/var/spack/repos/builtin/packages/mrbayes/package.py index 930bc04af9..bfc485eb31 100644 --- a/var/spack/repos/builtin/packages/mrbayes/package.py +++ b/var/spack/repos/builtin/packages/mrbayes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,21 +13,18 @@ class Mrbayes(AutotoolsPackage): of model parameters.""" homepage = "http://mrbayes.sourceforge.net" - git = "https://github.com/NBISweden/MrBayes.git" + url = "https://github.com/NBISweden/MrBayes/releases/download/v3.2.7a/mrbayes-3.2.7a.tar.gz" - version('2017-11-22', commit='8a9adb11bcc538cb95d91d57568dff383f924503') + version('3.2.7a', sha256='1a4670be84e6b968d59382328294db4c8ceb73e0c19c702265deec6f2177815c') + version('3.2.7', sha256='39d9eb269969b501268d5c27f77687c6eaa2c71ccf15c724e6f330fc405f24b9') variant('mpi', default=True, description='Enable MPI parallel support') variant('beagle', default=True, description='Enable BEAGLE library for speed benefits') - variant('sse', default=True, description='Enable SSE in order to substantially speed up execution') - - depends_on('autoconf', type='build') - depends_on('automake', type='build') - depends_on('libtool', type='build') - depends_on('m4', type='build') + variant('readline', default=False, description='Enable readline library, not recommended with MPI') depends_on('libbeagle', when='+beagle') depends_on('mpi', when='+mpi') + depends_on('readline', when='+readline') def configure_args(self): args = [] @@ -35,14 +32,14 @@ class Mrbayes(AutotoolsPackage): args.append('--with-beagle=no') else: args.append('--with-beagle=%s' % self.spec['libbeagle'].prefix) - if '~sse' in self.spec: - args.append('--enable-sse=no') + if '+readline' in self.spec: + args.append('--with-readline=yes') else: - args.append('--enable-sse=yes') + args.append('--with-readline=no') if '~mpi' in self.spec: - args.append('--enable-mpi=no') + args.append('--with-mpi=no') else: - args.append('--enable-mpi=yes') + args.append('--with-mpi=yes') return args def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py index 6cdbef3130..f18286118e 100644 --- a/var/spack/repos/builtin/packages/mrnet/package.py +++ b/var/spack/repos/builtin/packages/mrnet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,14 +20,11 @@ class Mrnet(AutotoolsPackage): version('4.1.0', sha256='94758191ac46a9dbfea931a8e61167fe7e8a5f880caa418305c44f1d12af5e45') version('4.0.0', sha256='7207c6d493b3f17c386667cfefa81364c96b9c8b831c67442d218d77813c5d38') - variant('cti', default=False, - description="Build the MRNet with the CTI startup option") variant('lwthreads', default=False, description="Also build the MRNet LW threadsafe libraries") parallel = False depends_on("boost") - depends_on("cti", when='+cti') def configure_args(self): spec = self.spec @@ -37,11 +34,5 @@ class Mrnet(AutotoolsPackage): # lwthreads variant is present if '+lwthreads' in spec: config_args.append('--enable-ltwt-threadsafe') - # Build the MRNet with CTI based start-up when - # the cti variant is present - if '+cti' in spec: - config_args.append('--with-startup=cray-cti') - cti = self.spec['cti'].prefix - config_args.append('--with-craycti-inc=-I%s/include' % cti) - config_args.append('--with-craycti-lib=-I%s/lib' % cti) + return config_args diff --git a/var/spack/repos/builtin/packages/mrtrix3/package.py b/var/spack/repos/builtin/packages/mrtrix3/package.py index 63d00a200b..4cb03770d6 100644 --- a/var/spack/repos/builtin/packages/mrtrix3/package.py +++ b/var/spack/repos/builtin/packages/mrtrix3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -35,5 +35,5 @@ class Mrtrix3(Package): build() install_tree('.', prefix) - def setup_environment(self, spac_env, run_env): - run_env.prepend_path('PATH', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/mscgen/package.py b/var/spack/repos/builtin/packages/mscgen/package.py index 34a3d921b4..a39bdc0e3c 100644 --- a/var/spack/repos/builtin/packages/mscgen/package.py +++ b/var/spack/repos/builtin/packages/mscgen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py index 114c760a3f..153c551369 100644 --- a/var/spack/repos/builtin/packages/msgpack-c/package.py +++ b/var/spack/repos/builtin/packages/msgpack-c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mshadow/package.py b/var/spack/repos/builtin/packages/mshadow/package.py index 4248beee1d..235ed182fa 100644 --- a/var/spack/repos/builtin/packages/mshadow/package.py +++ b/var/spack/repos/builtin/packages/mshadow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/msmc/package.py b/var/spack/repos/builtin/packages/msmc/package.py index 3caf431c3f..eec3682753 100644 --- a/var/spack/repos/builtin/packages/msmc/package.py +++ b/var/spack/repos/builtin/packages/msmc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mstk/package.py b/var/spack/repos/builtin/packages/mstk/package.py new file mode 100644 index 0000000000..07e21b9ba9 --- /dev/null +++ b/var/spack/repos/builtin/packages/mstk/package.py @@ -0,0 +1,115 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Mstk(CMakePackage): + """MSTK is a mesh framework that allows users to represent, + manipulate and query unstructured 3D arbitrary topology meshes + in a general manner without the need to code their own data + structures. MSTK is a flexible framework in that it allows a + variety of underlying representations for the mesh while + maintaining a common interface. It allows users to choose from + different mesh representations either at initialization (implemented) + or during the program execution (not yet implemented) so that the + optimal data structures are used for the particular algorithm. + The interaction of users and applications with MSTK is through a + functional interface that acts as though the mesh always contains + vertices, edges, faces and regions and maintains connectivity between + all these entities.""" + + homepage = "https://github.com/MeshToolkit/MSTK" + git = "https://github.com/MeshToolkit/MSTK" + url = "https://github.com/MeshToolkit/MSTK/archive/3.3.1.tar.gz" + + maintainers = ['raovgarimella', 'julienloiseau'] + + version('master', branch='master') + version('3.3.2', sha256='fb4ffa97af4d0a0d4771c8585d0b27538b013d8b1cfaff992e5e054fef62af0b') + version('3.3.1', sha256='9fdb0c33c1b68714d708b355d963547cf41332812658d4560d4db43904fc78de') + version('3.3.0', sha256='205c48fb5619937b5dd83788da739b7c2060155b7c41793e29ce05422b8f7dfb') + version('3.2.1', sha256='09bc6684abb576e34c324322db6f71f8987c6ec436a54256b85ef4db40185470') + version('3.2.0', sha256='57e58c5a7a456dbc608ce9f834a06c212a1aa64ac3ebc880ea0b8a19b000dab0') + version('3.1.3', sha256='03f6901cd6d563e1705a173c1a2fbbef10ab9a43f533f6ba758e357c03bdfa16') + version('3.1.2', sha256='1eb44c29554f45695f875fc60ab81554a2c46a041ef58a7224f3767d30e2846e') + version('3.1.1', sha256='5a03873c69fb38acd7ce27f2a5fa0643dd1cfcc3e214cff4aa26ee717651cc0b') + version('3.1.0', sha256='70e68d8a90cd2367015e0ab3459ed230a7995ad2297671742d9be6e28bc03dcf') + version('3.0.4', sha256='99e4c996bf22fd325335ed1391dfe735b0a338e8e4d733204d56dde7ef4eedf3') + version('3.0.3', sha256='618e371a48077f2b4ccfafd4d174c05f007b2ea7a51e0399df67442639409518') + version('3.0.2', sha256='b0172cd68e5137b8585d82c37b8a4af4b7e884f04d1b7d006a399d39447fe89e') + version('3.0.1', sha256='d44e4bf01b118b1d19710aa839b3f5f0c1a8391264a435f641ba4bd23bcf45ec') + version('3.0.0', sha256='d993ff5fc6c431067eb97e4089835c7790397d9c1ad88a56523c0591d451df19') + + variant('exodusii', default=False, description='Enable ExodusII') + variant('use_markers', default=True, description='Enable use of markers') + variant('parallel', default=False, description='Enable Parallel Support') + variant('partitioner', default='none', + values=('none', 'metis', 'zoltan', 'all'), + multi=False, description='Choose partitioner') + conflicts('partitioner=none', when='+parallel') + conflicts('partitioner=all', when='-parallel') + conflicts('partitioner=zoltan', when='-parallel') + + # MSTK turns on METIS only for parallel builds + conflicts('partitioner=metis', when='-parallel') + + # dependencies + depends_on('cmake@3.11:', type='build') + + # + depends_on('mpi', when='+parallel') + + depends_on('zoltan -fortran', when='partitioner=zoltan') + depends_on('zoltan -fortran', when='partitioner=all') + depends_on('metis', when='partitioner=metis') + depends_on('metis', when='partitioner=all') + + # Exodusii variant + # The default exodusii build with mpi support + depends_on('exodusii', when='+exodusii') + + # Unit testing variant + depends_on('unittest-cpp', type='test') + + def cmake_args(self): + options = [] + if '+use_markers' in self.spec: + options.append('-DMSTK_USE_MARKERS=ON') + else: + options.append('-DMSTK_USE_MARKERS=OFF') + + # Parallel variant + if '+parallel' in self.spec: + options.append('-DENABLE_PARALLEL=ON') + else: + options.append('-DENABLE_PARALLEL=OFF') + + if 'partitioner=none' in self.spec: + options.append('-DENABLE_METIS=OFF') + options.append('-DENABLE_ZOLTAN=OFF') + else: + if 'zoltan' in self.spec: + options.append('-DENABLE_ZOLTAN=ON') + else: + options.append('-DENABLE_ZOLTAN=OFF') + if 'metis' in self.spec: + options.append('-DENABLE_METIS=ON') + else: + options.append('-DENABLE_METIS=OFF') + + # ExodusII variant + if '+exodusii' in self.spec: + options.append('-DENABLE_ExodusII=ON') + else: + options.append('-DENABLE_ExodusII=OFF') + + # Unit test variant + if self.run_tests: + options.append('-DENABLE_Tests=ON') + else: + options.append('-DENABLE_Tests=OFF') + + return options diff --git a/var/spack/repos/builtin/packages/multitail/package.py b/var/spack/repos/builtin/packages/multitail/package.py index ab35455be1..78fbdcfd33 100644 --- a/var/spack/repos/builtin/packages/multitail/package.py +++ b/var/spack/repos/builtin/packages/multitail/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/multitime/package.py b/var/spack/repos/builtin/packages/multitime/package.py index c3fc5d6fdf..00510c5cbc 100644 --- a/var/spack/repos/builtin/packages/multitime/package.py +++ b/var/spack/repos/builtin/packages/multitime/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/multiverso/package.py b/var/spack/repos/builtin/packages/multiverso/package.py index c38696dba9..35535eff51 100644 --- a/var/spack/repos/builtin/packages/multiverso/package.py +++ b/var/spack/repos/builtin/packages/multiverso/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mummer/package.py b/var/spack/repos/builtin/packages/mummer/package.py index 7b8a3ca51e..e1edf39b8e 100644 --- a/var/spack/repos/builtin/packages/mummer/package.py +++ b/var/spack/repos/builtin/packages/mummer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 48e8cca29e..a56bc111e2 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -55,11 +55,6 @@ class Mumps(Package): patch('examples.patch', when='@5.1.1%clang^spectrum-mpi') patch('gfortran8.patch', when='@5.1.2') - # this function is not a patch function because in case scalapack - # is needed it uses self.spec['scalapack'].fc_link set by the - # setup_dependent_environment in scalapck. This happen after patch - # end before install - # def patch(self): def write_makefile_inc(self): if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and ( '+mpi' not in self.spec): @@ -119,6 +114,7 @@ class Mumps(Package): using_pgi = self.compiler.name == "pgi" using_intel = self.compiler.name == "intel" using_xl = self.compiler.name in ['xl', 'xl_r'] + using_fj = self.compiler.name == "fj" # The llvm compiler suite does not contain a Fortran compiler by # default. Its possible that a Spack user may have configured @@ -176,17 +172,18 @@ class Mumps(Package): "MUMPS_TYPE = par"]) else: makefile_conf.extend( - ["CC = cc", - "FC = fc", - "FL = fc", + ["CC = {0}".format(spack_cc), + "FC = {0}".format(spack_fc), + "FL = {0}".format(spack_fc), "MUMPS_TYPE = seq"]) # TODO: change the value to the correct one according to the # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER - if using_intel or using_pgi: - # Intel & PGI Fortran compiler provides the main() function so - # C examples linked with the Fortran compiler require a - # hack defined by _DMAIN_COMP (see examples/c_example.c) + if using_intel or using_pgi or using_fj: + # Intel, PGI, and Fujitsu Fortran compiler provides + # the main() function so C examples linked with the Fortran + # compiler require a hack defined by _DMAIN_COMP + # (see examples/c_example.c) makefile_conf.append("CDEFS = -DAdd_ -DMAIN_COMP") else: if not using_xlf: diff --git a/var/spack/repos/builtin/packages/munge/package.py b/var/spack/repos/builtin/packages/munge/package.py index d56768d29f..5c10720e77 100644 --- a/var/spack/repos/builtin/packages/munge/package.py +++ b/var/spack/repos/builtin/packages/munge/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py index 33800c9afa..3f0018e9d1 100644 --- a/var/spack/repos/builtin/packages/muparser/package.py +++ b/var/spack/repos/builtin/packages/muparser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/muscle/package.py b/var/spack/repos/builtin/packages/muscle/package.py index f1d5a71a16..4e62064362 100644 --- a/var/spack/repos/builtin/packages/muscle/package.py +++ b/var/spack/repos/builtin/packages/muscle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/muse/package.py b/var/spack/repos/builtin/packages/muse/package.py index 7481435bd2..4f1831416e 100644 --- a/var/spack/repos/builtin/packages/muse/package.py +++ b/var/spack/repos/builtin/packages/muse/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/musl/package.py b/var/spack/repos/builtin/packages/musl/package.py index cfbcf177bb..7c68735c20 100644 --- a/var/spack/repos/builtin/packages/musl/package.py +++ b/var/spack/repos/builtin/packages/musl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/muster/package.py b/var/spack/repos/builtin/packages/muster/package.py index a2a733e966..42c369f8d8 100644 --- a/var/spack/repos/builtin/packages/muster/package.py +++ b/var/spack/repos/builtin/packages/muster/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mutationpp/package.py b/var/spack/repos/builtin/packages/mutationpp/package.py index 26eabdf8c1..94abb0fbc4 100644 --- a/var/spack/repos/builtin/packages/mutationpp/package.py +++ b/var/spack/repos/builtin/packages/mutationpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -40,12 +40,12 @@ class Mutationpp(CMakePackage): if '+examples' in self.spec and os.path.isdir('examples'): install_tree('examples', self.prefix.examples) - def setup_environment(self, spack_env, run_env): - run_env.set('MPP_DIRECTORY', self.prefix) + def setup_run_environment(self, env): + env.set('MPP_DIRECTORY', self.prefix) if os.path.isdir(self.prefix.data): - run_env.set('MPP_DATA_DIRECTORY', self.prefix.data) + env.set('MPP_DATA_DIRECTORY', self.prefix.data) - def setup_dependent_environment(self, spack_env, run_env): - spack_env.set('MPP_DIRECTORY', self.prefix) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('MPP_DIRECTORY', self.prefix) if os.path.isdir(self.prefix.data): - spack_env.set('MPP_DATA_DIRECTORY', self.prefix.data) + env.set('MPP_DATA_DIRECTORY', self.prefix.data) diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index 1673316bb7..87e9f77848 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -1,21 +1,21 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os.path import sys -from spack import * - class Mvapich2(AutotoolsPackage): """MVAPICH2 is an MPI implementation for Infiniband networks.""" homepage = "http://mvapich.cse.ohio-state.edu/" - url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2.tar.gz" + url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.2.tar.gz" list_url = "http://mvapich.cse.ohio-state.edu/downloads/" # Prefer the latest stable release - version('2.3.1', sha256='314e12829f75f3ed83cd4779a972572d1787aac6543a3d024ea7c6080e0ee3bf', preferred=True) + version('2.3.2', sha256='30cc0d7bcaa075d204692f76bca4d65a539e0f661c7460ffa9f835d6249e1ebf') + version('2.3.1', sha256='314e12829f75f3ed83cd4779a972572d1787aac6543a3d024ea7c6080e0ee3bf') version('2.3', sha256='01d5fb592454ddd9ecc17e91c8983b6aea0e7559aa38f410b111c8ef385b50dd') version('2.3rc2', sha256='dc3801f879a54358d17002a56afd45186e2e83edc5b8367b5c317e282eb6d6bf') version('2.3rc1', sha256='607d309c864a6d57f5fa78fe6dd02368919736b8be0f4ddb938aba303ef9c45c') @@ -24,8 +24,10 @@ class Mvapich2(AutotoolsPackage): version('2.1', sha256='49f3225ad17d2f3b6b127236a0abdc979ca8a3efb8d47ab4b6cd4f5252d05d29') provides('mpi') - provides('mpi@:3.0') + provides('mpi@:3.1', when='@2.3:') + provides('mpi@:3.0', when='@2.1:') + variant('wrapperrpath', default=True, description='Enable wrapper rpath') variant('debug', default=False, description='Enable debug info and error messages at run-time') @@ -72,7 +74,7 @@ class Mvapich2(AutotoolsPackage): variant( 'fabrics', description='The fabric enabled for this build', - default='psm', + default='mrail', values=( 'psm', 'psm2', 'sock', 'nemesisib', 'nemesis', 'mrail', 'nemesisibtcp', 'nemesistcpib', 'nemesisofi' @@ -195,34 +197,35 @@ class Mvapich2(AutotoolsPackage): return opts - def setup_environment(self, spack_env, run_env): - spec = self.spec + def setup_build_environment(self, env): # mvapich2 configure fails when F90 and F90FLAGS are set - spack_env.unset('F90') - spack_env.unset('F90FLAGS') - if 'process_managers=slurm' in spec: - run_env.set('SLURM_MPI_TYPE', 'pmi2') + env.unset('F90') + env.unset('F90FLAGS') + + def setup_run_environment(self, env): + if 'process_managers=slurm' in self.spec: + env.set('SLURM_MPI_TYPE', 'pmi2') - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('MPICC', os.path.join(self.prefix.bin, 'mpicc')) + env.set('MPICXX', os.path.join(self.prefix.bin, 'mpicxx')) + env.set('MPIF77', os.path.join(self.prefix.bin, 'mpif77')) + env.set('MPIF90', os.path.join(self.prefix.bin, 'mpif90')) - spack_env.set('MPICH_CC', spack_cc) - spack_env.set('MPICH_CXX', spack_cxx) - spack_env.set('MPICH_F77', spack_f77) - spack_env.set('MPICH_F90', spack_fc) - spack_env.set('MPICH_FC', spack_fc) + env.set('MPICH_CC', spack_cc) + env.set('MPICH_CXX', spack_cxx) + env.set('MPICH_F77', spack_f77) + env.set('MPICH_F90', spack_fc) + env.set('MPICH_FC', spack_fc) def setup_dependent_package(self, module, dependent_spec): - self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') - self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx') - self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') - self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') + self.spec.mpicc = os.path.join(self.prefix.bin, 'mpicc') + self.spec.mpicxx = os.path.join(self.prefix.bin, 'mpicxx') + self.spec.mpifc = os.path.join(self.prefix.bin, 'mpif90') + self.spec.mpif77 = os.path.join(self.prefix.bin, 'mpif77') self.spec.mpicxx_shared_libs = [ - join_path(self.prefix.lib, 'libmpicxx.{0}'.format(dso_suffix)), - join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix)) + os.path.join(self.prefix.lib, 'libmpicxx.{0}'.format(dso_suffix)), + os.path.join(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix)) ] @run_before('configure') @@ -246,6 +249,8 @@ class Mvapich2(AutotoolsPackage): "--enable-threads={0}".format(spec.variants['threads'].value), "--with-ch3-rank-bits={0}".format( spec.variants['ch3_rank_bits'].value), + '--enable-wrapper-rpath={0}'.format('no' if '~wrapperrpath' in + spec else 'yes') ] args.extend(self.enable_or_disable('alloca')) diff --git a/var/spack/repos/builtin/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py index 17c5344031..1f57c2b95d 100644 --- a/var/spack/repos/builtin/packages/mxml/package.py +++ b/var/spack/repos/builtin/packages/mxml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/mxnet/package.py b/var/spack/repos/builtin/packages/mxnet/package.py index 43796ab7d8..f3b7cddb23 100644 --- a/var/spack/repos/builtin/packages/mxnet/package.py +++ b/var/spack/repos/builtin/packages/mxnet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,10 +11,9 @@ class Mxnet(MakefilePackage): designed for both efficiency and flexibility.""" homepage = "http://mxnet.io" - url = "https://github.com/apache/incubator-mxnet/archive/0.10.0.post2.tar.gz" + url = "https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz" - version('1.3.0', sha256='c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2', - url='https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz') + version('1.3.0', sha256='c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2') variant('cuda', default=False, description='Enable CUDA support') variant('opencv', default=True, description='Enable OpenCV support') diff --git a/var/spack/repos/builtin/packages/mysql/package.py b/var/spack/repos/builtin/packages/mysql/package.py index 497b8568a8..7501d57cbd 100644 --- a/var/spack/repos/builtin/packages/mysql/package.py +++ b/var/spack/repos/builtin/packages/mysql/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,9 @@ class Mysql(CMakePackage): homepage = "https://www.mysql.com/" url = "https://dev.mysql.com/get/Downloads/MySQL-8.0/mysql-8.0.15.tar.gz" + version('8.0.19', sha256='a62786d67b5e267eef928003967b4ccfe362d604b80f4523578e0688f5b9f834') + version('8.0.18', sha256='4cb39a315298eb243c25c53c184b3682b49c2a907a1d8432ba0620534806ade8') + version('8.0.17', sha256='c6e3f38199a77bfd8a4925ca00b252d3b6159b90e4980c7232f1c58d6ca759d6') version('8.0.16', sha256='8d9fe89920dc8bbbde2857b7b877ad2fa5ec2f231c68e941d484f3b72735eaea') version('8.0.15', sha256='bb1bca2dc2f23ee9dd395cc4db93b64561d4ac20b53be5d1dae563f7be64825e') version('8.0.14', sha256='bc53f4c914fb39650289700d144529121d71f38399d2d24a0f5c76e5a8abd204') @@ -122,7 +125,7 @@ class Mysql(CMakePackage): options.append('-DWITHOUT_SERVER:BOOL=ON') return options - def _fix_dtrace_shebang(self, build_env): + def _fix_dtrace_shebang(self, env): # dtrace may cause build to fail because it uses # '/usr/bin/python' in the shebang. To work around that we copy # the original script into a temporary folder, and change the @@ -141,13 +144,7 @@ class Mysql(CMakePackage): ) # To have our own copy of dtrace in PATH, we need to # prepend to PATH the temporary folder where it resides. - build_env.prepend_path('PATH', dtrace_copy_path) - - @run_before('cmake') - def _maybe_fix_dtrace_shebang(self): - if 'python' in self.spec.flat_dependencies() and \ - self.spec.satisfies('@:7.99.99'): - self._fix_dtrace_shebang(build_env) + env.prepend_path('PATH', dtrace_copy_path) def setup_build_environment(self, env): cxxstd = self.spec.variants['cxxstd'].value @@ -160,3 +157,7 @@ class Mysql(CMakePackage): '-Wno-deprecated-declarations') if int(cxxstd) > 14: env.append_flags('CXXFLAGS', '-Wno-error=register') + + if 'python' in self.spec.flat_dependencies() and \ + self.spec.satisfies('@:7.99.99'): + self._fix_dtrace_shebang(env) diff --git a/var/spack/repos/builtin/packages/nag/package.py b/var/spack/repos/builtin/packages/nag/package.py index 06e51c1cab..4e23559913 100644 --- a/var/spack/repos/builtin/packages/nag/package.py +++ b/var/spack/repos/builtin/packages/nag/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,10 +10,11 @@ import os class Nag(Package): """The NAG Fortran Compiler.""" homepage = "http://www.nag.com/nagware/np.asp" + maintainers = ['ThemosTsikas'] - version('6.2', sha256='e22f70f52949c4eb5526229c13920c924af5254d07a584cf54fefecd130fd29c') + version('7.0', sha256='fafd97ebb58753ab5b9f13822d2e3d24c2f488ea25928c4c3a13e4e2e350ab3e') + version('6.2', sha256='9b60f6ffa4f4be631079676963e74eea25e8824512e5c864eb06758b2a3cdd2d') version('6.1', sha256='32580e0004e6798abf1fa52f0070281b28abeb0da2387530a4cc41218e813c7c') - version('6.0', sha256='d5a326777a20303626b121da58522a122fcb1e3b4f2fcd657d9848e7b39fe7f8') # Licensing license_required = True @@ -37,6 +38,6 @@ class Nag(Package): # Run install script os.system('./INSTALLU.sh') - def setup_environment(self, spack_env, run_env): - run_env.set('F77', join_path(self.prefix.bin, 'nagfor')) - run_env.set('FC', join_path(self.prefix.bin, 'nagfor')) + def setup_run_environment(self, env): + env.set('F77', self.prefix.bin.nagfor) + env.set('FC', self.prefix.bin.nagfor) diff --git a/var/spack/repos/builtin/packages/nalu-wind/package.py b/var/spack/repos/builtin/packages/nalu-wind/package.py index 67af366156..9691f1f50e 100644 --- a/var/spack/repos/builtin/packages/nalu-wind/package.py +++ b/var/spack/repos/builtin/packages/nalu-wind/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nalu/package.py b/var/spack/repos/builtin/packages/nalu/package.py index f5f022d050..8e6abea569 100644 --- a/var/spack/repos/builtin/packages/nalu/package.py +++ b/var/spack/repos/builtin/packages/nalu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py index 7dde176df1..dcd80e94a8 100644 --- a/var/spack/repos/builtin/packages/namd/package.py +++ b/var/spack/repos/builtin/packages/namd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nano/package.py b/var/spack/repos/builtin/packages/nano/package.py index 4cd6cf1d4b..0901db0a05 100644 --- a/var/spack/repos/builtin/packages/nano/package.py +++ b/var/spack/repos/builtin/packages/nano/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nanoflann/package.py b/var/spack/repos/builtin/packages/nanoflann/package.py index 371df53487..faeb5d7b16 100644 --- a/var/spack/repos/builtin/packages/nanoflann/package.py +++ b/var/spack/repos/builtin/packages/nanoflann/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nanopb/package.py b/var/spack/repos/builtin/packages/nanopb/package.py index 75726c37e4..60829cbd91 100644 --- a/var/spack/repos/builtin/packages/nanopb/package.py +++ b/var/spack/repos/builtin/packages/nanopb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nasm/package.py b/var/spack/repos/builtin/packages/nasm/package.py index aa64098be3..da5d358a19 100644 --- a/var/spack/repos/builtin/packages/nasm/package.py +++ b/var/spack/repos/builtin/packages/nasm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,3 +22,6 @@ class Nasm(AutotoolsPackage): # Fix compilation with GCC 8 # https://bugzilla.nasm.us/show_bug.cgi?id=3392461 patch('https://src.fedoraproject.org/rpms/nasm/raw/0cc3eb244bd971df81a7f02bc12c5ec259e1a5d6/f/0001-Remove-invalid-pure_func-qualifiers.patch', level=1, sha256='ac9f315d204afa6b99ceefa1fe46d4eed2b8a23c7315d32d33c0f378d930e950', when='@2.13.03 %gcc@8:') + + conflicts('%intel@:14', when='@2.14:', + msg="Intel 14 has immature C11 support") diff --git a/var/spack/repos/builtin/packages/nauty/package.py b/var/spack/repos/builtin/packages/nauty/package.py index 444629efd7..cccacd8e6c 100644 --- a/var/spack/repos/builtin/packages/nauty/package.py +++ b/var/spack/repos/builtin/packages/nauty/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -47,9 +47,9 @@ class Nauty(AutotoolsPackage): ] } # Iterate over patches - for condition, urls in urls_for_patches.items(): - for url, sha256 in urls: - patch(url, when=condition, level=1, sha256=sha256) + for condition, url_and_sha256 in urls_for_patches.items(): + for path, sha256 in url_and_sha256: + patch(path, when=condition, level=1, sha256=sha256) depends_on('m4', type='build', when='@2.6r7') depends_on('autoconf', type='build', when='@2.6r7') diff --git a/var/spack/repos/builtin/packages/ncbi-magicblast/package.py b/var/spack/repos/builtin/packages/ncbi-magicblast/package.py index 74e755d610..eb93f59b9d 100644 --- a/var/spack/repos/builtin/packages/ncbi-magicblast/package.py +++ b/var/spack/repos/builtin/packages/ncbi-magicblast/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py index 66c24739c3..a0f7873c33 100644 --- a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py +++ b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py index 39dc3e8761..c3be024e81 100644 --- a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py +++ b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nccl/package.py b/var/spack/repos/builtin/packages/nccl/package.py index caef4bdb31..7fbc780525 100644 --- a/var/spack/repos/builtin/packages/nccl/package.py +++ b/var/spack/repos/builtin/packages/nccl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py index 6bf5fdb1b4..0e2a13f6f0 100644 --- a/var/spack/repos/builtin/packages/nccmp/package.py +++ b/var/spack/repos/builtin/packages/nccmp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,7 @@ class Nccmp(Package): version('1.8.2.0', sha256='7f5dad4e8670568a71f79d2bcebb08d95b875506d3d5faefafe1a8b3afa14f18') - depends_on('netcdf') + depends_on('netcdf-c') def install(self, spec, prefix): # Configure says: F90 and F90FLAGS are replaced by FC and diff --git a/var/spack/repos/builtin/packages/ncdu/package.py b/var/spack/repos/builtin/packages/ncdu/package.py index 5698930069..6218512e29 100644 --- a/var/spack/repos/builtin/packages/ncdu/package.py +++ b/var/spack/repos/builtin/packages/ncdu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ncftp/package.py b/var/spack/repos/builtin/packages/ncftp/package.py index 01593e419f..386d90b01a 100644 --- a/var/spack/repos/builtin/packages/ncftp/package.py +++ b/var/spack/repos/builtin/packages/ncftp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ncl/package.py b/var/spack/repos/builtin/packages/ncl/package.py index c3940136c4..0fa063c52c 100644 --- a/var/spack/repos/builtin/packages/ncl/package.py +++ b/var/spack/repos/builtin/packages/ncl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -42,8 +42,8 @@ class Ncl(Package): # Non-optional dependencies according to the manual: depends_on('jpeg') - depends_on('netcdf') - depends_on('cairo+X+pdf') + depends_on('netcdf-c') + depends_on('cairo+X+ft+pdf') # Extra dependencies that may be missing from build system: depends_on('bison', type='build') @@ -64,8 +64,9 @@ class Ncl(Package): depends_on('pixman') depends_on('bzip2') depends_on('freetype') + depends_on('fontconfig') - # In Spack, we do not have an option to compile netcdf without netcdf-4 + # In Spack, we do not have an option to compile netcdf-c without netcdf-4 # support, so we will tell the ncl configuration script that we want # support for netcdf-4, but the script assumes that hdf5 is compiled with # szip support. We introduce this restriction with the following dependency @@ -76,13 +77,13 @@ class Ncl(Package): # ESMF is only required at runtime (for ESMF_regridding.ncl) depends_on('esmf', type='run') - # In Spack, we also do not have an option to compile netcdf without DAP + # In Spack, we also do not have an option to compile netcdf-c without DAP # support, so we will tell the ncl configuration script that we have it. # Some of the optional dependencies according to the manual: depends_on('hdf', when='+hdf4') depends_on('gdal+proj@:2.4', when='+gdal') - depends_on('udunits2', when='+udunits2') + depends_on('udunits', when='+udunits2') # We need src files of triangle to appear in ncl's src tree if we want # triangle's features. @@ -123,8 +124,8 @@ class Ncl(Package): self.prepare_src_tree() make('Everything', parallel=False) - def setup_environment(self, spack_env, run_env): - run_env.set('NCARG_ROOT', self.spec.prefix) + def setup_run_environment(self, env): + env.set('NCARG_ROOT', self.spec.prefix) def prepare_site_config(self): fc_flags = [] @@ -224,6 +225,7 @@ class Ncl(Package): # Build GRIB2 support (optional) into NCL? 'n\n', # Enter local library search path(s) : + self.spec['fontconfig'].prefix.lib + ' ' + self.spec['pixman'].prefix.lib + ' ' + self.spec['bzip2'].prefix.lib + '\n', # Enter local include search path(s) : diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py index 951d6f5974..859dac6ab7 100644 --- a/var/spack/repos/builtin/packages/nco/package.py +++ b/var/spack/repos/builtin/packages/nco/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,10 +30,10 @@ class Nco(AutotoolsPackage): # See "Compilation Requirements" at: # http://nco.sourceforge.net/#bld - depends_on('netcdf') + depends_on('netcdf-c') depends_on('antlr@2.7.7+cxx') # required for ncap2 depends_on('gsl') # desirable for ncap2 - depends_on('udunits2') # allows dimensional unit transformations + depends_on('udunits') # allows dimensional unit transformations depends_on('flex', type='build') depends_on('bison', type='build') @@ -45,9 +45,9 @@ class Nco(AutotoolsPackage): spec = self.spec return ['--{0}-doc'.format('enable' if '+doc' in spec else 'disable')] - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('NETCDF_INC', spec['netcdf'].prefix.include) - spack_env.set('NETCDF_LIB', spec['netcdf'].prefix.lib) - spack_env.set('ANTLR_ROOT', spec['antlr'].prefix) - spack_env.set('UDUNITS2_PATH', spec['udunits2'].prefix) + env.set('NETCDF_INC', spec['netcdf-c'].prefix.include) + env.set('NETCDF_LIB', spec['netcdf-c'].prefix.lib) + env.set('ANTLR_ROOT', spec['antlr'].prefix) + env.set('UDUNITS2_PATH', spec['udunits'].prefix) diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py index 2e77799233..7b9b67b939 100644 --- a/var/spack/repos/builtin/packages/ncurses/package.py +++ b/var/spack/repos/builtin/packages/ncurses/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,7 +9,7 @@ from os.path import exists, join from os import makedirs -class Ncurses(AutotoolsPackage): +class Ncurses(AutotoolsPackage, GNUMirrorPackage): """The ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses terminfo format, supports pads and color and multiple highlights and forms @@ -18,7 +18,7 @@ class Ncurses(AutotoolsPackage): homepage = "http://invisible-island.net/ncurses/ncurses.html" # URL must remain http:// so Spack can bootstrap curl - url = "http://ftpmirror.gnu.org/ncurses/ncurses-6.1.tar.gz" + gnu_mirror_path = "ncurses/ncurses-6.1.tar.gz" version('6.1', sha256='aa057eeeb4a14d470101eff4597d5833dcef5965331be3528c08d99cebaa0d17') version('6.0', sha256='f551c24b30ce8bfb6e96d9f59b42fbea30fa3a6123384172f9e7284bcf647260') @@ -34,8 +34,8 @@ class Ncurses(AutotoolsPackage): patch('patch_gcc_5.txt', when='@6.0%gcc@5.0:') patch('sed_pgi.patch', when='@:6.0') - def setup_environment(self, spack_env, run_env): - spack_env.unset('TERMINFO') + def setup_build_environment(self, env): + env.unset('TERMINFO') def flag_handler(self, name, flags): if name == 'cflags' or name == 'cxxflags': @@ -45,6 +45,7 @@ class Ncurses(AutotoolsPackage): def configure(self, spec, prefix): opts = [ + '--disable-stripping', '--with-shared', '--with-cxx-shared', '--enable-overwrite', diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py index 3f1d6f4d8c..f142a435f2 100644 --- a/var/spack/repos/builtin/packages/ncview/package.py +++ b/var/spack/repos/builtin/packages/ncview/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,8 +13,8 @@ class Ncview(AutotoolsPackage): version('2.1.7', sha256='a14c2dddac0fc78dad9e4e7e35e2119562589738f4ded55ff6e0eca04d682c82') - depends_on('netcdf') - depends_on('udunits2') + depends_on('netcdf-c') + depends_on('udunits') depends_on('libpng') depends_on('libxaw') @@ -23,7 +23,7 @@ class Ncview(AutotoolsPackage): config_args = [] - if spec.satisfies('^netcdf+mpi'): + if spec.satisfies('^netcdf-c+mpi'): config_args.append('CC={0}'.format(spec['mpi'].mpicc)) return config_args diff --git a/var/spack/repos/builtin/packages/ndiff/package.py b/var/spack/repos/builtin/packages/ndiff/package.py index c2071af64d..a688a09241 100644 --- a/var/spack/repos/builtin/packages/ndiff/package.py +++ b/var/spack/repos/builtin/packages/ndiff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nek5000/package.py b/var/spack/repos/builtin/packages/nek5000/package.py index e2dfa2333b..86ccb6b090 100644 --- a/var/spack/repos/builtin/packages/nek5000/package.py +++ b/var/spack/repos/builtin/packages/nek5000/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nekbone/package.py b/var/spack/repos/builtin/packages/nekbone/package.py index 9d46ee8623..0ad37561e3 100644 --- a/var/spack/repos/builtin/packages/nekbone/package.py +++ b/var/spack/repos/builtin/packages/nekbone/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nekcem/package.py b/var/spack/repos/builtin/packages/nekcem/package.py index 710c465b07..e5f829677d 100644 --- a/var/spack/repos/builtin/packages/nekcem/package.py +++ b/var/spack/repos/builtin/packages/nekcem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nektar/package.py b/var/spack/repos/builtin/packages/nektar/package.py index d2cc96d92b..ed9a2bc966 100644 --- a/var/spack/repos/builtin/packages/nektar/package.py +++ b/var/spack/repos/builtin/packages/nektar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,7 @@ class Nektar(CMakePackage): homepage = "https://www.nektar.info/" url = "https://gitlab.nektar.info/nektar/nektar/-/archive/v4.4.1/nektar-v4.4.1.tar.bz2" + version('5.0.0', sha256='5c594453fbfaa433f732a55405da9bba27d4a00c32d7b9d7515767925fb4a818') version('4.4.1', sha256='71cfd93d848a751ae9ae5e5ba336cee4b4827d4abcd56f6b8dc5c460ed6b738c') variant('mpi', default=True, description='Builds with mpi support') diff --git a/var/spack/repos/builtin/packages/nektools/package.py b/var/spack/repos/builtin/packages/nektools/package.py index 61ea5b297e..c8a5b46a9f 100644 --- a/var/spack/repos/builtin/packages/nektools/package.py +++ b/var/spack/repos/builtin/packages/nektools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/neovim/package.py b/var/spack/repos/builtin/packages/neovim/package.py index 205607d4a6..8a574f58e9 100644 --- a/var/spack/repos/builtin/packages/neovim/package.py +++ b/var/spack/repos/builtin/packages/neovim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nest/package.py b/var/spack/repos/builtin/packages/nest/package.py index 5ecc403a3b..6524931f5e 100644 --- a/var/spack/repos/builtin/packages/nest/package.py +++ b/var/spack/repos/builtin/packages/nest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -147,5 +147,5 @@ class Nest(CMakePackage): self.stage.source_path, recursive=True): install(f, path_headers) - def setup_environment(self, spack_env, run_env): - run_env.set("NEST_INSTALL_DIR", self.spec.prefix) + def setup_run_environment(self, env): + env.set("NEST_INSTALL_DIR", self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf-c/package.py index 46a5695c58..01f2acf425 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf-c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,13 +16,13 @@ def is_integral(x): return False -class Netcdf(AutotoolsPackage): - """NetCDF is a set of software libraries and self-describing, - machine-independent data formats that support the creation, access, - and sharing of array-oriented scientific data.""" +class NetcdfC(AutotoolsPackage): + """NetCDF (network Common Data Form) is a set of software libraries and + machine-independent data formats that support the creation, access, and + sharing of array-oriented scientific data. This is the C distribution.""" homepage = "http://www.unidata.ucar.edu/software/netcdf" - git = "https://github.com/Unidata/netcdf-c" + git = "https://github.com/Unidata/netcdf-c.git" url = "https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-c-4.7.2.tar.gz" def url_for_version(self, version): @@ -34,6 +34,7 @@ class Netcdf(AutotoolsPackage): return url.format(version.dotted) version('master', branch='master') + version('4.7.3', sha256='8e8c9f4ee15531debcf83788594744bd6553b8489c06a43485a15c93b4e0448b') version('4.7.2', sha256='b751cc1f314ac8357df2e0a1bacf35a624df26fe90981d3ad3fa85a5bbd8989a') version('4.7.1', sha256='5c537c585773e575a16b28c3973b9608a98fdc4cf7c42893aa5223024e0001fc') version('4.7.0', sha256='a512d2b4828c6177dd4b96791c4163e4e06e6bfc7123bebfbfe01762d777d1cb') @@ -45,7 +46,7 @@ class Netcdf(AutotoolsPackage): # Version 4.4.1.1 is having problems in tests # https://github.com/Unidata/netcdf-c/issues/343 version('4.4.1.1', sha256='4d44c6f4d02a8faf10ea619bfe1ba8224cd993024f4da12988c7465f663c8cae') - # netcdf@4.4.1 can crash on you (in real life and in tests). See: + # Version 4.4.1 can crash on you (in real life and in tests). See: # https://github.com/Unidata/netcdf-c/issues/282 version('4.4.1', sha256='8915cc69817f7af6165fbe69a8d1dfe21d5929d7cca9d10b10f568669ec6b342') version('4.4.0', sha256='0d40cb7845abd03c363abcd5f57f16e3c0685a0faf8badb2c59867452f6bcf78') @@ -55,6 +56,9 @@ class Netcdf(AutotoolsPackage): # configure fails if curl is not installed. # See https://github.com/Unidata/netcdf-c/issues/1390 patch('https://github.com/Unidata/netcdf-c/commit/e5315da1e748dc541d50796fb05233da65e86b6b.patch', sha256='10a1c3f7fa05e2c82457482e272bbe04d66d0047b237ad0a73e87d63d848b16c', when='@4.7.0') + # fix headers + patch('https://github.com/Unidata/netcdf-c/pull/1505.patch', sha256='f52db13c61b9c19aafe03c2a865163b540e9f6dee36e3a5f808f05fac59f2030', when='@4.7.2') + patch('https://github.com/Unidata/netcdf-c/pull/1508.patch', sha256='56532470875b9a97f3cf2a7d9ed16ef1612df3265ee38880c109428322ff3a40', when='@4.7.2') variant('mpi', default=True, description='Enable parallel I/O for netcdf-4') @@ -121,20 +125,20 @@ class Netcdf(AutotoolsPackage): # Starting version 4.4.0, it became possible to disable parallel I/O even # if HDF5 supports it. For previous versions of the library we need # HDF5 without mpi support to disable parallel I/O. - # The following doesn't work if hdf5+mpi by default and netcdf~mpi is + # The following doesn't work if hdf5+mpi by default and netcdf-c~mpi is # specified in packages.yaml # depends_on('hdf5~mpi', when='@:4.3~mpi') # Thus, we have to introduce a conflict conflicts('~mpi', when='@:4.3^hdf5+mpi', - msg='netcdf@:4.3~mpi requires hdf5~mpi') + msg='netcdf-c@:4.3~mpi requires hdf5~mpi') # We need HDF5 with mpi support to enable parallel I/O. - # The following doesn't work if hdf5~mpi by default and netcdf+mpi is + # The following doesn't work if hdf5~mpi by default and netcdf-c+mpi is # specified in packages.yaml # depends_on('hdf5+mpi', when='+mpi') # Thus, we have to introduce a conflict conflicts('+mpi', when='^hdf5~mpi', - msg='netcdf+mpi requires hdf5+mpi') + msg='netcdf-c+mpi requires hdf5+mpi') # NetCDF 4.4.0 and prior have compatibility issues with HDF5 1.10 and later # https://github.com/Unidata/netcdf-c/issues/250 @@ -264,3 +268,10 @@ class Netcdf(AutotoolsPackage): def check(self): # h5_test fails when run in parallel make('check', parallel=False) + + @property + def libs(self): + shared = '+shared' in self.spec + return find_libraries( + 'libnetcdf', root=self.prefix, shared=shared, recursive=True + ) diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py index 94bb28412f..6a5f6aa183 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,7 +17,7 @@ class NetcdfCxx(AutotoolsPackage): version('4.2', sha256='95ed6ab49a0ee001255eac4e44aacb5ca4ea96ba850c08337a3e4c9a0872ccd1') - depends_on('netcdf') + depends_on('netcdf-c') variant( 'netcdf4', default=True, description='Compile with netCDF4 support') @@ -38,7 +38,7 @@ class NetcdfCxx(AutotoolsPackage): # Add these to LDFLAGS explicitly, so the linker doesn't accidentally # use system versions ldflags = [ - self.spec['netcdf'].libs.search_flags, + self.spec['netcdf-c'].libs.search_flags, self.spec['hdf5'].libs.search_flags, ] args.append('LDFLAGS=' + ' '.join(ldflags)) diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py index 938d74d6aa..ce1a851ce3 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,7 +7,9 @@ from spack import * class NetcdfCxx4(AutotoolsPackage): - """C++ interface for NetCDF4""" + """NetCDF (network Common Data Form) is a set of software libraries and + machine-independent data formats that support the creation, access, and + sharing of array-oriented scientific data. This is the C++ distribution.""" homepage = "https://www.unidata.ucar.edu/software/netcdf" url = "https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.3.1.tar.gz" @@ -19,7 +21,7 @@ class NetcdfCxx4(AutotoolsPackage): # force its usage with this variant. variant('pic', default=True, description='Produce position-independent code (for shared libs)') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('automake', type='build') depends_on('autoconf', type='build') @@ -32,7 +34,7 @@ class NetcdfCxx4(AutotoolsPackage): if name == 'cflags' and '+pic' in self.spec: flags.append(self.compiler.pic_flag) elif name == 'cppflags': - flags.append('-I' + self.spec['netcdf'].prefix.include) + flags.append('-I' + self.spec['netcdf-c'].prefix.include) return (None, None, flags) diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/no_parallel_build.patch b/var/spack/repos/builtin/packages/netcdf-fortran/no_parallel_build.patch new file mode 100644 index 0000000000..c232a62bc5 --- /dev/null +++ b/var/spack/repos/builtin/packages/netcdf-fortran/no_parallel_build.patch @@ -0,0 +1,12 @@ +--- a/fortran/Makefile.in 2019-09-18 12:29:45.000000000 -0500 ++++ b/fortran/Makefile.in 2020-01-24 10:56:03.660035265 -0600 +@@ -1095,6 +1095,9 @@ + @USE_LOGGING_TRUE@ echo ' integer nf_set_log_level' >> netcdf.inc + @USE_LOGGING_TRUE@ echo ' external nf_set_log_level' >> netcdf.inc + ++# Turn off parallel builds in this directory. ++.NOTPARALLEL: ++ + # Tell versions [3.59,3.63) of GNU make to not export all variables. + # Otherwise a system limit (for SysV at least) may be exceeded. + .NOEXPORT: diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py index d698ff1e8b..e3703fd609 100644 --- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py +++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,7 +7,10 @@ from spack import * class NetcdfFortran(AutotoolsPackage): - """Fortran interface for NetCDF4""" + """NetCDF (network Common Data Form) is a set of software libraries and + machine-independent data formats that support the creation, access, and + sharing of array-oriented scientific data. This is the Fortran + distribution.""" homepage = "https://www.unidata.ucar.edu/software/netcdf" url = "https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.5.2.tar.gz" @@ -17,27 +20,38 @@ class NetcdfFortran(AutotoolsPackage): version('4.4.4', sha256='b2d395175f8d283e68c8be516e231a96b191ade67ad0caafaf7fa01b1e6b5d75') version('4.4.3', sha256='330373aa163d5931e475b5e83da5c1ad041e855185f24e6a8b85d73b48d6cda9') + variant('mpi', default=True, + description='Enable parallel I/O for netcdf-4') variant('pic', default=True, description='Produce position-independent code (for shared libs)') - depends_on('netcdf') + # We need to build with MPI wrappers if parallel I/O features is enabled: + # https://www.unidata.ucar.edu/software/netcdf/docs/building_netcdf_fortran.html + depends_on('mpi', when='+mpi') + + depends_on('netcdf-c~mpi', when='~mpi') + depends_on('netcdf-c+mpi', when='+mpi') # The default libtool.m4 is too old to handle NAG compiler properly: # https://github.com/Unidata/netcdf-fortran/issues/94 patch('nag.patch', when='@:4.4.4%nag') + # Parallel builds do not work in the fortran directory. This patch is + # derived from https://github.com/Unidata/netcdf-fortran/pull/211 + patch('no_parallel_build.patch', when='@4.5.2') + def flag_handler(self, name, flags): if name in ['cflags', 'fflags'] and '+pic' in self.spec: flags.append(self.compiler.pic_flag) elif name == 'cppflags': - flags.append(self.spec['netcdf'].headers.cpp_flags) + flags.append(self.spec['netcdf-c'].headers.cpp_flags) elif name == 'ldflags': # We need to specify LDFLAGS to get correct dependency_libs # in libnetcdff.la, so packages that use libtool for linking # could correctly link to all the dependencies even when the # building takes place outside of Spack environment, i.e. # without Spack's compiler wrappers. - flags.append(self.spec['netcdf'].libs.search_flags) + flags.append(self.spec['netcdf-c'].libs.search_flags) return None, None, flags @@ -53,3 +67,13 @@ class NetcdfFortran(AutotoolsPackage): return find_libraries( libraries, root=self.prefix, shared=shared, recursive=True ) + + def configure_args(self): + config_args = [] + + if '+mpi' in self.spec: + config_args.append('CC=%s' % self.spec['mpi'].mpicc) + config_args.append('FC=%s' % self.spec['mpi'].mpifc) + config_args.append('F77=%s' % self.spec['mpi'].mpif77) + + return config_args diff --git a/var/spack/repos/builtin/packages/netgauge/package.py b/var/spack/repos/builtin/packages/netgauge/package.py index 1d4eee11e5..b367b6aecd 100644 --- a/var/spack/repos/builtin/packages/netgauge/package.py +++ b/var/spack/repos/builtin/packages/netgauge/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/netgen/package.py b/var/spack/repos/builtin/packages/netgen/package.py index 767ccec819..f22ae4a168 100644 --- a/var/spack/repos/builtin/packages/netgen/package.py +++ b/var/spack/repos/builtin/packages/netgen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index a4205e733f..91358bf60f 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/int_overflow.patch b/var/spack/repos/builtin/packages/netlib-scalapack/int_overflow.patch new file mode 100644 index 0000000000..b407fc840f --- /dev/null +++ b/var/spack/repos/builtin/packages/netlib-scalapack/int_overflow.patch @@ -0,0 +1,313 @@ +diff --git a/PBLAS/SRC/pdamax_.c b/PBLAS/SRC/pdamax_.c +index 3f4690a..89d8993 100644 +--- a/PBLAS/SRC/pdamax_.c ++++ b/PBLAS/SRC/pdamax_.c +@@ -233,7 +233,7 @@ void pdamax_( N, AMAX, INDX, X, IX, JX, DESCX, INCX ) + if( ( ( myrow == Xrow ) || ( Xrow < 0 ) ) && + ( ( mycol == Xcol ) || ( Xcol < 0 ) ) ) + { +- *INDX = *JX; *AMAX = X[Xii+Xjj*Xd[LLD_]]; ++ *INDX = *JX; *AMAX = *Mptr(X,Xii,Xjj,Xd[LLD_],1); + } + return; + } +@@ -260,9 +260,9 @@ void pdamax_( N, AMAX, INDX, X, IX, JX, DESCX, INCX ) + { + Xld = Xd[LLD_]; + Xlindx = Xjj - 1 + +- idamax_( &Xnq, ((char*)(X+(Xii+Xjj*Xld))), &Xld ); ++ idamax_( &Xnq, ((char*)Mptr(X,Xii,Xjj,Xld,1)), &Xld ); + Mindxl2g( Xgindx, Xlindx, Xinb, Xnb, mycol, Xsrc, npcol ); +- work[0] = X[Xii+Xlindx*Xld]; ++ work[0] = *Mptr(X,Xii,Xlindx,Xld,1); + work[1] = ((double)( Xgindx+1 )); + } + else +@@ -343,8 +343,8 @@ l_20: + */ + Xld = Xd[LLD_]; + Xlindx = Xjj - 1 + +- idamax_( &Xnq, ((char*)(X+(Xii+Xjj*Xld))), &Xld ); +- *AMAX = X[Xii+Xlindx*Xld]; ++ idamax_( &Xnq, ((char*)Mptr(X,Xii,Xjj,Xld,1)), &Xld ); ++ *AMAX = *Mptr(X,Xii,Xlindx,Xld,1); + } + else + { +@@ -419,9 +419,9 @@ l_20: + { + Xld = Xd[LLD_]; + Xlindx = Xii - 1 + +- idamax_( &Xnp, ((char*)(X+(Xii+Xjj*Xld))), INCX ); ++ idamax_( &Xnp, ((char*)Mptr(X,Xii,Xjj,Xld,1)), INCX ); + Mindxl2g( Xgindx, Xlindx, Ximb, Xmb, myrow, Xsrc, nprow ); +- work[0] = X[Xlindx+Xjj*Xld]; ++ work[0] = *Mptr(X,Xlindx,Xjj,Xld,1); + work[1] = ((double)( Xgindx+1 )); + } + else +@@ -503,8 +503,8 @@ l_40: + */ + Xld = Xd[LLD_]; + Xlindx = Xii - 1 + +- idamax_( &Xnp, ((char*)(X+(Xii+Xjj*Xld))), INCX ); +- *AMAX = X[Xlindx+Xjj*Xld]; ++ idamax_( &Xnp, ((char*)Mptr(X,Xii,Xjj,Xld,1)), INCX ); ++ *AMAX = *Mptr(X,Xlindx,Xjj,Xld,1); + } + else + { +diff --git a/PBLAS/SRC/pdasum_.c b/PBLAS/SRC/pdasum_.c +index 5b9ce8b..3a56c23 100644 +--- a/PBLAS/SRC/pdasum_.c ++++ b/PBLAS/SRC/pdasum_.c +@@ -225,7 +225,7 @@ void pdasum_( N, ASUM, X, IX, JX, DESCX, INCX ) + if( ( ( myrow == Xrow ) || ( Xrow < 0 ) ) && + ( ( mycol == Xcol ) || ( Xcol < 0 ) ) ) + { +- *ASUM = ABS( X[Xii+Xjj*Xd[LLD_]] ); ++ *ASUM = ABS( *Mptr(X,Xii,Xjj,Xd[LLD_],1) ); + } + return; + } +@@ -243,7 +243,7 @@ void pdasum_( N, ASUM, X, IX, JX, DESCX, INCX ) + if( Xnq > 0 ) + { + Xld = Xd[LLD_]; +- dvasum_( &Xnq, ((char *) ASUM), ((char *)( X+(Xii+Xjj*Xld) )), ++ dvasum_( &Xnq, ((char *) ASUM), ((char *)Mptr( X,Xii,Xjj,Xld,1 )), + &Xld ); + } + /* +@@ -276,7 +276,7 @@ void pdasum_( N, ASUM, X, IX, JX, DESCX, INCX ) + if( Xnp > 0 ) + { + dvasum_( &Xnp, ((char *) ASUM), +- ((char *)( X+(Xii+Xjj*Xd[LLD_]) )), INCX ); ++ ((char *)Mptr( X,Xii,Xjj,Xd[LLD_],1) ), INCX ); + } + /* + * If Xnp <= 0, ASUM is zero (see initialization above) +diff --git a/PBLAS/SRC/pdger_.c b/PBLAS/SRC/pdger_.c +index e84aa62..517a33c 100644 +--- a/PBLAS/SRC/pdger_.c ++++ b/PBLAS/SRC/pdger_.c +@@ -286,7 +286,7 @@ void pdger_( M, N, ALPHA, X, IX, JX, DESCX, INCX, Y, IY, JY, DESCY, + if( ( Amp > 0 ) && ( Anq > 0 ) ) + { + dger_( &Amp, &Anq, ((char *) ALPHA), XA, &ione, YA, &YAd[LLD_], +- ((char *) (A+(Aii+Ajj*Ald))), &Ald ); ++ ((char *)Mptr(A,Aii,Ajj,Ald,1)), &Ald ); + } + if( XAfr ) free( XA ); + if( YAfr ) free( YA ); +diff --git a/PBLAS/SRC/pdnrm2_.c b/PBLAS/SRC/pdnrm2_.c +index f5bfb1a..8e3bab9 100644 +--- a/PBLAS/SRC/pdnrm2_.c ++++ b/PBLAS/SRC/pdnrm2_.c +@@ -224,7 +224,7 @@ void pdnrm2_( N, NORM2, X, IX, JX, DESCX, INCX ) + */ + if( ( ( myrow == Xrow ) || ( Xrow < 0 ) ) && + ( ( mycol == Xcol ) || ( Xcol < 0 ) ) ) +- *NORM2 = ABS( X[Xii+Xjj*Xd[LLD_]] ); ++ *NORM2 = ABS( *Mptr(X,Xii,Xjj,Xd[LLD_],1) ); + return; + } + else if( *INCX == Xd[M_] ) +@@ -246,7 +246,7 @@ void pdnrm2_( N, NORM2, X, IX, JX, DESCX, INCX ) + if( Xnq > 0 ) + { + Xld = Xd[LLD_]; +- Xptr = X+(Xii+Xjj*Xld); ++ Xptr = Mptr(X,Xii,Xjj,Xld,1); + + for( k = 0; k < Xnq; k++ ) + { +@@ -366,7 +366,7 @@ l_20: + Xnp = PB_Cnumroc( *N, Xi, Xd[IMB_], Xd[MB_], myrow, Xd[RSRC_], nprow ); + if( Xnp > 0 ) + { +- Xptr = X+(Xii+Xjj*Xd[LLD_]); ++ Xptr = Mptr(X,Xii,Xjj,Xd[LLD_],1); + + for( k = 0; k < Xnp; k++ ) + { +diff --git a/PBLAS/SRC/pdscal_.c b/PBLAS/SRC/pdscal_.c +index 28ddc66..b7c0964 100644 +--- a/PBLAS/SRC/pdscal_.c ++++ b/PBLAS/SRC/pdscal_.c +@@ -210,12 +210,12 @@ void pdscal_( N, ALPHA, X, IX, JX, DESCX, INCX ) + Xld = Xd[LLD_]; + if( ALPHA[REAL_PART] == ZERO ) + { +- dset_( &Xnq, ((char *) ALPHA), ((char *)(X+(Xii+Xjj*Xld))), ++ dset_( &Xnq, ((char *) ALPHA), ((char *)Mptr(X,Xii,Xjj,Xld,1)), + &Xld ); + } + else + { +- dscal_( &Xnq, ((char *) ALPHA), ((char *)(X+(Xii+Xjj*Xld))), ++ dscal_( &Xnq, ((char *) ALPHA), ((char *)Mptr(X,Xii,Xjj,Xld,1)), + &Xld ); + } + } +@@ -239,12 +239,12 @@ void pdscal_( N, ALPHA, X, IX, JX, DESCX, INCX ) + if( ALPHA[REAL_PART] == ZERO ) + { + dset_( &Xnp, ((char *) ALPHA), +- ((char *)( X+(Xii+Xjj*Xd[LLD_]) )), INCX ); ++ ((char *)Mptr( X,Xii,Xjj,Xd[LLD_],1) ), INCX ); + } + else + { + dscal_( &Xnp, ((char *) ALPHA), +- ((char *)( X+(Xii+Xjj*Xd[LLD_]) )), INCX ); ++ ((char *)Mptr( X,Xii,Xjj,Xd[LLD_],1) ), INCX ); + } + } + } +diff --git a/PBLAS/SRC/psamax_.c b/PBLAS/SRC/psamax_.c +index a23b28a..8cdbd8e 100644 +--- a/PBLAS/SRC/psamax_.c ++++ b/PBLAS/SRC/psamax_.c +@@ -260,7 +260,7 @@ void psamax_( N, AMAX, INDX, X, IX, JX, DESCX, INCX ) + { + Xld = Xd[LLD_]; + Xlindx = Xjj - 1 + +- isamax_( &Xnq, ((char*)(X+(Xii+Xjj*Xld))), &Xld ); ++ isamax_( &Xnq, ((char*)(Mptr(X,Xii,Xjj,Xld,1))), &Xld ); + Mindxl2g( Xgindx, Xlindx, Xinb, Xnb, mycol, Xsrc, npcol ); + work[0] = X[Xii+Xlindx*Xld]; + work[1] = ((float )( Xgindx+1 )); +@@ -343,8 +343,8 @@ l_20: + */ + Xld = Xd[LLD_]; + Xlindx = Xjj - 1 + +- isamax_( &Xnq, ((char*)(X+(Xii+Xjj*Xld))), &Xld ); +- *AMAX = X[Xii+Xlindx*Xld]; ++ isamax_( &Xnq, ((char*)(Mptr(X,Xii,Xjj,Xld, 1))), &Xld ); ++ *AMAX = *Mptr(X,Xii,Xlindx,Xld,1); + } + else + { +@@ -419,9 +419,9 @@ l_20: + { + Xld = Xd[LLD_]; + Xlindx = Xii - 1 + +- isamax_( &Xnp, ((char*)(X+(Xii+Xjj*Xld))), INCX ); ++ isamax_( &Xnp, ((char*)Mptr(X,Xii,Xjj,Xld,1)), INCX ); + Mindxl2g( Xgindx, Xlindx, Ximb, Xmb, myrow, Xsrc, nprow ); +- work[0] = X[Xlindx+Xjj*Xld]; ++ work[0] = *Mptr(X,Xlindx,Xjj,Xld,1); + work[1] = ((float )( Xgindx+1 )); + } + else +diff --git a/PBLAS/SRC/psasum_.c b/PBLAS/SRC/psasum_.c +index a9820b3..dd6dcf1 100644 +--- a/PBLAS/SRC/psasum_.c ++++ b/PBLAS/SRC/psasum_.c +@@ -225,7 +225,7 @@ void psasum_( N, ASUM, X, IX, JX, DESCX, INCX ) + if( ( ( myrow == Xrow ) || ( Xrow < 0 ) ) && + ( ( mycol == Xcol ) || ( Xcol < 0 ) ) ) + { +- *ASUM = ABS( X[Xii+Xjj*Xd[LLD_]] ); ++ *ASUM = ABS( *Mptr(X,Xii,Xjj,Xd[LLD_],1) ); + } + return; + } +@@ -243,7 +243,7 @@ void psasum_( N, ASUM, X, IX, JX, DESCX, INCX ) + if( Xnq > 0 ) + { + Xld = Xd[LLD_]; +- svasum_( &Xnq, ((char *) ASUM), ((char *)( X+(Xii+Xjj*Xld) )), ++ svasum_( &Xnq, ((char *) ASUM), ((char *)Mptr( X,Xii,Xjj,Xld,1) ), + &Xld ); + } + /* +@@ -276,7 +276,7 @@ void psasum_( N, ASUM, X, IX, JX, DESCX, INCX ) + if( Xnp > 0 ) + { + svasum_( &Xnp, ((char *) ASUM), +- ((char *)( X+(Xii+Xjj*Xd[LLD_]) )), INCX ); ++ ((char *)Mptr( X,Xii,Xjj,Xd[LLD_],1) ), INCX ); + } + /* + * If Xnp <= 0, ASUM is zero (see initialization above) +diff --git a/PBLAS/SRC/psger_.c b/PBLAS/SRC/psger_.c +index f7774a4..47af5e5 100644 +--- a/PBLAS/SRC/psger_.c ++++ b/PBLAS/SRC/psger_.c +@@ -286,7 +286,7 @@ void psger_( M, N, ALPHA, X, IX, JX, DESCX, INCX, Y, IY, JY, DESCY, + if( ( Amp > 0 ) && ( Anq > 0 ) ) + { + sger_( &Amp, &Anq, ((char *) ALPHA), XA, &ione, YA, &YAd[LLD_], +- ((char *) (A+(Aii+Ajj*Ald))), &Ald ); ++ ((char *)Mptr(A,Aii,Ajj,Ald,1)), &Ald ); + } + if( XAfr ) free( XA ); + if( YAfr ) free( YA ); +diff --git a/PBLAS/SRC/psnrm2_.c b/PBLAS/SRC/psnrm2_.c +index ff047c2..05eb00b 100644 +--- a/PBLAS/SRC/psnrm2_.c ++++ b/PBLAS/SRC/psnrm2_.c +@@ -224,7 +224,7 @@ void psnrm2_( N, NORM2, X, IX, JX, DESCX, INCX ) + */ + if( ( ( myrow == Xrow ) || ( Xrow < 0 ) ) && + ( ( mycol == Xcol ) || ( Xcol < 0 ) ) ) +- *NORM2 = ABS( X[Xii+Xjj*Xd[LLD_]] ); ++ *NORM2 = ABS( *Mptr(X,Xii,Xjj,Xd[LLD_],1) ); + return; + } + else if( *INCX == Xd[M_] ) +@@ -246,7 +246,7 @@ void psnrm2_( N, NORM2, X, IX, JX, DESCX, INCX ) + if( Xnq > 0 ) + { + Xld = Xd[LLD_]; +- Xptr = X+(Xii+Xjj*Xld); ++ Xptr = Mptr(X,Xii,Xjj,Xld,1); + + for( k = 0; k < Xnq; k++ ) + { +@@ -366,7 +366,7 @@ l_20: + Xnp = PB_Cnumroc( *N, Xi, Xd[IMB_], Xd[MB_], myrow, Xd[RSRC_], nprow ); + if( Xnp > 0 ) + { +- Xptr = X+(Xii+Xjj*Xd[LLD_]); ++ Xptr = Mptr(X,Xii,Xjj,Xd[LLD_],1); + + for( k = 0; k < Xnp; k++ ) + { +diff --git a/PBLAS/SRC/psscal_.c b/PBLAS/SRC/psscal_.c +index d3652e2..6eb6ee7 100644 +--- a/PBLAS/SRC/psscal_.c ++++ b/PBLAS/SRC/psscal_.c +@@ -210,12 +210,12 @@ void psscal_( N, ALPHA, X, IX, JX, DESCX, INCX ) + Xld = Xd[LLD_]; + if( ALPHA[REAL_PART] == ZERO ) + { +- sset_( &Xnq, ((char *) ALPHA), ((char *)(X+(Xii+Xjj*Xld))), ++ sset_( &Xnq, ((char *) ALPHA), ((char *)Mptr(X,Xii,Xjj,Xld,1)), + &Xld ); + } + else + { +- sscal_( &Xnq, ((char *) ALPHA), ((char *)(X+(Xii+Xjj*Xld))), ++ sscal_( &Xnq, ((char *) ALPHA), ((char *)Mptr(X,Xii,Xjj,Xld,1)), + &Xld ); + } + } +@@ -239,12 +239,12 @@ void psscal_( N, ALPHA, X, IX, JX, DESCX, INCX ) + if( ALPHA[REAL_PART] == ZERO ) + { + sset_( &Xnp, ((char *) ALPHA), +- ((char *)( X+(Xii+Xjj*Xd[LLD_]) )), INCX ); ++ ((char *)Mptr( X,Xii,Xjj,Xd[LLD_],1) ), INCX ); + } + else + { + sscal_( &Xnp, ((char *) ALPHA), +- ((char *)( X+(Xii+Xjj*Xd[LLD_]) )), INCX ); ++ ((char *)Mptr( X,Xii,Xjj,Xd[LLD_],1 )), INCX ); + } + } + } diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index bd05e73d4b..a135e7b2ff 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,7 @@ class NetlibScalapack(CMakePackage): homepage = "http://www.netlib.org/scalapack/" url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz" + version('2.1.0', sha256='61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6') version('2.0.2', sha256='0c74aeae690fe5ee4db7926f49c5d0bb69ce09eea75beb915e00bba07530395c') version('2.0.1', sha256='a9b34278d4e10b40cbe084c6d87d09af8845e874250719bfbbc497b2a88bfde1') version('2.0.0', sha256='e51fbd9c3ef3a0dbd81385b868e2355900148eea689bf915c5383d72daf73114') @@ -40,9 +41,11 @@ class NetlibScalapack(CMakePackage): depends_on('cmake', when='@2.0.0:', type='build') # See: https://github.com/Reference-ScaLAPACK/scalapack/issues/9 - patch("cmake_fortran_mangle.patch", when='@2.0.2:') + patch("cmake_fortran_mangle.patch", when='@2.0.2:@2.0.99') # See: https://github.com/Reference-ScaLAPACK/scalapack/pull/10 - patch("mpi2-compatibility.patch", when='@2.0.2:') + patch("mpi2-compatibility.patch", when='@2.0.2:@2.0.99') + # See: https://github.com/Reference-ScaLAPACK/scalapack/pull/16 + patch("int_overflow.patch", when='@2.0.0:@2.1.0') @property def libs(self): diff --git a/var/spack/repos/builtin/packages/netlib-xblas/package.py b/var/spack/repos/builtin/packages/netlib-xblas/package.py index 330d030655..1431b78494 100644 --- a/var/spack/repos/builtin/packages/netlib-xblas/package.py +++ b/var/spack/repos/builtin/packages/netlib-xblas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/netperf/package.py b/var/spack/repos/builtin/packages/netperf/package.py new file mode 100644 index 0000000000..484c6b961c --- /dev/null +++ b/var/spack/repos/builtin/packages/netperf/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Netperf(AutotoolsPackage): + """Netperf is a benchmark that can be used to measure the performance + of many different types of networking. It provides tests for both + unidirectional throughput, and end-to-end latency.""" + + homepage = "https://github.com/HewlettPackard/netperf" + url = "https://github.com/HewlettPackard/netperf/archive/netperf-2.7.0.tar.gz" + + version('2.7.0', sha256='4569bafa4cca3d548eb96a486755af40bd9ceb6ab7c6abd81cc6aa4875007c4e') + version('2.6.0', sha256='560b9c0ef0eed826941f74708b3ac53d91ec13b0b8c565fb107a1b5e6d99ded4') + version('2.5.0', sha256='bebc94102fb74071cf289e0c116f83920dbd982f9e6c913ec0f1c7f6fcffbf77') diff --git a/var/spack/repos/builtin/packages/nettle/package.py b/var/spack/repos/builtin/packages/nettle/package.py index 8776e850ae..358294a22a 100644 --- a/var/spack/repos/builtin/packages/nettle/package.py +++ b/var/spack/repos/builtin/packages/nettle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Nettle(AutotoolsPackage): +class Nettle(AutotoolsPackage, GNUMirrorPackage): """The Nettle package contains the low-level cryptographic library that is designed to fit easily in many contexts.""" homepage = "https://www.lysator.liu.se/~nisse/nettle/" - url = "https://ftpmirror.gnu.org/nettle/nettle-3.3.tar.gz" + gnu_mirror_path = "nettle/nettle-3.3.tar.gz" version('3.4.1', sha256='f941cf1535cd5d1819be5ccae5babef01f6db611f9b5a777bae9c7604b8a92ad') version('3.4', sha256='ae7a42df026550b85daca8389b6a60ba6313b0567f374392e54918588a411e94') diff --git a/var/spack/repos/builtin/packages/neuron/package.py b/var/spack/repos/builtin/packages/neuron/package.py index 86fcf5ac84..15a0f94ea9 100644 --- a/var/spack/repos/builtin/packages/neuron/package.py +++ b/var/spack/repos/builtin/packages/neuron/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -189,14 +189,12 @@ class Neuron(Package): make('VERBOSE=1') make('install') - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): neuron_archdir = self.get_neuron_archdir() - run_env.prepend_path('PATH', join_path(neuron_archdir, 'bin')) - run_env.prepend_path( - 'LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib')) + env.prepend_path('PATH', join_path(neuron_archdir, 'bin')) + env.prepend_path('LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib')) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): neuron_archdir = self.get_neuron_archdir() - spack_env.prepend_path('PATH', join_path(neuron_archdir, 'bin')) - spack_env.prepend_path( - 'LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib')) + env.prepend_path('PATH', join_path(neuron_archdir, 'bin')) + env.prepend_path('LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib')) diff --git a/var/spack/repos/builtin/packages/nextflow/package.py b/var/spack/repos/builtin/packages/nextflow/package.py index c763aceb8e..a569e0f7e6 100644 --- a/var/spack/repos/builtin/packages/nextflow/package.py +++ b/var/spack/repos/builtin/packages/nextflow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nfft/package.py b/var/spack/repos/builtin/packages/nfft/package.py index 0b60277cb4..ccd1a8ade0 100644 --- a/var/spack/repos/builtin/packages/nfft/package.py +++ b/var/spack/repos/builtin/packages/nfft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nghttp2/package.py b/var/spack/repos/builtin/packages/nghttp2/package.py index 9f39e163d4..e5a6cb60dc 100644 --- a/var/spack/repos/builtin/packages/nghttp2/package.py +++ b/var/spack/repos/builtin/packages/nghttp2/package.py @@ -1,10 +1,12 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import os + class Nghttp2(AutotoolsPackage): """nghttp2 is an implementation of HTTP/2 and its header compression @@ -19,17 +21,17 @@ class Nghttp2(AutotoolsPackage): depends_on('py-cython@0.19:', type=('build', 'run')) depends_on('py-setuptools', type=('build')) - def setup_environment(self, spack_env, run_env): - site_packages_dir = '/'.join( - [self.spec.prefix.lib, - ('python' + str(self.spec['python'].version.up_to(2))), - 'site-packages']) - spack_env.prepend_path('PYTHONPATH', site_packages_dir) + def setup_build_environment(self, env): + site_packages_dir = os.path.join( + self.spec.prefix.lib, + 'python' + str(self.spec['python'].version.up_to(2)), + 'site-packages') + env.prepend_path('PYTHONPATH', site_packages_dir) @run_before('install') def ensure_install_dir_exists(self): - site_packages_dir = '/'.join( - [self.spec.prefix.lib, - ('python' + str(self.spec['python'].version.up_to(2))), - 'site-packages']) + site_packages_dir = os.path.join( + self.spec.prefix.lib, + 'python' + str(self.spec['python'].version.up_to(2)), + 'site-packages') mkdirp(site_packages_dir) diff --git a/var/spack/repos/builtin/packages/nginx/package.py b/var/spack/repos/builtin/packages/nginx/package.py index 32d7142a9e..8c2c6a32dd 100644 --- a/var/spack/repos/builtin/packages/nginx/package.py +++ b/var/spack/repos/builtin/packages/nginx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,6 +28,6 @@ class Nginx(AutotoolsPackage): args = ['--with-http_ssl_module'] return args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Prepend the sbin directory to PATH.""" - run_env.prepend_path('PATH', join_path(self.prefix, 'sbin')) + env.prepend_path('PATH', self.prefix.sbin) diff --git a/var/spack/repos/builtin/packages/ngmlr/package.py b/var/spack/repos/builtin/packages/ngmlr/package.py index 182643c08b..fba498e8d8 100644 --- a/var/spack/repos/builtin/packages/ngmlr/package.py +++ b/var/spack/repos/builtin/packages/ngmlr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nicstat/package.py b/var/spack/repos/builtin/packages/nicstat/package.py new file mode 100644 index 0000000000..37e931bb83 --- /dev/null +++ b/var/spack/repos/builtin/packages/nicstat/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Nicstat(MakefilePackage): + """ + Nicstat is a Solaris and Linux command-line that prints out network + statistics for all network interface cards (NICs), including packets, + kilobytes per second, average packet sizes and more. + """ + + homepage = "https://github.com/scotte/nicstat" + url = "https://jaist.dl.sourceforge.net/project/nicstat/nicstat-1.95.tar.gz" + + version('1.95', sha256='c4cc33f8838f4523f27c3d7584eedbe59f4c587f0821612f5ac2201adc18b367') + + def edit(self, spec, prefix): + copy('Makefile.Linux', 'makefile') + filter_file(r'CMODEL =\s+-m32', '', 'makefile') + filter_file('sudo', '', 'makefile', string=True) + + def install(self, spec, prefix): + install_tree(".", prefix) diff --git a/var/spack/repos/builtin/packages/nim/package.py b/var/spack/repos/builtin/packages/nim/package.py index 2457ea676c..bc5fb15916 100644 --- a/var/spack/repos/builtin/packages/nim/package.py +++ b/var/spack/repos/builtin/packages/nim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ninja-fortran/package.py b/var/spack/repos/builtin/packages/ninja-fortran/package.py index 4c6deda2a0..8e9fcb9851 100644 --- a/var/spack/repos/builtin/packages/ninja-fortran/package.py +++ b/var/spack/repos/builtin/packages/ninja-fortran/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ninja/package.py b/var/spack/repos/builtin/packages/ninja/package.py index 51f0a45f43..41e2a9d8d9 100644 --- a/var/spack/repos/builtin/packages/ninja/package.py +++ b/var/spack/repos/builtin/packages/ninja/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,7 @@ class Ninja(Package): git = "https://github.com/Kitware/ninja.git" version('kitware', branch='features-for-fortran') + version('1.10.0', sha256='3810318b08489435f8efc19c05525e80a993af5a55baa0dfeae0465a9d45f99f') version('1.9.0', sha256='5d7ec75828f8d3fd1a0c2f31b5b0cea780cdfe1031359228c428c1a48bfcd5b9') version('1.8.2', sha256='86b8700c3d0880c2b44c2ff67ce42774aaf8c28cbf57725cb881569288c1c6f4') version('1.7.2', sha256='2edda0a5421ace3cf428309211270772dd35a91af60c96f93f90df6bc41b16d9') diff --git a/var/spack/repos/builtin/packages/nix/package.py b/var/spack/repos/builtin/packages/nix/package.py index 528f330efa..7025b65dc1 100644 --- a/var/spack/repos/builtin/packages/nix/package.py +++ b/var/spack/repos/builtin/packages/nix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nlohmann-json/package.py b/var/spack/repos/builtin/packages/nlohmann-json/package.py index 628e4395bc..80bc0ddf1e 100644 --- a/var/spack/repos/builtin/packages/nlohmann-json/package.py +++ b/var/spack/repos/builtin/packages/nlohmann-json/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ class NlohmannJson(CMakePackage): url = "https://github.com/nlohmann/json/archive/v3.1.2.tar.gz" maintainers = ['ax3l'] + version('3.7.2', sha256='914c4af3f14bb98ff084172685fba5d32e8ce4390ec8ba5da45c63daa305df4d') version('3.7.0', sha256='d51a3a8d3efbb1139d7608e28782ea9efea7e7933157e8ff8184901efd8ee760') version('3.5.0', sha256='e0b1fc6cc6ca05706cce99118a87aca5248bd9db3113e703023d23f044995c1d') version('3.4.0', sha256='c377963a95989270c943d522bfefe7b889ef5ed0e1e15d535fd6f6f16ed70732') diff --git a/var/spack/repos/builtin/packages/nlopt/package.py b/var/spack/repos/builtin/packages/nlopt/package.py index 417e7f5cd6..c533bf60e8 100644 --- a/var/spack/repos/builtin/packages/nlopt/package.py +++ b/var/spack/repos/builtin/packages/nlopt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ class Nlopt(CMakePackage): url = "https://github.com/stevengj/nlopt/archive/v2.5.0.tar.gz" git = "https://github.com/stevengj/nlopt.git" - version('develop', branch='master') + version('master', branch='master') version('2.5.0', sha256='c6dd7a5701fff8ad5ebb45a3dc8e757e61d52658de3918e38bab233e7fd3b4ae') variant('shared', default=True, description='Enables the build of shared libraries') @@ -28,13 +28,14 @@ class Nlopt(CMakePackage): # Note: matlab is licenced - spack does not download automatically variant("matlab", default=False, description="Build the Matlab bindings.") - depends_on('cmake@3.0:', type='build', when='@develop') - depends_on('python', when='+python') + depends_on('cmake@3.0:', type='build', when='@master') + depends_on('python', when='+python', type=('build', 'run')) depends_on('py-numpy', when='+python', type=('build', 'run')) depends_on('swig', when='+python') depends_on('guile', when='+guile') depends_on('octave', when='+octave') depends_on('matlab', when='+matlab') + extends('python', when='+python') def cmake_args(self): # Add arguments other than @@ -43,7 +44,7 @@ class Nlopt(CMakePackage): args = [] # Specify on command line to alter defaults: - # eg: spack install nlopt@develop +guile -octave +cxx + # eg: spack install nlopt@master +guile -octave +cxx # Spack should locate python by default - but to point to a build if '+python' in spec: diff --git a/var/spack/repos/builtin/packages/nmap/package.py b/var/spack/repos/builtin/packages/nmap/package.py index 8bedd76b74..a7e3d1a4b2 100644 --- a/var/spack/repos/builtin/packages/nmap/package.py +++ b/var/spack/repos/builtin/packages/nmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nnvm/package.py b/var/spack/repos/builtin/packages/nnvm/package.py index 4bf85cfe51..b341fc315a 100644 --- a/var/spack/repos/builtin/packages/nnvm/package.py +++ b/var/spack/repos/builtin/packages/nnvm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/node-js/package.py b/var/spack/repos/builtin/packages/node-js/package.py index 93dd232143..155d030f29 100644 --- a/var/spack/repos/builtin/packages/node-js/package.py +++ b/var/spack/repos/builtin/packages/node-js/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,8 +13,15 @@ class NodeJs(Package): engine.""" homepage = "https://nodejs.org/" - url = "https://nodejs.org/download/release/v6.3.0/node-v6.3.0.tar.gz" + url = "https://nodejs.org/dist/v13.5.0/node-v13.5.0.tar.gz" + list_url = "https://nodejs.org/dist/" + list_depth = 1 + # Current (latest features) + version('13.5.0', sha256='4b8078d896a7550d7ed399c1b4ac9043e9f883be404d9b337185c8d8479f2db8') + + # LTS (recommended for most users) + version('12.14.0', sha256='5c1939867228f3845c808ef84a89c8ee93cc35f857bf7587ecee1b5a6d9da67b', preferred=True) version('11.1.0', sha256='3f53b5ac25b2d36ad538267083c0e603d9236867a936c22a9116d95fa10c60d5') version('10.13.0', sha256='aa06825fff375ece7c0d881ae0de5d402a857e8cabff9b4a50f2f0b7b44906be') version('8.9.1', sha256='32491b7fcc4696b2cdead45c47e52ad16bbed8f78885d32e873952fee0f971e1') @@ -22,30 +29,32 @@ class NodeJs(Package): version('6.3.0', sha256='4ed7a99985f8afee337cc22d5fef61b495ab4238dfff3750ac9019e87fc6aae6') version('6.2.2', sha256='b6baee57a0ede496c7c7765001f7495ad74c8dfe8c34f1a6fb2cd5d8d526ffce') - # variant('bash-completion', default=False, description='Build with bash-completion support for npm') # NOQA: ignore=E501 variant('debug', default=False, description='Include debugger support') variant('doc', default=False, description='Compile with documentation') variant('icu4c', default=False, description='Build with support for all locales instead of just English') variant('openssl', default=True, description='Build with Spacks OpenSSL instead of the bundled version') variant('zlib', default=True, description='Build with Spacks zlib instead of the bundled version') + # https://github.com/nodejs/node/blob/master/BUILDING.md#unix-and-macos + depends_on('gmake@3.81:', type='build') depends_on('libtool', type='build', when=sys.platform != 'darwin') depends_on('pkgconfig', type='build') - depends_on('python@2.7:2.8', type='build') + depends_on('python@2.7:2.8,3.5:', when='@12:', type='build') + depends_on('python@2.7:2.8', when='@:11', type='build') # depends_on('bash-completion', when="+bash-completion") depends_on('icu4c', when='+icu4c') depends_on('openssl@1.0.2d:1.0.99', when='@:9+openssl') depends_on('openssl@1.1:', when='@10:+openssl') depends_on('zlib', when='+zlib') - def install(self, spec, prefix): - options = [] - options.extend(['--prefix={0}'.format(prefix)]) + phases = ['configure', 'build', 'install'] - # Note: npm is updated more regularly than node.js, so we build the - # package instead of using the bundled version - options.extend(['--without-npm']) + def setup_build_environment(self, env): + # Force use of experimental Python 3 support + env.set('PYTHON', self.spec['python'].command.path) + env.set('NODE_GYP_FORCE_PYTHON', self.spec['python'].command.path) + def configure_args(self): # On OSX, the system libtool must be used # So, we ensure that this is the case by... if sys.platform == 'darwin': @@ -60,37 +69,52 @@ class NodeJs(Package): '(temporarily) remove \n %s or its link to libtool from' 'path') - # TODO: Add bash-completion + args = [ + '--prefix={0}'.format(self.prefix), + # Note: npm is updated more regularly than node.js, so we build + # the package instead of using the bundled version + '--without-npm' + ] - if '+debug' in spec: - options.extend(['--debug']) + if '+debug' in self.spec: + args.append('--debug') - if '+openssl' in spec: - options.extend([ + if '+openssl' in self.spec: + args.extend([ '--shared-openssl', - '--shared-openssl-includes=%s' % spec['openssl'].prefix.include, # NOQA: ignore=E501 - '--shared-openssl-libpath=%s' % spec['openssl'].prefix.lib, + '--shared-openssl-includes={0}'.format( + self.spec['openssl'].prefix.include), + '--shared-openssl-libpath={0}'.format( + self.spec['openssl'].prefix.lib), ]) - if '+zlib' in spec: - options.extend([ + if '+zlib' in self.spec: + args.extend([ '--shared-zlib', - '--shared-zlib-includes=%s' % spec['zlib'].prefix.include, - '--shared-zlib-libpath=%s' % spec['zlib'].prefix.lib, + '--shared-zlib-includes={0}'.format( + self.spec['zlib'].prefix.include), + '--shared-zlib-libpath={0}'.format( + self.spec['zlib'].prefix.lib), ]) - if '+icu4c' in spec: - options.extend(['--with-intl=full-icu']) - # else: - # options.extend(['--with-intl=system-icu']) + if '+icu4c' in self.spec: + args.append('--with-intl=full-icu') - configure(*options) + return args - if self.run_tests: - make('test') - make('test-addons') + def configure(self, spec, prefix): + python('configure.py', *self.configure_args()) + def build(self, spec, prefix): + make() if '+doc' in spec: make('doc') + @run_after('build') + @on_package_attributes(run_tests=True) + def test(self): + make('test') + make('test-addons') + + def install(self, spec, prefix): make('install') diff --git a/var/spack/repos/builtin/packages/notmuch/package.py b/var/spack/repos/builtin/packages/notmuch/package.py index 676a275f4c..6a79d0b421 100644 --- a/var/spack/repos/builtin/packages/notmuch/package.py +++ b/var/spack/repos/builtin/packages/notmuch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/npb/package.py b/var/spack/repos/builtin/packages/npb/package.py index 1f6499f09d..bc9a10cc0d 100644 --- a/var/spack/repos/builtin/packages/npb/package.py +++ b/var/spack/repos/builtin/packages/npb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/npm/package.py b/var/spack/repos/builtin/packages/npm/package.py index 76cc11703d..91b4345484 100644 --- a/var/spack/repos/builtin/packages/npm/package.py +++ b/var/spack/repos/builtin/packages/npm/package.py @@ -1,27 +1,63 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) import os +import shutil from spack import * -class Npm(AutotoolsPackage): +# NOTE: not actually an Autotools package +class Npm(Package): """npm: A package manager for javascript.""" homepage = "https://github.com/npm/npm" # base http://www.npmjs.com/ - url = "https://registry.npmjs.org/npm/-/npm-3.10.5.tgz" + url = "https://registry.npmjs.org/npm/-/npm-6.13.4.tgz" + version('6.13.4', sha256='a063290bd5fa06a8753de14169b7b243750432f42d01213fbd699e6b85916de7') version('3.10.9', sha256='fb0871b1aebf4b74717a72289fade356aedca83ee54e7386e38cb51874501dd6') version('3.10.5', sha256='ff019769e186152098841c1fa6325e5a79f7903a45f13bd0046a4dc8e63f845f') depends_on('node-js', type=('build', 'run')) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + # npm 6.13.4 ships with node-gyp 5.0.5, which contains several Python 3 + # compatibility issues on macOS. Manually update to node-gyp 6.0.1 for + # full Python 3 support. + resource(name='node-gyp', destination='node-gyp', + url='https://registry.npmjs.org/node-gyp/-/node-gyp-6.0.1.tgz', + sha256='bbc0e137e17a63676efc97a0e3b1fcf101498a1c2c01c3341cd9491f248711b8') + resource(name='env-paths', destination='env-paths', + url='https://registry.npmjs.org/env-paths/-/env-paths-2.2.0.tgz', + sha256='168b394fbca60ea81dc84b1824466df96246b9eb4d671c2541f55f408a264b4c') + + phases = ['configure', 'build', 'install'] + + def patch(self): + shutil.rmtree('node_modules/node-gyp') + install_tree('node-gyp/package', 'node_modules/node-gyp') + filter_file('"node-gyp": "^5.0.5"', '"node-gyp": "^6.0.1"', + 'package.json', string=True) + install_tree('env-paths/package', 'node_modules/env-paths') + + def configure(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + def build(self, spec, prefix): + make() + + def install(self, spec, prefix): + make('install') + + def setup_dependent_build_environment(self, env, dependent_spec): + npm_config_cache_dir = "%s/npm-cache" % dependent_spec.prefix + if not os.path.isdir(npm_config_cache_dir): + mkdir(npm_config_cache_dir) + env.set('npm_config_cache', npm_config_cache_dir) + + def setup_dependent_run_environment(self, env, dependent_spec): npm_config_cache_dir = "%s/npm-cache" % dependent_spec.prefix if not os.path.isdir(npm_config_cache_dir): mkdir(npm_config_cache_dir) - run_env.set('npm_config_cache', npm_config_cache_dir) - spack_env.set('npm_config_cache', npm_config_cache_dir) + env.set('npm_config_cache', npm_config_cache_dir) diff --git a/var/spack/repos/builtin/packages/npth/package.py b/var/spack/repos/builtin/packages/npth/package.py index 3cc30fea6c..e5a82c4e83 100644 --- a/var/spack/repos/builtin/packages/npth/package.py +++ b/var/spack/repos/builtin/packages/npth/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nrm/package.py b/var/spack/repos/builtin/packages/nrm/package.py index b15bc11323..d4d5bb4914 100644 --- a/var/spack/repos/builtin/packages/nrm/package.py +++ b/var/spack/repos/builtin/packages/nrm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,11 +16,11 @@ class Nrm(PythonPackage): depends_on('py-setuptools', type=('build')) depends_on('py-six', type=('build', 'run')) - depends_on('py-zmq@17.1.2', type=('build', 'run')) + depends_on('py-pyzmq@17.1.2', type=('build', 'run')) depends_on('py-pyyaml', type=('build', 'run')) depends_on('py-tornado@5.1.1', type=('build', 'run')) depends_on('py-numpy', type=('build', 'run')) - depends_on('py-argparse@1.2.1:', type=('build', 'run')) + depends_on('py-argparse@1.2.1:', type=('build', 'run'), when='^python@:2.6') depends_on('py-jsonschema@2.6.0', type=('build', 'run')) depends_on('py-warlock', type=('build', 'run')) depends_on('py-scipy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/nseg/package.py b/var/spack/repos/builtin/packages/nseg/package.py index ef552f2b36..26644f61ff 100644 --- a/var/spack/repos/builtin/packages/nseg/package.py +++ b/var/spack/repos/builtin/packages/nseg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nsimd/package.py b/var/spack/repos/builtin/packages/nsimd/package.py new file mode 100644 index 0000000000..1d22be943e --- /dev/null +++ b/var/spack/repos/builtin/packages/nsimd/package.py @@ -0,0 +1,65 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Nsimd(CMakePackage): + """NSIMD is a vectorization library that abstracts SIMD programming. + It was designed to exploit the maximum power of processors + at a low development cost.""" + + homepage = "https://agenium-scale.github.io/nsimd/" + url = "https://github.com/agenium-scale/nsimd/archive/v1.0.tar.gz" + + maintainers = ['eschnett'] + + version('1.0', sha256='523dae83f1d93eab30114321f1c9a67e2006a52595da4c51f121ca139abe0857') + + variant('simd', + default='none', + description='SIMD instruction set', + values=( + 'none', + 'CPU', + 'SSE2', 'SSE42', 'AVX', 'AVX2', 'AVX512_KNL', 'AVX512_SKYLAKE', + 'NEON128', 'AARCH64', 'SVE', + ), + multi=False) + variant('optionals', + default=(), + description='Optional SIMD features', + values=('FMA', 'FP16'), + multi=True) + + conflicts('simd=none', msg="SIMD instruction set not defined") + + # Requires a C++14 compiler for building. + # The C++ interface requires a C++11 compiler to use. + depends_on('cmake@2.8.7:', type='build') + depends_on('python@3:', type='build') + + # Add a 'generate_code' phase in the beginning + phases = ['generate_code'] + CMakePackage.phases + + def generate_code(self, spec, prefix): + """Auto-generates code in the build directory""" + options = [ + 'egg/hatch.py', + '--all', + '--force', + '--disable-clang-format', + ] + python = spec['python'].command + python(*options) + + def cmake_args(self): + simd = self.spec.variants['simd'].value + optionals = ';'.join(self.spec.variants['optionals'].value) + cmake_args = [ + "-DSIMD={0}".format(simd), + "-DSIMD_OPTIONALS={0}".format(optionals), + ] + return cmake_args diff --git a/var/spack/repos/builtin/packages/nspr/package.py b/var/spack/repos/builtin/packages/nspr/package.py index 83acbb01bc..5d697e6ddc 100644 --- a/var/spack/repos/builtin/packages/nspr/package.py +++ b/var/spack/repos/builtin/packages/nspr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ntpoly/package.py b/var/spack/repos/builtin/packages/ntpoly/package.py index d390e19dba..d83a0bba78 100644 --- a/var/spack/repos/builtin/packages/ntpoly/package.py +++ b/var/spack/repos/builtin/packages/ntpoly/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ class Ntpoly(CMakePackage): """ homepage = "https://william-dawson.github.io/NTPoly/" - url = "https://github.com/william-dawson/NTPoly/archive/ntpoly-v2.3.1-alpha.tar.gz" + url = "https://github.com/william-dawson/NTPoly/archive/ntpoly-v2.3.1.tar.gz" version('2.3.1', sha256='af8c7690321607fbdee9671b9cb3acbed945148014e0541435858cf82bfd887e') diff --git a/var/spack/repos/builtin/packages/numactl/package.py b/var/spack/repos/builtin/packages/numactl/package.py index eb2b7667fb..fabf18127a 100644 --- a/var/spack/repos/builtin/packages/numactl/package.py +++ b/var/spack/repos/builtin/packages/numactl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py index 3518a5545f..5205d0e1ac 100644 --- a/var/spack/repos/builtin/packages/numdiff/package.py +++ b/var/spack/repos/builtin/packages/numdiff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nut/package.py b/var/spack/repos/builtin/packages/nut/package.py index f159838c63..45eff1207a 100644 --- a/var/spack/repos/builtin/packages/nut/package.py +++ b/var/spack/repos/builtin/packages/nut/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,7 @@ class Nut(CMakePackage): and performance issues.""" homepage = "https://github.com/lanl/NuT" - url = "https://github.com/lanl/NuT/archive/0.1.0.tar.gz" + url = "https://github.com/lanl/NuT/archive/0.1.1.tar.gz" git = "https://github.com/lanl/NuT.git" tags = ['proxy-app'] @@ -29,11 +29,11 @@ class Nut(CMakePackage): conflicts('%xl', when='@serial') conflicts('%nag', when='@serial') - def setup_environment(self, spack_env, run_env): - spack_env.set('RANDOM123_DIR', self.spec['random123'].prefix) - build_targets = ['VERBOSE=on'] + def setup_build_environment(self, env): + env.set('RANDOM123_DIR', self.spec['random123'].prefix) + def install(self, spec, prefix): install('README.md', prefix) mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/nvptx-tools/package.py b/var/spack/repos/builtin/packages/nvptx-tools/package.py index 1e349971b3..775b53e3fa 100644 --- a/var/spack/repos/builtin/packages/nvptx-tools/package.py +++ b/var/spack/repos/builtin/packages/nvptx-tools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nwchem/package.py b/var/spack/repos/builtin/packages/nwchem/package.py index 6a18e54c5c..afc1451c0d 100644 --- a/var/spack/repos/builtin/packages/nwchem/package.py +++ b/var/spack/repos/builtin/packages/nwchem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/nyancat/package.py b/var/spack/repos/builtin/packages/nyancat/package.py index a53ddcaf00..e96079814b 100644 --- a/var/spack/repos/builtin/packages/nyancat/package.py +++ b/var/spack/repos/builtin/packages/nyancat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ocaml/package.py b/var/spack/repos/builtin/packages/ocaml/package.py index e3d3cb9c83..34ff99eb93 100644 --- a/var/spack/repos/builtin/packages/ocaml/package.py +++ b/var/spack/repos/builtin/packages/ocaml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,7 +20,7 @@ class Ocaml(Package): def url_for_version(self, version): url = "http://caml.inria.fr/pub/distrib/ocaml-{0}/ocaml-{1}.tar.gz" - return url.format(version.up_to(2), version) + return url.format(str(version)[:-2], version) def install(self, spec, prefix): configure('-prefix', '{0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/occa/package.py b/var/spack/repos/builtin/packages/occa/package.py index c6528f2960..314f79b121 100644 --- a/var/spack/repos/builtin/packages/occa/package.py +++ b/var/spack/repos/builtin/packages/occa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -41,7 +41,7 @@ class Occa(Package): conflicts('%gcc@7:', when='^cuda@:9') def install(self, spec, prefix): - # The build environment is set by the 'setup_environment' method. + # The build environment is set by the 'setup_build_environment' method. # Copy the source to the installation directory and build OCCA there. install_tree('.', prefix) make('-C', prefix) @@ -65,7 +65,7 @@ class Occa(Package): s_env.set('OCCA_CUDA_COMPILER', join_path(cuda_dir, 'bin', 'nvcc')) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec # The environment variable CXX is automatically set to the Spack # compiler wrapper. @@ -79,7 +79,7 @@ class Occa(Package): # the verbose output, so we keep both. cxxflags = spec.compiler_flags['cxxflags'] if cxxflags: - spack_env.set('CXXFLAGS', ' '.join(cxxflags)) + env.set('CXXFLAGS', ' '.join(cxxflags)) # For the cuda, openmp, and opencl variants, set the environment # variable OCCA_{CUDA,OPENMP,OPENCL}_ENABLED only if the variant is @@ -92,21 +92,23 @@ class Occa(Package): cuda_dir, shared=True, recursive=True) - spack_env.set('OCCA_INCLUDE_PATH', cuda_dir.include) - spack_env.set('OCCA_LIBRARY_PATH', ':'.join(cuda_libs.directories)) + env.set('OCCA_INCLUDE_PATH', cuda_dir.include) + env.set('OCCA_LIBRARY_PATH', ':'.join(cuda_libs.directories)) else: - spack_env.set('OCCA_CUDA_ENABLED', '0') + env.set('OCCA_CUDA_ENABLED', '0') if '~opencl' in spec: - spack_env.set('OCCA_OPENCL_ENABLED', '0') + env.set('OCCA_OPENCL_ENABLED', '0') # Setup run-time environment for testing. - spack_env.set('OCCA_VERBOSE', '1') - self._setup_runtime_flags(spack_env) - # The 'run_env' is included in the Spack generated module files. - self._setup_runtime_flags(run_env) + env.set('OCCA_VERBOSE', '1') + self._setup_runtime_flags(env) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_run_environment(self, env): + # The 'env' is included in the Spack generated module files. + self._setup_runtime_flags(env) + + def setup_dependent_build_environment(self, env, dependent_spec): # Export OCCA_* variables for everyone using this package from within # Spack. - self._setup_runtime_flags(spack_env) + self._setup_runtime_flags(env) diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index a285a5e025..dbd3f23182 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/oclint/package.py b/var/spack/repos/builtin/packages/oclint/package.py index 645e7090d4..8731f6b5ad 100644 --- a/var/spack/repos/builtin/packages/oclint/package.py +++ b/var/spack/repos/builtin/packages/oclint/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,7 +19,7 @@ class Oclint(Package): version('0.13', sha256='a0fd188673863e6357d6585b9bb9c3affe737df134b9383a1a5ed021d09ed848') depends_on('python', type=('build')) - depends_on('py-argparse', type=('build')) + depends_on('py-argparse', type=('build'), when='^python@:2.6') depends_on('git', type=('build')) depends_on('subversion', type=('build')) depends_on('cmake', type=('build')) diff --git a/var/spack/repos/builtin/packages/oclock/package.py b/var/spack/repos/builtin/packages/oclock/package.py index 816bb57f46..f0410e94d6 100644 --- a/var/spack/repos/builtin/packages/oclock/package.py +++ b/var/spack/repos/builtin/packages/oclock/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/octave-optim/package.py b/var/spack/repos/builtin/packages/octave-optim/package.py index bb63bfe429..2a5b736ec7 100644 --- a/var/spack/repos/builtin/packages/octave-optim/package.py +++ b/var/spack/repos/builtin/packages/octave-optim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/octave-splines/package.py b/var/spack/repos/builtin/packages/octave-splines/package.py index efa0893144..e100e9b840 100644 --- a/var/spack/repos/builtin/packages/octave-splines/package.py +++ b/var/spack/repos/builtin/packages/octave-splines/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/octave-struct/package.py b/var/spack/repos/builtin/packages/octave-struct/package.py index a8f679f06e..2d99125be6 100644 --- a/var/spack/repos/builtin/packages/octave-struct/package.py +++ b/var/spack/repos/builtin/packages/octave-struct/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/octave/helloworld.cc b/var/spack/repos/builtin/packages/octave/helloworld.cc new file mode 100644 index 0000000000..f2cb6d9c1e --- /dev/null +++ b/var/spack/repos/builtin/packages/octave/helloworld.cc @@ -0,0 +1,11 @@ +#include <octave/oct.h> + +DEFUN_DLD (helloworld, args, nargout, + "Hello World Help String") +{ + octave_stdout << "Hello World has " + << args.length () << " input arguments and " + << nargout << " output arguments.\n"; + + return octave_value_list (); +} diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index cdfa076c73..f70895bfda 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -1,24 +1,32 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * +import os.path +import shutil import sys +import tempfile + +import spack.util.environment -class Octave(AutotoolsPackage): +class Octave(AutotoolsPackage, GNUMirrorPackage): """GNU Octave is a high-level language, primarily intended for numerical - computations. It provides a convenient command line interface for solving - linear and nonlinear problems numerically, and for performing other - numerical experiments using a language that is mostly compatible with - Matlab. It may also be used as a batch-oriented language.""" + computations. + + It provides a convenient command line interface for solving linear and + nonlinear problems numerically, and for performing other numerical + experiments using a language that is mostly compatible with Matlab. + It may also be used as a batch-oriented language. + """ homepage = "https://www.gnu.org/software/octave/" - url = "https://ftpmirror.gnu.org/octave/octave-4.0.0.tar.gz" + gnu_mirror_path = "octave/octave-4.0.0.tar.gz" + maintainers = ['mtmiller'] extendable = True + version('5.1.0', sha256='e36b1124cac27c7caa51cc57de408c31676d5f0096349b4d50b57bfe1bcd7495') version('4.4.1', sha256='09fbd0f212f4ef21e53f1d9c41cf30ce3d7f9450fb44911601e21ed64c67ae97') version('4.4.0', sha256='72f846379fcec7e813d46adcbacd069d72c4f4d8f6003bcd92c3513aafcd6e96') version('4.2.2', sha256='77b84395d8e7728a1ab223058fe5e92dc38c03bc13f7358e6533aab36f76726e') @@ -75,7 +83,7 @@ class Octave(AutotoolsPackage): depends_on('glpk', when='+glpk') depends_on('gl2ps', when='+gl2ps') depends_on('gnuplot', when='+gnuplot') - depends_on('image-magick', when='+magick') + depends_on('imagemagick', when='+magick') depends_on('hdf5', when='+hdf5') depends_on('java', when='+jdk') # TODO: requires Java 6 ? depends_on('llvm', when='+llvm') @@ -87,6 +95,57 @@ class Octave(AutotoolsPackage): depends_on('suite-sparse', when='+suitesparse') depends_on('zlib', when='+zlib') + def patch(self): + # Filter mkoctfile.in.cc to use underlying compilers and not + # Spack compiler wrappers. We are patching the template file + # and not mkoctfile.cc since the latter is generated as part + # of the build. + mkoctfile_in = os.path.join( + self.stage.source_path, 'src', 'mkoctfile.in.cc' + ) + quote = lambda s: '"' + s + '"' + entries_to_patch = { + r'%OCTAVE_CONF_MKOCTFILE_CC%': quote(self.compiler.cc), + r'%OCTAVE_CONF_MKOCTFILE_CXX%': quote(self.compiler.cxx), + r'%OCTAVE_CONF_MKOCTFILE_F77%': quote(self.compiler.f77), + r'%OCTAVE_CONF_MKOCTFILE_DL_LD%': quote(self.compiler.cxx), + r'%OCTAVE_CONF_MKOCTFILE_LD_CXX%': quote(self.compiler.cxx) + } + + for pattern, subst in entries_to_patch.items(): + filter_file(pattern, subst, mkoctfile_in) + + @run_after('install') + @on_package_attributes(run_tests=True) + def check_mkoctfile_works_outside_of_build_env(self): + # Check that mkoctfile is properly configured and can compile + # Octave extensions outside of the build env + mkoctfile = Executable(os.path.join(self.prefix, 'bin', 'mkoctfile')) + helloworld_cc = os.path.join( + os.path.dirname(__file__), 'helloworld.cc' + ) + tmp_dir = tempfile.mkdtemp() + shutil.copy(helloworld_cc, tmp_dir) + + # We need to unset these variables since we are still within + # Spack's build environment when running tests + vars_to_unset = ['CC', 'CXX', 'F77', 'FC'] + + with spack.util.environment.preserve_environment(*vars_to_unset): + # Delete temporarily the environment variables that point + # to Spack compiler wrappers + for v in vars_to_unset: + del os.environ[v] + # Check that mkoctfile outputs the expected value for CC + cc = mkoctfile('-p', 'CC', output=str) + msg = "mkoctfile didn't output the expected CC compiler" + assert self.compiler.cc in cc, msg + + # Try to compile an Octave extension + shutil.copy(helloworld_cc, tmp_dir) + with working_dir(tmp_dir): + mkoctfile('helloworld.cc') + def configure_args(self): # See # https://github.com/macports/macports-ports/blob/master/math/octave/ @@ -156,7 +215,7 @@ class Octave(AutotoolsPackage): if '+magick' in spec: config_args.append("--with-magick=%s" - % spec['image-magick'].prefix.lib) + % spec['imagemagick'].prefix.lib) else: config_args.append("--without-magick") diff --git a/var/spack/repos/builtin/packages/octopus/package.py b/var/spack/repos/builtin/packages/octopus/package.py index 4e7aa3322e..1073965e81 100644 --- a/var/spack/repos/builtin/packages/octopus/package.py +++ b/var/spack/repos/builtin/packages/octopus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/of-catalyst/package.py b/var/spack/repos/builtin/packages/of-catalyst/package.py index 9dfc56d9d5..eb036b0db9 100644 --- a/var/spack/repos/builtin/packages/of-catalyst/package.py +++ b/var/spack/repos/builtin/packages/of-catalyst/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/of-precice/package.py b/var/spack/repos/builtin/packages/of-precice/package.py index 1b833da812..3cc9927f4a 100644 --- a/var/spack/repos/builtin/packages/of-precice/package.py +++ b/var/spack/repos/builtin/packages/of-precice/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/omega-h/package.py b/var/spack/repos/builtin/packages/omega-h/package.py index e459406164..2e7707e8d5 100644 --- a/var/spack/repos/builtin/packages/omega-h/package.py +++ b/var/spack/repos/builtin/packages/omega-h/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,7 +12,7 @@ class OmegaH(CMakePackage): """ homepage = "https://github.com/SNLComputation/omega_h" - url = "https://github.com/SNLComputation/omega_h/archive/v9.13.4.tar.gz" + url = "https://github.com/SNLComputation/omega_h/archive/v9.29.0.tar.gz" git = "https://github.com/SNLComputation/omega_h.git" maintainers = ['ibaned'] diff --git a/var/spack/repos/builtin/packages/ompss/package.py b/var/spack/repos/builtin/packages/ompss/package.py index be79dc958e..669116328c 100644 --- a/var/spack/repos/builtin/packages/ompss/package.py +++ b/var/spack/repos/builtin/packages/ompss/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ompt-openmp/package.py b/var/spack/repos/builtin/packages/ompt-openmp/package.py index fa23d0fd3c..7376efb76e 100644 --- a/var/spack/repos/builtin/packages/ompt-openmp/package.py +++ b/var/spack/repos/builtin/packages/ompt-openmp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/oniguruma/package.py b/var/spack/repos/builtin/packages/oniguruma/package.py index 9d9ccecdec..91259d7588 100644 --- a/var/spack/repos/builtin/packages/oniguruma/package.py +++ b/var/spack/repos/builtin/packages/oniguruma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,6 +10,25 @@ class Oniguruma(AutotoolsPackage): """Regular expression library.""" homepage = "https://github.com/kkos/oniguruma" - url = "https://github.com/kkos/oniguruma/releases/download/v6.1.3/onig-6.1.3.tar.gz" + url = "https://github.com/kkos/oniguruma/releases/download/v6.9.4/onig-6.9.4.tar.gz" + version('6.9.4', sha256='4669d22ff7e0992a7e93e116161cac9c0949cd8960d1c562982026726f0e6d53') version('6.1.3', sha256='480c850cd7c7f2fcaad0942b4a488e2af01fbb8e65375d34908f558b432725cf') + + @property + def libs(self): + return find_libraries('libonig', root=self.prefix, recursive=True) + + @run_after('install') + @on_package_attributes(run_tests=True) + def configuration_check(self): + onig_config = Executable(join_path(self.prefix.bin, 'onig-config')) + + assert onig_config('--cflags', output=str).rstrip() == \ + self.spec['oniguruma'].headers.include_flags + assert onig_config('--libs', output=str).rstrip() == \ + self.spec['oniguruma'].libs.ld_flags + assert onig_config('--prefix', output=str).rstrip() == \ + self.prefix + assert onig_config('--exec-prefix', output=str).rstrip() == \ + self.prefix diff --git a/var/spack/repos/builtin/packages/ont-albacore/package.py b/var/spack/repos/builtin/packages/ont-albacore/package.py index b9e070dcaf..b3bedf9da2 100644 --- a/var/spack/repos/builtin/packages/ont-albacore/package.py +++ b/var/spack/repos/builtin/packages/ont-albacore/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/opa-psm2/package.py b/var/spack/repos/builtin/packages/opa-psm2/package.py index 29e573e5bb..304c7adafe 100644 --- a/var/spack/repos/builtin/packages/opa-psm2/package.py +++ b/var/spack/repos/builtin/packages/opa-psm2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -35,12 +35,12 @@ class OpaPsm2(MakefilePackage): patch('opa-psm2-compiler.patch', when='@11.2.68:', sha256='fe31fda9aaee13acb87d178af2282446196d2cc0b21163034573706110b2e2d6') - def setup_environment(self, spack_env, run_env): - spack_env.set('DESTDIR', self.prefix) + def setup_build_environment(self, env): + env.set('DESTDIR', self.prefix) if '%intel' in self.spec: # this variable must be set when we use the Intel compilers to # ensure that the proper flags are set - spack_env.set('CCARCH', 'icc') + env.set('CCARCH', 'icc') def edit(self, spec, prefix): # Change the makefile so libraries and includes are not diff --git a/var/spack/repos/builtin/packages/opam/package.py b/var/spack/repos/builtin/packages/opam/package.py index bc32c26e52..179fad0bd9 100644 --- a/var/spack/repos/builtin/packages/opam/package.py +++ b/var/spack/repos/builtin/packages/opam/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,10 +23,10 @@ class Opam(AutotoolsPackage): parallel = False - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Environment variable setting taken from # https://github.com/Homebrew/homebrew-core/blob/master/Formula/opam.rb - spack_env.set('OCAMLPARAM', 'safe-string=0,_') # OCaml 4.06.0 compat + env.set('OCAMLPARAM', 'safe-string=0,_') # OCaml 4.06.0 compat def build(self, spec, prefix): make('lib-ext') diff --git a/var/spack/repos/builtin/packages/opari2/package.py b/var/spack/repos/builtin/packages/opari2/package.py index ec0f6df5a1..9899e51544 100644 --- a/var/spack/repos/builtin/packages/opari2/package.py +++ b/var/spack/repos/builtin/packages/opari2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openbabel/package.py b/var/spack/repos/builtin/packages/openbabel/package.py index 68fbff7fde..c847c9c1ee 100644 --- a/var/spack/repos/builtin/packages/openbabel/package.py +++ b/var/spack/repos/builtin/packages/openbabel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,18 +12,24 @@ class Openbabel(CMakePackage): search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.""" - homepage = "http://openbabel.org/wiki/Main_Page" - url = "https://sourceforge.net/projects/openbabel/files/openbabel/2.4.1/openbabel-2.4.1.tar.gz" + homepage = 'https://openbabel.org/wiki/Main_Page' + url = 'https://github.com/openbabel/openbabel/archive/openbabel-3-0-0.tar.gz' + git = 'https://github.com/openbabel/openbabel.git' - version('2.4.1', sha256='204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc') + version('master', branch='master') + version('3.0.0', tag='openbabel-3-0-0') + version('2.4.1', tag='openbabel-2-4-1') + version('2.4.0', tag='openbabel-2-4-0') variant('python', default=True, description='Build Python bindings') extends('python', when='+python') depends_on('python', type=('build', 'run'), when='+python') - depends_on('cmake@2.4.8:', type='build') - depends_on('pkgconfig', type='build') + depends_on('cmake@3.1:', type='build') + depends_on('pkgconfig', type='build') + depends_on('swig@2.0:', type='build', when='+python') + depends_on('boost') depends_on('cairo') # required to support PNG depiction depends_on('eigen@3.0:') # required if using the language bindings depends_on('libxml2') # required to read/write CML files, XML formats @@ -43,6 +49,7 @@ class Openbabel(CMakePackage): args.extend([ '-DPYTHON_BINDINGS=ON', '-DPYTHON_EXECUTABLE={0}'.format(spec['python'].command.path), + '-DRUN_SWIG=ON', ]) else: args.append('-DPYTHON_BINDINGS=OFF') @@ -56,6 +63,6 @@ class Openbabel(CMakePackage): obabel('-:C1=CC=CC=C1Br', '-omol') if '+python' in self.spec: - # Attempt to import the Python modules - for module in ['openbabel', 'pybel']: - python('-c', 'import {0}'.format(module)) + python('-c', 'import openbabel') + if self.spec.version < Version('3.0.0'): + python('-c', 'import pybel') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 97242ee45d..695dcec80c 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -1,13 +1,13 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) import os +import re from spack import * from spack.package_test import compare_output_file, compile_c_and_execute -import spack.architecture class Openblas(MakefilePackage): @@ -33,17 +33,9 @@ class Openblas(MakefilePackage): version('0.2.16', sha256='766f350d0a4be614812d535cead8c816fc3ad3b9afcd93167ea5e4df9d61869b') version('0.2.15', sha256='73c40ace5978282224e5e122a41c8388c5a19e65a6f2329c2b7c0b61bacc9044') - variant( - 'shared', - default=True, - description='Build shared libraries as well as static libs.' - ) - variant('ilp64', default=False, description='64 bit integers') + variant('ilp64', default=False, description='Force 64-bit Fortran native integers') variant('pic', default=True, description='Build position independent code') - - variant('cpu_target', default='auto', - description='Set CPU target architecture (leave empty for ' - 'autodetection; GENERIC, SSE_GENERIC, NEHALEM, ...)') + variant('shared', default=True, description='Build shared libraries') variant( 'threads', default='none', @@ -52,24 +44,6 @@ class Openblas(MakefilePackage): multi=False ) - variant( - 'virtual_machine', - default=False, - description="Adding options to build openblas on Linux virtual machine" - ) - - variant( - 'avx2', - default=True, - description='Enable use of AVX2 instructions' - ) - - variant( - 'avx512', - default=False, - description='Enable use of AVX512 instructions' - ) - # virtual dependency provides('blas') provides('lapack') @@ -142,14 +116,80 @@ class Openblas(MakefilePackage): 'OpenBLAS @:0.2.19 does not support OpenMP with clang!' ) + @staticmethod + def _read_targets(target_file): + """Parse a list of available targets from the OpenBLAS/TargetList.txt + file. + """ + micros = [] + re_target = re.compile(r'^[A-Z0-9_]+$') + for line in target_file: + match = re_target.match(line) + if match is not None: + micros.append(line.strip().lower()) + + return micros + + @staticmethod + def _microarch_target_args(microarch, available_targets): + """Given a spack microarchitecture and a list of targets found in + OpenBLAS' TargetList.txt, determine the best command-line arguments. + """ + args = [] # Return value + + # List of available architectures, and possible aliases + openblas_arch = set(['alpha', 'arm', 'ia64', 'mips', 'mips64', + 'power', 'sparc', 'zarch']) + openblas_arch_map = { + 'amd64': 'x86_64', + 'powerpc64': 'power', + 'i386': 'x86', + 'aarch64': 'arm64', + } + openblas_arch.update(openblas_arch_map.keys()) + openblas_arch.update(openblas_arch_map.values()) + + # Add spack-only microarchitectures to list + skylake = set(["skylake", "skylake_avx512"]) + available_targets = set(available_targets) | skylake | openblas_arch + + # Find closest ancestor that is known to build in blas + if microarch.name not in available_targets: + for microarch in microarch.ancestors: + if microarch.name in available_targets: + break + + arch_name = microarch.family.name + if arch_name in openblas_arch: + # Apply possible spack->openblas arch name mapping + arch_name = openblas_arch_map.get(arch_name, arch_name) + args.append('ARCH=' + arch_name) + + if microarch.vendor == 'generic': + # User requested a generic platform, or we couldn't find a good + # match for the requested one. Allow OpenBLAS to determine + # an optimized kernel at run time. + args.append('DYNAMIC_ARCH=1') + elif microarch.name in skylake: + # Special case for renaming skylake family + args.append('TARGET=SKYLAKEX') + if microarch.name == "skylake": + # Special case for disabling avx512 instructions + args.append('NO_AVX512=1') + else: + args.append('TARGET=' + microarch.name.upper()) + + return args + @property def make_defs(self): + spec = self.spec + # Configure fails to pick up fortran from FC=/abs/path/to/fc, but # works fine with FC=/abs/path/to/gfortran. # When mixing compilers make sure that # $SPACK_ROOT/lib/spack/env/<compiler> have symlinks with reasonable # names and hack them inside lib/spack/spack/compilers/<compiler>.py - make_defs = [ 'CC={0}'.format(spack_cc), 'FC={0}'.format(spack_fc), @@ -161,23 +201,15 @@ class Openblas(MakefilePackage): else: make_defs.append('MAKE_NB_JOBS=0') # flag provided by OpenBLAS - if self.spec.variants['virtual_machine'].value: - make_defs += [ - 'DYNAMIC_ARCH=1', - 'NUM_THREADS=64', # OpenBLAS stores present no of CPUs as max - ] - - if self.spec.variants['cpu_target'].value != 'auto': - make_defs += [ - 'TARGET={0}'.format(self.spec.variants['cpu_target'].value) - ] - # invoke make with the correct TARGET for aarch64 - elif 'aarch64' in spack.architecture.sys_type(): - make_defs += [ - 'TARGET=ARMV8' - ] - if self.spec.satisfies('%gcc@:4.8.4'): - make_defs += ['NO_AVX2=1'] + # Add target and architecture flags + targetlist_name = join_path(self.stage.source_path, "TargetList.txt") + if os.path.exists(targetlist_name): + with open(targetlist_name) as f: + avail_targets = self._read_targets(f) + else: + avail_targets = [] + make_defs += self._microarch_target_args(spec.target, avail_targets) + if '~shared' in self.spec: if '+pic' in self.spec: make_defs.extend([ @@ -201,11 +233,9 @@ class Openblas(MakefilePackage): if '+ilp64' in self.spec: make_defs += ['INTERFACE64=1'] - if self.spec.target.family == 'x86_64': - if '~avx2' in self.spec: - make_defs += ['NO_AVX2=1'] - if '~avx512' in self.spec: - make_defs += ['NO_AVX512=1'] + # Prevent errors in `as` assembler from newer instructions + if self.spec.satisfies('%gcc@:4.8.4'): + make_defs.append('NO_AVX2=1') return make_defs diff --git a/var/spack/repos/builtin/packages/opencascade/package.py b/var/spack/repos/builtin/packages/opencascade/package.py new file mode 100644 index 0000000000..8267716e78 --- /dev/null +++ b/var/spack/repos/builtin/packages/opencascade/package.py @@ -0,0 +1,67 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Opencascade(CMakePackage): + """Open CASCADE Technology is a software development kit (SDK) + intended for development of applications dealing with 3D CAD data, + freely available in open source. It includes a set of C++ class + libraries providing services for 3D surface and solid modeling, + visualization, data exchange and rapid application development.""" + + homepage = "https://www.opencascade.com" + url = "http://git.dev.opencascade.org/gitweb/?p=occt.git;a=snapshot;h=refs/tags/V7_4_0;sf=tgz" + + version('7.4.0', extension='tar.gz', + sha256='655da7717dac3460a22a6a7ee68860c1da56da2fec9c380d8ac0ac0349d67676') + + variant('tbb', default=False, + description='Build with Intel Threading Building Blocks') + variant('vtk', default=False, + description='Enable VTK support') + variant('freeimage', default=False, + description='Build with FreeImage') + variant('rapidjson', default=False, + description='Build with rapidjson') + + depends_on('intel-tbb', when='+tbb') + depends_on('vtk', when='+vtk') + depends_on('freeimage', when='+freeimage') + depends_on('rapidjson', when='+rapidjson') + + def cmake_args(self): + args = [] + + if '+tbb' in self.spec: + args.append('-DUSE_TBB=ON') + args.append('-D3RDPARTY_VTK_DIR=%s' % + self.spec['intel-tbb'].prefix) + else: + args.append('-DUSE_TBB=OFF') + + if '+vtk' in self.spec: + args.append('-DUSE_VTK=ON') + args.append('-D3RDPARTY_VTK_DIR=%s' % + self.spec['vtk'].prefix) + else: + args.append('-DUSE_VTK=OFF') + + if '+freeimage' in self.spec: + args.append('-DUSE_FREEIMAGE=ON') + args.append('-D3RDPARTY_FREEIMAGE_DIR=%s' % + self.spec['freeimage'].prefix) + else: + args.append('-DUSE_FREEIMAGE=OFF') + + if '+rapidjson' in self.spec: + args.append('-DUSE_RAPIDJSON=ON') + args.append('-D3RDPARTY_RAPIDJSON_DIR=%s' % + self.spec['rapidjson'].prefix) + else: + args.append('-DUSE_RAPIDJSON=OFF') + + return args diff --git a/var/spack/repos/builtin/packages/opencoarrays/package.py b/var/spack/repos/builtin/packages/opencoarrays/package.py index 9cd2b31cb6..d2d55add98 100644 --- a/var/spack/repos/builtin/packages/opencoarrays/package.py +++ b/var/spack/repos/builtin/packages/opencoarrays/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py index bf74f64418..fcd3cb7424 100644 --- a/var/spack/repos/builtin/packages/opencv/package.py +++ b/var/spack/repos/builtin/packages/opencv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Opencv(CMakePackage): +class Opencv(CMakePackage, CudaPackage): """OpenCV is released under a BSD license and hence it's free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for @@ -60,6 +60,7 @@ class Opencv(CMakePackage): # OpenCV modules variant('calib3d', default=True, description='calib3d module') variant('core', default=True, description='Include opencv_core module into the OpenCV build') + variant('cudacodec', default=False, description='Enable video encoding/decoding with CUDA') variant('dnn', default=True, description='Build DNN support') variant('features2d', default=True, description='features2d module') variant('flann', default=True, description='flann module') @@ -78,9 +79,6 @@ class Opencv(CMakePackage): variant('videoio', default=True, description='videoio module') # Optional 3rd party components - variant('cuda', default=True, description='Activates support for CUDA') - # Cuda@10.0.130 does not support gcc > 7 - conflicts('%gcc@7:', when='+cuda') variant('eigen', default=True, description='Activates support for eigen') variant('ipp', default=True, description='Activates support for IPP') variant('ipp_iw', default=True, description='Build IPP IW from source') @@ -124,6 +122,11 @@ class Opencv(CMakePackage): depends_on('ffmpeg', when='+videoio') depends_on('mpi', when='+videoio') + # TODO For Cuda >= 10, make sure 'dynlink_nvcuvid.h' or 'nvcuvid.h' + # exists, otherwise build will fail + # See https://github.com/opencv/opencv_contrib/issues/1786 + conflicts('cuda@10:', when='+cudacodec') + extends('python', when='+python') def cmake_args(self): @@ -150,6 +153,8 @@ class Opencv(CMakePackage): 'ON' if '+calib3d' in spec else 'OFF')), '-DBUILD_opencv_core:BOOL={0}'.format(( 'ON' if '+core' in spec else 'OFF')), + '-DBUILD_opencv_cudacodec={0}'.format(( + 'ON' if '+cudacodec' in spec else 'OFF')), '-DBUILD_opencv_dnn:BOOL={0}'.format(( 'ON' if '+dnn' in spec else 'OFF')), '-DBUILD_opencv_features2d={0}'.format(( diff --git a/var/spack/repos/builtin/packages/openexr/package.py b/var/spack/repos/builtin/packages/openexr/package.py index c5d2188405..9663fd9ab7 100644 --- a/var/spack/repos/builtin/packages/openexr/package.py +++ b/var/spack/repos/builtin/packages/openexr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openfast/package.py b/var/spack/repos/builtin/packages/openfast/package.py index 4a9f12b2da..70e49a8c4f 100644 --- a/var/spack/repos/builtin/packages/openfast/package.py +++ b/var/spack/repos/builtin/packages/openfast/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openfdtd/package.py b/var/spack/repos/builtin/packages/openfdtd/package.py index 50a4049bd3..5af480448f 100644 --- a/var/spack/repos/builtin/packages/openfdtd/package.py +++ b/var/spack/repos/builtin/packages/openfdtd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openfoam-org/package.py b/var/spack/repos/builtin/packages/openfoam-org/package.py index 363cc32f05..d7ca0f6908 100644 --- a/var/spack/repos/builtin/packages/openfoam-org/package.py +++ b/var/spack/repos/builtin/packages/openfoam-org/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -62,6 +62,10 @@ class OpenfoamOrg(Package): git = "https://github.com/OpenFOAM/OpenFOAM-dev.git" version('develop', branch='master') + version('7', sha256='12389cf092dc032372617785822a597aee434a50a62db2a520ab35ba5a7548b5', + url=baseurl + '/OpenFOAM-7/archive/version-7.tar.gz') + version('6', sha256='32a6af4120e691ca2df29c5b9bd7bc7a3e11208947f9bccf6087cfff5492f025', + url=baseurl + '/OpenFOAM-6/archive/version-6.tar.gz') version('5.0', sha256='9057d6a8bb9fa18802881feba215215699065e0b3c5cdd0c0e84cb29c9916c89', url=baseurl + '/OpenFOAM-5.x/archive/version-5.0.tar.gz') version('4.1', sha256='2de18de64e7abdb1b649ad8e9d2d58b77a2b188fb5bcb6f7c2a038282081fd31', @@ -75,6 +79,8 @@ class OpenfoamOrg(Package): description='Compile with 32-bit scalar (single-precision)') variant('source', default=True, description='Install library/application sources and tutorials') + variant('metis', default=False, + description='With metis decomposition') depends_on('mpi') depends_on('zlib') @@ -85,12 +91,17 @@ class OpenfoamOrg(Package): depends_on('scotch~metis+mpi~int64', when='~int64') depends_on('scotch~metis+mpi+int64', when='+int64') + depends_on('metis@5:', when='+metis') + depends_on('metis+int64', when='+metis+int64') + # General patches - foamEtcFile as per openfoam.com (robuster) common = ['spack-Allwmake', 'README-spack'] assets = ['bin/foamEtcFile'] # Version-specific patches - patch('50-etc.patch', when='@5.0:') + patch('https://github.com/OpenFOAM/OpenFOAM-7/commit/ef33cf38ac9b811072a8970c71fbda35a90f6641.patch', + sha256='73103e6b1bdbf3b1e0d517cbbd11562e98c6e9464df5f43e5125e9a5b457d1c5', when='@7') + patch('50-etc.patch', when='@5.0:5.9') patch('41-etc.patch', when='@4.1') patch('41-site.patch', when='@4.1:') patch('240-etc.patch', when='@2.4.0') @@ -126,24 +137,32 @@ class OpenfoamOrg(Package): settings['label-size'] = False return settings - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # This should be similar to the openfoam package, # but sourcing the etc/bashrc here seems to exit with an error. # ... this needs to be examined in more detail. # # Minimal environment only. - run_env.set('FOAM_PROJECT_DIR', self.projectdir) - run_env.set('WM_PROJECT_DIR', self.projectdir) + env.set('FOAM_PROJECT_DIR', self.projectdir) + env.set('WM_PROJECT_DIR', self.projectdir) for d in ['wmake', self.archbin]: # bin already added automatically - run_env.prepend_path('PATH', join_path(self.projectdir, d)) + env.prepend_path('PATH', join_path(self.projectdir, d)) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Location of the OpenFOAM project directory. This is identical to the WM_PROJECT_DIR value, but we avoid that variable since it would mask the normal OpenFOAM cleanup of previous versions. """ - spack_env.set('FOAM_PROJECT_DIR', self.projectdir) + env.set('FOAM_PROJECT_DIR', self.projectdir) + + def setup_dependent_run_environment(self, env, dependent_spec): + """Location of the OpenFOAM project directory. + This is identical to the WM_PROJECT_DIR value, but we avoid that + variable since it would mask the normal OpenFOAM cleanup of + previous versions. + """ + env.set('FOAM_PROJECT_DIR', self.projectdir) @property def projectdir(self): @@ -246,6 +265,11 @@ class OpenfoamOrg(Package): 'SCOTCH_VERSION': 'scotch-{0}'.format(spec['scotch'].version), } + if '+metis' in spec: + self.etc_config['metis'] = { + 'METIS_ARCH_PATH': spec['metis'].prefix, + } + # Write prefs files according to the configuration. # Only need prefs.sh for building, but install both for end-users if self.etc_prefs: diff --git a/var/spack/repos/builtin/packages/openfoam/common/spack-Allwmake b/var/spack/repos/builtin/packages/openfoam/common/spack-Allwmake index a98d7d0db2..91287383d8 100755 --- a/var/spack/repos/builtin/packages/openfoam/common/spack-Allwmake +++ b/var/spack/repos/builtin/packages/openfoam/common/spack-Allwmake @@ -1,8 +1,8 @@ #!/bin/bash # Build wrapper script - FOAM_INST_DIR is only required by foam-extend export FOAM_INST_DIR=$(cd .. && pwd -L) -. $PWD/etc/bashrc '' # No arguments -mkdir -p $FOAM_APPBIN $FOAM_LIBBIN 2>/dev/null # Allow interrupt +. "$PWD/etc/bashrc" '' # No arguments +mkdir -p "$FOAM_APPBIN" "$FOAM_LIBBIN" 2>/dev/null # Allow build interrupt echo "Build openfoam with SPACK ($@)" echo "WM_PROJECT_DIR = $WM_PROJECT_DIR" @@ -12,6 +12,7 @@ then ./Allwmake-spack $@ # Pass arguments else ./Allwmake $@ # Pass arguments + ##echo "Disabled build of openfoam" # When testing environment only # Generate manpages if [ -x bin/tools/foamCreateManpage ] @@ -23,13 +24,13 @@ fi # Link non-dummy MPI_FOAM type to parent-dir, where rpath can find it -if [ "${FOAM_MPI:=dummy}" != dummy -a -d "$FOAM_LIBBIN/$FOAM_MPI" ] +if [ "${FOAM_MPI:=dummy}" != dummy ] && [ -d "$FOAM_LIBBIN/$FOAM_MPI" ] then ( cd "$FOAM_LIBBIN" || exit 1 - for i in $FOAM_MPI/lib*.so + for i in "$FOAM_MPI"/lib*.so do - [ -f $i ] && ln -sf $i "${i##*/}" + [ -f "$i" ] && ln -sf "$i" "${i##*/}" done ) fi diff --git a/var/spack/repos/builtin/packages/openfoam/package.py b/var/spack/repos/builtin/packages/openfoam/package.py index d0d6dac390..f741db61d9 100644 --- a/var/spack/repos/builtin/packages/openfoam/package.py +++ b/var/spack/repos/builtin/packages/openfoam/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -38,7 +38,7 @@ # - Combining +mgridgen with +int64 or +float32 probably won't work. # # The spack 'develop' version of openfoam retains the upstream -# WM_PROJECT_VERSION=plus naming internally. +# WM_PROJECT_VERSION=com naming internally. # ############################################################################## import glob @@ -259,12 +259,16 @@ class Openfoam(Package): maintainers = ['olesenm'] homepage = "http://www.openfoam.com/" url = "https://sourceforge.net/projects/openfoam/files/v1906/OpenFOAM-v1906.tgz" - git = "https://develop.openfoam.com/Development/OpenFOAM-plus.git" + git = "https://develop.openfoam.com/Development/openfoam.git" list_url = "https://sourceforge.net/projects/openfoam/files/" list_depth = 2 version('develop', branch='develop', submodules='True') - version('1906', sha256='15e38c2dc659b63753a0dd3dff913222cc46d6a40089a1b76973dd741145f61a') + version('master', branch='master', submodules='True') + version('1912', sha256='437feadf075419290aa8bf461673b723a60dc39525b23322850fb58cb48548f2') + version('1906_191103', sha256='631a7fcd926ccbcdef0ab737a9dc55e58d6bedae2f3acaa041ea679db6c9303b') + version('1906', sha256='bee03c4b1da0d2c9f98eb469eeffbce3a8614728ef8e87f664042a7490976537') + version('1812_191001', sha256='857a3d476696679313ea9a3f022b33446ddef2bcd417049a9486d504c12038dd') version('1812_190531', sha256='51f0ef49a199edf3cd94e2ccfc7330e54e93c8e4ddb29ee66fe3e6b443583b34') version('1812', sha256='d4d23d913419c6a364b1fe91509c1fadb5661bdf2eedb8fe9a8a005924eb2032') version('1806', sha256='6951aab6405294fe59cec90b0a4e425f5403043191cda02ebaaa890ce1fcc819') @@ -338,7 +342,7 @@ class Openfoam(Package): # Version-specific patches patch('1612-spack-patches.patch', when='@1612') # kahip patch (wmake) - patch('https://develop.openfoam.com/Development/OpenFOAM-plus/commit/4068c03c616a4964472e06d5fb5b9bc2dd0bf1b7.patch', + patch('https://develop.openfoam.com/Development/openfoam/commit/8831dfc58b0295d0d301a78341dd6f4599073d45.patch', when='@1806', sha256='21f1ab68c82dfa41ed1a4439427c94c43ddda02c84175c30da623d905d3e5d61' ) @@ -368,29 +372,41 @@ class Openfoam(Package): # def url_for_version(self, version): - # Prior to 1706 had additional '+' in the naming - fmt = self.list_url + """Handles locations for patched and unpatched versions. + Patched version (eg '1906_191103') are located in the + corresponding unpatched directories (eg '1906'). + Older versions (eg, v1612+) had additional '+' in naming + """ + tty.info('openfoam: {0}'.format(version)) if version <= Version('1612'): - fmt += 'v{0}+/OpenFOAM-v{0}+.tgz' + fmt = 'v{0}+/OpenFOAM-v{1}+.tgz' else: - fmt += 'v{0}/OpenFOAM-v{0}.tgz' - return fmt.format(version, version) + fmt = 'v{0}/OpenFOAM-v{1}.tgz' + return self.list_url + fmt.format(version.up_to(1), version) + + def setup_minimal_environment(self, env): + """Sets a minimal openfoam environment. + """ + tty.info('OpenFOAM minimal env {0}'.format(self.prefix)) + env.set('FOAM_PROJECT_DIR', self.projectdir) + env.set('WM_PROJECT_DIR', self.projectdir) + for d in ['wmake', self.archbin]: # bin added automatically + env.prepend_path('PATH', join_path(self.projectdir, d)) + + def setup_build_environment(self, env): + """Sets the build environment (prior to unpacking the sources). + """ + pass - def setup_environment(self, spack_env, run_env): - """Add environment variables to the generated module file. - These environment variables come from running: + def setup_run_environment(self, env): + """Sets the run environment (post-installation). + The environment comes from running: .. code-block:: console $ . $WM_PROJECT_DIR/etc/bashrc """ - # NOTE: Spack runs setup_environment twice. - # 1) pre-build to set up the build environment - # 2) post-install to determine runtime environment variables - # The etc/bashrc is only available (with corrrect content) - # post-installation. - bashrc = join_path(self.projectdir, 'etc', 'bashrc') minimal = True if os.path.isfile(bashrc): @@ -427,8 +443,7 @@ class Openfoam(Package): 'MPI_ARCH_PATH', # Can be needed for compilation ]) - run_env.extend(mods) - spack_env.extend(mods) + env.extend(mods) minimal = False tty.info('OpenFOAM bashrc env: {0}'.format(bashrc)) except Exception: @@ -436,22 +451,23 @@ class Openfoam(Package): if minimal: # pre-build or minimal environment - tty.info('OpenFOAM minimal env {0}'.format(self.prefix)) - run_env.set('FOAM_PROJECT_DIR', self.projectdir) - run_env.set('WM_PROJECT_DIR', self.projectdir) - spack_env.set('FOAM_PROJECT_DIR', self.projectdir) - spack_env.set('WM_PROJECT_DIR', self.projectdir) - for d in ['wmake', self.archbin]: # bin added automatically - run_env.prepend_path('PATH', join_path(self.projectdir, d)) - spack_env.prepend_path('PATH', join_path(self.projectdir, d)) - - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - """Location of the OpenFOAM project directory. - This is identical to the WM_PROJECT_DIR value, but we avoid that - variable since it would mask the normal OpenFOAM cleanup of - previous versions. + self.setup_minimal_environment(env) + + def setup_dependent_build_environment(self, env, dependent_spec): + """Use full OpenFOAM environment when building. + Mirror WM_PROJECT_DIR value as FOAM_PROJECT_DIR to avoid + masking the normal OpenFOAM cleanup of previous versions. + """ + self.setup_run_environment(env) + env.set('FOAM_PROJECT_DIR', self.projectdir) + + def setup_dependent_run_environment(self, env, dependent_spec): + """Use full OpenFOAM environment when running. + Mirror WM_PROJECT_DIR value as FOAM_PROJECT_DIR to avoid + masking the normal OpenFOAM cleanup of previous versions. """ - self.setup_environment(spack_env, run_env) + self.setup_run_environment(env) + env.set('FOAM_PROJECT_DIR', self.projectdir) @property def projectdir(self): diff --git a/var/spack/repos/builtin/packages/openfst/package.py b/var/spack/repos/builtin/packages/openfst/package.py index d699657f74..d8f6b01475 100644 --- a/var/spack/repos/builtin/packages/openfst/package.py +++ b/var/spack/repos/builtin/packages/openfst/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,6 +16,7 @@ class Openfst(AutotoolsPackage): url = "http://www.openfst.org/twiki/pub/FST/FstDownload/openfst-1.6.1.tar.gz" list_url = "http://www.openfst.org/twiki/bin/view/FST/FstDownload" + version('1.6.7', sha256='e21a486d827cde6a592c8e91721e4540ad01a5ae35a60423cf17be4d716017f7') version('1.6.1', sha256='5245af8ebccb96208eec2dfe3b3a81143d3565a4d41220bff299287fb3333f7d') version('1.6.0', sha256='c03467951631af3f74a6f33ffd50f04285bc4562f79127afd95785120379d293') version('1.5.4', sha256='acc115aaaa33de53de62dae44120ab368fabaea06f52606b77714081ecd32657') diff --git a/var/spack/repos/builtin/packages/opengl/package.py b/var/spack/repos/builtin/packages/opengl/package.py index fe3a29607c..603dc9cb88 100644 --- a/var/spack/repos/builtin/packages/opengl/package.py +++ b/var/spack/repos/builtin/packages/opengl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openglu/package.py b/var/spack/repos/builtin/packages/openglu/package.py index 87ab191df7..f4e5504a8e 100644 --- a/var/spack/repos/builtin/packages/openglu/package.py +++ b/var/spack/repos/builtin/packages/openglu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openimageio/package.py b/var/spack/repos/builtin/packages/openimageio/package.py index cf971fa337..5c3a1487f6 100644 --- a/var/spack/repos/builtin/packages/openimageio/package.py +++ b/var/spack/repos/builtin/packages/openimageio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openjdk/package.py b/var/spack/repos/builtin/packages/openjdk/package.py index 0e7e10588b..9d0b3d54e4 100644 --- a/var/spack/repos/builtin/packages/openjdk/package.py +++ b/var/spack/repos/builtin/packages/openjdk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,25 +12,15 @@ class Openjdk(Package): homepage = "https://jdk.java.net" - version( - "11.0.2", - sha256="99be79935354f5c0df1ad293620ea36d13f48ec3ea870c838f20c504c9668b57", - url="https://download.java.net/java/GA/jdk11/9/GPL/openjdk-11.0.2_linux-x64_bin.tar.gz", - ) - - version( - "11.0.1", - sha256="7a6bb980b9c91c478421f865087ad2d69086a0583aeeb9e69204785e8e97dcfd", - url="https://download.java.net/java/GA/jdk11/13/GPL/openjdk-11.0.1_linux-x64_bin.tar.gz", - ) - - version( - "1.8.0_202-b08", - sha256="533dcd8d9ca15df231a1eb392fa713a66bca85a8e76d9b4ee30975f3823636b7", - url="https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u202-b08/OpenJDK8U-jdk_x64_linux_openj9_8u202b08_openj9-0.12.0.tar.gz", - ) - - provides('java') + version("11.0.2", sha256="99be79935354f5c0df1ad293620ea36d13f48ec3ea870c838f20c504c9668b57", + url="https://download.java.net/java/GA/jdk11/9/GPL/openjdk-11.0.2_linux-x64_bin.tar.gz") + version("11.0.1", sha256="7a6bb980b9c91c478421f865087ad2d69086a0583aeeb9e69204785e8e97dcfd", + url="https://download.java.net/java/GA/jdk11/13/GPL/openjdk-11.0.1_linux-x64_bin.tar.gz") + version("1.8.0_202-b08", sha256="533dcd8d9ca15df231a1eb392fa713a66bca85a8e76d9b4ee30975f3823636b7", + url="https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u202-b08/OpenJDK8U-jdk_x64_linux_openj9_8u202b08_openj9-0.12.0.tar.gz") + version('1.8.0_40-b25', sha256='79e96dce03a14271040023231a7d0ae374b755d48adf68bbdaec30294e4e2b88', + url='https://download.java.net/openjdk/jdk8u40/ri/jdk_ri-8u40-b25-linux-x64-10_feb_2015.tar.gz') + provides('java@11', when='@11.0:11.99') provides('java@8', when='@1.8.0:1.8.999') @@ -83,18 +73,18 @@ class Openjdk(Package): def install(self, spec, prefix): install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set JAVA_HOME.""" - run_env.set('JAVA_HOME', self.home) + env.set('JAVA_HOME', self.home) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Set JAVA_HOME and CLASSPATH. CLASSPATH contains the installation prefix for the extension and any other Java extensions it depends on.""" - spack_env.set('JAVA_HOME', self.home) + env.set('JAVA_HOME', self.home) class_paths = [] for d in dependent_spec.traverse(deptype=('build', 'run', 'test')): @@ -102,14 +92,19 @@ class Openjdk(Package): class_paths.extend(find(d.prefix, '*.jar')) classpath = os.pathsep.join(class_paths) - spack_env.set('CLASSPATH', classpath) + env.set('CLASSPATH', classpath) + + def setup_dependent_run_environment(self, env, dependent_spec): + """Set CLASSPATH. + CLASSPATH contains the installation prefix for the extension and any + other Java extensions it depends on.""" # For runtime environment set only the path for # dependent_spec and prepend it to CLASSPATH if dependent_spec.package.extends(self.spec): class_paths = find(dependent_spec.prefix, '*.jar') classpath = os.pathsep.join(class_paths) - run_env.prepend_path('CLASSPATH', classpath) + env.prepend_path('CLASSPATH', classpath) def setup_dependent_package(self, module, dependent_spec): """Allows spec['java'].home to work.""" diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py index 980819c8bb..c451758ef0 100644 --- a/var/spack/repos/builtin/packages/openjpeg/package.py +++ b/var/spack/repos/builtin/packages/openjpeg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -50,3 +50,8 @@ class Openjpeg(CMakePackage): 'https://github.com/uclouvain/openjpeg/archive/version.{0}.tar.gz' return url_fmt.format(version) + + @property + def libs(self): + return find_libraries('libopenjp{0}'.format(self.version.up_to(1)), + root=self.prefix, recursive=True) diff --git a/var/spack/repos/builtin/packages/openkim-models/package.py b/var/spack/repos/builtin/packages/openkim-models/package.py index 8ac09dc1cb..6e8819da66 100644 --- a/var/spack/repos/builtin/packages/openkim-models/package.py +++ b/var/spack/repos/builtin/packages/openkim-models/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openldap/package.py b/var/spack/repos/builtin/packages/openldap/package.py index 3c8a9e453e..0ef3a63f01 100644 --- a/var/spack/repos/builtin/packages/openldap/package.py +++ b/var/spack/repos/builtin/packages/openldap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,7 +17,7 @@ class Openldap(AutotoolsPackage): """ homepage = "https://www.openldap.org/" - url = "ftp://ftp.openldap.org/pub/OpenLDAP/openldap-release/openldap-2.4.9.tgz" + url = "ftp://ftp.openldap.org/pub/OpenLDAP/openldap-release/openldap-2.4.48.tgz" version('2.4.48', sha256='d9523ffcab5cd14b709fcf3cb4d04e8bc76bb8970113255f372bc74954c6074d') diff --git a/var/spack/repos/builtin/packages/openmc/package.py b/var/spack/repos/builtin/packages/openmc/package.py index 5627ac0dc6..60ce6f4bba 100644 --- a/var/spack/repos/builtin/packages/openmc/package.py +++ b/var/spack/repos/builtin/packages/openmc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openmolcas/package.py b/var/spack/repos/builtin/packages/openmolcas/package.py new file mode 100644 index 0000000000..d8c8b0fe84 --- /dev/null +++ b/var/spack/repos/builtin/packages/openmolcas/package.py @@ -0,0 +1,37 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Openmolcas(CMakePackage): + """OpenMolcas is a quantum chemistry software package. + The key feature of OpenMolcas is the multiconfigurational approach to + the electronic structure.""" + + homepage = "https://gitlab.com/Molcas/OpenMolcas" + url = "https://github.com/Molcas/OpenMolcas/archive/v19.11.tar.gz" + + version('19.11', sha256='8ebd1dcce98fc3f554f96e54e34f1e8ad566c601196ee68153763b6c0a04c7b9') + + depends_on('hdf5') + depends_on('lapack') + depends_on('openblas+ilp64') + depends_on('python@3.7:', type=('build', 'run')) + depends_on('py-pyparsing', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) + + def setup_build_environment(self, env): + env.set('MOLCAS', self.prefix) + + def setup_run_environment(self, env): + env.set('MOLCAS', self.prefix) + + def cmake_args(self): + return [ + '-DLINALG=OpenBLAS', + '-DOPENBLASROOT=%s' % self.spec['openblas'].prefix, + '-DPYTHON_EXECUTABLE=%s' % self.spec['python'].command.path, + ] diff --git a/var/spack/repos/builtin/packages/openmpi/fix-ucx-1.7.0-api-instability.patch b/var/spack/repos/builtin/packages/openmpi/fix-ucx-1.7.0-api-instability.patch new file mode 100644 index 0000000000..59d9b06d50 --- /dev/null +++ b/var/spack/repos/builtin/packages/openmpi/fix-ucx-1.7.0-api-instability.patch @@ -0,0 +1,254 @@ +diff --git a/opal/mca/btl/uct/btl_uct.h b/opal/mca/btl/uct/btl_uct.h +index 3875679443..0e4ec9a949 100644 +--- a/opal/mca/btl/uct/btl_uct.h ++++ b/opal/mca/btl/uct/btl_uct.h +@@ -12,6 +12,7 @@ + * All rights reserved. + * Copyright (c) 2015-2018 Los Alamos National Security, LLC. All rights + * reserved. ++ * Copyright (c) 2019 Google, LLC. All rights reserved. + * $COPYRIGHT$ + * + * Additional copyrights may follow +@@ -85,6 +86,10 @@ struct mca_btl_uct_module_t { + /** array containing the am_tl and rdma_tl */ + mca_btl_uct_tl_t *comm_tls[2]; + ++#if UCT_API >= UCT_VERSION(1, 7) ++ uct_component_h uct_component; ++#endif ++ + /** registration cache */ + mca_rcache_base_module_t *rcache; + +diff --git a/opal/mca/btl/uct/btl_uct_amo.c b/opal/mca/btl/uct/btl_uct_amo.c +index f7d0232688..72398ce736 100644 +--- a/opal/mca/btl/uct/btl_uct_amo.c ++++ b/opal/mca/btl/uct/btl_uct_amo.c +@@ -110,7 +110,7 @@ int mca_btl_uct_afop (struct mca_btl_base_module_t *btl, struct mca_btl_base_end + mca_btl_uct_uct_completion_release (comp); + } + +- uct_rkey_release (&rkey); ++ mca_btl_uct_rkey_release (uct_btl, &rkey); + + return rc; + } +@@ -184,7 +184,7 @@ int mca_btl_uct_acswap (struct mca_btl_base_module_t *btl, struct mca_btl_base_e + mca_btl_uct_uct_completion_release (comp); + } + +- uct_rkey_release (&rkey); ++ mca_btl_uct_rkey_release (uct_btl, &rkey); + + return rc; + } +diff --git a/opal/mca/btl/uct/btl_uct_component.c b/opal/mca/btl/uct/btl_uct_component.c +index f968cb9c31..bff160736b 100644 +--- a/opal/mca/btl/uct/btl_uct_component.c ++++ b/opal/mca/btl/uct/btl_uct_component.c +@@ -314,7 +314,12 @@ ucs_status_t mca_btl_uct_am_handler (void *arg, void *data, size_t length, unsig + return UCS_OK; + } + ++#if UCT_API >= UCT_VERSION(1, 7) ++static int mca_btl_uct_component_process_uct_md (uct_component_h component, uct_md_resource_desc_t *md_desc, ++ char **allowed_ifaces) ++#else + static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc, char **allowed_ifaces) ++#endif + { + mca_rcache_base_resources_t rcache_resources; + uct_tl_resource_desc_t *tl_desc; +@@ -348,8 +353,14 @@ static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc + + md = OBJ_NEW(mca_btl_uct_md_t); + ++ ++#if UCT_API >= UCT_VERSION(1, 7) ++ uct_md_config_read (component, NULL, NULL, &uct_config); ++ uct_md_open (component, md_desc->md_name, uct_config, &md->uct_md); ++#else + uct_md_config_read (md_desc->md_name, NULL, NULL, &uct_config); + uct_md_open (md_desc->md_name, uct_config, &md->uct_md); ++#endif + uct_config_release (uct_config); + + uct_md_query (md->uct_md, &md_attr); +@@ -375,6 +386,10 @@ static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc + return OPAL_ERR_NOT_AVAILABLE; + } + ++#if UCT_API >= UCT_VERSION(1, 7) ++ module->uct_component = component; ++#endif ++ + mca_btl_uct_component.modules[mca_btl_uct_component.module_count++] = module; + + /* NTH: a registration cache shouldn't be necessary when using UCT but there are measurable +@@ -400,6 +415,42 @@ static int mca_btl_uct_component_process_uct_md (uct_md_resource_desc_t *md_desc + return OPAL_SUCCESS; + } + ++#if UCT_API >= UCT_VERSION(1, 7) ++static int mca_btl_uct_component_process_uct_component (uct_component_h component, char **allowed_ifaces) ++{ ++ uct_component_attr_t attr = {.field_mask = UCT_COMPONENT_ATTR_FIELD_NAME | ++ UCT_COMPONENT_ATTR_FIELD_MD_RESOURCE_COUNT}; ++ ucs_status_t ucs_status; ++ int rc; ++ ++ ucs_status = uct_component_query (component, &attr); ++ if (UCS_OK != ucs_status) { ++ return OPAL_ERROR; ++ } ++ ++ BTL_VERBOSE(("processing uct component %s", attr.name)); ++ ++ attr.md_resources = calloc (attr.md_resource_count, sizeof (*attr.md_resources)); ++ attr.field_mask |= UCT_COMPONENT_ATTR_FIELD_MD_RESOURCES; ++ ucs_status = uct_component_query (component, &attr); ++ if (UCS_OK != ucs_status) { ++ return OPAL_ERROR; ++ } ++ ++ for (int i = 0 ; i < attr.md_resource_count ; ++i) { ++ rc = mca_btl_uct_component_process_uct_md (component, attr.md_resources + i, ++ allowed_ifaces); ++ if (OPAL_SUCCESS != rc) { ++ break; ++ } ++ } ++ ++ free (attr.md_resources); ++ ++ return OPAL_SUCCESS; ++} ++#endif /* UCT_API >= UCT_VERSION(1, 7) */ ++ + /* + * UCT component initialization: + * (1) read interface list from kernel and compare against component parameters +@@ -415,6 +466,7 @@ static mca_btl_base_module_t **mca_btl_uct_component_init (int *num_btl_modules, + struct mca_btl_base_module_t **base_modules; + uct_md_resource_desc_t *resources; + unsigned resource_count; ++ ucs_status_t ucs_status; + char **allowed_ifaces; + int rc; + +@@ -431,10 +483,32 @@ static mca_btl_base_module_t **mca_btl_uct_component_init (int *num_btl_modules, + return NULL; + } + +- uct_query_md_resources (&resources, &resource_count); +- + mca_btl_uct_component.module_count = 0; + ++#if UCT_API >= UCT_VERSION(1, 7) ++ uct_component_h *components; ++ unsigned num_components; ++ ++ ucs_status = uct_query_components(&components, &num_components); ++ if (UCS_OK != ucs_status) { ++ BTL_ERROR(("could not query UCT components")); ++ return NULL; ++ } ++ ++ /* generate all suitable btl modules */ ++ for (unsigned i = 0 ; i < num_components ; ++i) { ++ rc = mca_btl_uct_component_process_uct_component (components[i], allowed_ifaces); ++ if (OPAL_SUCCESS != rc) { ++ break; ++ } ++ } ++ ++ uct_release_component_list (components); ++ ++#else /* UCT 1.6 and older */ ++ ++ uct_query_md_resources (&resources, &resource_count); ++ + /* generate all suitable btl modules */ + for (unsigned i = 0 ; i < resource_count ; ++i) { + rc = mca_btl_uct_component_process_uct_md (resources + i, allowed_ifaces); +@@ -443,9 +517,11 @@ static mca_btl_base_module_t **mca_btl_uct_component_init (int *num_btl_modules, + } + } + +- opal_argv_free (allowed_ifaces); + uct_release_md_resource_list (resources); + ++#endif /* UCT_API >= UCT_VERSION(1, 7) */ ++ ++ opal_argv_free (allowed_ifaces); + mca_btl_uct_modex_send (); + + /* pass module array back to caller */ +diff --git a/opal/mca/btl/uct/btl_uct_rdma.c b/opal/mca/btl/uct/btl_uct_rdma.c +index 2d2d1c3f04..9ee9530f26 100644 +--- a/opal/mca/btl/uct/btl_uct_rdma.c ++++ b/opal/mca/btl/uct/btl_uct_rdma.c +@@ -132,7 +132,7 @@ int mca_btl_uct_get (mca_btl_base_module_t *btl, mca_btl_base_endpoint_t *endpoi + + BTL_VERBOSE(("get issued. status = %d", ucs_status)); + +- uct_rkey_release (&rkey); ++ mca_btl_uct_rkey_release (uct_btl, &rkey); + + return OPAL_LIKELY(UCS_OK == ucs_status) ? OPAL_SUCCESS : OPAL_ERR_RESOURCE_BUSY; + } +@@ -237,7 +237,7 @@ int mca_btl_uct_put (mca_btl_base_module_t *btl, mca_btl_base_endpoint_t *endpoi + mca_btl_uct_uct_completion_release (comp); + } + +- uct_rkey_release (&rkey); ++ mca_btl_uct_rkey_release (uct_btl, &rkey); + + return OPAL_LIKELY(UCS_OK == ucs_status) ? OPAL_SUCCESS : OPAL_ERR_RESOURCE_BUSY; + } +diff --git a/opal/mca/btl/uct/btl_uct_rdma.h b/opal/mca/btl/uct/btl_uct_rdma.h +index e9b0d6b19d..ab790371af 100644 +--- a/opal/mca/btl/uct/btl_uct_rdma.h ++++ b/opal/mca/btl/uct/btl_uct_rdma.h +@@ -55,8 +55,22 @@ static inline int mca_btl_uct_get_rkey (mca_btl_uct_module_t *module, + return rc; + } + ++#if UCT_API >= UCT_VERSION(1, 7) ++ ucs_status = uct_rkey_unpack (module->uct_component, (void *) remote_handle, rkey); ++#else + ucs_status = uct_rkey_unpack ((void *) remote_handle, rkey); ++#endif + return (UCS_OK == ucs_status) ? OPAL_SUCCESS : OPAL_ERROR; + } + ++static inline void mca_btl_uct_rkey_release (mca_btl_uct_module_t *uct_btl, uct_rkey_bundle_t *rkey) ++{ ++#if UCT_API >= UCT_VERSION(1, 7) ++ uct_rkey_release (uct_btl->uct_component, rkey); ++#else ++ (void) uct_btl; ++ uct_rkey_release (rkey); ++#endif ++} ++ + #endif /* !defined(BTL_UCT_RDMA_H) */ +diff --git a/opal/mca/btl/uct/btl_uct_tl.c b/opal/mca/btl/uct/btl_uct_tl.c +index a711a41ce9..e69c769b41 100644 +--- a/opal/mca/btl/uct/btl_uct_tl.c ++++ b/opal/mca/btl/uct/btl_uct_tl.c +@@ -516,7 +516,13 @@ static int mca_btl_uct_evaluate_tl (mca_btl_uct_module_t *module, mca_btl_uct_tl + * come up with a better estimate. */ + + /* UCT bandwidth is in bytes/sec, BTL is in MB/sec */ ++#if UCT_API >= UCT_VERSION(1, 7) ++ module->super.btl_bandwidth = (uint32_t) ((MCA_BTL_UCT_TL_ATTR(tl, 0).bandwidth.dedicated + ++ MCA_BTL_UCT_TL_ATTR(tl, 0).bandwidth.shared / ++ (opal_process_info.num_local_peers + 1)) / 1048576.0); ++#else + module->super.btl_bandwidth = (uint32_t) (MCA_BTL_UCT_TL_ATTR(tl, 0).bandwidth / 1048576.0); ++#endif + /* TODO -- figure out how to translate UCT latency to us */ + module->super.btl_latency = 1; + } diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index b5ddba6355..aac0c4c60b 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -75,24 +75,30 @@ class Openmpi(AutotoolsPackage): list_url = "http://www.open-mpi.org/software/ompi/" git = "https://github.com/open-mpi/ompi.git" + maintainers = ['hppritcha'] + version('develop', branch='master') # Current - version('4.0.1', sha256='cce7b6d20522849301727f81282201d609553103ac0b09162cf28d102efb9709') # libmpi.so.40.20.1 + version('4.0.2', sha256='900bf751be72eccf06de9d186f7b1c4b5c2fa9fa66458e53b77778dffdfe4057') # libmpi.so.40.20.2 # Still supported + version('4.0.1', sha256='cce7b6d20522849301727f81282201d609553103ac0b09162cf28d102efb9709') # libmpi.so.40.20.1 version('4.0.0', sha256='2f0b8a36cfeb7354b45dda3c5425ef8393c9b04115570b615213faaa3f97366b') # libmpi.so.40.20.0 - version('3.1.4', preferred=True, sha256='17a69e0054db530c7dc119f75bd07d079efa147cf94bf27e590905864fe379d6') # libmpi.so.40.10.4 + version('3.1.5', preferred=True, sha256='fbf0075b4579685eec8d56d34d4d9c963e6667825548554f5bf308610af72133') # libmpi.so.40.10.4 + version('3.1.4', sha256='17a69e0054db530c7dc119f75bd07d079efa147cf94bf27e590905864fe379d6') # libmpi.so.40.10.4 version('3.1.3', sha256='8be04307c00f51401d3fb9d837321781ea7c79f2a5a4a2e5d4eaedc874087ab6') # libmpi.so.40.10.3 version('3.1.2', sha256='c654ed847f34a278c52a15c98add40402b4a90f0c540779f1ae6c489af8a76c5') # libmpi.so.40.10.2 version('3.1.1', sha256='3f11b648dd18a8b878d057e9777f2c43bf78297751ad77ae2cef6db0fe80c77c') # libmpi.so.40.10.1 version('3.1.0', sha256='b25c044124cc859c0b4e6e825574f9439a51683af1950f6acda1951f5ccdf06c') # libmpi.so.40.10.0 + version('3.0.5', sha256='f8976b95f305efc435aa70f906b82d50e335e34cffdbf5d78118a507b1c6efe8') # libmpi.so.40.00.5 version('3.0.4', sha256='2ff4db1d3e1860785295ab95b03a2c0f23420cda7c1ae845c419401508a3c7b5') # libmpi.so.40.00.5 version('3.0.3', sha256='fb228e42893fe6a912841a94cd8a0c06c517701ae505b73072409218a12cf066') # libmpi.so.40.00.4 version('3.0.2', sha256='d2eea2af48c1076c53cabac0a1f12272d7470729c4e1cb8b9c2ccd1985b2fb06') # libmpi.so.40.00.2 version('3.0.1', sha256='663450d1ee7838b03644507e8a76edfb1fba23e601e9e0b5b2a738e54acd785d') # libmpi.so.40.00.1 version('3.0.0', sha256='f699bff21db0125d8cccfe79518b77641cd83628725a1e1ed3e45633496a82d7') # libmpi.so.40.00.0 + # Retired version('2.1.6', sha256='98b8e1b8597bbec586a0da79fcd54a405388190247aa04d48e8c40944d4ca86e') # libmpi.so.20.10.3 version('2.1.5', sha256='b807ccab801f27c3159a5edf29051cd3331d3792648919f9c4cee48e987e7794') # libmpi.so.20.10.3 version('2.1.4', sha256='3e03695ca8bd663bc2d89eda343c92bb3d4fc79126b178f5ddcb68a8796b24e2') # libmpi.so.20.10.3 @@ -101,7 +107,6 @@ class Openmpi(AutotoolsPackage): version('2.1.1', sha256='bd7badd4ff3afa448c0d7f3ca0ee6ce003b957e9954aa87d8e4435759b5e4d16') # libmpi.so.20.10.1 version('2.1.0', sha256='b169e15f5af81bf3572db764417670f508c0df37ce86ff50deb56bd3acb43957') # libmpi.so.20.10.0 - # Retired version('2.0.4', sha256='4f82d5f7f294becbd737319f74801206b08378188a95b70abe706fdc77a0c20b') # libmpi.so.20.0.4 version('2.0.3', sha256='b52c0204c0e5954c9c57d383bb22b4181c09934f97783292927394d29f2a808a') # libmpi.so.20.0.3 version('2.0.2', sha256='cae396e643f9f91f0a795f8d8694adf7bacfb16f967c22fb39e9e28d477730d3') # libmpi.so.20.0.2 @@ -188,6 +193,7 @@ class Openmpi(AutotoolsPackage): patch('llnl-platforms.patch', when="@1.6.5") patch('configure.patch', when="@1.10.1") patch('fix_multidef_pmi_class.patch', when="@2.0.0:2.0.1") + patch('fix-ucx-1.7.0-api-instability.patch', when='@4.0.0:4.0.3') # Vader Bug: https://github.com/open-mpi/ompi/issues/5375 # Haven't release fix for 2.1.x @@ -269,6 +275,8 @@ class Openmpi(AutotoolsPackage): depends_on('zlib', when='@3.0.0:') depends_on('valgrind~mpi', when='+memchecker') depends_on('ucx', when='fabrics=ucx') + depends_on('ucx +thread_multiple', when='fabrics=ucx +thread_multiple') + depends_on('ucx +thread_multiple', when='@3.0.0: fabrics=ucx') depends_on('libfabric', when='fabrics=libfabric') depends_on('slurm', when='schedulers=slurm') depends_on('lsf', when='schedulers=lsf') @@ -311,16 +319,16 @@ class Openmpi(AutotoolsPackage): libraries, root=self.prefix, shared=True, recursive=True ) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) + env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) + env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) + env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) - spack_env.set('OMPI_CC', spack_cc) - spack_env.set('OMPI_CXX', spack_cxx) - spack_env.set('OMPI_FC', spack_fc) - spack_env.set('OMPI_F77', spack_f77) + env.set('OMPI_CC', spack_cc) + env.set('OMPI_CXX', spack_cxx) + env.set('OMPI_FC', spack_fc) + env.set('OMPI_F77', spack_f77) def setup_dependent_package(self, module, dependent_spec): self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') @@ -421,6 +429,10 @@ class Openmpi(AutotoolsPackage): if spec.satisfies('@3.0.0:', strict=True): config_args.append('--with-zlib={0}'.format(spec['zlib'].prefix)) + if spec.satisfies('@4.0.0:4.0.2'): + # uct btl doesn't work with some UCX versions so just disable + config_args.append('--enable-mca-no-build=btl-uct') + # some scientific packages ignore deprecated/remove symbols. Re-enable # them for now, for discussion see # https://github.com/open-mpi/ompi/issues/6114#issuecomment-446279495 @@ -430,6 +442,13 @@ class Openmpi(AutotoolsPackage): # Fabrics if 'fabrics=auto' not in spec: config_args.extend(self.with_or_without('fabrics')) + # The wrappers fail to automatically link libfabric. This will cause + # undefined references unless we add the appropriate flags. + if 'fabrics=libfabric' in spec: + config_args.append('--with-wrapper-ldflags=-L{0} -Wl,-rpath={0}' + .format(spec['libfabric'].prefix.lib)) + config_args.append('--with-wrapper-libs=-lfabric') + # Schedulers if 'schedulers=auto' not in spec: config_args.extend(self.with_or_without('schedulers')) @@ -444,7 +463,6 @@ class Openmpi(AutotoolsPackage): # Hwloc support if spec.satisfies('@1.5.2:'): config_args.append('--with-hwloc={0}'.format(spec['hwloc'].prefix)) - # Java support if spec.satisfies('@1.7.4:'): if '+java' in spec: diff --git a/var/spack/repos/builtin/packages/openmx/package.py b/var/spack/repos/builtin/packages/openmx/package.py index 53f470c804..9bfe2a6af5 100644 --- a/var/spack/repos/builtin/packages/openmx/package.py +++ b/var/spack/repos/builtin/packages/openmx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/opennurbs/package.py b/var/spack/repos/builtin/packages/opennurbs/package.py index 0ea61fa36f..5df4a1dbf6 100644 --- a/var/spack/repos/builtin/packages/opennurbs/package.py +++ b/var/spack/repos/builtin/packages/opennurbs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openpa/package.py b/var/spack/repos/builtin/packages/openpa/package.py index 829bee8f3c..7271d579e1 100644 --- a/var/spack/repos/builtin/packages/openpa/package.py +++ b/var/spack/repos/builtin/packages/openpa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openpmd-api/package.py b/var/spack/repos/builtin/packages/openpmd-api/package.py index fe9972776f..f05caa68f5 100644 --- a/var/spack/repos/builtin/packages/openpmd-api/package.py +++ b/var/spack/repos/builtin/packages/openpmd-api/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,10 @@ class OpenpmdApi(CMakePackage): maintainers = ['ax3l'] version('develop', branch='dev') + version('0.10.3', tag='0.10.3-alpha') + version('0.10.2', tag='0.10.2-alpha') + version('0.10.1', tag='0.10.1-alpha') + version('0.10.0', tag='0.10.0-alpha') variant('shared', default=True, description='Build a shared version of the library') @@ -24,27 +28,25 @@ class OpenpmdApi(CMakePackage): description='Enable HDF5 support') variant('adios1', default=False, description='Enable ADIOS1 support') - variant('adios2', default=False, + variant('adios2', default=True, description='Enable ADIOS2 support') - variant('json', default=True, - description='Enable JSON support') variant('python', default=False, description='Enable Python bindings') depends_on('cmake@3.11.0:', type='build') depends_on('mpark-variant@1.4.0:') - depends_on('catch@2.6.1: ~single_header', type='test') + depends_on('catch2@2.6.1: ~single_header', type='test') depends_on('mpi@2.3:', when='+mpi') # might become MPI 3.0+ depends_on('hdf5@1.8.13:', when='+hdf5') depends_on('hdf5@1.8.13: ~mpi', when='~mpi +hdf5') depends_on('hdf5@1.8.13: +mpi', when='+mpi +hdf5') - depends_on('adios@1.13.1:', when='+adios1') - depends_on('adios@1.13.1: ~mpi', when='~mpi +adios1') - depends_on('adios@1.13.1: +mpi', when='+mpi +adios1') - depends_on('adios2@2.4.0:', when='+adios2') - depends_on('adios2@2.4.0: ~mpi', when='~mpi +adios2') - depends_on('adios2@2.4.0: +mpi', when='+mpi +adios2') - depends_on('nlohmann-json@3.7.0:', when='+json') + depends_on('adios@1.13.1: ~sz', when='+adios1') + depends_on('adios@1.13.1: ~mpi ~sz', when='~mpi +adios1') + depends_on('adios@1.13.1: +mpi ~sz', when='+mpi +adios1') + depends_on('adios2@2.5.0:', when='+adios2') + depends_on('adios2@2.5.0: ~mpi', when='~mpi +adios2') + depends_on('adios2@2.5.0: +mpi', when='+mpi +adios2') + depends_on('nlohmann-json@3.7.0:') depends_on('py-pybind11@2.3.0:', when='+python', type='link') depends_on('py-numpy@1.15.1:', when='+python', type=['test', 'run']) depends_on('py-mpi4py@2.1.0:', when='+python +mpi', type=['test', 'run']) @@ -67,8 +69,6 @@ class OpenpmdApi(CMakePackage): 'ON' if '+adios1' in spec else 'OFF'), '-DopenPMD_USE_ADIOS2:BOOL={0}'.format( 'ON' if '+adios2' in spec else 'OFF'), - '-DopenPMD_USE_JSON:BOOL={0}'.format( - 'ON' if '+json' in spec else 'OFF'), '-DopenPMD_USE_PYTHON:BOOL={0}'.format( 'ON' if '+python' in spec else 'OFF'), # tests and examples @@ -84,34 +84,34 @@ class OpenpmdApi(CMakePackage): args.append('-DPYTHON_EXECUTABLE:FILEPATH={0}'.format( self.spec['python'].command.path)) - if spec.satisfies('+json'): - args.append('-DopenPMD_USE_INTERNAL_JSON:BOOL=OFF') - - args.append('-DopenPMD_USE_INTERNAL_VARIANT:BOOL=OFF') + args.extend([ + '-DopenPMD_USE_INTERNAL_JSON:BOOL=OFF', + '-DopenPMD_USE_INTERNAL_VARIANT:BOOL=OFF' + ]) if self.run_tests: args.append('-DopenPMD_USE_INTERNAL_CATCH:BOOL=OFF') return args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): spec = self.spec # pre-load dependent CMake-PUBLIC header-only libs - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['mpark-variant'].prefix) - run_env.prepend_path('CPATH', spec['mpark-variant'].prefix.include) + env.prepend_path('CMAKE_PREFIX_PATH', spec['mpark-variant'].prefix) + env.prepend_path('CPATH', spec['mpark-variant'].prefix.include) # more deps searched in openPMDConfig.cmake if spec.satisfies("+mpi"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['mpi'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['mpi'].prefix) if spec.satisfies("+adios1"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['adios'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['adios'].prefix) + env.prepend_path('PATH', spec['adios'].prefix.bin) # adios-config if spec.satisfies("+adios2"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['adios2'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['adios2'].prefix) if spec.satisfies("+hdf5"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['hdf5'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['hdf5'].prefix) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): # pre-load dependent CMake-PUBLIC header-only libs - spack_env.prepend_path('CMAKE_PREFIX_PATH', - self.spec['mpark-variant'].prefix) - spack_env.prepend_path('CPATH', - self.spec['mpark-variant'].prefix.include) + env.prepend_path('CMAKE_PREFIX_PATH', + self.spec['mpark-variant'].prefix) + prepend_path('CPATH', self.spec['mpark-variant'].prefix.include) diff --git a/var/spack/repos/builtin/packages/openresty/package.py b/var/spack/repos/builtin/packages/openresty/package.py new file mode 100644 index 0000000000..23708b280d --- /dev/null +++ b/var/spack/repos/builtin/packages/openresty/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Openresty(AutotoolsPackage): + """ + OpenResty is a full-fledged web application server by bundling the + standard nginx core, lots of 3rd-party nginx modules, as well as + most of their external dependencies. + """ + + homepage = "https://github.com/openresty" + url = "https://github.com/openresty/openresty/releases/download/v1.15.8.2/openresty-1.15.8.2.tar.gz" + + version('1.15.8.2', sha256='bf92af41d3ad22880047a8b283fc213d59c7c1b83f8dae82e50d14b64d73ac38') + version('1.15.8.1', sha256='89a1238ca177692d6903c0adbea5bdf2a0b82c383662a73c03ebf5ef9f570842') + version('1.13.6.2', sha256='946e1958273032db43833982e2cec0766154a9b5cb8e67868944113208ff2942') + + depends_on('pcre', type='build') + + def configure_args(self): + args = ['--without-http_rewrite_module'] + return args diff --git a/var/spack/repos/builtin/packages/openscenegraph/package.py b/var/spack/repos/builtin/packages/openscenegraph/package.py index 03b4de98b0..c0cb024c14 100644 --- a/var/spack/repos/builtin/packages/openscenegraph/package.py +++ b/var/spack/repos/builtin/packages/openscenegraph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openslide/package.py b/var/spack/repos/builtin/packages/openslide/package.py index b3cb4d55f2..d86af5a1aa 100644 --- a/var/spack/repos/builtin/packages/openslide/package.py +++ b/var/spack/repos/builtin/packages/openslide/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openspeedshop-utils/package.py b/var/spack/repos/builtin/packages/openspeedshop-utils/package.py index b4e1fe97bd..33bd293fa2 100644 --- a/var/spack/repos/builtin/packages/openspeedshop-utils/package.py +++ b/var/spack/repos/builtin/packages/openspeedshop-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -96,8 +96,7 @@ class OpenspeedshopUtils(CMakePackage): depends_on("dyninst@develop", when='@develop') depends_on("dyninst@10:", when='@2.3.1.3:9999') - depends_on("python", when='@develop', type=('build', 'run')) - depends_on("python@2.7.14:2.7.99", when='@2.3.1.3:9999', type=('build', 'run')) + depends_on("python@2.7.14:2.7.99", type=('build', 'run')) depends_on("libxml2") @@ -269,7 +268,7 @@ class OpenspeedshopUtils(CMakePackage): cmake_options.extend(mpi_options) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set up the compile and runtime environments for a package.""" # Find Dyninst library path, this is needed to @@ -281,26 +280,26 @@ class OpenspeedshopUtils(CMakePackage): shared=True, recursive=True) # Set Dyninst RT library path to support OSS loop resolution code - run_env.set('DYNINSTAPI_RT_LIB', dyninst_libdir[0]) + env.set('DYNINSTAPI_RT_LIB', dyninst_libdir[0]) # Find openspeedshop library path oss_libdir = find_libraries( 'libopenss-framework', root=self.spec['openspeedshop-utils'].prefix, shared=True, recursive=True) - run_env.prepend_path('LD_LIBRARY_PATH', - os.path.dirname(oss_libdir.joined())) + env.prepend_path('LD_LIBRARY_PATH', + os.path.dirname(oss_libdir.joined())) - run_env.set('OPENSS_RAWDATA_DIR', '.') + env.set('OPENSS_RAWDATA_DIR', '.') cbtf_mc = '/sbin/cbtf_mrnet_commnode' cbtf_lmb = '/sbin/cbtf_libcbtf_mrnet_backend' - run_env.set('XPLAT_RSH', 'ssh') - run_env.set('MRNET_COMM_PATH', - join_path(self.spec['cbtf-krell'].prefix + cbtf_mc)) - run_env.set('CBTF_MRNET_BACKEND_PATH', - join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb)) - run_env.prepend_path('PATH', self.spec['mrnet'].prefix.bin) - run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin) - run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin) - run_env.prepend_path('PATH', self.spec['python'].prefix.bin) + env.set('XPLAT_RSH', 'ssh') + env.set('MRNET_COMM_PATH', + join_path(self.spec['cbtf-krell'].prefix + cbtf_mc)) + env.set('CBTF_MRNET_BACKEND_PATH', + join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb)) + env.prepend_path('PATH', self.spec['mrnet'].prefix.bin) + env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin) + env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin) + env.prepend_path('PATH', self.spec['python'].prefix.bin) diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py index 349ddee052..88ac7e3547 100644 --- a/var/spack/repos/builtin/packages/openspeedshop/package.py +++ b/var/spack/repos/builtin/packages/openspeedshop/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -92,8 +92,7 @@ class Openspeedshop(CMakePackage): depends_on("dyninst@develop", when='@develop') depends_on("dyninst@10:", when='@2.3.1.3:9999') - depends_on("python", when='@develop', type=('build', 'run')) - depends_on("python@2.7.14:2.7.99", when='@2.3.1.3:9999', type=('build', 'run')) + depends_on("python@2.7.14:2.7.99", type=('build', 'run')) depends_on("libxml2") @@ -278,7 +277,7 @@ class Openspeedshop(CMakePackage): cmake_options.extend(mpi_options) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set up the compile and runtime environments for a package.""" # Find Dyninst library path, this is needed to @@ -290,9 +289,9 @@ class Openspeedshop(CMakePackage): shared=True, recursive=True) # Set Dyninst RT library path to support OSS loop resolution code - run_env.set('DYNINSTAPI_RT_LIB', dyninst_libdir[0]) + env.set('DYNINSTAPI_RT_LIB', dyninst_libdir[0]) - run_env.set('OPENSS_RAWDATA_DIR', '.') + env.set('OPENSS_RAWDATA_DIR', '.') # Set the openspeedshop plugin path if os.path.isdir(self.prefix.lib64): @@ -301,13 +300,13 @@ class Openspeedshop(CMakePackage): lib_dir = self.prefix.lib plugin_path = '/openspeedshop' oss_plugin_path = lib_dir + plugin_path - run_env.set('OPENSS_PLUGIN_PATH', oss_plugin_path) + env.set('OPENSS_PLUGIN_PATH', oss_plugin_path) cbtf_mc = '/sbin/cbtf_mrnet_commnode' cbtf_lmb = '/sbin/cbtf_libcbtf_mrnet_backend' - run_env.set('XPLAT_RSH', 'ssh') - run_env.set('MRNET_COMM_PATH', - join_path(self.spec['cbtf-krell'].prefix + cbtf_mc)) + env.set('XPLAT_RSH', 'ssh') + env.set('MRNET_COMM_PATH', + join_path(self.spec['cbtf-krell'].prefix + cbtf_mc)) # Set CBTF_MPI_IMPLEMENTATON to the appropriate mpi implementation # This is needed by O|SS and CBTF tools to deploy the correct @@ -315,23 +314,25 @@ class Openspeedshop(CMakePackage): # Users may have to set the CBTF_MPI_IMPLEMENTATION variable # manually if multiple mpi's are specified in the build if self.spec.satisfies('+mpich'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mpich") + env.set('CBTF_MPI_IMPLEMENTATION', "mpich") if self.spec.satisfies('+mvapich'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich") + env.set('CBTF_MPI_IMPLEMENTATION', "mvapich") if self.spec.satisfies('+mvapich2'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2") + env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2") if self.spec.satisfies('+mpt'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "mpt") + env.set('CBTF_MPI_IMPLEMENTATION', "mpt") if self.spec.satisfies('+openmpi'): - run_env.set('CBTF_MPI_IMPLEMENTATION', "openmpi") - - run_env.set('CBTF_MRNET_BACKEND_PATH', - join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb)) - run_env.prepend_path('PATH', self.spec['mrnet'].prefix.bin) - run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin) - run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin) - run_env.prepend_path('PATH', self.spec['python'].prefix.bin) + env.set('CBTF_MPI_IMPLEMENTATION', "openmpi") + + env.set('CBTF_MRNET_BACKEND_PATH', + join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb)) + env.prepend_path('PATH', self.spec['mrnet'].prefix.bin) + env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin) + env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin) + mpath = '/share/man' + env.prepend_path('MANPATH', self.spec['cbtf-krell'].prefix + mpath) + env.prepend_path('PATH', self.spec['python'].prefix.bin) diff --git a/var/spack/repos/builtin/packages/openssh/package.py b/var/spack/repos/builtin/packages/openssh/package.py index 59252cc833..71f15f731e 100644 --- a/var/spack/repos/builtin/packages/openssh/package.py +++ b/var/spack/repos/builtin/packages/openssh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 4c3a93c325..450990c179 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/openstf/package.py b/var/spack/repos/builtin/packages/openstf/package.py index 8ed190b03b..52f50b046a 100644 --- a/var/spack/repos/builtin/packages/openstf/package.py +++ b/var/spack/repos/builtin/packages/openstf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/opentsdb/package.py b/var/spack/repos/builtin/packages/opentsdb/package.py new file mode 100644 index 0000000000..04ba715d8e --- /dev/null +++ b/var/spack/repos/builtin/packages/opentsdb/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Opentsdb(AutotoolsPackage): + """ + OpenTSDB is a distributed, scalable Time Series Database (TSDB) written on + top of HBase. OpenTSDB was written to address a common need: store, index + and serve metrics collected from computer systems (network gear, operating + systems, applications) at a large scale, and make this data easily + accessible and graphable. + """ + + homepage = "https://github.com/OpenTSDB" + url = "https://github.com/OpenTSDB/opentsdb/archive/v2.4.0.tar.gz" + + version('2.4.0', sha256='eb6bf323d058bd456a3b92132f872ca0e4f4a0b0d5e3ed325ebc03dcd64abfd0') + version('2.3.2', sha256='5de8a3ff21bfa431d53859e278e23100fddde239aa2f25e8dee7810098cfd131') + version('2.3.1', sha256='cc3c13aa18a733e1d353558623b5d3620d5322f3894a84d84cb24c024a70a8d7') + version('2.3.0', sha256='c5641ff63a617a5f1ba787b17a10f102dceb3826ce7a4f3b6fd74d1b6409f722') + version('2.2.2', sha256='031fb2b8fab083ad035dafecdac259a1316af0f1c6d28f8846e07ad03d36ff02') + version('2.2.1', sha256='e2f335dcb3dfdc74cc80b2f70dc3c68d239d0832c4bf9af278b7df5a58c06990') + version('2.2.0', sha256='fa9856e17fcd9c804878ea0be59377b64cca3ce25bc8424ed1ab786dce2432a0') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('java', type='run') diff --git a/var/spack/repos/builtin/packages/opium/package.py b/var/spack/repos/builtin/packages/opium/package.py index 13d2c3ef97..f593889dd4 100644 --- a/var/spack/repos/builtin/packages/opium/package.py +++ b/var/spack/repos/builtin/packages/opium/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/optional-lite/package.py b/var/spack/repos/builtin/packages/optional-lite/package.py index 6c4d2193f0..347ed93e87 100644 --- a/var/spack/repos/builtin/packages/optional-lite/package.py +++ b/var/spack/repos/builtin/packages/optional-lite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/optipng/package.py b/var/spack/repos/builtin/packages/optipng/package.py index 3b44c7838c..364c2cb02d 100644 --- a/var/spack/repos/builtin/packages/optipng/package.py +++ b/var/spack/repos/builtin/packages/optipng/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/opus/package.py b/var/spack/repos/builtin/packages/opus/package.py index 7efac2e296..b59de759a7 100644 --- a/var/spack/repos/builtin/packages/opus/package.py +++ b/var/spack/repos/builtin/packages/opus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/orca/package.py b/var/spack/repos/builtin/packages/orca/package.py index bb36f8f759..c541544d78 100644 --- a/var/spack/repos/builtin/packages/orca/package.py +++ b/var/spack/repos/builtin/packages/orca/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/orfm/package.py b/var/spack/repos/builtin/packages/orfm/package.py index 0d55ca4243..8c98bd4f1b 100644 --- a/var/spack/repos/builtin/packages/orfm/package.py +++ b/var/spack/repos/builtin/packages/orfm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/orthofiller/package.py b/var/spack/repos/builtin/packages/orthofiller/package.py index 1319f721f3..b5376c7d2f 100644 --- a/var/spack/repos/builtin/packages/orthofiller/package.py +++ b/var/spack/repos/builtin/packages/orthofiller/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/orthofinder/package.py b/var/spack/repos/builtin/packages/orthofinder/package.py index bb16a134c5..af6820cf16 100644 --- a/var/spack/repos/builtin/packages/orthofinder/package.py +++ b/var/spack/repos/builtin/packages/orthofinder/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/orthomcl/package.py b/var/spack/repos/builtin/packages/orthomcl/package.py index 1d93968899..f06da0e2dc 100644 --- a/var/spack/repos/builtin/packages/orthomcl/package.py +++ b/var/spack/repos/builtin/packages/orthomcl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,5 +26,5 @@ class Orthomcl(Package): install_tree('doc', prefix.doc) install_tree('lib', prefix.lib) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PERL5LIB', self.prefix.lib) + def setup_run_environment(self, env): + env.prepend_path('PERL5LIB', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/osmctools/package.py b/var/spack/repos/builtin/packages/osmctools/package.py index dd86f9da08..84c23714bf 100644 --- a/var/spack/repos/builtin/packages/osmctools/package.py +++ b/var/spack/repos/builtin/packages/osmctools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/osqp/package.py b/var/spack/repos/builtin/packages/osqp/package.py index bed4d87d11..6597e9a701 100644 --- a/var/spack/repos/builtin/packages/osqp/package.py +++ b/var/spack/repos/builtin/packages/osqp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py index 333287c80a..b291fc1aab 100644 --- a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py +++ b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,8 +15,9 @@ class OsuMicroBenchmarks(AutotoolsPackage): and can be used for both traditional and GPU-enhanced nodes.""" homepage = "http://mvapich.cse.ohio-state.edu/benchmarks/" - url = "http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.3.tar.gz" + url = "http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.6.2.tar.gz" + version('5.6.2', sha256='2ecb90abd85398786823c0716d92448d7094657d3f017c65d270ffe39afc7b95') version('5.6.1', sha256='943c426a653a6c56200193d747755efaa4c4e6f23b3571b0e3ef81ecd21b1063') version('5.5', sha256='1e5a4ae5ef2b03143a815b21fefc23373c1b079cc163c2fa1ed1e0c9b83c28ad') version('5.4', sha256='e1ca762e13a07205a59b59ad85e85ce0f826b70f76fd555ce5568efb1f2a8f33') @@ -46,9 +47,9 @@ class OsuMicroBenchmarks(AutotoolsPackage): return config_args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): mpidir = join_path(self.prefix.libexec, 'osu-micro-benchmarks', 'mpi') - run_env.prepend_path('PATH', join_path(mpidir, 'startup')) - run_env.prepend_path('PATH', join_path(mpidir, 'pt2pt')) - run_env.prepend_path('PATH', join_path(mpidir, 'one-sided')) - run_env.prepend_path('PATH', join_path(mpidir, 'collective')) + env.prepend_path('PATH', join_path(mpidir, 'startup')) + env.prepend_path('PATH', join_path(mpidir, 'pt2pt')) + env.prepend_path('PATH', join_path(mpidir, 'one-sided')) + env.prepend_path('PATH', join_path(mpidir, 'collective')) diff --git a/var/spack/repos/builtin/packages/otf/package.py b/var/spack/repos/builtin/packages/otf/package.py index eeab4e105e..cb19e3ee1b 100644 --- a/var/spack/repos/builtin/packages/otf/package.py +++ b/var/spack/repos/builtin/packages/otf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/otf2/package.py b/var/spack/repos/builtin/packages/otf2/package.py index 1feae614d6..a44ebc4451 100644 --- a/var/spack/repos/builtin/packages/otf2/package.py +++ b/var/spack/repos/builtin/packages/otf2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/p3dfft3/package.py b/var/spack/repos/builtin/packages/p3dfft3/package.py new file mode 100644 index 0000000000..a4dfe41941 --- /dev/null +++ b/var/spack/repos/builtin/packages/p3dfft3/package.py @@ -0,0 +1,103 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class P3dfft3(AutotoolsPackage): + """P3DFFT++ (a.k.a. P3DFFT v. 3) is a new generation of P3DFFT library + that aims to provide a comprehensive framework for simulating multiscale + phenomena. It takes the essence of P3DFFT further by creating an + extensible, modular structure uniquely adaptable to a greater range + of use cases.""" + + homepage = "https://www.p3dfft.net" + url = "https://github.com/sdsc/p3dfft.3/archive/v3.0.0.tar.gz" + git = "https://github.com/sdsc/p3dfft.3.git" + + version('develop', branch='master') + version('3.0.0', sha256='1c549e78097d1545d18552b039be0d11cdb96be46efe99a16b65fd5d546dbfa7') + + variant('fftw', default=True, + description='Builds with FFTW library') + variant('essl', default=False, + description='Builds with ESSL library') + variant('mpi', default=True, + description="Enable MPI support.") + variant('measure', default=False, + description="Define if you want to use" + "the measure fftw planner flag") + variant('estimate', default=False, + description="Define if you want to" + "use the estimate fftw planner flag") + variant('patient', default=False, + description="Define if you want to" + "use the patient fftw planner flag") + + # TODO: Add more configure options! + + depends_on('mpi', when='+mpi') + depends_on('fftw', when='+fftw') + depends_on('essl', when='+essl') + + def configure_args(self): + args = [] + + if '%gcc' in self.spec: + args.append('--enable-gnu') + + if '%intel' in self.spec: + args.append('--enable-intel') + + if '%xl' in self.spec: + args.append('--enable-ibm') + + if '%cce' in self.spec: + args.append('--enable-cray') + + if '%pgi' in self.spec: + args.append('--enable-pgi') + + if '+mpi' in self.spec: + args.append('CC=%s' % self.spec['mpi'].mpicc) + args.append('CXX=%s' % self.spec['mpi'].mpicxx) + args.append('FC=%s' % self.spec['mpi'].mpifc) + + if '+openmpi' in self.spec: + args.append('--enable-openmpi') + + if '+fftw' in self.spec: + args.append('--enable-fftw') + + if '@:3.0.0' in self.spec: + args.append('--with-fftw-lib=%s' % + self.spec['fftw'].prefix.lib) + args.append('--with-fftw-inc=%s' % + self.spec['fftw'].prefix.include) + else: + args.append('--with-fftw=%s' % self.spec['fftw'].prefix) + + if 'fftw+measure' in self.spec: + args.append('--enable-fftwmeasure') + if 'fftw+estimate' in self.spec: + args.append('--enable-fftwestimate') + if 'fftw+patient' in self.spec: + args.append('--enable-fftwpatient') + + if '+essl' in self.spec: + args.append('--enable-essl') + args.append('--with-essl-lib=%s' % + self.spec['essl'].prefix.lib) + args.append('--with-essl-inc=%s' % + self.spec['essl'].prefix.include) + + if '+mkl' in self.spec: + args.append('--enable-mkl') + args.append('--with-mkl-lib=%s' % + self.spec['mkl'].prefix.lib) + args.append('--with-mkl-inc=%s' % + self.spec['mkl'].prefix.include) + + return args diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py index 9eda813a1a..e5ec4998da 100644 --- a/var/spack/repos/builtin/packages/p4est/package.py +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/p7zip/package.py b/var/spack/repos/builtin/packages/p7zip/package.py index 160cf82565..0f13335ae6 100644 --- a/var/spack/repos/builtin/packages/p7zip/package.py +++ b/var/spack/repos/builtin/packages/p7zip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pacbio-daligner/package.py b/var/spack/repos/builtin/packages/pacbio-daligner/package.py index 07738d14ee..b3b6420ac1 100644 --- a/var/spack/repos/builtin/packages/pacbio-daligner/package.py +++ b/var/spack/repos/builtin/packages/pacbio-daligner/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pacbio-damasker/package.py b/var/spack/repos/builtin/packages/pacbio-damasker/package.py index d904e3ece2..876e602a76 100644 --- a/var/spack/repos/builtin/packages/pacbio-damasker/package.py +++ b/var/spack/repos/builtin/packages/pacbio-damasker/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py b/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py index 0ccb68842b..f5b0958bfb 100644 --- a/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py +++ b/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pacbio-dextractor/package.py b/var/spack/repos/builtin/packages/pacbio-dextractor/package.py index 9fea4ecd78..5d4d1bcd7f 100644 --- a/var/spack/repos/builtin/packages/pacbio-dextractor/package.py +++ b/var/spack/repos/builtin/packages/pacbio-dextractor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/packmol/package.py b/var/spack/repos/builtin/packages/packmol/package.py index ebfdfd4aa3..0d4465c958 100644 --- a/var/spack/repos/builtin/packages/packmol/package.py +++ b/var/spack/repos/builtin/packages/packmol/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pacvim/package.py b/var/spack/repos/builtin/packages/pacvim/package.py index af9e8e7258..6df19aee63 100644 --- a/var/spack/repos/builtin/packages/pacvim/package.py +++ b/var/spack/repos/builtin/packages/pacvim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pagit/package.py b/var/spack/repos/builtin/packages/pagit/package.py index 7cc1496b53..e0fef6b568 100644 --- a/var/spack/repos/builtin/packages/pagit/package.py +++ b/var/spack/repos/builtin/packages/pagit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,10 +18,6 @@ class Pagit(Package): depends_on('java', type=('build', 'run')) depends_on('perl', type=('build', 'run')) - def url_for_version(self, version): - url = 'ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V{0}.64bit.tgz' - return url.format(version) - def install(self, spec, prefix): with working_dir('PAGIT'): install_tree('ABACAS', prefix.ABACAS) @@ -31,19 +27,18 @@ class Pagit(Package): install_tree('lib', prefix.lib) install_tree('RATT', prefix.RATT) - def setup_environment(self, spack_env, run_env): - run_env.set('PAGIT_HOME', self.prefix) - run_env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5')) - run_env.set('ICORN_HOME', self.prefix.icorn) - run_env.set('SNPOMATIC_HOME', self.prefix.bin) - run_env.set('RATT_HOME', self.prefix.RATT) - run_env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config')) - run_env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5', - 'ssaha2')) - run_env.prepend_path('PATH', join_path(self.prefix.bin, - 'pileup_v0.5')) - run_env.prepend_path('PATH', self.prefix.IMAGE) - run_env.prepend_path('PATH', self.prefix.ABACAS) - run_env.prepend_path('PATH', self.prefix.ICORN) - run_env.prepend_path('PATH', self.prefix.RATT) - run_env.prepend_path('PERL5LIB', self.prefix.lib) + def setup_run_environment(self, env): + env.set('PAGIT_HOME', self.prefix) + env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5')) + env.set('ICORN_HOME', self.prefix.icorn) + env.set('SNPOMATIC_HOME', self.prefix.bin) + env.set('RATT_HOME', self.prefix.RATT) + env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config')) + env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5', + 'ssaha2')) + env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5')) + env.prepend_path('PATH', self.prefix.IMAGE) + env.prepend_path('PATH', self.prefix.ABACAS) + env.prepend_path('PATH', self.prefix.ICORN) + env.prepend_path('PATH', self.prefix.RATT) + env.prepend_path('PERL5LIB', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/pagmo/package.py b/var/spack/repos/builtin/packages/pagmo/package.py index 11a8b922a8..406372843b 100644 --- a/var/spack/repos/builtin/packages/pagmo/package.py +++ b/var/spack/repos/builtin/packages/pagmo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pal/package.py b/var/spack/repos/builtin/packages/pal/package.py index 480dc2539f..53e092f70c 100644 --- a/var/spack/repos/builtin/packages/pal/package.py +++ b/var/spack/repos/builtin/packages/pal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/paml/package.py b/var/spack/repos/builtin/packages/paml/package.py index 91063e7faf..b56da09036 100644 --- a/var/spack/repos/builtin/packages/paml/package.py +++ b/var/spack/repos/builtin/packages/paml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/panda/package.py b/var/spack/repos/builtin/packages/panda/package.py index e607f12627..df0bf63a87 100644 --- a/var/spack/repos/builtin/packages/panda/package.py +++ b/var/spack/repos/builtin/packages/panda/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pandaseq/package.py b/var/spack/repos/builtin/packages/pandaseq/package.py index 4ad9060d56..a4693e7056 100644 --- a/var/spack/repos/builtin/packages/pandaseq/package.py +++ b/var/spack/repos/builtin/packages/pandaseq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pandoc/package.py b/var/spack/repos/builtin/packages/pandoc/package.py index c0efc2cb8c..9983a4e597 100644 --- a/var/spack/repos/builtin/packages/pandoc/package.py +++ b/var/spack/repos/builtin/packages/pandoc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py index 35fd629b54..52874160fc 100644 --- a/var/spack/repos/builtin/packages/pango/package.py +++ b/var/spack/repos/builtin/packages/pango/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,7 +25,7 @@ class Pango(AutotoolsPackage): depends_on("pkgconfig", type="build") depends_on("harfbuzz") - depends_on("cairo") + depends_on("cairo+ft+fc") depends_on("cairo~X", when='~X') depends_on("cairo+X", when='+X') depends_on("libxft", when='+X') @@ -56,8 +56,8 @@ class Pango(AutotoolsPackage): def install(self, spec, prefix): make("install", parallel=False) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path("XDG_DATA_DIRS", - self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", - self.prefix.share) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) diff --git a/var/spack/repos/builtin/packages/pangomm/package.py b/var/spack/repos/builtin/packages/pangomm/package.py index 0fec54ba4e..e77aaf711b 100644 --- a/var/spack/repos/builtin/packages/pangomm/package.py +++ b/var/spack/repos/builtin/packages/pangomm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,21 @@ class Pangomm(AutotoolsPackage): homepage = "http://www.pango.org/" url = "https://ftp.gnome.org/pub/GNOME/sources/pangomm/2.14/pangomm-2.14.1.tar.gz" + version('2.43.1', sha256='00483967b4ed0869da09dc0617de45625b9ab846c7b07aa25dfc940a4fc540a4') + version('2.42.0', sha256='ca6da067ff93a6445780c0b4b226eb84f484ab104b8391fb744a45cbc7edbf56') + version('2.41.5', sha256='5131830d5b37b181ca4fa8f641ad86faa985c0bb7dcc833c98672d294367b304') + version('2.40.2', sha256='0a97aa72513db9088ca3034af923484108746dba146e98ed76842cf858322d05') + version('2.39.1', sha256='10c06bbf12a03963ffe9c697887b57c72f1dac1671d09dba45cecd25db5dc6ed') + version('2.38.1', sha256='effb18505b36d81fc32989a39ead8b7858940d0533107336a30bc3eef096bc8b') + version('2.37.2', sha256='bb83d769f4d4256e0b108e84a4f0441065da8483c7cc51518b0634668ed094f5') + version('2.36.0', sha256='a8d96952c708d7726bed260d693cece554f8f00e48b97cccfbf4f5690b6821f0') + version('2.35.1', sha256='3eb4d11014d09627b2b7c532c65b54fa182905b4c9688901ae11cdfb506dbc55') + version('2.34.0', sha256='0e82bbff62f626692a00f3772d8b17169a1842b8cc54d5f2ddb1fec2cede9e41') + version('2.28.4', sha256='778dcb66a793cbfd52a9f92ee5a71b888c3603a913fc1ddc48a30204de6d6c82') + version('2.27.1', sha256='0d707b4a9e632223f7f27215f83fff679166cc89b9b7f209e7fe049af7b4562e') + version('2.26.3', sha256='4f68e4d2d4b6c4ae82327ebd9e69f2cbc4379e502d12856c36943399b87d71a2') + version('2.25.1', sha256='25684058138050a35ebb4f4e13899aea12045dfb00cc351dfe78f01cb1a1f21c') + version('2.24.0', sha256='24c7b8782b8986fa8f6224ac1e5f1a02412b7d8bc21b53d14d6df9c7d9b59a3f') version('2.14.1', sha256='2ea6cee273cca1aae2ee5a5dac0c416b4dc354e46debb51f20c6eeba828f5ed5') version('2.14.0', sha256='baa3b231c9498fb1140254e3feb4eb93c638f07e6e26ae0e36c3699ec14d80fd') diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index 7f863fa7f6..c6dc408eb6 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,11 +17,12 @@ class Papi(Package): enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of - components that expose performance measurement opportunites + components that expose performance measurement opportunities across the hardware and software stack.""" homepage = "http://icl.cs.utk.edu/papi/index.html" + maintainers = ['G-Ragghianti'] - url = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz" + url = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz" version('5.7.0', sha256='d1a3bb848e292c805bc9f29e09c27870e2ff4cda6c2fba3b7da8b4bba6547589') version('5.6.0', sha256='49b7293f9ca2d74d6d80bd06b5c4be303663123267b4ac0884cbcae4c914dc47') version('5.5.1', sha256='49dc2c2323f6164c4a7e81b799ed690ee73158671205e71501f849391dd2c2d4') @@ -30,11 +31,27 @@ class Papi(Package): version('5.4.1', sha256='e131c1449786fe870322a949e44f974a5963824f683232e653fb570cc65d4e87') version('5.3.0', sha256='99f2f36398b370e75d100b4a189d5bc0ac4f5dd66df44d441f88fd32e1421524') + variant('example', default=True, description='Install the example files') + variant('infiniband', default=False, description='Enable Infiniband support') + variant('powercap', default=False, description='Enable powercap interface support') + variant('rapl', default=False, description='Enable RAPL support') + variant('lmsensors', default=False, description='Enable lm_sensors support') + + depends_on('lm-sensors', when='+lmsensors') + # Does not build with newer versions of gcc, see # https://bitbucket.org/icl/papi/issues/46/cannot-compile-on-arch-linux patch('https://bitbucket.org/icl/papi/commits/53de184a162b8a7edff48fed01a15980664e15b1/raw', sha256='64c57b3ad4026255238cc495df6abfacc41de391a0af497c27d0ac819444a1f8', when='@5.4.0:5.6.99%gcc@8:') def install(self, spec, prefix): + if '+lmsensors' in spec: + with working_dir("src/components/lmsensors"): + configure_args = [ + "--with-sensors_incdir=%s/sensors" % + spec['lm-sensors'].headers.directories[0], + "--with-sensors_libdir=%s" % + spec['lm-sensors'].libs.directories[0]] + configure(*configure_args) with working_dir("src"): configure_args = ["--prefix=%s" % prefix] @@ -44,6 +61,10 @@ class Papi(Package): # fail, so that PAPI does not get confused configure_args.append('MPICC=:') + configure_args.append( + '--with-components={0}'.format(' '.join( + filter(lambda x: spec.variants[x].value, spec.variants)))) + configure(*configure_args) # Don't use <malloc.h> diff --git a/var/spack/repos/builtin/packages/papyrus/package.py b/var/spack/repos/builtin/packages/papyrus/package.py index 4a5119deb0..a0e51c9f5f 100644 --- a/var/spack/repos/builtin/packages/papyrus/package.py +++ b/var/spack/repos/builtin/packages/papyrus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py index bb22dd6e14..c235acbdc8 100644 --- a/var/spack/repos/builtin/packages/paradiseo/package.py +++ b/var/spack/repos/builtin/packages/paradiseo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py index 3e78f8ad9a..34a1af5984 100644 --- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py +++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,6 +27,7 @@ class ParallelNetcdf(AutotoolsPackage): version('develop', branch='develop') version('master', branch='master') + version('1.12.1', sha256='56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2') version('1.11.2', sha256='d2c18601b364c35b5acb0a0b46cd6e14cae456e0eb854e5c789cf65f3cd6a2a7') version('1.11.1', sha256='0c587b707835255126a23c104c66c9614be174843b85b897b3772a590be45779') version('1.11.0', sha256='a18a1a43e6c4fd7ef5827dbe90e9dcf1363b758f513af1f1356ed6c651195a9f') diff --git a/var/spack/repos/builtin/packages/parallel/package.py b/var/spack/repos/builtin/packages/parallel/package.py index 596bb814e3..09b8f729b6 100644 --- a/var/spack/repos/builtin/packages/parallel/package.py +++ b/var/spack/repos/builtin/packages/parallel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,14 +6,14 @@ from spack import * -class Parallel(AutotoolsPackage): +class Parallel(AutotoolsPackage, GNUMirrorPackage): """GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. """ homepage = "http://www.gnu.org/software/parallel/" - url = "https://ftpmirror.gnu.org/parallel/parallel-20170122.tar.bz2" + gnu_mirror_path = "parallel/parallel-20170122.tar.bz2" version('20190222', sha256='86b1badc56ee2de1483107c2adf634604fd72789c91f65e40138d21425906b1c') version('20170322', sha256='f8f810040088bf3c52897a2ee0c0c71bd8d097e755312364b946f107ae3553f6') diff --git a/var/spack/repos/builtin/packages/paraver/package.py b/var/spack/repos/builtin/packages/paraver/package.py index 8bcfc5952c..fe9e31b2f2 100644 --- a/var/spack/repos/builtin/packages/paraver/package.py +++ b/var/spack/repos/builtin/packages/paraver/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index 938004b97c..823e9b0f03 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,7 +12,7 @@ class Paraview(CMakePackage, CudaPackage): visualization application.""" homepage = 'https://www.paraview.org' - url = "https://www.paraview.org/files/v5.6/ParaView-v5.6.2.tar.xz" + url = "https://www.paraview.org/files/v5.7/ParaView-v5.7.0.tar.xz" list_url = "https://www.paraview.org/files" list_depth = 1 git = "https://gitlab.kitware.com/paraview/paraview.git" @@ -20,6 +20,7 @@ class Paraview(CMakePackage, CudaPackage): maintainers = ['chuckatkins', 'danlipsa'] version('develop', branch='master', submodules=True) + version('5.7.0', sha256='e41e597e1be462974a03031380d9e5ba9a7efcdb22e4ca2f3fec50361f310874') version('5.6.2', sha256='1f3710b77c58a46891808dbe23dc59a1259d9c6b7bb123aaaeaa6ddf2be882ea') version('5.6.0', sha256='cb8c4d752ad9805c74b4a08f8ae6e83402c3f11e38b274dba171b99bb6ac2460') version('5.5.2', sha256='64561f34c4402b88f3cb20a956842394dde5838efd7ebb301157a837114a0e2d') @@ -43,10 +44,13 @@ class Paraview(CMakePackage, CudaPackage): variant('opengl2', default=True, description='Enable OpenGL2 backend') variant('examples', default=False, description="Build examples") variant('hdf5', default=False, description="Use external HDF5") + variant('shared', default=True, + description='Builds a shared version of the library') conflicts('+python', when='+python3') conflicts('+python', when='@5.6:') conflicts('+python3', when='@:5.5') + conflicts('+shared', when='+cuda') # Workaround for # adding the following to your packages.yaml @@ -63,13 +67,13 @@ class Paraview(CMakePackage, CudaPackage): depends_on('python@2.7:2.8', when='+python', type=('build', 'run')) depends_on('python@3:', when='+python3', type=('build', 'run')) - depends_on('py-numpy', when='+python', type=('build', 'run')) + depends_on('py-numpy@:1.15.4', when='+python', type=('build', 'run')) depends_on('py-numpy', when='+python3', type=('build', 'run')) depends_on('py-mpi4py', when='+python+mpi', type=('build', 'run')) depends_on('py-mpi4py', when='+python3+mpi', type=('build', 'run')) depends_on('py-matplotlib@:2', when='+python', type='run') - depends_on('py-matplotlib@3:', when='+python3', type='run') + depends_on('py-matplotlib', when='+python3', type='run') depends_on('mpi', when='+mpi') depends_on('qt+opengl', when='@5.3.0:+qt+opengl2') @@ -92,7 +96,7 @@ class Paraview(CMakePackage, CudaPackage): depends_on('libpng') depends_on('libtiff') depends_on('libxml2') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('expat') # depends_on('netcdf-cxx') # depends_on('protobuf') # version mismatches? @@ -126,16 +130,16 @@ class Paraview(CMakePackage, CudaPackage): """The paraview subdirectory name as paraview-major.minor""" return 'paraview-{0}'.format(self.spec.version.up_to(2)) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): if os.path.isdir(self.prefix.lib64): lib_dir = self.prefix.lib64 else: lib_dir = self.prefix.lib - spack_env.set('ParaView_DIR', self.prefix) - spack_env.set('PARAVIEW_VTK_DIR', - join_path(lib_dir, 'cmake', self.paraview_subdir)) + env.set('ParaView_DIR', self.prefix) + env.set('PARAVIEW_VTK_DIR', + join_path(lib_dir, 'cmake', self.paraview_subdir)) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # paraview 5.5 and later # - cmake under lib/cmake/paraview-5.5 # - libs under lib @@ -145,31 +149,31 @@ class Paraview(CMakePackage, CudaPackage): else: lib_dir = self.prefix.lib - run_env.set('ParaView_DIR', self.prefix) - run_env.set('PARAVIEW_VTK_DIR', - join_path(lib_dir, 'cmake', self.paraview_subdir)) + env.set('ParaView_DIR', self.prefix) + env.set('PARAVIEW_VTK_DIR', + join_path(lib_dir, 'cmake', self.paraview_subdir)) if self.spec.version <= Version('5.4.1'): lib_dir = join_path(lib_dir, self.paraview_subdir) - run_env.prepend_path('LIBRARY_PATH', lib_dir) - run_env.prepend_path('LD_LIBRARY_PATH', lib_dir) + env.prepend_path('LIBRARY_PATH', lib_dir) + env.prepend_path('LD_LIBRARY_PATH', lib_dir) if '+python' in self.spec or '+python3' in self.spec: if self.spec.version <= Version('5.4.1'): pv_pydir = join_path(lib_dir, 'site-packages') - run_env.prepend_path('PYTHONPATH', pv_pydir) - run_env.prepend_path('PYTHONPATH', join_path(pv_pydir, 'vtk')) + env.prepend_path('PYTHONPATH', pv_pydir) + env.prepend_path('PYTHONPATH', join_path(pv_pydir, 'vtk')) else: python_version = self.spec['python'].version.up_to(2) pv_pydir = join_path(lib_dir, 'python{0}'.format(python_version), 'site-packages') - run_env.prepend_path('PYTHONPATH', pv_pydir) + env.prepend_path('PYTHONPATH', pv_pydir) # The Trilinos Catalyst adapter requires # the vtkmodules directory in PYTHONPATH - run_env.prepend_path('PYTHONPATH', join_path(pv_pydir, - 'vtkmodules')) + env.prepend_path('PYTHONPATH', join_path(pv_pydir, + 'vtkmodules')) def cmake_args(self): """Populate cmake arguments for ParaView.""" @@ -234,6 +238,15 @@ class Paraview(CMakePackage, CudaPackage): '-DMPI_Fortran_COMPILER:PATH=%s' % spec['mpi'].mpifc ]) + if '+shared' in spec: + cmake_args.append( + '-DPARAVIEW_BUILD_SHARED_LIBS:BOOL=ON' + ) + else: + cmake_args.append( + '-DPARAVIEW_BUILD_SHARED_LIBS:BOOL=OFF' + ) + if '+cuda' in spec: cmake_args.extend([ '-DPARAVIEW_USE_CUDA:BOOL=ON', diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index bf487a80f2..076e447877 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/parmgridgen/package.py b/var/spack/repos/builtin/packages/parmgridgen/package.py index 74305fc907..95ab72060d 100644 --- a/var/spack/repos/builtin/packages/parmgridgen/package.py +++ b/var/spack/repos/builtin/packages/parmgridgen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/parquet/package.py b/var/spack/repos/builtin/packages/parquet-cpp/package.py index ac130b359f..38e43f33d3 100644 --- a/var/spack/repos/builtin/packages/parquet/package.py +++ b/var/spack/repos/builtin/packages/parquet-cpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Parquet(CMakePackage): +class ParquetCpp(CMakePackage): """C++ bindings for the Apache Parquet columnar data format. """ diff --git a/var/spack/repos/builtin/packages/parsimonator/package.py b/var/spack/repos/builtin/packages/parsimonator/package.py index 4ebbac8498..d83dbab338 100644 --- a/var/spack/repos/builtin/packages/parsimonator/package.py +++ b/var/spack/repos/builtin/packages/parsimonator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/parsplice/package.py b/var/spack/repos/builtin/packages/parsplice/package.py index 6301f6ea5e..308bcd79f4 100644 --- a/var/spack/repos/builtin/packages/parsplice/package.py +++ b/var/spack/repos/builtin/packages/parsplice/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/partitionfinder/package.py b/var/spack/repos/builtin/packages/partitionfinder/package.py index e810982505..302ead2b40 100644 --- a/var/spack/repos/builtin/packages/partitionfinder/package.py +++ b/var/spack/repos/builtin/packages/partitionfinder/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pasta/package.py b/var/spack/repos/builtin/packages/pasta/package.py index 885e0673c9..cb1c073c08 100644 --- a/var/spack/repos/builtin/packages/pasta/package.py +++ b/var/spack/repos/builtin/packages/pasta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,9 +25,9 @@ class Pasta(Package): destination='.' ) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): tools = join_path(self.prefix, 'sate-tools-linux') - spack_env.set('PASTA_TOOLS_DEVDIR', tools) + env.set('PASTA_TOOLS_DEVDIR', tools) def install(self, spec, prefix): # build process for pasta is very hacky -- uses hard links to source diff --git a/var/spack/repos/builtin/packages/patch/package.py b/var/spack/repos/builtin/packages/patch/package.py index d67d564280..a5e9a0f4bc 100644 --- a/var/spack/repos/builtin/packages/patch/package.py +++ b/var/spack/repos/builtin/packages/patch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,14 +6,14 @@ from spack import * -class Patch(AutotoolsPackage): +class Patch(AutotoolsPackage, GNUMirrorPackage): """Patch takes a patch file containing a difference listing produced by the diff program and applies those differences to one or more original files, producing patched versions. """ homepage = "http://savannah.gnu.org/projects/patch/" - url = "https://ftpmirror.gnu.org/patch/patch-2.7.6.tar.xz" + gnu_mirror_path = "patch/patch-2.7.6.tar.xz" version('2.7.6', sha256='ac610bda97abe0d9f6b7c963255a11dcb196c25e337c61f94e4778d632f1d8fd') version('2.7.5', sha256='fd95153655d6b95567e623843a0e77b81612d502ecf78a489a4aed7867caa299') diff --git a/var/spack/repos/builtin/packages/patchelf/package.py b/var/spack/repos/builtin/packages/patchelf/package.py index 6d4d979b16..d17bb3bea1 100644 --- a/var/spack/repos/builtin/packages/patchelf/package.py +++ b/var/spack/repos/builtin/packages/patchelf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pathfinder/package.py b/var/spack/repos/builtin/packages/pathfinder/package.py index 3f5bf368e2..3208448d81 100644 --- a/var/spack/repos/builtin/packages/pathfinder/package.py +++ b/var/spack/repos/builtin/packages/pathfinder/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class Pathfinder(MakefilePackage): """Proxy Application. Signature search.""" homepage = "https://mantevo.org/packages/" - url = "http://mantevo.org/downloads/releaseTarballs/miniapps/PathFinder/PathFinder_1.0.0.tgz" + url = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/PathFinder_1.0.0.tgz" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/pax-utils/package.py b/var/spack/repos/builtin/packages/pax-utils/package.py index 85013e69da..62776831c0 100644 --- a/var/spack/repos/builtin/packages/pax-utils/package.py +++ b/var/spack/repos/builtin/packages/pax-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pbbam/package.py b/var/spack/repos/builtin/packages/pbbam/package.py index 97486e1606..26622715e9 100644 --- a/var/spack/repos/builtin/packages/pbbam/package.py +++ b/var/spack/repos/builtin/packages/pbbam/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -38,6 +38,6 @@ class Pbbam(CMakePackage): install_tree('spack-build/lib', prefix.lib) install_tree('include/pbbam', prefix.include.pbbam) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('PacBioBAM_LIBRARIES', self.prefix.lib) - spack_env.set('PacBioBAM_INCLUDE_DIRS', self.prefix.include) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('PacBioBAM_LIBRARIES', self.prefix.lib) + env.set('PacBioBAM_INCLUDE_DIRS', self.prefix.include) diff --git a/var/spack/repos/builtin/packages/pbmpi/package.py b/var/spack/repos/builtin/packages/pbmpi/package.py index edb9960d5c..205af53280 100644 --- a/var/spack/repos/builtin/packages/pbmpi/package.py +++ b/var/spack/repos/builtin/packages/pbmpi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pbsuite/package.py b/var/spack/repos/builtin/packages/pbsuite/package.py index b29b734f4c..ee45037755 100644 --- a/var/spack/repos/builtin/packages/pbsuite/package.py +++ b/var/spack/repos/builtin/packages/pbsuite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,5 +24,5 @@ class Pbsuite(Package): install_tree('pbsuite', prefix.pbsuite) install_tree('bin', prefix.bin) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PYTHONPATH', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('PYTHONPATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/pcma/fix_return_type_err.patch b/var/spack/repos/builtin/packages/pcma/fix_return_type_err.patch new file mode 100644 index 0000000000..1b34a36013 --- /dev/null +++ b/var/spack/repos/builtin/packages/pcma/fix_return_type_err.patch @@ -0,0 +1,42 @@ +diff -ur spack-src.org/alcomp2.c spack-src/alcomp2.c +--- spack-src.org/alcomp2.c 2020-01-21 15:13:59.483665899 +0900 ++++ spack-src/alcomp2.c 2020-01-21 15:15:25.702732353 +0900 +@@ -155,7 +155,7 @@ + int *ScoreOverColumn (int colScore, int flag1, int flag2, int flag3, int flag4, int flag5, int flag6, int *column_Score); + + void *ReadRef (char *inputfile); +-int CompareAlnVsReferenceAln (int *apos1, int *apos2, int *aposref1, int *aposref2, int start_ref1, int start_ref2, int end_ref1, int end_ref2 /* , int coverage1, int coverage2, int accuracy1, int accuracy2*/ ); ++void CompareAlnVsReferenceAln (int *apos1, int *apos2, int *aposref1, int *aposref2, int start_ref1, int start_ref2, int end_ref1, int end_ref2 /* , int coverage1, int coverage2, int accuracy1, int accuracy2*/ ); + + double p_dayhoff[]={0, 0.0143859, 0.0384319, 0.0352742, 0.0195027, 0.086209, 0.048466, 0.0708956, 0.0866279, 0.0193078, + 0.0832518, 0.0457631, 0.0610127, 0.0695179, 0.0390894, 0.0367281, 0.0570451, 0.0580589, 0.0244313, 0.043972, 0.0620286}; +@@ -1738,7 +1738,7 @@ + int **ali; + readali(filename); + +-if (flag_errread==1) return; ++if (flag_errread==1) return NULL; + + ali=ali_char2int(aseq,start_num,start_seq); + return ali; +@@ -3247,7 +3247,7 @@ + reflen_nogp = pos; + } + +-int CompareAlnVsReferenceAln (int *apos1, int *apos2, int *aposref1, int *aposref2, int start_ref1, int start_ref2, int end_ref1, int end_ref2 /*, int coverage1, int coverage2, int accuracy1, int accuracy2 */) ++void CompareAlnVsReferenceAln (int *apos1, int *apos2, int *aposref1, int *aposref2, int start_ref1, int start_ref2, int end_ref1, int end_ref2 /*, int coverage1, int coverage2, int accuracy1, int accuracy2 */) + { + int i,j,k; + int start_ali1, start_ali2, end_ali1, end_ali2; +diff -ur spack-src.org/interface.c spack-src/interface.c +--- spack-src.org/interface.c 2020-01-21 15:13:59.483665899 +0900 ++++ spack-src/interface.c 2020-01-21 15:14:23.466183088 +0900 +@@ -202,7 +202,7 @@ + match[i] = 0; + } + +- if(args[0]==NULL) return; ++ if(args[0]==NULL) return 0; + + params[0]=(char *)ckalloc((strlen(args[0])+1)*sizeof(char)); + if (args[0][0]!=COMMANDSEP) diff --git a/var/spack/repos/builtin/packages/pcma/package.py b/var/spack/repos/builtin/packages/pcma/package.py index baaf935f90..efde640c07 100644 --- a/var/spack/repos/builtin/packages/pcma/package.py +++ b/var/spack/repos/builtin/packages/pcma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,3 +22,6 @@ class Pcma(MakefilePackage): def install(self, spec, prefix): mkdirp(prefix.bin) install('pcma', prefix.bin) + + # set return value and change return type of function [-Wreturn-type] + patch('fix_return_type_err.patch') diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py index f2a4e494a5..a488ef3644 100644 --- a/var/spack/repos/builtin/packages/pcre/package.py +++ b/var/spack/repos/builtin/packages/pcre/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pcre2/package.py b/var/spack/repos/builtin/packages/pcre2/package.py index abe62d70fd..eaa5928ae2 100644 --- a/var/spack/repos/builtin/packages/pcre2/package.py +++ b/var/spack/repos/builtin/packages/pcre2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pdf2svg/package.py b/var/spack/repos/builtin/packages/pdf2svg/package.py index 00f242f671..da10b3f5b0 100644 --- a/var/spack/repos/builtin/packages/pdf2svg/package.py +++ b/var/spack/repos/builtin/packages/pdf2svg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pdftk/package.py b/var/spack/repos/builtin/packages/pdftk/package.py index 8f06385f14..0788be1861 100644 --- a/var/spack/repos/builtin/packages/pdftk/package.py +++ b/var/spack/repos/builtin/packages/pdftk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pdsh/package.py b/var/spack/repos/builtin/packages/pdsh/package.py index 8b58fb595d..d28c2f695d 100644 --- a/var/spack/repos/builtin/packages/pdsh/package.py +++ b/var/spack/repos/builtin/packages/pdsh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pdt/package.py b/var/spack/repos/builtin/packages/pdt/package.py index dd4c1110da..2d099b8dff 100644 --- a/var/spack/repos/builtin/packages/pdt/package.py +++ b/var/spack/repos/builtin/packages/pdt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -43,6 +43,10 @@ class Pdt(AutotoolsPackage): options.append('-icpc') elif self.compiler.name == 'pgi': options.append('-pgCC') + elif self.compiler.name == 'gcc': + options.append('-GNU') + else: + raise InstallError('Unknown/unsupported compiler family') configure(*options) diff --git a/var/spack/repos/builtin/packages/pegtl/package.py b/var/spack/repos/builtin/packages/pegtl/package.py index 749b1dbd2c..0da4bfe16f 100644 --- a/var/spack/repos/builtin/packages/pegtl/package.py +++ b/var/spack/repos/builtin/packages/pegtl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pennant/package.py b/var/spack/repos/builtin/packages/pennant/package.py index 372db4559f..80f79b0ecc 100644 --- a/var/spack/repos/builtin/packages/pennant/package.py +++ b/var/spack/repos/builtin/packages/pennant/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/percept/package.py b/var/spack/repos/builtin/packages/percept/package.py index fe72d79ded..745643f335 100644 --- a/var/spack/repos/builtin/packages/percept/package.py +++ b/var/spack/repos/builtin/packages/percept/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-acme-damn/package.py b/var/spack/repos/builtin/packages/perl-acme-damn/package.py index 62fbd15301..ac5a5c0cad 100644 --- a/var/spack/repos/builtin/packages/perl-acme-damn/package.py +++ b/var/spack/repos/builtin/packages/perl-acme-damn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py b/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py index f44c8452b5..9936e43f85 100644 --- a/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py +++ b/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-alien-build/package.py b/var/spack/repos/builtin/packages/perl-alien-build/package.py index db96518659..7e227821aa 100644 --- a/var/spack/repos/builtin/packages/perl-alien-build/package.py +++ b/var/spack/repos/builtin/packages/perl-alien-build/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py b/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py index 98c0a488d9..0ec9551e4a 100644 --- a/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py +++ b/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class PerlAlienLibxml2(PerlPackage): """This module provides libxml2 for other modules to use.""" homepage = "https://metacpan.org/pod/Alien::Libxml2" - url = "https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/Alien-Libxml2-0.09.tar.gz" + url = "https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/Alien-Libxml2-0.10_01.tar.gz" version('0.10_01', sha256='2f45b308b33503292f48bf46a75fe1e653d6b209ba5caf0628d8cc103f8d61ac') diff --git a/var/spack/repos/builtin/packages/perl-app-cmd/package.py b/var/spack/repos/builtin/packages/perl-app-cmd/package.py index faef6535e3..39fe52402c 100644 --- a/var/spack/repos/builtin/packages/perl-app-cmd/package.py +++ b/var/spack/repos/builtin/packages/perl-app-cmd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-array-utils/package.py b/var/spack/repos/builtin/packages/perl-array-utils/package.py index 6216eeea2e..beb3619ecb 100644 --- a/var/spack/repos/builtin/packages/perl-array-utils/package.py +++ b/var/spack/repos/builtin/packages/perl-array-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py b/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py index 3ffa56d0a4..2fde7fc975 100644 --- a/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py +++ b/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-bio-perl/package.py b/var/spack/repos/builtin/packages/perl-bioperl/package.py index a8680d8b2e..de0f367141 100644 --- a/var/spack/repos/builtin/packages/perl-bio-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-bioperl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,7 +7,7 @@ from spack import * import inspect -class PerlBioPerl(PerlPackage): +class PerlBioperl(PerlPackage): """BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are @@ -35,9 +35,10 @@ class PerlBioPerl(PerlPackage): homepage = "https://metacpan.org/pod/BioPerl" url = "https://cpan.metacpan.org/authors/id/C/CD/CDRAUG/BioPerl-1.7.6.tar.gz" - version('1.7.6', sha256='df2a3efc991b9b5d7cc9d038a1452c6dac910c9ad2a0e47e408dd692c111688d') - version('1.7.2', sha256='17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1', - url="http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz") + version('1.7.6', + sha256='df2a3efc991b9b5d7cc9d038a1452c6dac910c9ad2a0e47e408dd692c111688d', + preferred=True) + version('1.007002', sha256='17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1') # According to cpandeps.grinnz.com Module-Build is both a build and run # time dependency for BioPerl diff --git a/var/spack/repos/builtin/packages/perl-bit-vector/package.py b/var/spack/repos/builtin/packages/perl-bit-vector/package.py index 380d79191c..6d4fcbc44d 100644 --- a/var/spack/repos/builtin/packages/perl-bit-vector/package.py +++ b/var/spack/repos/builtin/packages/perl-bit-vector/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-cairo/package.py b/var/spack/repos/builtin/packages/perl-cairo/package.py index 3b4ebe9dc9..6ac4f1e682 100644 --- a/var/spack/repos/builtin/packages/perl-cairo/package.py +++ b/var/spack/repos/builtin/packages/perl-cairo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-capture-tiny/package.py b/var/spack/repos/builtin/packages/perl-capture-tiny/package.py index 041ee0903a..0f6c7df5b3 100644 --- a/var/spack/repos/builtin/packages/perl-capture-tiny/package.py +++ b/var/spack/repos/builtin/packages/perl-capture-tiny/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-carp-clan/package.py b/var/spack/repos/builtin/packages/perl-carp-clan/package.py index 19b046d2bd..74058a6206 100644 --- a/var/spack/repos/builtin/packages/perl-carp-clan/package.py +++ b/var/spack/repos/builtin/packages/perl-carp-clan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-cgi/package.py b/var/spack/repos/builtin/packages/perl-cgi/package.py index 009b018e59..63b10b5ce2 100644 --- a/var/spack/repos/builtin/packages/perl-cgi/package.py +++ b/var/spack/repos/builtin/packages/perl-cgi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py b/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py index d5e8c7e392..71cd1db575 100644 --- a/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py +++ b/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-class-inspector/package.py b/var/spack/repos/builtin/packages/perl-class-inspector/package.py index 5f04cf5b25..a1d1b87605 100644 --- a/var/spack/repos/builtin/packages/perl-class-inspector/package.py +++ b/var/spack/repos/builtin/packages/perl-class-inspector/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-class-load-xs/package.py b/var/spack/repos/builtin/packages/perl-class-load-xs/package.py index 7133d8bd12..6e4eb2b317 100644 --- a/var/spack/repos/builtin/packages/perl-class-load-xs/package.py +++ b/var/spack/repos/builtin/packages/perl-class-load-xs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-class-load/package.py b/var/spack/repos/builtin/packages/perl-class-load/package.py index 3e7ef53f9e..e2890a406d 100644 --- a/var/spack/repos/builtin/packages/perl-class-load/package.py +++ b/var/spack/repos/builtin/packages/perl-class-load/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-clone-choose/package.py b/var/spack/repos/builtin/packages/perl-clone-choose/package.py index bdc58a87ad..903afa8800 100644 --- a/var/spack/repos/builtin/packages/perl-clone-choose/package.py +++ b/var/spack/repos/builtin/packages/perl-clone-choose/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-clone/package.py b/var/spack/repos/builtin/packages/perl-clone/package.py index 0f3fffd451..baf0625396 100644 --- a/var/spack/repos/builtin/packages/perl-clone/package.py +++ b/var/spack/repos/builtin/packages/perl-clone/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py b/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py index 56cd8605f3..4935df1e1c 100644 --- a/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py +++ b/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py b/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py index 8fdbd023e6..4e850c1ca7 100644 --- a/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py +++ b/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-config-general/package.py b/var/spack/repos/builtin/packages/perl-config-general/package.py index 803efa55d0..3cbc8cf636 100644 --- a/var/spack/repos/builtin/packages/perl-config-general/package.py +++ b/var/spack/repos/builtin/packages/perl-config-general/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-contextual-return/package.py b/var/spack/repos/builtin/packages/perl-contextual-return/package.py index 3330a5175a..1e7c993917 100644 --- a/var/spack/repos/builtin/packages/perl-contextual-return/package.py +++ b/var/spack/repos/builtin/packages/perl-contextual-return/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py b/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py index 79bdc6cd0c..cdaf06be25 100644 --- a/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py +++ b/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-data-dumper/package.py b/var/spack/repos/builtin/packages/perl-data-dumper/package.py index 3fc0dca758..8c5d73a14e 100644 --- a/var/spack/repos/builtin/packages/perl-data-dumper/package.py +++ b/var/spack/repos/builtin/packages/perl-data-dumper/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-data-optlist/package.py b/var/spack/repos/builtin/packages/perl-data-optlist/package.py index 11e3573410..d1e17f1ab8 100644 --- a/var/spack/repos/builtin/packages/perl-data-optlist/package.py +++ b/var/spack/repos/builtin/packages/perl-data-optlist/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-data-stag/package.py b/var/spack/repos/builtin/packages/perl-data-stag/package.py index eae912d679..f18fb9f255 100644 --- a/var/spack/repos/builtin/packages/perl-data-stag/package.py +++ b/var/spack/repos/builtin/packages/perl-data-stag/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-dbfile/package.py b/var/spack/repos/builtin/packages/perl-db-file/package.py index c56d98f842..47791806a6 100644 --- a/var/spack/repos/builtin/packages/perl-dbfile/package.py +++ b/var/spack/repos/builtin/packages/perl-db-file/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PerlDbfile(PerlPackage): +class PerlDbFile(PerlPackage): """DB_File is a module which allows Perl programs to make use of the facilities provided by Berkeley DB version 1.x (if you have a newer version of DB, see "Using DB_File with Berkeley DB version 2 or greater"). @@ -20,3 +20,8 @@ class PerlDbfile(PerlPackage): version('1.840', sha256='b7864707fad0f2d1488c748c4fa08f1fb8bcfd3da247c36909fd42f20bfab2c4') depends_on('perl-extutils-makemaker', type='build') + depends_on('berkeley-db', type='build') + + def patch(self): + filter_file('/usr/local/BerkeleyDB', + self.spec['berkeley-db'].prefix, 'config.in') diff --git a/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py b/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py index fa56bfc8a6..d7358ccca9 100644 --- a/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py +++ b/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-dbd-pg/package.py b/var/spack/repos/builtin/packages/perl-dbd-pg/package.py index b54b7864b0..04ed9af3b3 100644 --- a/var/spack/repos/builtin/packages/perl-dbd-pg/package.py +++ b/var/spack/repos/builtin/packages/perl-dbd-pg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-dbd-sqlite/package.py b/var/spack/repos/builtin/packages/perl-dbd-sqlite/package.py index cee85f4b7f..9a082332aa 100644 --- a/var/spack/repos/builtin/packages/perl-dbd-sqlite/package.py +++ b/var/spack/repos/builtin/packages/perl-dbd-sqlite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-dbi/package.py b/var/spack/repos/builtin/packages/perl-dbi/package.py index e2024c71b1..1bfb8c5f94 100644 --- a/var/spack/repos/builtin/packages/perl-dbi/package.py +++ b/var/spack/repos/builtin/packages/perl-dbi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-devel-cycle/package.py b/var/spack/repos/builtin/packages/perl-devel-cycle/package.py index 6b90cfb6ae..36d47053c2 100644 --- a/var/spack/repos/builtin/packages/perl-devel-cycle/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-cycle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py b/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py index e5c76cfec8..888d592842 100644 --- a/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py b/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py index 5c8f30a268..a1d11b5d24 100644 --- a/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py b/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py index d5629f2283..2f6a7c1696 100644 --- a/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-devel-symdump/package.py b/var/spack/repos/builtin/packages/perl-devel-symdump/package.py index 9dfdc5ae98..83084c0d46 100644 --- a/var/spack/repos/builtin/packages/perl-devel-symdump/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-symdump/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,6 +10,6 @@ class PerlDevelSymdump(PerlPackage): """Devel::Symdump - dump symbol names or the symbol table""" homepage = "https://metacpan.org/pod/Devel::Symdump" - url = "https://cpan.metacpan.org/authors/id/A/AN/ANDK/Devel-Symdump-2.18.tar.gz" + url = "https://cpan.metacpan.org/authors/id/A/AN/ANDK/Devel-Symdump-2.0604.tar.gz" version('2.0604', sha256='1f9eaa557733f775ccaa852e846566274c017e6fee380aeb8d08e425cfa86d3e') diff --git a/var/spack/repos/builtin/packages/perl-digest-md5/package.py b/var/spack/repos/builtin/packages/perl-digest-md5/package.py index ee90d90556..577e223cf2 100644 --- a/var/spack/repos/builtin/packages/perl-digest-md5/package.py +++ b/var/spack/repos/builtin/packages/perl-digest-md5/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py b/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py index a1984ef6a0..7a11c4ca3b 100644 --- a/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py +++ b/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-encode-locale/package.py b/var/spack/repos/builtin/packages/perl-encode-locale/package.py index aa7b098174..225c8c7752 100644 --- a/var/spack/repos/builtin/packages/perl-encode-locale/package.py +++ b/var/spack/repos/builtin/packages/perl-encode-locale/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-error/package.py b/var/spack/repos/builtin/packages/perl-error/package.py index 0289506bc7..f274b4e78c 100644 --- a/var/spack/repos/builtin/packages/perl-error/package.py +++ b/var/spack/repos/builtin/packages/perl-error/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-eval-closure/package.py b/var/spack/repos/builtin/packages/perl-eval-closure/package.py index 3e3ce2bed2..5341d59640 100644 --- a/var/spack/repos/builtin/packages/perl-eval-closure/package.py +++ b/var/spack/repos/builtin/packages/perl-eval-closure/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-exception-class/package.py b/var/spack/repos/builtin/packages/perl-exception-class/package.py index 6df79cbc54..893c2f817a 100644 --- a/var/spack/repos/builtin/packages/perl-exception-class/package.py +++ b/var/spack/repos/builtin/packages/perl-exception-class/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py b/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py index 993544506e..f8fef2eada 100644 --- a/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py +++ b/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-extutils-config/package.py b/var/spack/repos/builtin/packages/perl-extutils-config/package.py index c6aa6140c9..65a426a239 100644 --- a/var/spack/repos/builtin/packages/perl-extutils-config/package.py +++ b/var/spack/repos/builtin/packages/perl-extutils-config/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-extutils-depends/package.py b/var/spack/repos/builtin/packages/perl-extutils-depends/package.py index 3034f2e3cb..e10e1848a3 100644 --- a/var/spack/repos/builtin/packages/perl-extutils-depends/package.py +++ b/var/spack/repos/builtin/packages/perl-extutils-depends/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-extutils-helpers/package.py b/var/spack/repos/builtin/packages/perl-extutils-helpers/package.py index fcb782d1e7..f6ba584389 100644 --- a/var/spack/repos/builtin/packages/perl-extutils-helpers/package.py +++ b/var/spack/repos/builtin/packages/perl-extutils-helpers/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-extutils-installpaths/package.py b/var/spack/repos/builtin/packages/perl-extutils-installpaths/package.py index 621a329c4b..4688f37daf 100644 --- a/var/spack/repos/builtin/packages/perl-extutils-installpaths/package.py +++ b/var/spack/repos/builtin/packages/perl-extutils-installpaths/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py b/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py index d1b40ef043..0a7668428d 100644 --- a/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py +++ b/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py b/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py index e6ce7863e8..bbe10419ce 100644 --- a/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-ffi-checklib/package.py b/var/spack/repos/builtin/packages/perl-ffi-checklib/package.py index 461259ead0..c2a83e1952 100644 --- a/var/spack/repos/builtin/packages/perl-ffi-checklib/package.py +++ b/var/spack/repos/builtin/packages/perl-ffi-checklib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-file-chdir/package.py b/var/spack/repos/builtin/packages/perl-file-chdir/package.py index b628ca12e5..d6d56f7760 100644 --- a/var/spack/repos/builtin/packages/perl-file-chdir/package.py +++ b/var/spack/repos/builtin/packages/perl-file-chdir/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,6 +18,6 @@ class PerlFileChdir(PerlPackage): combine all the power of chdir(), File::Spec and Cwd.""" homepage = "https://metacpan.org/pod/File::chdir" - url = "https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/File-chdir-0.1010.tar.gz" + url = "https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/File-chdir-0.1011.tar.gz" version('0.1011', sha256='31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79') diff --git a/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py b/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py index b7971013c9..d4f2fe9705 100644 --- a/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py +++ b/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-file-homedir/package.py b/var/spack/repos/builtin/packages/perl-file-homedir/package.py index df87fae468..08ca6a0854 100644 --- a/var/spack/repos/builtin/packages/perl-file-homedir/package.py +++ b/var/spack/repos/builtin/packages/perl-file-homedir/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-file-listing/package.py b/var/spack/repos/builtin/packages/perl-file-listing/package.py index 89eaabc0c8..f40ede5793 100644 --- a/var/spack/repos/builtin/packages/perl-file-listing/package.py +++ b/var/spack/repos/builtin/packages/perl-file-listing/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-file-pushd/package.py b/var/spack/repos/builtin/packages/perl-file-pushd/package.py index b0e8b998f3..4d6ae057e1 100644 --- a/var/spack/repos/builtin/packages/perl-file-pushd/package.py +++ b/var/spack/repos/builtin/packages/perl-file-pushd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py b/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py index 227e4a4889..89eec13d46 100644 --- a/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py +++ b/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py b/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py index 0596513ca5..881110d542 100644 --- a/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py +++ b/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-file-slurper/package.py b/var/spack/repos/builtin/packages/perl-file-slurper/package.py index b792a441ea..075ef52fe1 100644 --- a/var/spack/repos/builtin/packages/perl-file-slurper/package.py +++ b/var/spack/repos/builtin/packages/perl-file-slurper/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-file-which/package.py b/var/spack/repos/builtin/packages/perl-file-which/package.py index 4ba1404103..636e8ae3ec 100644 --- a/var/spack/repos/builtin/packages/perl-file-which/package.py +++ b/var/spack/repos/builtin/packages/perl-file-which/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-font-ttf/package.py b/var/spack/repos/builtin/packages/perl-font-ttf/package.py index 7d995027e1..20d1d374df 100644 --- a/var/spack/repos/builtin/packages/perl-font-ttf/package.py +++ b/var/spack/repos/builtin/packages/perl-font-ttf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-forks/package.py b/var/spack/repos/builtin/packages/perl-forks/package.py index 51fe7762db..b4fddbdd5e 100644 --- a/var/spack/repos/builtin/packages/perl-forks/package.py +++ b/var/spack/repos/builtin/packages/perl-forks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-gd/package.py b/var/spack/repos/builtin/packages/perl-gd/package.py index ffedf63d8c..0990c198f8 100644 --- a/var/spack/repos/builtin/packages/perl-gd/package.py +++ b/var/spack/repos/builtin/packages/perl-gd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-gdgraph-histogram/package.py b/var/spack/repos/builtin/packages/perl-gdgraph-histogram/package.py index 0ae0a50487..3c550e758c 100644 --- a/var/spack/repos/builtin/packages/perl-gdgraph-histogram/package.py +++ b/var/spack/repos/builtin/packages/perl-gdgraph-histogram/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-gd-graph/package.py b/var/spack/repos/builtin/packages/perl-gdgraph/package.py index a4c83eefc4..3897af23cc 100644 --- a/var/spack/repos/builtin/packages/perl-gd-graph/package.py +++ b/var/spack/repos/builtin/packages/perl-gdgraph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PerlGdGraph(PerlPackage): +class PerlGdgraph(PerlPackage): """Graph Plotting Module for Perl 5""" homepage = "http://search.cpan.org/~bwarfield/GDGraph/Graph.pm" @@ -16,5 +16,5 @@ class PerlGdGraph(PerlPackage): depends_on('perl-capture-tiny', type=('build', 'run')) depends_on('perl-test-exception', type=('build', 'run')) - depends_on('perl-gd-text', type=('build', 'run')) + depends_on('perl-gdtextutil', type=('build', 'run')) depends_on('perl-gd', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-gd-text/package.py b/var/spack/repos/builtin/packages/perl-gdtextutil/package.py index 1988eeaf70..4be0490125 100644 --- a/var/spack/repos/builtin/packages/perl-gd-text/package.py +++ b/var/spack/repos/builtin/packages/perl-gdtextutil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PerlGdText(PerlPackage): +class PerlGdtextutil(PerlPackage): """Text utilities for use with GD""" homepage = "http://search.cpan.org/~mverb/GDTextUtil-0.86/Text.pm" diff --git a/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py b/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py index 05559cccf5..b89ca46e9f 100644 --- a/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py +++ b/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-graph/package.py b/var/spack/repos/builtin/packages/perl-graph/package.py index 67a6c31ebf..6022a74c66 100644 --- a/var/spack/repos/builtin/packages/perl-graph/package.py +++ b/var/spack/repos/builtin/packages/perl-graph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-hash-merge/package.py b/var/spack/repos/builtin/packages/perl-hash-merge/package.py index 2290098a0c..9fbcf05055 100644 --- a/var/spack/repos/builtin/packages/perl-hash-merge/package.py +++ b/var/spack/repos/builtin/packages/perl-hash-merge/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-html-parser/package.py b/var/spack/repos/builtin/packages/perl-html-parser/package.py index 8fab2f83c6..cef4f955cf 100644 --- a/var/spack/repos/builtin/packages/perl-html-parser/package.py +++ b/var/spack/repos/builtin/packages/perl-html-parser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-html-tagset/package.py b/var/spack/repos/builtin/packages/perl-html-tagset/package.py index d7a67697cd..523a597370 100644 --- a/var/spack/repos/builtin/packages/perl-html-tagset/package.py +++ b/var/spack/repos/builtin/packages/perl-html-tagset/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-http-cookies/package.py b/var/spack/repos/builtin/packages/perl-http-cookies/package.py index fc383c709b..25e3a81d89 100644 --- a/var/spack/repos/builtin/packages/perl-http-cookies/package.py +++ b/var/spack/repos/builtin/packages/perl-http-cookies/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-http-daemon/package.py b/var/spack/repos/builtin/packages/perl-http-daemon/package.py index eac9e93f02..18ba0e506c 100644 --- a/var/spack/repos/builtin/packages/perl-http-daemon/package.py +++ b/var/spack/repos/builtin/packages/perl-http-daemon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-http-date/package.py b/var/spack/repos/builtin/packages/perl-http-date/package.py index 6f5491d257..ae330f69e5 100644 --- a/var/spack/repos/builtin/packages/perl-http-date/package.py +++ b/var/spack/repos/builtin/packages/perl-http-date/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-http-message/package.py b/var/spack/repos/builtin/packages/perl-http-message/package.py index 57b3127177..bedcb7d315 100644 --- a/var/spack/repos/builtin/packages/perl-http-message/package.py +++ b/var/spack/repos/builtin/packages/perl-http-message/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-http-negotiate/package.py b/var/spack/repos/builtin/packages/perl-http-negotiate/package.py index 6e3b7cd5a1..dbb407ac05 100644 --- a/var/spack/repos/builtin/packages/perl-http-negotiate/package.py +++ b/var/spack/repos/builtin/packages/perl-http-negotiate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-inline-c/package.py b/var/spack/repos/builtin/packages/perl-inline-c/package.py index dfcd457c6e..f41c070d28 100644 --- a/var/spack/repos/builtin/packages/perl-inline-c/package.py +++ b/var/spack/repos/builtin/packages/perl-inline-c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-inline/package.py b/var/spack/repos/builtin/packages/perl-inline/package.py index baa0d78621..001553c399 100644 --- a/var/spack/repos/builtin/packages/perl-inline/package.py +++ b/var/spack/repos/builtin/packages/perl-inline/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-io-all/package.py b/var/spack/repos/builtin/packages/perl-io-all/package.py index 6d45ed5b8a..9e55fc06e8 100644 --- a/var/spack/repos/builtin/packages/perl-io-all/package.py +++ b/var/spack/repos/builtin/packages/perl-io-all/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-io-compress/package.py b/var/spack/repos/builtin/packages/perl-io-compress/package.py index eec1245daa..b28bf0c935 100644 --- a/var/spack/repos/builtin/packages/perl-io-compress/package.py +++ b/var/spack/repos/builtin/packages/perl-io-compress/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-io-html/package.py b/var/spack/repos/builtin/packages/perl-io-html/package.py index 8809663b76..42950079dc 100644 --- a/var/spack/repos/builtin/packages/perl-io-html/package.py +++ b/var/spack/repos/builtin/packages/perl-io-html/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-io-prompt/package.py b/var/spack/repos/builtin/packages/perl-io-prompt/package.py index 2bf4144990..9947434642 100644 --- a/var/spack/repos/builtin/packages/perl-io-prompt/package.py +++ b/var/spack/repos/builtin/packages/perl-io-prompt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,5 +31,5 @@ class PerlIoPrompt(PerlPackage): depends_on('perl-module-build', type='build') - depends_on('perl-term-readkey', type=('build', 'run')) + depends_on('perl-termreadkey', type=('build', 'run')) depends_on('perl-want', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py b/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py index 215eb239da..6f94b59fd8 100644 --- a/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py +++ b/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py b/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py index 88dc0008a1..71fa915734 100644 --- a/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py +++ b/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-io-string/package.py b/var/spack/repos/builtin/packages/perl-io-string/package.py index a117b578fe..364e6eab6a 100644 --- a/var/spack/repos/builtin/packages/perl-io-string/package.py +++ b/var/spack/repos/builtin/packages/perl-io-string/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-io-stringy/package.py b/var/spack/repos/builtin/packages/perl-io-stringy/package.py index 826414418b..063c7b747b 100644 --- a/var/spack/repos/builtin/packages/perl-io-stringy/package.py +++ b/var/spack/repos/builtin/packages/perl-io-stringy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-io-tty/package.py b/var/spack/repos/builtin/packages/perl-io-tty/package.py index 217b4fb71b..1700a20c84 100644 --- a/var/spack/repos/builtin/packages/perl-io-tty/package.py +++ b/var/spack/repos/builtin/packages/perl-io-tty/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,6 @@ class PerlIoTty(PerlPackage): For a list of importable constants, see IO::Tty::Constant.""" homepage = "https://metacpan.org/pod/IO::Tty" - url = "https://cpan.metacpan.org/authors/id/T/TO/TODDR/IO-Tty-1.12.tar.gz" + url = "https://cpan.metacpan.org/authors/id/T/TO/TODDR/IO-Tty-1.13_01.tar.gz" version('1.13_01', sha256='89798eba7c31d9c169ef2f38ff49490aa769b1d9a68033de365595cfaf9cc258') diff --git a/var/spack/repos/builtin/packages/perl-ipc-run/package.py b/var/spack/repos/builtin/packages/perl-ipc-run/package.py index 228d76877f..26247138ee 100644 --- a/var/spack/repos/builtin/packages/perl-ipc-run/package.py +++ b/var/spack/repos/builtin/packages/perl-ipc-run/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-json/package.py b/var/spack/repos/builtin/packages/perl-json/package.py index a62663777a..c1dbe2634d 100644 --- a/var/spack/repos/builtin/packages/perl-json/package.py +++ b/var/spack/repos/builtin/packages/perl-json/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py index 63a36a0e65..f82663cdef 100644 --- a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,6 +16,7 @@ class PerlLibwwwPerl(PerlPackage): url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.33.tar.gz" version('6.33', sha256='97417386f11f007ae129fe155b82fd8969473ce396a971a664c8ae6850c69b99') + version('6.29', sha256='4c6f2697999d2d0e6436b584116b12b30dc39990ec0622751c1a6cec2c0e6662') depends_on('perl-encode-locale', type=('build', 'run')) depends_on('perl-file-listing', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-libxml-perl/package.py b/var/spack/repos/builtin/packages/perl-libxml-perl/package.py index 70fbfda3ab..06b598b36f 100644 --- a/var/spack/repos/builtin/packages/perl-libxml-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-libxml-perl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-list-moreutils-xs/package.py b/var/spack/repos/builtin/packages/perl-list-moreutils-xs/package.py index 0020e88313..36812e5efc 100644 --- a/var/spack/repos/builtin/packages/perl-list-moreutils-xs/package.py +++ b/var/spack/repos/builtin/packages/perl-list-moreutils-xs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-list-moreutils/package.py b/var/spack/repos/builtin/packages/perl-list-moreutils/package.py index 17ae5cce70..9e11513683 100644 --- a/var/spack/repos/builtin/packages/perl-list-moreutils/package.py +++ b/var/spack/repos/builtin/packages/perl-list-moreutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py index ef7faad32c..c63584e302 100644 --- a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py +++ b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,6 +10,6 @@ class PerlLogLog4perl(PerlPackage): """Log4j implementation for Perl""" homepage = "http://search.cpan.org/~mschilli/Log-Log4perl-1.44/lib/Log/Log4perl.pm" - url = "https://github.com/mschilli/log4perl/archive/rel_146.tar.gz" + url = "https://cpan.metacpan.org/authors/id/M/MS/MSCHILLI/Log-Log4perl-1.46.tar.gz" - version('146', sha256='a361e483095795753b97f8a506b40c24c753cf73828bb8697665499ef8596402') + version('1.46', sha256='31011a17c04e78016e73eaa4865d0481d2ffc3dc22813c61065d90ad73c64e6f') diff --git a/var/spack/repos/builtin/packages/perl-logger-simple/package.py b/var/spack/repos/builtin/packages/perl-logger-simple/package.py index c92f535cbb..4db26ae672 100644 --- a/var/spack/repos/builtin/packages/perl-logger-simple/package.py +++ b/var/spack/repos/builtin/packages/perl-logger-simple/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py b/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py index a3fa8365b8..9fc269ae5d 100644 --- a/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py +++ b/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py index 0974a00bc7..8d2da894b0 100644 --- a/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py +++ b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,4 +18,4 @@ class PerlLwpProtocolHttps(PerlPackage): depends_on('perl-io-socket-ssl', type=('build', 'run')) depends_on('perl-net-http', type=('build', 'run')) depends_on('perl-mozilla-ca', type=('build', 'run')) - depends_on('perl-lwp', type=('build', 'run')) + depends_on('perl-libwww-perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-lwp/package.py b/var/spack/repos/builtin/packages/perl-lwp/package.py deleted file mode 100644 index 4cbe00854e..0000000000 --- a/var/spack/repos/builtin/packages/perl-lwp/package.py +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class PerlLwp(PerlPackage): - """The World-Wide Web library for Perl""" - - homepage = "http://search.cpan.org/~oalders/libwww-perl-6.29/lib/LWP.pm" - url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.29.tar.gz" - - version('6.29', sha256='4c6f2697999d2d0e6436b584116b12b30dc39990ec0622751c1a6cec2c0e6662') - - depends_on('perl-test-requiresinternet', type=('build', 'run')) - depends_on('perl-http-message', type=('build', 'run')) - depends_on('perl-file-listing', type=('build', 'run')) - depends_on('perl-http-daemon', type=('build', 'run')) - depends_on('perl-html-parser', type=('build', 'run')) - depends_on('perl-http-cookies', type=('build', 'run')) - depends_on('perl-www-robotrules', type=('build', 'run')) - depends_on('perl-test-fatal', type=('build', 'run')) - depends_on('perl-http-negotiate', type=('build', 'run')) - depends_on('perl-net-http', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-mailtools/package.py b/var/spack/repos/builtin/packages/perl-mailtools/package.py index 9c4237c2e6..ae53c07582 100644 --- a/var/spack/repos/builtin/packages/perl-mailtools/package.py +++ b/var/spack/repos/builtin/packages/perl-mailtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-math-bezier/package.py b/var/spack/repos/builtin/packages/perl-math-bezier/package.py index 9d7e8ead79..d53aa00e33 100644 --- a/var/spack/repos/builtin/packages/perl-math-bezier/package.py +++ b/var/spack/repos/builtin/packages/perl-math-bezier/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-math-cdf/package.py b/var/spack/repos/builtin/packages/perl-math-cdf/package.py index d53b414955..0572e5a8cd 100644 --- a/var/spack/repos/builtin/packages/perl-math-cdf/package.py +++ b/var/spack/repos/builtin/packages/perl-math-cdf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-math-cephes/package.py b/var/spack/repos/builtin/packages/perl-math-cephes/package.py index 3550414a02..70eea6616c 100644 --- a/var/spack/repos/builtin/packages/perl-math-cephes/package.py +++ b/var/spack/repos/builtin/packages/perl-math-cephes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py b/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py index 697289b2b9..66d742daad 100644 --- a/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py +++ b/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-math-round/package.py b/var/spack/repos/builtin/packages/perl-math-round/package.py index d6898524f8..f9f94857be 100644 --- a/var/spack/repos/builtin/packages/perl-math-round/package.py +++ b/var/spack/repos/builtin/packages/perl-math-round/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-math-vecstat/package.py b/var/spack/repos/builtin/packages/perl-math-vecstat/package.py index b4588294f5..404c92b762 100644 --- a/var/spack/repos/builtin/packages/perl-math-vecstat/package.py +++ b/var/spack/repos/builtin/packages/perl-math-vecstat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-module-build-tiny/package.py b/var/spack/repos/builtin/packages/perl-module-build-tiny/package.py index ad67f5029a..8cbfbe2651 100644 --- a/var/spack/repos/builtin/packages/perl-module-build-tiny/package.py +++ b/var/spack/repos/builtin/packages/perl-module-build-tiny/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-module-build/package.py b/var/spack/repos/builtin/packages/perl-module-build/package.py index bb54259cc6..2bb7ee2014 100644 --- a/var/spack/repos/builtin/packages/perl-module-build/package.py +++ b/var/spack/repos/builtin/packages/perl-module-build/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-module-implementation/package.py b/var/spack/repos/builtin/packages/perl-module-implementation/package.py index ef802b6b11..0f7fc9d2ea 100644 --- a/var/spack/repos/builtin/packages/perl-module-implementation/package.py +++ b/var/spack/repos/builtin/packages/perl-module-implementation/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py b/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py index c86a6a641a..3ee858b6e5 100644 --- a/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py +++ b/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-module-runtime/package.py b/var/spack/repos/builtin/packages/perl-module-runtime/package.py index b7f172aa51..811fc818a5 100644 --- a/var/spack/repos/builtin/packages/perl-module-runtime/package.py +++ b/var/spack/repos/builtin/packages/perl-module-runtime/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-moose/package.py b/var/spack/repos/builtin/packages/perl-moose/package.py index 11dbe467f8..e6fe33a7a1 100644 --- a/var/spack/repos/builtin/packages/perl-moose/package.py +++ b/var/spack/repos/builtin/packages/perl-moose/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py b/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py index c5a4e0c5d6..dcb7b7fbec 100644 --- a/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py +++ b/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-mro-compat/package.py b/var/spack/repos/builtin/packages/perl-mro-compat/package.py index fa25854b43..777dda8b19 100644 --- a/var/spack/repos/builtin/packages/perl-mro-compat/package.py +++ b/var/spack/repos/builtin/packages/perl-mro-compat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-namespace-clean/package.py b/var/spack/repos/builtin/packages/perl-namespace-clean/package.py index 749313e756..8434b43622 100644 --- a/var/spack/repos/builtin/packages/perl-namespace-clean/package.py +++ b/var/spack/repos/builtin/packages/perl-namespace-clean/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-net-http/package.py b/var/spack/repos/builtin/packages/perl-net-http/package.py index 0d7667bd8a..95abf9018d 100644 --- a/var/spack/repos/builtin/packages/perl-net-http/package.py +++ b/var/spack/repos/builtin/packages/perl-net-http/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py b/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py index c1c0dc2f33..bb56e653ed 100644 --- a/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py +++ b/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-net-ssleay/package.py b/var/spack/repos/builtin/packages/perl-net-ssleay/package.py index 58f4d237f3..90d622752b 100644 --- a/var/spack/repos/builtin/packages/perl-net-ssleay/package.py +++ b/var/spack/repos/builtin/packages/perl-net-ssleay/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-number-format/package.py b/var/spack/repos/builtin/packages/perl-number-format/package.py index 4a11a132ae..9743a62d0e 100644 --- a/var/spack/repos/builtin/packages/perl-number-format/package.py +++ b/var/spack/repos/builtin/packages/perl-number-format/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-object-insideout/package.py b/var/spack/repos/builtin/packages/perl-object-insideout/package.py index 6d356daf6f..9eb1b1e216 100644 --- a/var/spack/repos/builtin/packages/perl-object-insideout/package.py +++ b/var/spack/repos/builtin/packages/perl-object-insideout/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py b/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py index 4213a1bc0f..a230fb68b0 100644 --- a/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py +++ b/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py b/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py index a607a40acc..fc4638e5f9 100644 --- a/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py +++ b/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-package-stash/package.py b/var/spack/repos/builtin/packages/perl-package-stash/package.py index 600315fc24..d5691e3166 100644 --- a/var/spack/repos/builtin/packages/perl-package-stash/package.py +++ b/var/spack/repos/builtin/packages/perl-package-stash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-padwalker/package.py b/var/spack/repos/builtin/packages/perl-padwalker/package.py index 03bb145f79..8722fcd46f 100644 --- a/var/spack/repos/builtin/packages/perl-padwalker/package.py +++ b/var/spack/repos/builtin/packages/perl-padwalker/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py b/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py index 9277b3b2f3..dd6f3e8e26 100644 --- a/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py +++ b/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-params-util/package.py b/var/spack/repos/builtin/packages/perl-params-util/package.py index 4989953449..4c21dff3f0 100644 --- a/var/spack/repos/builtin/packages/perl-params-util/package.py +++ b/var/spack/repos/builtin/packages/perl-params-util/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-params-validate/package.py b/var/spack/repos/builtin/packages/perl-params-validate/package.py index d69be62199..e23f51433a 100644 --- a/var/spack/repos/builtin/packages/perl-params-validate/package.py +++ b/var/spack/repos/builtin/packages/perl-params-validate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py b/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py index 3c5d3ae7fd..7d3668fcef 100644 --- a/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py +++ b/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-path-tiny/package.py b/var/spack/repos/builtin/packages/perl-path-tiny/package.py index e721884387..6579aa788c 100644 --- a/var/spack/repos/builtin/packages/perl-path-tiny/package.py +++ b/var/spack/repos/builtin/packages/perl-path-tiny/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-pdf-api2/package.py b/var/spack/repos/builtin/packages/perl-pdf-api2/package.py index 200d2c02e1..5f80edeb0f 100644 --- a/var/spack/repos/builtin/packages/perl-pdf-api2/package.py +++ b/var/spack/repos/builtin/packages/perl-pdf-api2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-pegex/package.py b/var/spack/repos/builtin/packages/perl-pegex/package.py index 96fb751d1c..af916be11e 100644 --- a/var/spack/repos/builtin/packages/perl-pegex/package.py +++ b/var/spack/repos/builtin/packages/perl-pegex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-perl-unsafe-signals/package.py b/var/spack/repos/builtin/packages/perl-perl-unsafe-signals/package.py index 4efa679d62..36af1d8355 100644 --- a/var/spack/repos/builtin/packages/perl-perl-unsafe-signals/package.py +++ b/var/spack/repos/builtin/packages/perl-perl-unsafe-signals/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-version/package.py b/var/spack/repos/builtin/packages/perl-perl-version/package.py index a1413c0c37..d059adea86 100644 --- a/var/spack/repos/builtin/packages/perl-version/package.py +++ b/var/spack/repos/builtin/packages/perl-perl-version/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PerlVersion(PerlPackage): +class PerlPerlVersion(PerlPackage): """Parse and manipulate Perl version strings""" homepage = "http://search.cpan.org/~bdfoy/Perl-Version-1.013/lib/Perl/Version.pm" diff --git a/var/spack/repos/builtin/packages/perl-perl4-corelibs/package.py b/var/spack/repos/builtin/packages/perl-perl4-corelibs/package.py index 46827fc761..3f721225ef 100644 --- a/var/spack/repos/builtin/packages/perl-perl4-corelibs/package.py +++ b/var/spack/repos/builtin/packages/perl-perl4-corelibs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py b/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py index 32e1fe7a91..b6b4d1f154 100644 --- a/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py +++ b/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py b/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py index e70ca30720..a25481e7e0 100644 --- a/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py +++ b/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py b/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py index 24b8bde83a..f34077aca8 100644 --- a/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py +++ b/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-readonly/package.py b/var/spack/repos/builtin/packages/perl-readonly/package.py index 876529c1c8..83c47b1af3 100644 --- a/var/spack/repos/builtin/packages/perl-readonly/package.py +++ b/var/spack/repos/builtin/packages/perl-readonly/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-regexp-common/package.py b/var/spack/repos/builtin/packages/perl-regexp-common/package.py index fb0862c5bd..4468a61eb9 100644 --- a/var/spack/repos/builtin/packages/perl-regexp-common/package.py +++ b/var/spack/repos/builtin/packages/perl-regexp-common/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-scalar-list-utils/package.py b/var/spack/repos/builtin/packages/perl-scalar-list-utils/package.py index 3a35b567e3..a7e5af124c 100644 --- a/var/spack/repos/builtin/packages/perl-scalar-list-utils/package.py +++ b/var/spack/repos/builtin/packages/perl-scalar-list-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-scalar-util-numeric/package.py b/var/spack/repos/builtin/packages/perl-scalar-util-numeric/package.py index eb4336c8d8..10047fbb8c 100644 --- a/var/spack/repos/builtin/packages/perl-scalar-util-numeric/package.py +++ b/var/spack/repos/builtin/packages/perl-scalar-util-numeric/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-intervaltree/package.py b/var/spack/repos/builtin/packages/perl-set-intervaltree/package.py index 5f875cdd6e..222895ef49 100644 --- a/var/spack/repos/builtin/packages/perl-intervaltree/package.py +++ b/var/spack/repos/builtin/packages/perl-set-intervaltree/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PerlIntervaltree(PerlPackage): +class PerlSetIntervaltree(PerlPackage): """Set::IntervalTree uses Interval Trees to store and efficiently look up ranges using a range-based lookup.""" diff --git a/var/spack/repos/builtin/packages/perl-set-intspan/package.py b/var/spack/repos/builtin/packages/perl-set-intspan/package.py index 19684dd83d..eb02324284 100644 --- a/var/spack/repos/builtin/packages/perl-set-intspan/package.py +++ b/var/spack/repos/builtin/packages/perl-set-intspan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-set-scalar/package.py b/var/spack/repos/builtin/packages/perl-set-scalar/package.py index 9ea860541e..9129381b0d 100644 --- a/var/spack/repos/builtin/packages/perl-set-scalar/package.py +++ b/var/spack/repos/builtin/packages/perl-set-scalar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-soap-lite/package.py b/var/spack/repos/builtin/packages/perl-soap-lite/package.py index 78563d69ca..0d79c0f9c1 100644 --- a/var/spack/repos/builtin/packages/perl-soap-lite/package.py +++ b/var/spack/repos/builtin/packages/perl-soap-lite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-star-fusion/package.py b/var/spack/repos/builtin/packages/perl-star-fusion/package.py index ccab3095ad..4c5a1b050d 100644 --- a/var/spack/repos/builtin/packages/perl-star-fusion/package.py +++ b/var/spack/repos/builtin/packages/perl-star-fusion/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,9 +23,9 @@ class PerlStarFusion(Package): depends_on('star', type=('build', 'run')) depends_on('perl', type=('build', 'run')) - depends_on('perl-intervaltree', type=('build', 'run')) + depends_on('perl-set-intervaltree', type=('build', 'run')) depends_on('perl-dbi', type=('build', 'run')) - depends_on('perl-dbfile', type=('build', 'run')) + depends_on('perl-db-file', type=('build', 'run')) depends_on('perl-uri', type=('build', 'run')) def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/perl-statistics-basic/package.py b/var/spack/repos/builtin/packages/perl-statistics-basic/package.py index 6c3add643a..275ea7c29d 100644 --- a/var/spack/repos/builtin/packages/perl-statistics-basic/package.py +++ b/var/spack/repos/builtin/packages/perl-statistics-basic/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py b/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py index 0860ab9e3d..a4567cb9ad 100644 --- a/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py +++ b/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-statistics-pca/package.py b/var/spack/repos/builtin/packages/perl-statistics-pca/package.py index 7e2ffea511..9fd21bc7f3 100644 --- a/var/spack/repos/builtin/packages/perl-statistics-pca/package.py +++ b/var/spack/repos/builtin/packages/perl-statistics-pca/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py b/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py index 86136fc0d8..d583c203a7 100644 --- a/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-sub-exporter/package.py b/var/spack/repos/builtin/packages/perl-sub-exporter/package.py index a9b8966efc..c500800417 100644 --- a/var/spack/repos/builtin/packages/perl-sub-exporter/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-exporter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-sub-identify/package.py b/var/spack/repos/builtin/packages/perl-sub-identify/package.py index 945ea81a06..8f7cfe8e83 100644 --- a/var/spack/repos/builtin/packages/perl-sub-identify/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-identify/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-sub-install/package.py b/var/spack/repos/builtin/packages/perl-sub-install/package.py index c6b99426d7..6b3adf0925 100644 --- a/var/spack/repos/builtin/packages/perl-sub-install/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-install/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-sub-name/package.py b/var/spack/repos/builtin/packages/perl-sub-name/package.py index 4eaeb16cbe..3d98a9d9ec 100644 --- a/var/spack/repos/builtin/packages/perl-sub-name/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-name/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py b/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py index 4c8d6ff6e4..9efb3f8515 100644 --- a/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py +++ b/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-svg/package.py b/var/spack/repos/builtin/packages/perl-svg/package.py index 290d1ef9ef..5f916455ef 100644 --- a/var/spack/repos/builtin/packages/perl-svg/package.py +++ b/var/spack/repos/builtin/packages/perl-svg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-swissknife/package.py b/var/spack/repos/builtin/packages/perl-swissknife/package.py index 91c5a6024c..dcec6f3b78 100644 --- a/var/spack/repos/builtin/packages/perl-swissknife/package.py +++ b/var/spack/repos/builtin/packages/perl-swissknife/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-sys-sigaction/package.py b/var/spack/repos/builtin/packages/perl-sys-sigaction/package.py index 50118db548..d8c50b5c46 100644 --- a/var/spack/repos/builtin/packages/perl-sys-sigaction/package.py +++ b/var/spack/repos/builtin/packages/perl-sys-sigaction/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-task-weaken/package.py b/var/spack/repos/builtin/packages/perl-task-weaken/package.py index 5c3e680f94..3ca09779a8 100644 --- a/var/spack/repos/builtin/packages/perl-task-weaken/package.py +++ b/var/spack/repos/builtin/packages/perl-task-weaken/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-term-readline-gnu/package.py b/var/spack/repos/builtin/packages/perl-term-readline-gnu/package.py new file mode 100644 index 0000000000..2db6ca8d1a --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-term-readline-gnu/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class PerlTermReadlineGnu(PerlPackage): + """Perl extension for the GNU Readline/History Library.""" + + homepage = "https://metacpan.org/pod/Term::ReadLine::Gnu" + url = "https://cpan.metacpan.org/authors/id/H/HA/HAYASHI/Term-ReadLine-Gnu-1.36.tar.gz" + + version('1.36', sha256='9a08f7a4013c9b865541c10dbba1210779eb9128b961250b746d26702bab6925') + + depends_on('readline') diff --git a/var/spack/repos/builtin/packages/perl-term-readkey/package.py b/var/spack/repos/builtin/packages/perl-termreadkey/package.py index 0e89420d33..dab402ed10 100644 --- a/var/spack/repos/builtin/packages/perl-term-readkey/package.py +++ b/var/spack/repos/builtin/packages/perl-termreadkey/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PerlTermReadkey(PerlPackage): +class PerlTermreadkey(PerlPackage): """Term::ReadKey is a compiled perl module dedicated to providing simple control over terminal driver modes (cbreak, raw, cooked, etc.,) support for non-blocking reads, if the architecture allows, and some generalized diff --git a/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py b/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py index 29aa07bbcc..84239d7d57 100644 --- a/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py +++ b/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-deep/package.py b/var/spack/repos/builtin/packages/perl-test-deep/package.py index 9d5cf6a6bf..cb8aa6f76c 100644 --- a/var/spack/repos/builtin/packages/perl-test-deep/package.py +++ b/var/spack/repos/builtin/packages/perl-test-deep/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-differences/package.py b/var/spack/repos/builtin/packages/perl-test-differences/package.py index e53aa7f406..90d3a1f21f 100644 --- a/var/spack/repos/builtin/packages/perl-test-differences/package.py +++ b/var/spack/repos/builtin/packages/perl-test-differences/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-exception/package.py b/var/spack/repos/builtin/packages/perl-test-exception/package.py index 12374856e9..fffa271abc 100644 --- a/var/spack/repos/builtin/packages/perl-test-exception/package.py +++ b/var/spack/repos/builtin/packages/perl-test-exception/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-fatal/package.py b/var/spack/repos/builtin/packages/perl-test-fatal/package.py index 9582184f0e..b2ae23ddb2 100644 --- a/var/spack/repos/builtin/packages/perl-test-fatal/package.py +++ b/var/spack/repos/builtin/packages/perl-test-fatal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py b/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py index 514bfc8fea..497e0f6932 100644 --- a/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py +++ b/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-most/package.py b/var/spack/repos/builtin/packages/perl-test-most/package.py index 609414d870..63fb0c8ea2 100644 --- a/var/spack/repos/builtin/packages/perl-test-most/package.py +++ b/var/spack/repos/builtin/packages/perl-test-most/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-needs/package.py b/var/spack/repos/builtin/packages/perl-test-needs/package.py index 5696ea096d..5ac982eae2 100644 --- a/var/spack/repos/builtin/packages/perl-test-needs/package.py +++ b/var/spack/repos/builtin/packages/perl-test-needs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-requires/package.py b/var/spack/repos/builtin/packages/perl-test-requires/package.py index 4246cdb409..ac812e33f1 100644 --- a/var/spack/repos/builtin/packages/perl-test-requires/package.py +++ b/var/spack/repos/builtin/packages/perl-test-requires/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py b/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py index d583bdc6af..1300688bff 100644 --- a/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py +++ b/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-warn/package.py b/var/spack/repos/builtin/packages/perl-test-warn/package.py index c2dc269384..0708909ba2 100644 --- a/var/spack/repos/builtin/packages/perl-test-warn/package.py +++ b/var/spack/repos/builtin/packages/perl-test-warn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-test-warnings/package.py b/var/spack/repos/builtin/packages/perl-test-warnings/package.py index 2193dc1f52..a9385eaae6 100644 --- a/var/spack/repos/builtin/packages/perl-test-warnings/package.py +++ b/var/spack/repos/builtin/packages/perl-test-warnings/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-text-csv/package.py b/var/spack/repos/builtin/packages/perl-text-csv/package.py index 9616677c83..8c86a4ccb6 100644 --- a/var/spack/repos/builtin/packages/perl-text-csv/package.py +++ b/var/spack/repos/builtin/packages/perl-text-csv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-text-diff/package.py b/var/spack/repos/builtin/packages/perl-text-diff/package.py index 5ef6589a51..54b87ec592 100644 --- a/var/spack/repos/builtin/packages/perl-text-diff/package.py +++ b/var/spack/repos/builtin/packages/perl-text-diff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-text-format/package.py b/var/spack/repos/builtin/packages/perl-text-format/package.py index 137f3cd2aa..2f38503de9 100644 --- a/var/spack/repos/builtin/packages/perl-text-format/package.py +++ b/var/spack/repos/builtin/packages/perl-text-format/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-text-simpletable/package.py b/var/spack/repos/builtin/packages/perl-text-simpletable/package.py index 444d27c0d9..b0da48547e 100644 --- a/var/spack/repos/builtin/packages/perl-text-simpletable/package.py +++ b/var/spack/repos/builtin/packages/perl-text-simpletable/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-text-soundex/package.py b/var/spack/repos/builtin/packages/perl-text-soundex/package.py index ade3ce0d6e..34c20e0f54 100644 --- a/var/spack/repos/builtin/packages/perl-text-soundex/package.py +++ b/var/spack/repos/builtin/packages/perl-text-soundex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-text-unidecode/package.py b/var/spack/repos/builtin/packages/perl-text-unidecode/package.py index ebc31b7e00..e91f502234 100644 --- a/var/spack/repos/builtin/packages/perl-text-unidecode/package.py +++ b/var/spack/repos/builtin/packages/perl-text-unidecode/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-time-hires/package.py b/var/spack/repos/builtin/packages/perl-time-hires/package.py index 0e98a78111..dd628ecbe3 100644 --- a/var/spack/repos/builtin/packages/perl-time-hires/package.py +++ b/var/spack/repos/builtin/packages/perl-time-hires/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-time-piece/package.py b/var/spack/repos/builtin/packages/perl-time-piece/package.py index fae533f4d2..ec607ecef7 100644 --- a/var/spack/repos/builtin/packages/perl-time-piece/package.py +++ b/var/spack/repos/builtin/packages/perl-time-piece/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-timedate/package.py b/var/spack/repos/builtin/packages/perl-timedate/package.py index b887ce8513..f5891903c7 100644 --- a/var/spack/repos/builtin/packages/perl-timedate/package.py +++ b/var/spack/repos/builtin/packages/perl-timedate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-try-tiny/package.py b/var/spack/repos/builtin/packages/perl-try-tiny/package.py index 67c655970f..7c21b12f77 100644 --- a/var/spack/repos/builtin/packages/perl-try-tiny/package.py +++ b/var/spack/repos/builtin/packages/perl-try-tiny/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-uri/package.py b/var/spack/repos/builtin/packages/perl-uri/package.py index d9c42fd7d9..057ff43d87 100644 --- a/var/spack/repos/builtin/packages/perl-uri/package.py +++ b/var/spack/repos/builtin/packages/perl-uri/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-want/package.py b/var/spack/repos/builtin/packages/perl-want/package.py index 4255901836..8cf43446ba 100644 --- a/var/spack/repos/builtin/packages/perl-want/package.py +++ b/var/spack/repos/builtin/packages/perl-want/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-www-robotrules/package.py b/var/spack/repos/builtin/packages/perl-www-robotrules/package.py index 720a2aa158..e1cda90585 100644 --- a/var/spack/repos/builtin/packages/perl-www-robotrules/package.py +++ b/var/spack/repos/builtin/packages/perl-www-robotrules/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-dom-xpath/package.py b/var/spack/repos/builtin/packages/perl-xml-dom-xpath/package.py index 0227d4e509..36408595df 100644 --- a/var/spack/repos/builtin/packages/perl-xml-dom-xpath/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-dom-xpath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-dom/package.py b/var/spack/repos/builtin/packages/perl-xml-dom/package.py index e0c3d97d11..3eeec70b70 100644 --- a/var/spack/repos/builtin/packages/perl-xml-dom/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-dom/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-filter-buffertext/package.py b/var/spack/repos/builtin/packages/perl-xml-filter-buffertext/package.py index 59950576f0..28e9035034 100644 --- a/var/spack/repos/builtin/packages/perl-xml-filter-buffertext/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-filter-buffertext/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-libxml/package.py b/var/spack/repos/builtin/packages/perl-xml-libxml/package.py index bc6d4f4c05..3a4a21727c 100644 --- a/var/spack/repos/builtin/packages/perl-xml-libxml/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-libxml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-libxslt/package.py b/var/spack/repos/builtin/packages/perl-xml-libxslt/package.py new file mode 100644 index 0000000000..86312928e1 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-xml-libxslt/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class PerlXmlLibxslt(PerlPackage): + """Interface to the GNOME libxslt library.""" + + homepage = "https://metacpan.org/pod/XML::LibXSLT" + url = "https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/XML-LibXSLT-1.96.tar.gz" + + version('1.96', sha256='2a5e374edaa2e9f9d26b432265bfea9b4bb7a94c9fbfef9047b298fce844d473') + + depends_on('libxslt') + depends_on('perl-xml-libxml') diff --git a/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py b/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py index cb7e58bcd1..91f50a70d5 100644 --- a/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,6 @@ class PerlXmlNamespacesupport(PerlPackage): prefix to namespace URI map, and provides a number of basic checks.""" homepage = "https://metacpan.org/pod/XML::NamespaceSupport" - url = "https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-NamespaceSupport-1.12.tar.gz" + url = "https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-NamespaceSupport-1.12_9.tar.gz" version('1.12_9', sha256='2e84a057f0a8c845a612d212742cb94fca4fc8a433150b5721bd448f77d1e4a9') diff --git a/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py b/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py index 57b4406be7..6ba82d6eb9 100644 --- a/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-parser/package.py b/var/spack/repos/builtin/packages/perl-xml-parser/package.py index 9730132af0..5f4aafa3fd 100644 --- a/var/spack/repos/builtin/packages/perl-xml-parser/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-parser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-quote/package.py b/var/spack/repos/builtin/packages/perl-xml-quote/package.py index 2c6702225e..d08e170109 100644 --- a/var/spack/repos/builtin/packages/perl-xml-quote/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-quote/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-regexp/package.py b/var/spack/repos/builtin/packages/perl-xml-regexp/package.py index 30ecb45a67..1a7ad14196 100644 --- a/var/spack/repos/builtin/packages/perl-xml-regexp/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-regexp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-sax-base/package.py b/var/spack/repos/builtin/packages/perl-xml-sax-base/package.py index b9943e6d0d..3fa83dff5c 100644 --- a/var/spack/repos/builtin/packages/perl-xml-sax-base/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-sax-base/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-sax-writer/package.py b/var/spack/repos/builtin/packages/perl-xml-sax-writer/package.py index 6de6611f09..ce276ea045 100644 --- a/var/spack/repos/builtin/packages/perl-xml-sax-writer/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-sax-writer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-sax/package.py b/var/spack/repos/builtin/packages/perl-xml-sax/package.py index 78138fca65..87646a73c1 100644 --- a/var/spack/repos/builtin/packages/perl-xml-sax/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-sax/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-simple/package.py b/var/spack/repos/builtin/packages/perl-xml-simple/package.py index 709fde6b3e..eb7d89b92c 100644 --- a/var/spack/repos/builtin/packages/perl-xml-simple/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-simple/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-twig/package.py b/var/spack/repos/builtin/packages/perl-xml-twig/package.py index e2c81fef04..f17251ea63 100644 --- a/var/spack/repos/builtin/packages/perl-xml-twig/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-twig/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-writer/package.py b/var/spack/repos/builtin/packages/perl-xml-writer/package.py index 29c39ca8f2..da5fdf7f6f 100644 --- a/var/spack/repos/builtin/packages/perl-xml-writer/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-writer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-xml-xpathengine/package.py b/var/spack/repos/builtin/packages/perl-xml-xpathengine/package.py index 241d806d6c..cf514e9b52 100644 --- a/var/spack/repos/builtin/packages/perl-xml-xpathengine/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-xpathengine/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py b/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py index b5df47fb81..2e141c982b 100644 --- a/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py +++ b/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl-yaml/package.py b/var/spack/repos/builtin/packages/perl-yaml/package.py index fdf1a2d05e..7d55b590ef 100644 --- a/var/spack/repos/builtin/packages/perl-yaml/package.py +++ b/var/spack/repos/builtin/packages/perl-yaml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py index 5df5692895..847bf83765 100644 --- a/var/spack/repos/builtin/packages/perl/package.py +++ b/var/spack/repos/builtin/packages/perl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,10 +31,12 @@ class Perl(Package): # Perl doesn't use Autotools, it should subclass Package # explanation of version numbering scheme # Development releases (odd numbers) + version('5.31.7', sha256='d05c4e72128f95ef6ffad42728ecbbd0d9437290bf0f88268b51af011f26b57d') version('5.31.4', sha256='418a7e6fe6485cc713a86d1227ef112f0bb3f80322e3b715ffe42851d97804a5') # Maintenance releases (even numbers, recommended) - version('5.30.0', sha256='851213c754d98ccff042caa40ba7a796b2cee88c5325f121be5cbb61bbf975f2', preferred=True) + version('5.30.1', sha256='bf3d25571ff1ee94186177c2cdef87867fd6a14aa5a84f0b1fb7bf798f42f964', preferred=True) + version('5.30.0', sha256='851213c754d98ccff042caa40ba7a796b2cee88c5325f121be5cbb61bbf975f2') # End of life releases version('5.28.0', sha256='7e929f64d4cb0e9d1159d4a59fc89394e27fa1f7004d0836ca0d514685406ea8') @@ -137,6 +139,9 @@ class Perl(Package): # Perl doesn't use Autotools, it should subclass Package if '+threads' in spec: config_args.append('-Dusethreads') + if spec.satisfies('@5.31'): + config_args.append('-Dusedevel') + return config_args def configure(self, spec, prefix): @@ -165,43 +170,24 @@ class Perl(Package): # Perl doesn't use Autotools, it should subclass Package make() make('install') - def setup_dependent_build_environment(self, env, dependent_spec): + def _setup_dependent_env(self, env, dependent_spec, deptypes): """Set PATH and PERL5LIB to include the extension and any other perl extensions it depends on, assuming they were installed with INSTALL_BASE defined.""" - perl_lib_dirs = [join_path(self.spec.prefix.lib, - str(self.spec.version))] - perl_bin_dirs = [self.spec.prefix.bin] - for d in dependent_spec.traverse( - deptype=('build', 'run'), deptype_query='run'): + perl_lib_dirs = [] + for d in dependent_spec.traverse(deptype=deptypes): if d.package.extends(self.spec): perl_lib_dirs.append(d.prefix.lib.perl5) - perl_bin_dirs.append(d.prefix.bin) - if perl_bin_dirs: - perl_bin_path = ':'.join(perl_bin_dirs) - env.prepend_path('PATH', perl_bin_path) if perl_lib_dirs: perl_lib_path = ':'.join(perl_lib_dirs) env.prepend_path('PERL5LIB', perl_lib_path) + def setup_dependent_build_environment(self, env, dependent_spec): + self._setup_dependent_env(env, dependent_spec, + deptypes=('build', 'run')) + def setup_dependent_run_environment(self, env, dependent_spec): - """Set PATH and PERL5LIB to include the extension and - any other perl extensions it depends on, - assuming they were installed with INSTALL_BASE defined.""" - perl_lib_dirs = [join_path(self.spec.prefix.lib, - str(self.spec.version))] - perl_bin_dirs = [self.spec.prefix.bin] - for d in dependent_spec.traverse( - deptype=('run',), deptype_query='run'): - if d.package.extends(self.spec): - perl_lib_dirs.append(d.prefix.lib.perl5) - perl_bin_dirs.append(d.prefix.bin) - if perl_bin_dirs: - perl_bin_path = ':'.join(perl_bin_dirs) - env.prepend_path('PATH', perl_bin_path) - if perl_lib_dirs: - perl_lib_path = ':'.join(perl_lib_dirs) - env.prepend_path('PERL5LIB', perl_lib_path) + self._setup_dependent_env(env, dependent_spec, deptypes=('run',)) def setup_dependent_package(self, module, dependent_spec): """Called before perl modules' install() methods. @@ -309,3 +295,21 @@ class Perl(Package): # Perl doesn't use Autotools, it should subclass Package # Make deactivate idempotent if ext_pkg.name in exts: del exts[ext_pkg.name] + + @property + def command(self): + """Returns the Perl command, which may vary depending on the version + of Perl. In general, Perl comes with a ``perl`` command. However, + development releases have a ``perlX.Y.Z`` command. + + Returns: + Executable: the Perl command + """ + for ver in ('', self.spec.version): + path = os.path.join(self.prefix.bin, '{0}{1}'.format( + self.spec.name, ver)) + if os.path.exists(path): + return Executable(path) + else: + msg = 'Unable to locate {0} command in {1}' + raise RuntimeError(msg.format(self.spec.name, self.prefix.bin)) diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index e436ffd02f..88332caec9 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,6 +24,8 @@ class Petsc(Package): version('develop', branch='master') version('xsdk-0.2.0', tag='xsdk-0.2.0') + version('3.12.3', sha256='91f77d7b0f54056f085b9e27938922db3d9bb1734a2e2a6d26f43d3e6c0cf631') + version('3.12.2', sha256='d874b2e198c4cb73551c2eca1d2c5d27da710be4d00517adb8f9eb3d6d0375e8') version('3.12.1', sha256='b72d895d0f4a79acb13ebc782b47b26d10d4e5706d399f533afcd5b3dba13737') version('3.12.0', sha256='ba9ecf69783c7ebf05bd1c91dd1d4b38bf09b7a2d5f9a774aa6bb46deff7cb14') version('3.11.4', sha256='319cb5a875a692a67fe5b1b90009ba8f182e21921ae645d38106544aff20c3c1') diff --git a/var/spack/repos/builtin/packages/pexsi/package.py b/var/spack/repos/builtin/packages/pexsi/package.py index 12cbbcdb61..cfb188ab7c 100644 --- a/var/spack/repos/builtin/packages/pexsi/package.py +++ b/var/spack/repos/builtin/packages/pexsi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pfft/package.py b/var/spack/repos/builtin/packages/pfft/package.py index 61a14682cf..c682ee63ce 100644 --- a/var/spack/repos/builtin/packages/pfft/package.py +++ b/var/spack/repos/builtin/packages/pfft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pflotran/package.py b/var/spack/repos/builtin/packages/pflotran/package.py index bd772b741f..72a41d3f2d 100644 --- a/var/spack/repos/builtin/packages/pflotran/package.py +++ b/var/spack/repos/builtin/packages/pflotran/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,6 +18,7 @@ class Pflotran(AutotoolsPackage): maintainers = ['ghammond86', 'balay'] version('develop') + version('xsdk-0.5.0', commit='98a959c591b72f73373febf5f9735d2c523b4c20') version('xsdk-0.4.0', commit='c851cbc94fc56a32cfdb0678f3c24b9936a5584e') version('xsdk-0.3.0', branch='release/xsdk-0.3.0') version('xsdk-0.2.0', commit='4da763c6136df57caff43f98c926433958cfdea6') @@ -25,11 +26,11 @@ class Pflotran(AutotoolsPackage): depends_on('mpi') depends_on('hdf5@1.8.12:+mpi+fortran') depends_on('petsc@develop:+hdf5+metis', when='@develop') + depends_on('petsc@3.12:+hdf5+metis', when='@xsdk-0.5.0') depends_on('petsc@3.10:+hdf5+metis', when='@xsdk-0.4.0') depends_on('petsc@xsdk-0.2.0+hdf5+metis', when='@xsdk-0.2.0') depends_on('petsc@3.8.0:+hdf5+metis', when='@xsdk-0.3.0') @property def parallel(self): - return (self.spec.satisfies('@develop') or - self.spec.satisfies('@xsdk-0.4.0')) + return (self.spec.satisfies('@xsdk-0.4.0:')) diff --git a/var/spack/repos/builtin/packages/pfunit/package.py b/var/spack/repos/builtin/packages/pfunit/package.py index 418701241b..30704ac62e 100644 --- a/var/spack/repos/builtin/packages/pfunit/package.py +++ b/var/spack/repos/builtin/packages/pfunit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -82,12 +82,14 @@ class Pfunit(CMakePackage): return value raise InstallError('Unsupported compiler.') - def setup_environment(self, spack_env, run_env): - spack_env.set('PFUNIT', self.spec.prefix) - run_env.set('PFUNIT', self.spec.prefix) - spack_env.set('F90_VENDOR', self.compiler_vendor()) - run_env.set('F90_VENDOR', self.compiler_vendor()) + def setup_build_environment(self, env): + env.set('PFUNIT', self.spec.prefix) + env.set('F90_VENDOR', self.compiler_vendor()) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('PFUNIT', self.spec.prefix) - spack_env.set('F90_VENDOR', self.compiler_vendor()) + def setup_run_environment(self, env): + env.set('PFUNIT', self.spec.prefix) + env.set('F90_VENDOR', self.compiler_vendor()) + + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('PFUNIT', self.spec.prefix) + env.set('F90_VENDOR', self.compiler_vendor()) diff --git a/var/spack/repos/builtin/packages/pgdspider/package.py b/var/spack/repos/builtin/packages/pgdspider/package.py index e8bb15987b..3c6f7ab1f3 100644 --- a/var/spack/repos/builtin/packages/pgdspider/package.py +++ b/var/spack/repos/builtin/packages/pgdspider/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py index c61611e22f..783bf75faa 100644 --- a/var/spack/repos/builtin/packages/pgi/package.py +++ b/var/spack/repos/builtin/packages/pgi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -87,16 +87,10 @@ class Pgi(Package): # Run install script os.system("./install") - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): prefix = Prefix(join_path(self.prefix, 'linux86-64', self.version)) - run_env.set('CC', join_path(prefix.bin, 'pgcc')) - run_env.set('CXX', join_path(prefix.bin, 'pgc++')) - run_env.set('F77', join_path(prefix.bin, 'pgfortran')) - run_env.set('FC', join_path(prefix.bin, 'pgfortran')) - - run_env.prepend_path('PATH', prefix.bin) - run_env.prepend_path('CPATH', prefix.include) - run_env.prepend_path('LIBRARY_PATH', prefix.lib) - run_env.prepend_path('LD_LIBRARY_PATH', prefix.lib) - run_env.prepend_path('MANPATH', prefix.man) + env.set('CC', join_path(prefix.bin, 'pgcc')) + env.set('CXX', join_path(prefix.bin, 'pgc++')) + env.set('F77', join_path(prefix.bin, 'pgfortran')) + env.set('FC', join_path(prefix.bin, 'pgfortran')) diff --git a/var/spack/repos/builtin/packages/pgmath/libpgmath_symbols.patch b/var/spack/repos/builtin/packages/pgmath/libpgmath_symbols.patch new file mode 100644 index 0000000000..65b7d40bea --- /dev/null +++ b/var/spack/repos/builtin/packages/pgmath/libpgmath_symbols.patch @@ -0,0 +1,91 @@ +diff --git a/runtime/libpgmath/lib/common/ceil.c b/runtime/libpgmath/lib/common/ceil.c +index 3b66ca5c..341c5194 100644 +--- a/runtime/libpgmath/lib/common/ceil.c ++++ b/runtime/libpgmath/lib/common/ceil.c +@@ -16,9 +16,11 @@ + */ + + #include "mthdecls.h" ++/* + #if defined(__SSE4_1__) || defined(__AVX__) + #include <immintrin.h> + #endif ++*/ + + float + __mth_i_ceil(float x) +diff --git a/runtime/libpgmath/lib/common/dceil.c b/runtime/libpgmath/lib/common/dceil.c +index 67482ef2..5dae82f9 100644 +--- a/runtime/libpgmath/lib/common/dceil.c ++++ b/runtime/libpgmath/lib/common/dceil.c +@@ -16,6 +16,7 @@ + */ + + #include "mthdecls.h" ++/* + #if defined(__SSE4_1__) || defined(__AVX__) + #include <immintrin.h> + #endif +@@ -33,9 +34,12 @@ __mth_i_dceil_sse(double x) + return _mm_cvtsd_f64(_mm_ceil_sd(_mm_set1_pd(x), _mm_set1_pd(x))); + } + #else ++*/ + double + __mth_i_dceil(double x) + { + return ceil(x); + } ++/* + #endif ++*/ +diff --git a/runtime/libpgmath/lib/common/dfloor.c b/runtime/libpgmath/lib/common/dfloor.c +index f947ef33..8b955897 100644 +--- a/runtime/libpgmath/lib/common/dfloor.c ++++ b/runtime/libpgmath/lib/common/dfloor.c +@@ -16,6 +16,7 @@ + */ + + #include "mthdecls.h" ++/* + #if defined(__SSE4_1__) || defined(__AVX__) + #include <immintrin.h> + #endif +@@ -33,9 +34,12 @@ __mth_i_dfloor_sse(double x) + return _mm_cvtsd_f64(_mm_floor_sd(_mm_set1_pd(x), _mm_set1_pd(x))); + } + #else ++*/ + double + __mth_i_dfloor(double x) + { + return floor(x); + } ++/* + #endif ++*/ +diff --git a/runtime/libpgmath/lib/common/floor.c b/runtime/libpgmath/lib/common/floor.c +index 7865bedc..c13872df 100644 +--- a/runtime/libpgmath/lib/common/floor.c ++++ b/runtime/libpgmath/lib/common/floor.c +@@ -16,6 +16,7 @@ + */ + + #include "mthdecls.h" ++/* + #if defined(__SSE4_1__) || defined(__AVX__) + #include <immintrin.h> + #endif +@@ -33,9 +34,12 @@ __mth_i_floor_sse(float x) + return _mm_cvtss_f32(_mm_floor_ss(_mm_set1_ps(x), _mm_set1_ps(x))); + } + #else ++*/ + float + __mth_i_floor(float x) + { + return floorf(x); + } ++/* + #endif ++*/ diff --git a/var/spack/repos/builtin/packages/pgmath/package.py b/var/spack/repos/builtin/packages/pgmath/package.py index bd554890a0..bd08ba8b40 100644 --- a/var/spack/repos/builtin/packages/pgmath/package.py +++ b/var/spack/repos/builtin/packages/pgmath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,13 +11,27 @@ class Pgmath(CMakePackage): """Flang's math library""" homepage = "https://github.com/flang-compiler/flang" - url = "https://github.com/flang-compiler/flang/archive/flang_20180612.tar.gz" + url = "https://github.com/flang-compiler/flang/archive/flang_20190329.tar.gz" git = "https://github.com/flang-compiler/flang.git" - version('develop', branch='master') + maintainers = ['naromero77'] + + version('master', branch='master') + version('20190329', sha256='b8c621da53829f8c53bad73125556fb1839c9056d713433b05741f7e445199f2') + version('20181226', sha256='00e716bea258c3bb60d6a5bb0c82bc79f67000062dc89939693e75f501883c36') version('20180921', sha256='f33bd1f054e474f1e8a204bb6f78d42f8f6ecf7a894fdddc3999f7c272350784') version('20180612', sha256='6af858bea013548e091371a97726ac784edbd4ff876222575eaae48a3c2920ed') + # work around for this issue + # https://github.com/flang-compiler/flang/issues/602 + patch('https://github.com/flang-compiler/flang/commit/7fcd6346a9427977afe4534c0f19bbbba04c99a3.diff', + sha256='4014df1e5855dd21242b0fc938a4e7835941c20f9a89c3a7a5314e74b6232bcb', + when='@20190329') + + # workaround for this issue + # https://github.com/flang-compiler/flang/issues/838 + patch('libpgmath_symbols.patch', when='@20190329,master') + depends_on("awk", type="build") conflicts("%gcc@:7.1.9999") diff --git a/var/spack/repos/builtin/packages/phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py index 8811cc3491..317d0e753d 100644 --- a/var/spack/repos/builtin/packages/phantompeakqualtools/package.py +++ b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/phast/package.py b/var/spack/repos/builtin/packages/phast/package.py index 1d98d353ca..7f787eb023 100644 --- a/var/spack/repos/builtin/packages/phast/package.py +++ b/var/spack/repos/builtin/packages/phast/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/phasta/package.py b/var/spack/repos/builtin/packages/phasta/package.py index 2dfb565499..6040d3f875 100644 --- a/var/spack/repos/builtin/packages/phasta/package.py +++ b/var/spack/repos/builtin/packages/phasta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/phist/package.py b/var/spack/repos/builtin/packages/phist/package.py index 344a091113..42ad816dfa 100644 --- a/var/spack/repos/builtin/packages/phist/package.py +++ b/var/spack/repos/builtin/packages/phist/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/phrap-crossmatch-swat/package.py b/var/spack/repos/builtin/packages/phrap-crossmatch-swat/package.py index ec58b57cb6..7cc86e5c7a 100644 --- a/var/spack/repos/builtin/packages/phrap-crossmatch-swat/package.py +++ b/var/spack/repos/builtin/packages/phrap-crossmatch-swat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/phred/package.py b/var/spack/repos/builtin/packages/phred/package.py index 9744305f47..cdfc8a41b3 100644 --- a/var/spack/repos/builtin/packages/phred/package.py +++ b/var/spack/repos/builtin/packages/phred/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/phylip/package.py b/var/spack/repos/builtin/packages/phylip/package.py index 9233b98b7a..8eefcbe512 100644 --- a/var/spack/repos/builtin/packages/phylip/package.py +++ b/var/spack/repos/builtin/packages/phylip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/phyluce/package.py b/var/spack/repos/builtin/packages/phyluce/package.py index 3cbf553957..2d6942b383 100644 --- a/var/spack/repos/builtin/packages/phyluce/package.py +++ b/var/spack/repos/builtin/packages/phyluce/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/picard/package.py b/var/spack/repos/builtin/packages/picard/package.py index d7fdbdb3f2..b8c0ac199d 100644 --- a/var/spack/repos/builtin/packages/picard/package.py +++ b/var/spack/repos/builtin/packages/picard/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -63,10 +63,9 @@ class Picard(Package): filter_file('picard.jar', join_path(prefix.bin, 'picard.jar'), script, **kwargs) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """The Picard docs suggest setting this as a convenience.""" - run_env.prepend_path('PICARD', - join_path(self.prefix, 'bin', 'picard.jar')) + env.prepend_path('PICARD', join_path(self.prefix.bin, 'picard.jar')) def url_for_version(self, version): if version < Version('2.6.0'): diff --git a/var/spack/repos/builtin/packages/picsar/package.py b/var/spack/repos/builtin/packages/picsar/package.py index 0f876d0679..fc5335a91b 100644 --- a/var/spack/repos/builtin/packages/picsar/package.py +++ b/var/spack/repos/builtin/packages/picsar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/picsarlite/package.py b/var/spack/repos/builtin/packages/picsarlite/package.py index a144fac0d8..5c752e9345 100644 --- a/var/spack/repos/builtin/packages/picsarlite/package.py +++ b/var/spack/repos/builtin/packages/picsarlite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pidx/package.py b/var/spack/repos/builtin/packages/pidx/package.py index 5f9e912050..2f51f09301 100644 --- a/var/spack/repos/builtin/packages/pidx/package.py +++ b/var/spack/repos/builtin/packages/pidx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pig/package.py b/var/spack/repos/builtin/packages/pig/package.py new file mode 100644 index 0000000000..1a4e37b357 --- /dev/null +++ b/var/spack/repos/builtin/packages/pig/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Pig(Package): + """ + Pig is a dataflow programming environment for processing very large files. + Pig's language is called Pig Latin. A Pig Latin program consists of a + directed acyclic graph where each node represents an operation that + transforms data. + """ + + homepage = "http://archive.apache.org" + url = "http://archive.apache.org/dist/hadoop/pig/stable/pig-0.7.0.tar.gz" + + version('0.7.0', sha256='fa7211fb339f547f679a3dd90055f1ddc45d5754d88463e4cc39c380ddf8b02a') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/pigz/package.py b/var/spack/repos/builtin/packages/pigz/package.py index fdcf42e8a7..c54a518993 100644 --- a/var/spack/repos/builtin/packages/pigz/package.py +++ b/var/spack/repos/builtin/packages/pigz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pilon/package.py b/var/spack/repos/builtin/packages/pilon/package.py index e6e416e18b..75600c5854 100644 --- a/var/spack/repos/builtin/packages/pilon/package.py +++ b/var/spack/repos/builtin/packages/pilon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pindel/package.py b/var/spack/repos/builtin/packages/pindel/package.py index b99920b0ea..ef7052b06f 100644 --- a/var/spack/repos/builtin/packages/pindel/package.py +++ b/var/spack/repos/builtin/packages/pindel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pipework/package.py b/var/spack/repos/builtin/packages/pipework/package.py new file mode 100644 index 0000000000..ad92723f64 --- /dev/null +++ b/var/spack/repos/builtin/packages/pipework/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Pipework(Package): + """ + Pipework lets you connect together containers in arbitrarily complex + scenarios. + """ + + homepage = "https://github.com/jpetazzo/pipework" + git = "https://github.com/jpetazzo/pipework.git" + + version('master', branch='master') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/piranha/package.py b/var/spack/repos/builtin/packages/piranha/package.py index c045e994de..c8681c1607 100644 --- a/var/spack/repos/builtin/packages/piranha/package.py +++ b/var/spack/repos/builtin/packages/piranha/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pism/package.py b/var/spack/repos/builtin/packages/pism/package.py index 10bc658dff..e25fab43c6 100644 --- a/var/spack/repos/builtin/packages/pism/package.py +++ b/var/spack/repos/builtin/packages/pism/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class Pism(CMakePackage): """Parallel Ice Sheet Model""" homepage = "http://pism-docs.org/wiki/doku.php:=" - url = "https://github.com/pism/pism/archive/v0.7.3.tar.gz" + url = "https://github.com/pism/pism/archive/v1.1.4.tar.gz" git = "https://github.com/pism/pism.git" maintainers = ['citibeth'] @@ -73,9 +73,9 @@ class Pism(CMakePackage): depends_on('fftw') depends_on('gsl') depends_on('mpi') - depends_on('netcdf') # Only the C interface is used, no netcdf-cxx4 + depends_on('netcdf-c') # Only the C interface is used, no netcdf-cxx4 depends_on('petsc') - depends_on('udunits2') + depends_on('udunits') depends_on('proj@:4') depends_on('everytrace', when='+everytrace') @@ -116,7 +116,7 @@ class Pism(CMakePackage): '-DPism_USE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO')] - def setup_environment(self, spack_env, env): + def setup_run_environment(self, env): env.set('PISM_PREFIX', self.prefix) env.set('PISM_BIN', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/pixman/package.py b/var/spack/repos/builtin/packages/pixman/package.py index 5cbc9b9498..eef9b116ca 100644 --- a/var/spack/repos/builtin/packages/pixman/package.py +++ b/var/spack/repos/builtin/packages/pixman/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pixz/package.py b/var/spack/repos/builtin/packages/pixz/package.py index 223c025790..5fad0583bb 100644 --- a/var/spack/repos/builtin/packages/pixz/package.py +++ b/var/spack/repos/builtin/packages/pixz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pkg-config/package.py b/var/spack/repos/builtin/packages/pkg-config/package.py index 5a68b5ab4a..bdbf1b5d3d 100644 --- a/var/spack/repos/builtin/packages/pkg-config/package.py +++ b/var/spack/repos/builtin/packages/pkg-config/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,10 +27,9 @@ class PkgConfig(AutotoolsPackage): parallel = False - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Adds the ACLOCAL path for autotools.""" - spack_env.append_path('ACLOCAL_PATH', - join_path(self.prefix.share, 'aclocal')) + env.append_path('ACLOCAL_PATH', self.prefix.share.aclocal) def configure_args(self): config_args = ['--enable-shared'] diff --git a/var/spack/repos/builtin/packages/pkgconf/package.py b/var/spack/repos/builtin/packages/pkgconf/package.py index 36b78c0713..06fcefcc6c 100644 --- a/var/spack/repos/builtin/packages/pkgconf/package.py +++ b/var/spack/repos/builtin/packages/pkgconf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,10 +30,9 @@ class Pkgconf(AutotoolsPackage): # TODO: Add a package for the kyua testing framework # depends_on('kyua', type='test') - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Adds the ACLOCAL path for autotools.""" - spack_env.append_path('ACLOCAL_PATH', - join_path(self.prefix.share, 'aclocal')) + env.append_path('ACLOCAL_PATH', self.prefix.share.aclocal) @run_after('install') def link_pkg_config(self): diff --git a/var/spack/repos/builtin/packages/pktools/package.py b/var/spack/repos/builtin/packages/pktools/package.py index db60c3ddc8..ae26bba54a 100644 --- a/var/spack/repos/builtin/packages/pktools/package.py +++ b/var/spack/repos/builtin/packages/pktools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/planck-likelihood/package.py b/var/spack/repos/builtin/packages/planck-likelihood/package.py index 70ab82de2e..7277ce5298 100644 --- a/var/spack/repos/builtin/packages/planck-likelihood/package.py +++ b/var/spack/repos/builtin/packages/planck-likelihood/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -107,17 +107,15 @@ class PlanckLikelihood(Package): for dir in dirs: install_tree(dir, join_path(prefix, 'share', 'clik', dir)) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - prefix = self.prefix - spack_env.set('CLIK_PATH', prefix) - spack_env.set('CLIK_DATA', join_path(prefix, 'share', 'clik')) - spack_env.set('CLIK_PLUGIN', 'rel2015') + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('CLIK_PATH', self.prefix) + env.set('CLIK_DATA', self.prefix.share.clik) + env.set('CLIK_PLUGIN', 'rel2015') - def setup_environment(self, spack_env, run_env): - prefix = self.prefix - run_env.set('CLIK_PATH', prefix) - run_env.set('CLIK_DATA', join_path(prefix, 'share', 'clik')) - run_env.set('CLIK_PLUGIN', 'rel2015') + def setup_run_environment(self, env): + env.set('CLIK_PATH', self.prefix) + env.set('CLIK_DATA', self.prefix.share.clik) + env.set('CLIK_PLUGIN', 'rel2015') @run_after('install') @on_package_attributes(run_tests=True) diff --git a/var/spack/repos/builtin/packages/plasma/package.py b/var/spack/repos/builtin/packages/plasma/package.py index d0def35fcc..bf4d8c68ee 100644 --- a/var/spack/repos/builtin/packages/plasma/package.py +++ b/var/spack/repos/builtin/packages/plasma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/platypus/package.py b/var/spack/repos/builtin/packages/platypus/package.py index ba09c53869..841464d5ec 100644 --- a/var/spack/repos/builtin/packages/platypus/package.py +++ b/var/spack/repos/builtin/packages/platypus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/plink/package.py b/var/spack/repos/builtin/packages/plink/package.py index 3a5096d93d..83bc26409a 100644 --- a/var/spack/repos/builtin/packages/plink/package.py +++ b/var/spack/repos/builtin/packages/plink/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/plplot/package.py b/var/spack/repos/builtin/packages/plplot/package.py index bfbbf73895..d080606965 100644 --- a/var/spack/repos/builtin/packages/plplot/package.py +++ b/var/spack/repos/builtin/packages/plplot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,8 @@ class Plplot(CMakePackage): homepage = "http://plplot.sourceforge.net/" url = "https://sourceforge.net/projects/plplot/files/plplot/5.13.0%20Source/plplot-5.13.0.tar.gz/download" + version('5.15.0', sha256='b92de4d8f626a9b20c84fc94f4f6a9976edd76e33fb1eae44f6804bdcc628c7b') + version('5.14.0', sha256='331009037c9cad9fcefacd7dbe9c7cfae25e766f5590f9efd739a294c649df97') version('5.13.0', sha256='ec36bbee8b03d9d1c98f8fd88f7dc3415560e559b53eb1aa991c2dcf61b25d2b') version('5.12.0', sha256='8dc5da5ef80e4e19993d4c3ef2a84a24cc0e44a5dade83201fca7160a6d352ce') version('5.11.0', sha256='bfa8434e6e1e7139a5651203ec1256c8581e2fac3122f907f7d8d25ed3bd5f7e') diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index 8acc721cff..c8b1f8e9b9 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,9 +21,16 @@ class Plumed(AutotoolsPackage): and C/C++ codes. """ homepage = 'http://www.plumed.org/' - url = 'https://github.com/plumed/plumed2/archive/v2.5.0.tar.gz' - + url = 'https://github.com/plumed/plumed2/archive/v2.5.3.tar.gz' + git = 'https://github.com/plumed/plumed2.git' + + version('master', branch='master') + version('2.6b', sha256='3ecda9d46967c8ddd08e820aed974794d926cffb78b262f9d42cdbece3b15677') + version('2.5.3', preferred=True, sha256='543288be667dc4201fc461ecd2dd4878ddfbeac682d0c021c99ea8e501c7c9dc') + version('2.5.2', sha256='85d10cc46e2e37c7719cf51c0931278f56c2c8f8a9d86188b2bf97c2535a2ab4') + version('2.5.1', sha256='de309980dcfd6f6e0e70e138856f4bd9eb4d8a513906a5e6389f18a5af7f2eba') version('2.5.0', sha256='53e08187ec9f8af2326fa84407e34644a7c51d2af93034309fb70675eee5e4f7') + version('2.4.6', sha256='c22ad19f5cd36ce9fe4ba0b53158fc2a3d985c48fc04606e3f3b3e835b994cb3') version('2.4.4', sha256='1e5c24109314481fad404da97d61c7339b219e27e120c9c80bacc79c9f6a51a8') version('2.4.2', sha256='528ce57f1f5330480bcd403140166a4580efd2acaea39c85dfeca5e2cd649321') version('2.4.1', sha256='f00410ebdd739c2ddf55fcd714ff4bd88a1029e02d2fc9cea0b5fca34e0fc4eb') @@ -53,7 +60,7 @@ class Plumed(AutotoolsPackage): depends_on('lapack') # For libmatheval support through the 'function' module # which is enabled by default (or when optional_modules=all) - depends_on('libmatheval') + depends_on('libmatheval', when='@:2.4.99') depends_on('mpi', when='+mpi') depends_on('gsl', when='+gsl') diff --git a/var/spack/repos/builtin/packages/pmdk/package.py b/var/spack/repos/builtin/packages/pmdk/package.py index 2f8aca78e0..c8c836e4eb 100644 --- a/var/spack/repos/builtin/packages/pmdk/package.py +++ b/var/spack/repos/builtin/packages/pmdk/package.py @@ -1,10 +1,9 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * -import spack.architecture class Pmdk(Package): @@ -18,13 +17,15 @@ class Pmdk(Package): git = "https://github.com/pmem/pmdk.git" version('develop', branch='master') + version('1.8', sha256='a241ea76ef76d233cb92826b6823ed48091a2fb6963282a4fea848dbce68aa21') version('1.7', sha256='865ce1b422bc83109cb4a63dcff8fd1077eea3617e668faf6a043208d8be03ca') version('1.6', sha256='3b99e6c30709326a94d2e73a9247a8dfb58d0a394c5b7714e5c3d8a3ad2e2e9f') version('1.5', sha256='6b069d7207febeb62440e89245e8b18fcdf40b6170d2ec2ef33c252ed16db2d4') depends_on('ncurses', when='@1.6:') # documentation requires doxygen and a bunch of other dependencies - patch('0001-make-doc-building-explicit.patch') + patch('0001-make-doc-building-explicit.patch', when="@:1.7") + patch('pmem-1.8-disable-docs.patch', when='@1.8') def install(self, spec, prefix): make_args = [ @@ -34,9 +35,9 @@ class Pmdk(Package): 'BUILD_RPMEM=n', ] - # pmdk is particular about the ARCH specification, must be - # exactly "x86_64" for build to work - if 'x86_64' in spack.architecture.sys_type(): + # pmdk prior to 1.8 was particular about the ARCH specification, must + # be exactly "x86_64" for build to work + if spec.target.family == 'x86_64': make_args += ['ARCH=x86_64'] make("install", *make_args) diff --git a/var/spack/repos/builtin/packages/pmdk/pmem-1.8-disable-docs.patch b/var/spack/repos/builtin/packages/pmdk/pmem-1.8-disable-docs.patch new file mode 100644 index 0000000000..f850e70e0f --- /dev/null +++ b/var/spack/repos/builtin/packages/pmdk/pmem-1.8-disable-docs.patch @@ -0,0 +1,19 @@ +--- pmdk-1.8/Makefile 2020-01-31 06:42:27.000000000 -0500 ++++ pmdk-1.8.nodocs/Makefile 2020-02-03 13:51:24.844691000 -0500 +@@ -79,7 +79,7 @@ rpm : override DESTDIR="$(CURDIR)/$(RPM_ + dpkg: override DESTDIR="$(CURDIR)/$(DPKG_BUILDDIR)" + rpm dpkg: override prefix=/usr + +-all: doc ++all: + $(MAKE) -C src $@ + + doc: +@@ -151,7 +151,6 @@ install: all + + install uninstall: + $(MAKE) -C src $@ +- $(MAKE) -C doc $@ + + .PHONY: all clean clobber test check cstyle check-license install uninstall\ + source rpm dpkg pkg-clean pcheck check-remote format doc require-rpmem\ diff --git a/var/spack/repos/builtin/packages/pmgr-collective/package.py b/var/spack/repos/builtin/packages/pmgr-collective/package.py index 3ce2f597cd..80cb96cfc3 100644 --- a/var/spack/repos/builtin/packages/pmgr-collective/package.py +++ b/var/spack/repos/builtin/packages/pmgr-collective/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pmix/package.py b/var/spack/repos/builtin/packages/pmix/package.py index 9bfe28a081..0ebdce7987 100644 --- a/var/spack/repos/builtin/packages/pmix/package.py +++ b/var/spack/repos/builtin/packages/pmix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pmlib/package.py b/var/spack/repos/builtin/packages/pmlib/package.py index a6e721a62b..3c7ea4a0ed 100644 --- a/var/spack/repos/builtin/packages/pmlib/package.py +++ b/var/spack/repos/builtin/packages/pmlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pnfft/package.py b/var/spack/repos/builtin/packages/pnfft/package.py index 6518e49c3e..209263a440 100644 --- a/var/spack/repos/builtin/packages/pnfft/package.py +++ b/var/spack/repos/builtin/packages/pnfft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pngquant/package.py b/var/spack/repos/builtin/packages/pngquant/package.py index 130bdf93ab..73d3946b48 100644 --- a/var/spack/repos/builtin/packages/pngquant/package.py +++ b/var/spack/repos/builtin/packages/pngquant/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pngwriter/package.py b/var/spack/repos/builtin/packages/pngwriter/package.py index b14a672c96..a544f48247 100644 --- a/var/spack/repos/builtin/packages/pngwriter/package.py +++ b/var/spack/repos/builtin/packages/pngwriter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pnmpi/package.py b/var/spack/repos/builtin/packages/pnmpi/package.py index 9e0c64faae..8c936455b7 100644 --- a/var/spack/repos/builtin/packages/pnmpi/package.py +++ b/var/spack/repos/builtin/packages/pnmpi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/poamsa/package.py b/var/spack/repos/builtin/packages/poamsa/package.py index a6cf51dbde..deba0f0544 100644 --- a/var/spack/repos/builtin/packages/poamsa/package.py +++ b/var/spack/repos/builtin/packages/poamsa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pocl/package.py b/var/spack/repos/builtin/packages/pocl/package.py index f3a13d8877..f9b343271a 100644 --- a/var/spack/repos/builtin/packages/pocl/package.py +++ b/var/spack/repos/builtin/packages/pocl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/polymake/package.py b/var/spack/repos/builtin/packages/polymake/package.py index 556d31a587..f32033188c 100644 --- a/var/spack/repos/builtin/packages/polymake/package.py +++ b/var/spack/repos/builtin/packages/polymake/package.py @@ -1,9 +1,7 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) - - from spack import * @@ -12,18 +10,28 @@ class Polymake(Package): homepage = "https://polymake.org/doku.php" url = "https://polymake.org/lib/exe/fetch.php/download/polymake-3.0r1.tar.bz2" + version('3.5', sha256='c649f8536ccef5a5e22b82c514a09278ebcd99d0815aa7170461fe12843109bd') version('3.0r2', sha256='e7c0f8e3a45ea288d2fb4ae781a1dcea913ef9c275fed401632cdb11a672d6dc') version('3.0r1', sha256='cdc223716b1cc3f4f3cc126089a438f9d12390caeed78291a87565717c7b504d') # Note: Could also be built with nauty instead of bliss - depends_on("bliss") depends_on("boost") depends_on("cddlib") depends_on("gmp") depends_on("lrslib") depends_on("mpfr") + depends_on("ninja", type='build', when='@3.2:') + depends_on("perl") + depends_on("perl-json") + depends_on("perl-termreadkey") + depends_on("perl-term-readline-gnu") + depends_on("perl-xml-libxml") + depends_on("perl-xml-libxslt") + depends_on("perl-xml-writer") depends_on("ppl") + depends_on("ppl@1.2:", when='@3.2:') + depends_on("readline") def install(self, spec, prefix): configure("--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/poppler-data/package.py b/var/spack/repos/builtin/packages/poppler-data/package.py index 7bf3cd94b5..19d0c0e3c7 100644 --- a/var/spack/repos/builtin/packages/poppler-data/package.py +++ b/var/spack/repos/builtin/packages/poppler-data/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/poppler/package.py b/var/spack/repos/builtin/packages/poppler/package.py index 23f2db8002..8689f817e5 100644 --- a/var/spack/repos/builtin/packages/poppler/package.py +++ b/var/spack/repos/builtin/packages/poppler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/popt/package.py b/var/spack/repos/builtin/packages/popt/package.py index c87e290320..b03670f417 100644 --- a/var/spack/repos/builtin/packages/popt/package.py +++ b/var/spack/repos/builtin/packages/popt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/porta/package.py b/var/spack/repos/builtin/packages/porta/package.py index d3bc8a466b..b61ed84db0 100644 --- a/var/spack/repos/builtin/packages/porta/package.py +++ b/var/spack/repos/builtin/packages/porta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/portage/p_intel_ice.patch b/var/spack/repos/builtin/packages/portage/p_intel_ice.patch new file mode 100644 index 0000000000..98832ea8b7 --- /dev/null +++ b/var/spack/repos/builtin/packages/portage/p_intel_ice.patch @@ -0,0 +1,24 @@ +--- portage.orig/portage/search/pairs.cc 2018-07-16 13:42:12.000000000 -0600 ++++ portage/portage/search/pairs.cc 2020-01-09 15:32:43.289085000 -0700 +@@ -323,8 +323,8 @@ + // check for completely outside source boxes + bool outside = false; + for (size_t m=0;m<dim;m++) { +- if (y[m][j]<=cminmax[0][m]) outside=true; +- if (y[m][j]>=cminmax[1][m]) outside=true; ++ if (y[m][j]<=cminmax[0][m]) { outside=true; break; } ++ if (y[m][j]>=cminmax[1][m]) { outside=true; break; } + } + if (outside) return pairlist; + +@@ -347,8 +347,8 @@ + // check that y is contained + bool inside = true; + for(size_t m=0; m<dim; m++) { +- if (y[m][j] <= xll[m]) inside = false; +- if (y[m][j] >= xur[m]) inside = false; ++ if (y[m][j] <= xll[m]) { inside = false; break; } ++ if (y[m][j] >= xur[m]) { inside = false; break; } + } + + // add pair: put x's in this y-cell onto neighbor list, if inside diff --git a/var/spack/repos/builtin/packages/portage/package.py b/var/spack/repos/builtin/packages/portage/package.py index 91fc5fa4dc..097ec9aab1 100644 --- a/var/spack/repos/builtin/packages/portage/package.py +++ b/var/spack/repos/builtin/packages/portage/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,6 +31,9 @@ class Portage(CMakePackage): # fixed in version above 1.2.2 patch('rel-with-deb-info.patch', when='@1.2.2') + # intel/19.0.4 got an ICE (internal compiler error) compiling pairs.cc + patch('p_intel_ice.patch', when='@1.2.2') + variant('mpi', default=True, description='Support MPI') depends_on("cmake@3.1:", type='build') @@ -51,7 +54,12 @@ class Portage(CMakePackage): else: options.append('-DENABLE_MPI=OFF') - options.append("-DLAPACKE_LIBRARIES=" + + options.append('-DBLA_VENDOR=' + self.spec['blas'].name.upper()) + options.append('-DBLAS_LIBRARIES=' + self.spec['blas'].libs.joined()) + options.append('-DLAPACK_LIBRARIES=' + + self.spec['lapack'].libs.joined()) + + options.append("-DLAPACKE_LIBRARY=" + self.spec["lapack"].libs.joined(";")) return options diff --git a/var/spack/repos/builtin/packages/portcullis/package.py b/var/spack/repos/builtin/packages/portcullis/package.py index 9b91a9fb39..6c4d0222c2 100644 --- a/var/spack/repos/builtin/packages/portcullis/package.py +++ b/var/spack/repos/builtin/packages/portcullis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/postgresql/package.py b/var/spack/repos/builtin/packages/postgresql/package.py index 63c76cbf35..328203138c 100644 --- a/var/spack/repos/builtin/packages/postgresql/package.py +++ b/var/spack/repos/builtin/packages/postgresql/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -87,25 +87,32 @@ class Postgresql(AutotoolsPackage): else: AutotoolsPackage.install(self, spec, prefix) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): spec = self.spec if '+perl' in spec: - run_env.prepend_path('PERL5LIB', self.prefix.lib) + env.prepend_path('PERL5LIB', self.prefix.lib) if '+tcl' in spec: - run_env.prepend_path('TCLLIBPATH', self.prefix.lib) + env.prepend_path('TCLLIBPATH', self.prefix.lib) if '+python' in spec: - run_env.prepend_path('PYTHONPATH', self.prefix.lib) + env.prepend_path('PYTHONPATH', self.prefix.lib) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): spec = self.spec if '+perl' in spec: - spack_env.prepend_path('PERL5LIB', self.prefix.lib) - run_env.prepend_path('PERL5LIB', self.prefix.lib) + env.prepend_path('PERL5LIB', self.prefix.lib) if '+tcl' in spec: - spack_env.prepend_path('TCLLIBPATH', self.prefix.lib) - run_env.prepend_path('TCLLIBPATH', self.prefix.lib) + env.prepend_path('TCLLIBPATH', self.prefix.lib) if '+python' in spec: - spack_env.prepend_path('PYTHONPATH', self.prefix.lib) - run_env.prepend_path('PYTHONPATH', self.prefix.lib) + env.prepend_path('PYTHONPATH', self.prefix.lib) + + def setup_dependent_run_environment(self, env, dependent_spec): + spec = self.spec + + if '+perl' in spec: + env.prepend_path('PERL5LIB', self.prefix.lib) + if '+tcl' in spec: + env.prepend_path('TCLLIBPATH', self.prefix.lib) + if '+python' in spec: + env.prepend_path('PYTHONPATH', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/powerapi/add_space.patch b/var/spack/repos/builtin/packages/powerapi/add_space.patch new file mode 100644 index 0000000000..307abafb29 --- /dev/null +++ b/var/spack/repos/builtin/packages/powerapi/add_space.patch @@ -0,0 +1,186 @@ +diff -ur spack-src.org/src/pwr/deviceStat.cc spack-src/src/pwr/deviceStat.cc +--- spack-src.org/src/pwr/deviceStat.cc 2020-01-28 11:00:47.690108007 +0900 ++++ spack-src/src/pwr/deviceStat.cc 2020-01-28 11:04:02.630472034 +0900 +@@ -47,7 +47,7 @@ + + int DeviceStat::startObj( ) { + int retval = m_obj->attrStartLog( m_attrName ); +- DBGX("%s time=%"PRIu64" sec\n",objTypeToString(m_obj->type()),m_startTime); ++ DBGX("%s time=%" PRIu64 " sec\n",objTypeToString(m_obj->type()),m_startTime); + return retval; + } + +@@ -64,7 +64,7 @@ + return PWR_RET_SUCCESS; + } + int DeviceStat::stopObj( ) { +- DBGX("%s time=%"PRIu64" sec\n",objTypeToString(m_obj->type()),m_startTime); ++ DBGX("%s time=%" PRIu64 " sec\n",objTypeToString(m_obj->type()),m_startTime); + int retval = m_obj->attrStopLog( m_attrName ); + return retval; + } +@@ -85,7 +85,7 @@ + int DeviceStat::stop( ) { + m_isLogging = false; + m_stopTime = getTime(); +- DBGX("time=%"PRIu64" sec\n",m_stopTime); ++ DBGX("time=%" PRIu64 " sec\n",m_stopTime); + if ( m_obj ) { + return stopObj(); + } else { +@@ -135,7 +135,7 @@ + + statTimes->start = timeStamp; + statTimes->stop = timeStamp + nSamples * m_period * 1000000000 ; +- DBGX("actual: start=%lf stop=%lf count=%"PRIu32"\n", ++ DBGX("actual: start=%lf stop=%lf count=%" PRIu32 "\n", + (double) timeStamp/1000000000, + (double) statTimes->stop/1000000000, nSamples); + +@@ -146,7 +146,7 @@ + statTimes->instant = statTimes->start + pos * m_period * 1000000000; + } + +- DBGX("actual: start=%lf stop=%lf instant=%lf count=%"PRIu32"\n", ++ DBGX("actual: start=%lf stop=%lf instant=%lf count=%" PRIu32 "\n", + (double) timeStamp/1000000000, + (double) statTimes->stop/1000000000, + (double) statTimes->instant/1000000000,nSamples); +diff -ur spack-src.org/src/pwr/distRequest.cc spack-src/src/pwr/distRequest.cc +--- spack-src.org/src/pwr/distRequest.cc 2020-01-28 11:00:47.690108007 +0900 ++++ spack-src/src/pwr/distRequest.cc 2020-01-28 11:05:11.687685948 +0900 +@@ -56,7 +56,7 @@ + // can we use "this" + void DistRequest::getSamples( DistCommReq* req, CommGetSamplesRespEvent* ev ) + { +- DBGX("count %"PRIu32"\n",ev->count); ++ DBGX("count %" PRIu32 "\n",ev->count); + + #if 0 + // FIX ME +@@ -67,7 +67,7 @@ + for ( unsigned i = 0; i< ev->count; i++ ) { + ((uint64_t*)value[0])[i] = ev->data[i]; + } +- DBGX("start time %"PRIu64", samples %"PRIu32"n",*timeStamp[0], ev->count); ++ DBGX("start time %" PRIu64 ", samples %" PRIu32 "n",*timeStamp[0], ev->count); + *timeStamp[0] = ev->startTime; + m_commReqs.erase( req ); + } +diff -ur spack-src.org/tools/pwrdaemon/router/commCreateEvent.cc spack-src/tools/pwrdaemon/router/commCreateEvent.cc +--- spack-src.org/tools/pwrdaemon/router/commCreateEvent.cc 2020-01-28 11:00:47.730112186 +0900 ++++ spack-src/tools/pwrdaemon/router/commCreateEvent.cc 2020-01-28 11:12:35.644062899 +0900 +@@ -21,7 +21,7 @@ + bool RtrCommCreateEvent::process( EventGenerator* _rtr, EventChannel* ec ) { + Router& rtr = *static_cast<Router*>(_rtr); + Router::Client* client = rtr.getClient( ec ); +- DBGX("id=%"PRIx64"\n",commID); ++ DBGX("id=%" PRIx64 "\n",commID); + + client->addComm( commID, this ); + +diff -ur spack-src.org/tools/pwrdaemon/router/commGetSamplesEvent.h spack-src/tools/pwrdaemon/router/commGetSamplesEvent.h +--- spack-src.org/tools/pwrdaemon/router/commGetSamplesEvent.h 2020-01-28 11:00:47.730112186 +0900 ++++ spack-src/tools/pwrdaemon/router/commGetSamplesEvent.h 2020-01-28 11:07:20.211111872 +0900 +@@ -45,7 +45,7 @@ + info->resp->id = id; + id = (EventId) info; + +- DBGX("commID=%" PRIx64 " eventId=%"PRIx64" new eventId=%p\n", ++ DBGX("commID=%" PRIx64 " eventId=%" PRIx64 " new eventId=%p\n", + commID, id, info ); + + for ( unsigned int i=0; i < commList.size(); i++ ) { +diff -ur spack-src.org/tools/pwrdaemon/router/commLogEvents.h spack-src/tools/pwrdaemon/router/commLogEvents.h +--- spack-src.org/tools/pwrdaemon/router/commLogEvents.h 2020-01-28 11:00:47.730112186 +0900 ++++ spack-src/tools/pwrdaemon/router/commLogEvents.h 2020-01-28 11:09:28.254487649 +0900 +@@ -46,7 +46,7 @@ + info->resp->id = id; + id = (EventId) info; + +- DBGX("commID=%"PRIu64" eventId=%" PRIx64 " new eventId=%p\n", ++ DBGX("commID=%" PRIu64 " eventId=%" PRIx64 " new eventId=%p\n", + commID, id, info ); + + for ( unsigned int i=0; i < commList.size(); i++ ) { +diff -ur spack-src.org/tools/pwrdaemon/router/commReqEvent.h spack-src/tools/pwrdaemon/router/commReqEvent.h +--- spack-src.org/tools/pwrdaemon/router/commReqEvent.h 2020-01-28 11:00:47.730112186 +0900 ++++ spack-src/tools/pwrdaemon/router/commReqEvent.h 2020-01-28 11:09:59.347735739 +0900 +@@ -35,7 +35,7 @@ + + CommReqInfo* info = new CommReqInfo; + +- DBGX("commID=%"PRIx64" eventId=%"PRIx64" new eventId=%p\n", ++ DBGX("commID=%" PRIx64 " eventId=%" PRIx64 " new eventId=%p\n", + commID, id, info ); + + info->src = ec; +diff -ur spack-src.org/tools/pwrdaemon/router/commRespEvent.h spack-src/tools/pwrdaemon/router/commRespEvent.h +--- spack-src.org/tools/pwrdaemon/router/commRespEvent.h 2020-01-28 11:00:47.730112186 +0900 ++++ spack-src/tools/pwrdaemon/router/commRespEvent.h 2020-01-28 11:10:43.862385866 +0900 +@@ -33,7 +33,7 @@ + + bool process( EventGenerator* _rtr, EventChannel* ) { + +- DBGX("id=%p status=%"PRIi32" grpIndex=%" PRIu64 "\n", ++ DBGX("id=%p status=%" PRIi32 " grpIndex=%" PRIu64 "\n", + (void*)id, status, grpIndex ); + + CommReqInfo* info = (CommReqInfo*) id; +@@ -44,7 +44,7 @@ + + CommRespEvent* resp = static_cast<CommRespEvent*>(info->resp); + if ( Get == info->ev->op ) { +- DBGX("index %"PRIu64" is ready, num attrs %zu\n", ++ DBGX("index %" PRIu64 " is ready, num attrs %zu\n", + grpIndex, info->valueOp.size() ); + resp->timeStamp[grpIndex].resize( info->valueOp.size() ); + resp->value[grpIndex].resize( info->valueOp.size() ); +diff -ur spack-src.org/tools/pwrdaemon/router/rtrRouterEvent.h spack-src/tools/pwrdaemon/router/rtrRouterEvent.h +--- spack-src.org/tools/pwrdaemon/router/rtrRouterEvent.h 2020-01-28 11:00:47.730112186 +0900 ++++ spack-src/tools/pwrdaemon/router/rtrRouterEvent.h 2020-01-28 11:11:05.824680110 +0900 +@@ -25,7 +25,7 @@ + + bool process( EventGenerator* _rtr, EventChannel* ec ) { + Router& rtr = *static_cast<Router*>(_rtr); +- DBGX("dest=%"PRIx64"\n",dest); ++ DBGX("dest=%" PRIx64 "\n",dest); + rtr.sendEvent( dest, this ); + + return true; +diff -ur spack-src.org/tools/pwrdaemon/server/commCreateEvent.h spack-src/tools/pwrdaemon/server/commCreateEvent.h +--- spack-src.org/tools/pwrdaemon/server/commCreateEvent.h 2020-01-28 11:00:47.740113231 +0900 ++++ spack-src/tools/pwrdaemon/server/commCreateEvent.h 2020-01-28 11:13:00.426651760 +0900 +@@ -21,7 +21,7 @@ + bool process( EventGenerator* gen, EventChannel* ) { + Server& info = *static_cast<Server*>(gen); + +- DBGX("commID=%"PRIx64"\n", commID); ++ DBGX("commID=%" PRIx64 "\n", commID); + + CommInfo& cInfo = info.m_commMap[commID]; + cInfo.objects.resize( members.size() ); +diff -ur spack-src.org/tools/pwrdaemon/server/commDestroyEvent.h spack-src/tools/pwrdaemon/server/commDestroyEvent.h +--- spack-src.org/tools/pwrdaemon/server/commDestroyEvent.h 2020-01-28 11:00:47.740113231 +0900 ++++ spack-src/tools/pwrdaemon/server/commDestroyEvent.h 2020-01-28 11:11:42.438504895 +0900 +@@ -24,7 +24,7 @@ + bool process( EventGenerator* gen, EventChannel* ) { + Server& info = *static_cast<Server*>(gen); + +- DBGX("commID=%"PRIx64"\n", commID); ++ DBGX("commID=%" PRIx64 "\n", commID); + + // We have a bunch of PWR_Obj hanging off of the comm. + // How/should we clean them up? +diff -ur spack-src.org/tools/pwrdaemon/server/commReqEvent.h spack-src/tools/pwrdaemon/server/commReqEvent.h +--- spack-src.org/tools/pwrdaemon/server/commReqEvent.h 2020-01-28 11:00:47.740113231 +0900 ++++ spack-src/tools/pwrdaemon/server/commReqEvent.h 2020-01-28 11:12:06.881058234 +0900 +@@ -31,7 +31,7 @@ + + PWR_Obj obj = m_info->m_commMap[commID].objects[0]; + +- DBGX("commID=%"PRIx64" grpIndex=%"PRIu64"\n",commID, grpIndex); ++ DBGX("commID=%" PRIx64 " grpIndex=%" PRIu64 "\n",commID, grpIndex); + char name[100]; + PWR_ObjGetName(obj,name,100); + diff --git a/var/spack/repos/builtin/packages/powerapi/package.py b/var/spack/repos/builtin/packages/powerapi/package.py index aa7132a043..ccb8ffe780 100644 --- a/var/spack/repos/builtin/packages/powerapi/package.py +++ b/var/spack/repos/builtin/packages/powerapi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,6 +26,9 @@ class Powerapi(AutotoolsPackage): depends_on('hwloc', when='+hwloc') depends_on('mpi', when='+mpi') + # C++11 requires a space between literal and identifier. + patch('add_space.patch') + def autoreconf(self, spec, prefix): bash = which('bash') bash('./autogen.sh') diff --git a/var/spack/repos/builtin/packages/ppl/package.py b/var/spack/repos/builtin/packages/ppl/package.py index e511f00158..0fc42092ae 100644 --- a/var/spack/repos/builtin/packages/ppl/package.py +++ b/var/spack/repos/builtin/packages/ppl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,6 +23,7 @@ class Ppl(Package): homepage = "http://bugseng.com/products/ppl/" url = "http://bugseng.com/products/ppl/download/ftp/releases/1.1/ppl-1.1.tar.gz" + version('1.2', sha256='6bc36dd4a87abc429d8f9c00c53e334e5041a9b0857cfc00dbad6ef14294aac8') version('1.1', sha256='46f073c0626234f0b1a479356c0022fe5dc3c9cf10df1a246c9cde81f7cf284d') depends_on("gmp") diff --git a/var/spack/repos/builtin/packages/pplacer/package.py b/var/spack/repos/builtin/packages/pplacer/package.py index f971cdff73..af928f8247 100644 --- a/var/spack/repos/builtin/packages/pplacer/package.py +++ b/var/spack/repos/builtin/packages/pplacer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py index 0eb0050d34..e87fca199e 100644 --- a/var/spack/repos/builtin/packages/prank/package.py +++ b/var/spack/repos/builtin/packages/prank/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class Prank(Package): """A powerful multiple sequence alignment browser.""" homepage = "http://wasabiapp.org/software/prank/" - url = "http://wasabiapp.org/download/prank/prank.source.150803.tgz" + url = "http://wasabiapp.org/download/prank/prank.source.170427.tgz" version('170427', sha256='623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859') @@ -21,6 +21,15 @@ class Prank(Package): def install(self, spec, prefix): with working_dir('src'): + + filter_file('gcc', '{0}'.format(spack_cc), + 'Makefile', string=True) + filter_file('g++', '{0}'.format(spack_cxx), + 'Makefile', string=True) + if not spec.target.family == 'x86_64': + filter_file('-m64', '', 'Makefile', string=True) + filter_file('-pipe', '', 'Makefile', string=True) + make() mkdirp(prefix.bin) install('prank', prefix.bin) diff --git a/var/spack/repos/builtin/packages/precice/package.py b/var/spack/repos/builtin/packages/precice/package.py index d9cbae147a..c3f37f7d69 100644 --- a/var/spack/repos/builtin/packages/precice/package.py +++ b/var/spack/repos/builtin/packages/precice/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,7 +31,7 @@ class Precice(CMakePackage): # Skip version 1.1.1 entirely, the cmake was lacking install. variant('mpi', default=True, description='Enable MPI support') - variant('petsc', default=False, description='Enable PETSc support') + variant('petsc', default=True, description='Enable PETSc support') variant('python', default=False, description='Enable Python support') variant('shared', default=True, description='Build shared libraries') @@ -48,6 +48,13 @@ class Precice(CMakePackage): # numpy 1.17+ requires Python 3 depends_on('py-numpy@:1.16', when='+python', type=('build', 'run')) + # We require C++11 compiler support as well as + # library support for time manipulators (N2071, N2072) + conflicts('%gcc@:4') + conflicts('%clang@:3.7') + conflicts('%intel@:14') + conflicts('%pgi@:14') + def cmake_args(self): """Populate cmake arguments for precice.""" spec = self.spec diff --git a/var/spack/repos/builtin/packages/presentproto/package.py b/var/spack/repos/builtin/packages/presentproto/package.py index 66a7ebbcd7..0e9652e4be 100644 --- a/var/spack/repos/builtin/packages/presentproto/package.py +++ b/var/spack/repos/builtin/packages/presentproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/preseq/package.py b/var/spack/repos/builtin/packages/preseq/package.py index 1315a2fa0c..a446ad53c6 100644 --- a/var/spack/repos/builtin/packages/preseq/package.py +++ b/var/spack/repos/builtin/packages/preseq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,5 +21,5 @@ class Preseq(MakefilePackage): depends_on('samtools') depends_on('gsl') - def setup_environment(self, spack_env, run_env): - spack_env.set('PREFIX', self.prefix) + def setup_build_environment(self, env): + env.set('PREFIX', self.prefix) diff --git a/var/spack/repos/builtin/packages/price/package.py b/var/spack/repos/builtin/packages/price/package.py index 3ab85f8724..746079fb17 100644 --- a/var/spack/repos/builtin/packages/price/package.py +++ b/var/spack/repos/builtin/packages/price/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/primer3/package.py b/var/spack/repos/builtin/packages/primer3/package.py index b05adff2ea..f54d1d6828 100644 --- a/var/spack/repos/builtin/packages/primer3/package.py +++ b/var/spack/repos/builtin/packages/primer3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/prinseq-lite/package.py b/var/spack/repos/builtin/packages/prinseq-lite/package.py index dd64857c83..a101a7dcfa 100644 --- a/var/spack/repos/builtin/packages/prinseq-lite/package.py +++ b/var/spack/repos/builtin/packages/prinseq-lite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/printproto/package.py b/var/spack/repos/builtin/packages/printproto/package.py index 22d2561ad4..d2ab937913 100644 --- a/var/spack/repos/builtin/packages/printproto/package.py +++ b/var/spack/repos/builtin/packages/printproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/prng/package.py b/var/spack/repos/builtin/packages/prng/package.py index 0a82a494af..b892c9bcb4 100644 --- a/var/spack/repos/builtin/packages/prng/package.py +++ b/var/spack/repos/builtin/packages/prng/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/probconsrna/package.py b/var/spack/repos/builtin/packages/probconsrna/package.py index c2a649cb0b..8db95ecb53 100644 --- a/var/spack/repos/builtin/packages/probconsrna/package.py +++ b/var/spack/repos/builtin/packages/probconsrna/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/procps/package.py b/var/spack/repos/builtin/packages/procps/package.py index ff51b4e57a..f8b4ed2633 100644 --- a/var/spack/repos/builtin/packages/procps/package.py +++ b/var/spack/repos/builtin/packages/procps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/prodigal/package.py b/var/spack/repos/builtin/packages/prodigal/package.py index 2cf8fedafd..429d6d78a6 100644 --- a/var/spack/repos/builtin/packages/prodigal/package.py +++ b/var/spack/repos/builtin/packages/prodigal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,5 +18,5 @@ class Prodigal(MakefilePackage): def install(self, spec, prefix): make('INSTALLDIR={0}'.format(self.prefix), 'install') - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py index 6c3febcd7b..19de7a7909 100644 --- a/var/spack/repos/builtin/packages/proj/package.py +++ b/var/spack/repos/builtin/packages/proj/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/protobuf-c/package.py b/var/spack/repos/builtin/packages/protobuf-c/package.py index 87a1df2dab..020e6297df 100644 --- a/var/spack/repos/builtin/packages/protobuf-c/package.py +++ b/var/spack/repos/builtin/packages/protobuf-c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/protobuf/package.py b/var/spack/repos/builtin/packages/protobuf/package.py index de252690d0..513d5653b4 100644 --- a/var/spack/repos/builtin/packages/protobuf/package.py +++ b/var/spack/repos/builtin/packages/protobuf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,23 +12,30 @@ class Protobuf(CMakePackage): """Google's data interchange format.""" homepage = "https://developers.google.com/protocol-buffers" - url = "https://github.com/protocolbuffers/protobuf/archive/v3.2.0.tar.gz" + url = "https://github.com/protocolbuffers/protobuf/archive/v3.10.1.tar.gz" root_cmakelists_dir = "cmake" - version('3.7.1', sha256='f1748989842b46fa208b2a6e4e2785133cfcc3e4d43c17fecb023733f0f5443f') - version('3.7.0', sha256='a19dcfe9d156ae45d209b15e0faed5c7b5f109b6117bfc1974b6a7b98a850320') - version('3.6.1', sha256='3d4e589d81b2006ca603c1ab712c9715a76227293032d05b26fca603f90b3f5b') - version('3.5.2', sha256='4ffd420f39f226e96aebc3554f9c66a912f6cad6261f39f194f16af8a1f6dab2') + version('3.11.2', sha256='e8c7601439dbd4489fe5069c33d374804990a56c2f710e00227ee5d8fd650e67') + version('3.11.1', sha256='4f8e805825c53bbc3c9f6b6abc009b5b5679e4702bccfca1121c42ff5ec801c7') + version('3.11.0', sha256='6d356a6279cc76d2d5c4dfa6541641264b59eae0bc96b852381361e3400d1f1c') + version('3.10.1', sha256='6adf73fd7f90409e479d6ac86529ade2d45f50494c5c10f539226693cb8fe4f7') + version('3.10.0', sha256='758249b537abba2f21ebc2d02555bf080917f0f2f88f4cbe2903e0e28c4187ed') + version('3.9.2', sha256='1fbf1c2962af287607232b2eddeaec9b4f4a7a6f5934e1a9276e9af76952f7e0') + version('3.9.1', sha256='98e615d592d237f94db8bf033fba78cd404d979b0b70351a9e5aaff725398357') + version('3.7.1', sha256='f1748989842b46fa208b2a6e4e2785133cfcc3e4d43c17fecb023733f0f5443f') + version('3.7.0', sha256='a19dcfe9d156ae45d209b15e0faed5c7b5f109b6117bfc1974b6a7b98a850320') + version('3.6.1', sha256='3d4e589d81b2006ca603c1ab712c9715a76227293032d05b26fca603f90b3f5b') + version('3.5.2', sha256='4ffd420f39f226e96aebc3554f9c66a912f6cad6261f39f194f16af8a1f6dab2') version('3.5.1.1', sha256='56b5d9e1ab2bf4f5736c4cfba9f4981fbc6976246721e7ded5602fbaee6d6869') version('3.5.1', sha256='826425182ee43990731217b917c5c3ea7190cfda141af4869e6d4ad9085a740f') version('3.5.0.1', sha256='86be71e61c76575c60839452a4f265449a6ea51570d7983cb929f06ad294b5f5') version('3.5.0', sha256='0cc6607e2daa675101e9b7398a436f09167dffb8ca0489b0307ff7260498c13c') version('3.4.1', sha256='8e0236242106e680b4f9f576cc44b8cd711e948b20a9fc07769b0a20ceab9cc4') - version('3.4.0', sha256='f6600abeee3babfa18591961a0ff21e7db6a6d9ef82418a261ec4fee44ee6d44') - version('3.3.0', sha256='9a36bc1265fa83b8e818714c0d4f08b8cec97a1910de0754a321b11e66eb76de') - version('3.2.0', sha256='a839d3f1519ff9d68ab908de5a0f269650ef1fc501c10f6eefd4cae51d29b86f') - version('3.1.0', sha256='fb2a314f4be897491bb2446697be693d489af645cb0e165a85e7e64e07eb134d') - version('3.0.2', sha256='a0a265bcc9d4e98c87416e59c33afc37cede9fb277292523739417e449b18c1e') + version('3.4.0', sha256='f6600abeee3babfa18591961a0ff21e7db6a6d9ef82418a261ec4fee44ee6d44') + version('3.3.0', sha256='9a36bc1265fa83b8e818714c0d4f08b8cec97a1910de0754a321b11e66eb76de') + version('3.2.0', sha256='a839d3f1519ff9d68ab908de5a0f269650ef1fc501c10f6eefd4cae51d29b86f') + version('3.1.0', sha256='fb2a314f4be897491bb2446697be693d489af645cb0e165a85e7e64e07eb134d') + version('3.0.2', sha256='a0a265bcc9d4e98c87416e59c33afc37cede9fb277292523739417e449b18c1e') variant('shared', default=True, description='Enables the build of shared libraries') diff --git a/var/spack/repos/builtin/packages/proxymngr/package.py b/var/spack/repos/builtin/packages/proxymngr/package.py index 6331b991f7..7dae3ca36a 100644 --- a/var/spack/repos/builtin/packages/proxymngr/package.py +++ b/var/spack/repos/builtin/packages/proxymngr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/prrte/package.py b/var/spack/repos/builtin/packages/prrte/package.py index 8d38b510a3..c8fa0ede0d 100644 --- a/var/spack/repos/builtin/packages/prrte/package.py +++ b/var/spack/repos/builtin/packages/prrte/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pruners-ninja/package.py b/var/spack/repos/builtin/packages/pruners-ninja/package.py index 4213cd95c0..6ea2b448f7 100644 --- a/var/spack/repos/builtin/packages/pruners-ninja/package.py +++ b/var/spack/repos/builtin/packages/pruners-ninja/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ps-lite/package.py b/var/spack/repos/builtin/packages/ps-lite/package.py index 92a0b7ff88..525633514e 100644 --- a/var/spack/repos/builtin/packages/ps-lite/package.py +++ b/var/spack/repos/builtin/packages/ps-lite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,6 @@ class PsLite(CMakePackage): version('20170328', commit='acdb698fa3bb80929ef83bb37c705f025e119b82') depends_on('protobuf@3:') - depends_on('zeromq') + depends_on('libzmq') patch('cmake.patch') diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py index be9d5046eb..64cb85a5ee 100644 --- a/var/spack/repos/builtin/packages/psi4/package.py +++ b/var/spack/repos/builtin/packages/psi4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pslib/package.py b/var/spack/repos/builtin/packages/pslib/package.py index 7cb6601b2c..38e1e40dc5 100644 --- a/var/spack/repos/builtin/packages/pslib/package.py +++ b/var/spack/repos/builtin/packages/pslib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/psm/package.py b/var/spack/repos/builtin/packages/psm/package.py index 387299b8a5..bf31fc4c90 100644 --- a/var/spack/repos/builtin/packages/psm/package.py +++ b/var/spack/repos/builtin/packages/psm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/psmc/package.py b/var/spack/repos/builtin/packages/psmc/package.py index 8db04ce5bc..243c740453 100644 --- a/var/spack/repos/builtin/packages/psmc/package.py +++ b/var/spack/repos/builtin/packages/psmc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,8 +17,8 @@ class Psmc(MakefilePackage): depends_on('zlib', type='link') - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', prefix.bin.utils) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix.bin.utils) def build(self, spec, prefix): make() diff --git a/var/spack/repos/builtin/packages/pstreams/package.py b/var/spack/repos/builtin/packages/pstreams/package.py index fc4bbff2d7..48afbe9388 100644 --- a/var/spack/repos/builtin/packages/pstreams/package.py +++ b/var/spack/repos/builtin/packages/pstreams/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pugixml/package.py b/var/spack/repos/builtin/packages/pugixml/package.py index 52b4bfa383..d4035f8e32 100644 --- a/var/spack/repos/builtin/packages/pugixml/package.py +++ b/var/spack/repos/builtin/packages/pugixml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pumi/package.py b/var/spack/repos/builtin/packages/pumi/package.py index 827ed6187a..62b771aa99 100644 --- a/var/spack/repos/builtin/packages/pumi/package.py +++ b/var/spack/repos/builtin/packages/pumi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,10 +24,9 @@ class Pumi(CMakePackage): # We will use the scorec/core master branch as the 'nightly' version # of pumi in spack. The master branch is more stable than the # scorec/core develop branch and we perfer not to expose spack users - # to the added instability. The spack version string is 'develop' since - # it compares greater than a numbered version (e.g., 2.1.0). The spack - # version string 'master' compares less than a numbered version. - version('develop', branch='master') + # to the added instability. + version('master', submodules=True, branch='master') + version('2.2.2', commit='bc34e3f7cfd8ab314968510c71486b140223a68f') # tag 2.2.2 version('2.2.1', commit='cd826205db21b8439026db1f6af61a8ed4a18564') # tag 2.2.1 version('2.2.0', commit='8c7e6f13943893b2bc1ece15003e4869a0e9634f') # tag 2.2.0 version('2.1.0', commit='840fbf6ec49a63aeaa3945f11ddb224f6055ac9f') @@ -41,6 +40,9 @@ class Pumi(CMakePackage): description="Enable Simmetrix SimModSuite Support: 'base' enables " "the minimum set of functionality, 'kernels' adds CAD kernel " "support to 'base', and 'full' enables all functionality.") + variant('simmodsuite_version_check', default=True, + description="Enable check of Simmetrix SimModSuite version. " + "Disable the check for testing new versions.") depends_on('mpi') depends_on('cmake@3:', type='build') @@ -69,7 +71,10 @@ class Pumi(CMakePackage): '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc, '-DPUMI_FORTRAN_INTERFACE=%s' % ('ON' if '+fortran' in spec else 'OFF'), - '-DMDS_ID_TYPE=%s' % ('long' if '+int64' in spec else 'int') + '-DMDS_ID_TYPE=%s' % ('long' if '+int64' in spec else 'int'), + '-DSKIP_SIMMETRIX_VERSION_CHECK=%s' % + ('ON' if '~simmodsuite_version_check' in spec else 'OFF'), + '-DMESHES=%s' % join_path(self.stage.source_path, 'pumi_meshes') ] if self.spec.satisfies('simmodsuite=base'): args.append('-DENABLE_SIMMETRIX=ON') @@ -82,3 +87,11 @@ class Pumi(CMakePackage): mpi_id = spec['mpi'].name + spec['mpi'].version.string args.append('-DSIM_MPI=' + mpi_id) return args + + @run_after('build') + @on_package_attributes(run_tests=True) + def check(self): + """Run ctest after building project.""" + + with working_dir(self.build_directory): + ctest(parallel=False) diff --git a/var/spack/repos/builtin/packages/pv/package.py b/var/spack/repos/builtin/packages/pv/package.py index 5e9d55a0e8..6b9ecb0e4a 100644 --- a/var/spack/repos/builtin/packages/pv/package.py +++ b/var/spack/repos/builtin/packages/pv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pvm/package.py b/var/spack/repos/builtin/packages/pvm/package.py index 0d19dd9f21..cb76f739bb 100644 --- a/var/spack/repos/builtin/packages/pvm/package.py +++ b/var/spack/repos/builtin/packages/pvm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -38,7 +38,7 @@ class Pvm(MakefilePackage): install_tree(join_path('lib', pvm_arch), prefix.lib) install_tree('man', prefix.man) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # Before running PVM, you must set the environment # variable "PVM_ROOT" to the path where PVM resides - run_env.set('PVM_ROOT', self.prefix) + env.set('PVM_ROOT', self.prefix) diff --git a/var/spack/repos/builtin/packages/pxz/package.py b/var/spack/repos/builtin/packages/pxz/package.py index c0d695175a..cbc64a0e88 100644 --- a/var/spack/repos/builtin/packages/pxz/package.py +++ b/var/spack/repos/builtin/packages/pxz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-3to2/package.py b/var/spack/repos/builtin/packages/py-3to2/package.py index 23866e18c2..facf4b4067 100644 --- a/var/spack/repos/builtin/packages/py-3to2/package.py +++ b/var/spack/repos/builtin/packages/py-3to2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-4suite-xml/package.py b/var/spack/repos/builtin/packages/py-4suite-xml/package.py index b3114bbff0..a848e1a63a 100644 --- a/var/spack/repos/builtin/packages/py-4suite-xml/package.py +++ b/var/spack/repos/builtin/packages/py-4suite-xml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-abipy/package.py b/var/spack/repos/builtin/packages/py-abipy/package.py index aef20708b4..b9b476b096 100644 --- a/var/spack/repos/builtin/packages/py-abipy/package.py +++ b/var/spack/repos/builtin/packages/py-abipy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-absl-py/package.py b/var/spack/repos/builtin/packages/py-absl-py/package.py index 8c9e6a72e0..4ebb9527be 100644 --- a/var/spack/repos/builtin/packages/py-absl-py/package.py +++ b/var/spack/repos/builtin/packages/py-absl-py/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-adios/package.py b/var/spack/repos/builtin/packages/py-adios/package.py index 0ce34ef3ca..aace2cd98a 100644 --- a/var/spack/repos/builtin/packages/py-adios/package.py +++ b/var/spack/repos/builtin/packages/py-adios/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-advancedhtmlparser/package.py b/var/spack/repos/builtin/packages/py-advancedhtmlparser/package.py index ed752e76de..11daf7db41 100644 --- a/var/spack/repos/builtin/packages/py-advancedhtmlparser/package.py +++ b/var/spack/repos/builtin/packages/py-advancedhtmlparser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-aenum/package.py b/var/spack/repos/builtin/packages/py-aenum/package.py index cdeae51f60..3fa4c63a80 100644 --- a/var/spack/repos/builtin/packages/py-aenum/package.py +++ b/var/spack/repos/builtin/packages/py-aenum/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-affine/package.py b/var/spack/repos/builtin/packages/py-affine/package.py index a9e6946ec1..d473915436 100644 --- a/var/spack/repos/builtin/packages/py-affine/package.py +++ b/var/spack/repos/builtin/packages/py-affine/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-agate-dbf/package.py b/var/spack/repos/builtin/packages/py-agate-dbf/package.py new file mode 100644 index 0000000000..e5a64ed299 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-agate-dbf/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAgateDbf(PythonPackage): + """agate-dbf adds read support for dbf files to agate.""" + + homepage = "https://agate-dbf.readthedocs.io/en/latest/" + url = "https://pypi.io/packages/source/a/agate-dbf/agate-dbf-0.2.1.tar.gz" + + version('0.2.1', sha256='00c93c498ec9a04cc587bf63dd7340e67e2541f0df4c9a7259d7cb3dd4ce372f') + + depends_on('py-setuptools', type='build') + depends_on('py-agate@1.5.0:', type=('build', 'run')) + depends_on('py-dbfread@2.0.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-agate-excel/package.py b/var/spack/repos/builtin/packages/py-agate-excel/package.py new file mode 100644 index 0000000000..f129ff9b5c --- /dev/null +++ b/var/spack/repos/builtin/packages/py-agate-excel/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAgateExcel(PythonPackage): + """agate-excel adds read support for Excel files (xls and xlsx) to + agate.""" + + homepage = "https://agate-excel.readthedocs.io/en/latest/" + url = "https://pypi.io/packages/source/a/agate-excel/agate-excel-0.2.3.tar.gz" + + version('0.2.3', sha256='8f255ef2c87c436b7132049e1dd86c8e08bf82d8c773aea86f3069b461a17d52') + + depends_on('py-setuptools', type='build') + depends_on('py-agate@1.5.0:', type=('build', 'run')) + depends_on('py-xlrd@0.9.4:', type=('build', 'run')) + depends_on('py-openpyxl@2.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-agate-sql/package.py b/var/spack/repos/builtin/packages/py-agate-sql/package.py new file mode 100644 index 0000000000..340ac94245 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-agate-sql/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAgateSql(PythonPackage): + """agate-sql adds SQL read/write support to agate.""" + + homepage = "https://agate-sql.readthedocs.io/en/latest/" + url = "https://pypi.io/packages/source/a/agate-sql/agate-sql-0.5.4.tar.gz" + + version('0.5.4', sha256='9277490ba8b8e7c747a9ae3671f52fe486784b48d4a14e78ca197fb0e36f281b') + + depends_on('py-setuptools', type='build') + depends_on('py-agate@1.5.0:', type=('build', 'run')) + depends_on('py-sqlalchemy@1.0.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-agate/package.py b/var/spack/repos/builtin/packages/py-agate/package.py new file mode 100644 index 0000000000..849e65574b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-agate/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAgate(PythonPackage): + """agate is a Python data analysis library that is optimized for humans + instead of machines. It is an alternative to numpy and pandas that solves + real-world problems with readable code.""" + + homepage = "https://agate.readthedocs.io/en/latest/" + url = "https://pypi.io/packages/source/a/agate/agate-1.6.1.tar.gz" + + version('1.6.1', sha256='c93aaa500b439d71e4a5cf088d0006d2ce2c76f1950960c8843114e5f361dfd3') + + depends_on('py-setuptools', type='build') + depends_on('py-six@1.9.0:', type=('build', 'run')) + depends_on('py-pytimeparse@1.1.5:', type=('build', 'run')) + depends_on('py-parsedatetime@2.1:', type=('build', 'run')) + depends_on('py-babel@2.0:', type=('build', 'run')) + depends_on('py-isodate@0.5.4:', type=('build', 'run')) + depends_on('py-python-slugify@1.2.1:', type=('build', 'run')) + depends_on('py-leather@0.3.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-alabaster/package.py b/var/spack/repos/builtin/packages/py-alabaster/package.py index d28f2085a0..5d623519b7 100644 --- a/var/spack/repos/builtin/packages/py-alabaster/package.py +++ b/var/spack/repos/builtin/packages/py-alabaster/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-alembic/package.py b/var/spack/repos/builtin/packages/py-alembic/package.py index c3ccdf23c5..86b75bc361 100644 --- a/var/spack/repos/builtin/packages/py-alembic/package.py +++ b/var/spack/repos/builtin/packages/py-alembic/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-altgraph/package.py b/var/spack/repos/builtin/packages/py-altgraph/package.py index db27953995..221fc3de85 100644 --- a/var/spack/repos/builtin/packages/py-altgraph/package.py +++ b/var/spack/repos/builtin/packages/py-altgraph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-amqp/package.py b/var/spack/repos/builtin/packages/py-amqp/package.py new file mode 100644 index 0000000000..b592a20688 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-amqp/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAmqp(PythonPackage): + """Low-level AMQP client for Python (fork of amqplib).""" + + homepage = "https://pypi.org/project/amqp/" + url = "https://pypi.io/packages/source/a/amqp/amqp-2.4.1.tar.gz" + + version('2.5.2', sha256='77f1aef9410698d20eaeac5b73a87817365f457a507d82edf292e12cbb83b08d') + version('2.4.2', sha256='043beb485774ca69718a35602089e524f87168268f0d1ae115f28b88d27f92d7') + version('2.4.1', sha256='6816eed27521293ee03aa9ace300a07215b11fee4e845588a9b863a7ba30addb') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + + depends_on('py-setuptools', type='build') + depends_on('py-vine@1.1.3:4.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-ansible/package.py b/var/spack/repos/builtin/packages/py-ansible/package.py new file mode 100644 index 0000000000..c3df51f2f2 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-ansible/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAnsible(PythonPackage): + """ + Ansible is a radically simple IT automation platform that makes your + applications and systems easier to deploy. + """ + + homepage = "https://github.com/ansible" + url = "https://github.com/ansible/ansible/archive/v2.9.1.tar.gz" + + version('2.9.2', sha256='27673726435e8773ef031ef6ffb121b8ec75b85b07b7684454b430c3c9a848a9') + version('2.9.1', sha256='087a7644890e27c26171b0d24fc5d64024f12201ffb81d222aaa5704987e4c12') + version('2.9.0', sha256='a2a9b1a74f3d47b82f9ea9da10ebf3573fa10c1783b7ed9b7eb937c7052fcb13') + version('2.8.7', sha256='1f7c765bf2a60e3f8d634a7eb3739a70522ba93a77e9266b07c119d29e08d484') + version('2.8.6', sha256='94c96aaf781417c073b340381c83992e4880f2a660b46888530909bc7c57ef71') + version('2.7.15', sha256='84f020f3b09575536fb200a3ff8e9bc98dce1ba3d8dd830134691237c9cb9a85') + version('2.7.14', sha256='92f0be1de4f9d1c0a3a35963fb853a6d7831360fd1e734cb36d601495a71770c') + version('2.6.20', sha256='55962e79e24a67a5534bf08aa0482d5f7322ad3f112a3ebffc4a58ae02b82277') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-jinja2', type=('build', 'run')) + depends_on('py-pyyaml', type=('build', 'run')) + depends_on('py-cryptography', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-antlr4-python3-runtime/package.py b/var/spack/repos/builtin/packages/py-antlr4-python3-runtime/package.py index 58e081045a..2684416f08 100644 --- a/var/spack/repos/builtin/packages/py-antlr4-python3-runtime/package.py +++ b/var/spack/repos/builtin/packages/py-antlr4-python3-runtime/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-apache-libcloud/package.py b/var/spack/repos/builtin/packages/py-apache-libcloud/package.py index 690d62281c..2b2034d98d 100644 --- a/var/spack/repos/builtin/packages/py-apache-libcloud/package.py +++ b/var/spack/repos/builtin/packages/py-apache-libcloud/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-apipkg/package.py b/var/spack/repos/builtin/packages/py-apipkg/package.py index 36881719ef..6799ad8f26 100644 --- a/var/spack/repos/builtin/packages/py-apipkg/package.py +++ b/var/spack/repos/builtin/packages/py-apipkg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-appdirs/package.py b/var/spack/repos/builtin/packages/py-appdirs/package.py index 1145924a7b..29b6c4f85b 100644 --- a/var/spack/repos/builtin/packages/py-appdirs/package.py +++ b/var/spack/repos/builtin/packages/py-appdirs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-appnope/package.py b/var/spack/repos/builtin/packages/py-appnope/package.py index 068f6e2426..07640da7f9 100644 --- a/var/spack/repos/builtin/packages/py-appnope/package.py +++ b/var/spack/repos/builtin/packages/py-appnope/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-apscheduler/package.py b/var/spack/repos/builtin/packages/py-apscheduler/package.py index 12aa3aa325..a4ba440e90 100644 --- a/var/spack/repos/builtin/packages/py-apscheduler/package.py +++ b/var/spack/repos/builtin/packages/py-apscheduler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-argcomplete/package.py b/var/spack/repos/builtin/packages/py-argcomplete/package.py index c5c8cc34fc..6a4ad018bd 100644 --- a/var/spack/repos/builtin/packages/py-argcomplete/package.py +++ b/var/spack/repos/builtin/packages/py-argcomplete/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-argparse/package.py b/var/spack/repos/builtin/packages/py-argparse/package.py index 63f726ad56..976e99d2a9 100644 --- a/var/spack/repos/builtin/packages/py-argparse/package.py +++ b/var/spack/repos/builtin/packages/py-argparse/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-arrow/package.py b/var/spack/repos/builtin/packages/py-arrow/package.py new file mode 100644 index 0000000000..ad2cd6bfce --- /dev/null +++ b/var/spack/repos/builtin/packages/py-arrow/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyArrow(PythonPackage): + """Arrow is a Python library that offers a sensible and human-friendly + approach to creating, manipulating, formatting and converting dates, + times and timestamps. It implements and updates the datetime type, + plugging gaps in functionality and providing an intelligent module API + that supports many common creation scenarios. Simply put, it helps you + work with dates and times with fewer imports and a lot less code.""" + + homepage = "https://arrow.readthedocs.io/en/latest/" + url = "https://pypi.io/packages/source/a/arrow/arrow-0.14.7.tar.gz" + + version('0.14.7', sha256='67f8be7c0cf420424bc62d8d7dc40b44e4bb2f7b515f9cc2954fb36e35797656') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-backports-functools-lru-cache@1.2.1:', type=('build', 'run'), when='^python@2.7:2.8') + depends_on('py-python-dateutil', type=('build', 'run')) + depends_on('py-chai', type='test') + depends_on('py-mock', type='test') + depends_on('py-pytz@2019.0:', type='test') diff --git a/var/spack/repos/builtin/packages/py-asciitree/package.py b/var/spack/repos/builtin/packages/py-asciitree/package.py new file mode 100644 index 0000000000..adbd103c5b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-asciitree/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAsciitree(PythonPackage): + """Draws ASCII trees.""" + + homepage = "https://github.com/mbr/asciitree" + url = "https://pypi.io/packages/source/a/asciitree/asciitree-0.3.3.tar.gz" + + version('0.3.3', sha256='4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-asdf/package.py b/var/spack/repos/builtin/packages/py-asdf/package.py index 4873c2a132..6fad12565d 100644 --- a/var/spack/repos/builtin/packages/py-asdf/package.py +++ b/var/spack/repos/builtin/packages/py-asdf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ase/package.py b/var/spack/repos/builtin/packages/py-ase/package.py index 39aaaea9ef..1e9c27921f 100644 --- a/var/spack/repos/builtin/packages/py-ase/package.py +++ b/var/spack/repos/builtin/packages/py-ase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-asn1crypto/package.py b/var/spack/repos/builtin/packages/py-asn1crypto/package.py index ad51bd828a..6f42673ef2 100644 --- a/var/spack/repos/builtin/packages/py-asn1crypto/package.py +++ b/var/spack/repos/builtin/packages/py-asn1crypto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-aspy-yaml/package.py b/var/spack/repos/builtin/packages/py-aspy-yaml/package.py new file mode 100644 index 0000000000..fb697e1f75 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-aspy-yaml/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAspyYaml(PythonPackage): + """Some extensions to pyyaml.""" + + homepage = "https://github.com/asottile/aspy.yaml/" + url = "https://pypi.io/packages/source/a/aspy.yaml/aspy.yaml-1.3.0.tar.gz" + + version('1.3.0', sha256='e7c742382eff2caed61f87a39d13f99109088e5e93f04d76eb8d4b28aa143f45') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-pyyaml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-asserts/package.py b/var/spack/repos/builtin/packages/py-asserts/package.py new file mode 100644 index 0000000000..36f9b16d98 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-asserts/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAsserts(PythonPackage): + """Stand-alone Assertions.""" + + homepage = "https://github.com/srittau/python-asserts" + url = "https://github.com/srittau/python-asserts/archive/v0.10.0.tar.gz" + + version('0.10.0', sha256='3466cf32c36d97ee2802121438003693546f590be81095317d0d698066bb5df7') + version('0.9.1', sha256='a73ea6b2ddc77364a5f0e13197f00662485944a6dd31c1f7555ff2f99c0f7319') + version('0.9.0', sha256='e3b8b06309234f9a7c6e4679e0f3cc127cf18da95c30fbb524ff47d439e22b17') + version('0.8.6', sha256='8a477746dbc501ac0d1fe9e593a1faafa7d361ceca79d994d3b2ebeecc7fbf32') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-astor/package.py b/var/spack/repos/builtin/packages/py-astor/package.py index 872941a377..38c77c5196 100644 --- a/var/spack/repos/builtin/packages/py-astor/package.py +++ b/var/spack/repos/builtin/packages/py-astor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,9 +14,16 @@ class PyAstor(PythonPackage): url = "https://pypi.io/packages/source/a/astor/astor-0.8.0.tar.gz" version('0.8.0', sha256='37a6eed8b371f1228db08234ed7f6cfdc7817a3ed3824797e20cbb11dc2a7862') - version('0.6', sha256='175ec395cde36aa0178c5a3120d03954c65d1ef4bb19ec4aa30e9d7a7cc426c4') + version('0.6', sha256='175ec395cde36aa0178c5a3120d03954c65d1ef4bb19ec4aa30e9d7a7cc426c4') - depends_on('python@2.7:2.8,3.4:') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-nose', type='test') depends_on('py-astunparse', type='test') + + # Build fails with newer versions of setuptools + # https://github.com/berkerpeksag/astor/issues/162 + # https://github.com/berkerpeksag/astor/pull/163 + patch('https://github.com/berkerpeksag/astor/pull/163/commits/30059dac4eb832e58ab2109db84508b294ba366d.patch', + sha256='edc5eeddabe153b08e938f52edaeb2d880ee3128082967f310db0f98510fe6e0', + when='@0.8.0') diff --git a/var/spack/repos/builtin/packages/py-astroid/package.py b/var/spack/repos/builtin/packages/py-astroid/package.py index fe4c4410e4..c75781daa9 100644 --- a/var/spack/repos/builtin/packages/py-astroid/package.py +++ b/var/spack/repos/builtin/packages/py-astroid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py index 1eb605e2d6..1e85cbf070 100644 --- a/var/spack/repos/builtin/packages/py-astropy/package.py +++ b/var/spack/repos/builtin/packages/py-astropy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-astunparse/package.py b/var/spack/repos/builtin/packages/py-astunparse/package.py index 3af8ed847b..87ca432f56 100644 --- a/var/spack/repos/builtin/packages/py-astunparse/package.py +++ b/var/spack/repos/builtin/packages/py-astunparse/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-async-generator/package.py b/var/spack/repos/builtin/packages/py-async-generator/package.py index 55cab55258..45d452d1d1 100644 --- a/var/spack/repos/builtin/packages/py-async-generator/package.py +++ b/var/spack/repos/builtin/packages/py-async-generator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-atomicwrites/package.py b/var/spack/repos/builtin/packages/py-atomicwrites/package.py index d2a8406547..de8ec7788b 100644 --- a/var/spack/repos/builtin/packages/py-atomicwrites/package.py +++ b/var/spack/repos/builtin/packages/py-atomicwrites/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-atropos/package.py b/var/spack/repos/builtin/packages/py-atropos/package.py index 2e92394a75..b08f3a818e 100644 --- a/var/spack/repos/builtin/packages/py-atropos/package.py +++ b/var/spack/repos/builtin/packages/py-atropos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-attrs/package.py b/var/spack/repos/builtin/packages/py-attrs/package.py index 1127684233..0c772a6219 100644 --- a/var/spack/repos/builtin/packages/py-attrs/package.py +++ b/var/spack/repos/builtin/packages/py-attrs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-autopep8/package.py b/var/spack/repos/builtin/packages/py-autopep8/package.py index c701382661..4cb29e5a55 100644 --- a/var/spack/repos/builtin/packages/py-autopep8/package.py +++ b/var/spack/repos/builtin/packages/py-autopep8/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py index 029745dec1..614d29196d 100644 --- a/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py +++ b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,9 +10,9 @@ class PyAvroJsonSerializer(PythonPackage): """Serializes data into a JSON format using AVRO schema.""" homepage = "https://github.com/linkedin/python-avro-json-serializer" - url = "https://github.com/linkedin/python-avro-json-serializer/archive/0.4.tar.gz" + url = "https://pypi.io/packages/source/a/avro_json_serializer/avro_json_serializer-0.4.tar.gz" - version('0.4', sha256='58df57e6c85b1b453668eb0bff2b049efcfd83d6e5dfa72cee1df220f330820d') + version('0.4', sha256='f9dac2dac92036c5dd5aba8c716545fc0a0630cc365a51ab15bc2ac47eac28f1') depends_on('py-setuptools', type='build') depends_on('py-simplejson', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-avro/package.py b/var/spack/repos/builtin/packages/py-avro/package.py index 4a90296429..35c903a411 100644 --- a/var/spack/repos/builtin/packages/py-avro/package.py +++ b/var/spack/repos/builtin/packages/py-avro/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-babel/package.py b/var/spack/repos/builtin/packages/py-babel/package.py index 8208ac3d72..efc1d5c61f 100644 --- a/var/spack/repos/builtin/packages/py-babel/package.py +++ b/var/spack/repos/builtin/packages/py-babel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-backcall/package.py b/var/spack/repos/builtin/packages/py-backcall/package.py index 1dbef69ac3..084f6f833b 100644 --- a/var/spack/repos/builtin/packages/py-backcall/package.py +++ b/var/spack/repos/builtin/packages/py-backcall/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-backports-abc/package.py b/var/spack/repos/builtin/packages/py-backports-abc/package.py index b0851e1420..5fec14d0ae 100644 --- a/var/spack/repos/builtin/packages/py-backports-abc/package.py +++ b/var/spack/repos/builtin/packages/py-backports-abc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py b/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py index 634638d5fa..aedc9c9ca7 100644 --- a/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py +++ b/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py b/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py index d06efbd5bb..43ea3b0cca 100644 --- a/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py +++ b/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,5 +19,5 @@ class PyBackportsShutilGetTerminalSize(PythonPackage): # newer setuptools version mess with "namespace" packages in an # incompatible way cf. https://github.com/pypa/setuptools/issues/900 - depends_on('py-setuptools@:30.999.999', type='build') + depends_on('py-setuptools@:30.999.999,41:', type='build') depends_on('python@:3.2') diff --git a/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py b/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py index 25582a47b4..5a3559edef 100644 --- a/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py +++ b/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-backports-tempfile/package.py b/var/spack/repos/builtin/packages/py-backports-tempfile/package.py index 59863d19d7..b3771f02e1 100644 --- a/var/spack/repos/builtin/packages/py-backports-tempfile/package.py +++ b/var/spack/repos/builtin/packages/py-backports-tempfile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-backports-weakref/package.py b/var/spack/repos/builtin/packages/py-backports-weakref/package.py index 566a0841a0..b3e5ad65bc 100644 --- a/var/spack/repos/builtin/packages/py-backports-weakref/package.py +++ b/var/spack/repos/builtin/packages/py-backports-weakref/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,7 @@ class PyBackportsWeakref(PythonPackage): homepage = "https://github.com/PiDelport/backports.weakref" url = "https://pypi.org/packages/source/b/backports.weakref/backports.weakref-1.0.post1.tar.gz" - version('1.0.post1', sha256='bc4170a29915f8b22c9e7c4939701859650f2eb84184aee80da329ac0b9825c2') + version('1.0.post1', sha256='bc4170a29915f8b22c9e7c4939701859650f2eb84184aee80da329ac0b9825c2', preferred=True) + version('1.0rc1', sha256='8813bf712a66b3d8b85dc289e1104ed220f1878cf981e2fe756dfaabe9a82892') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-basemap/package.py b/var/spack/repos/builtin/packages/py-basemap/package.py index 1403e24e9a..cc062ef347 100644 --- a/var/spack/repos/builtin/packages/py-basemap/package.py +++ b/var/spack/repos/builtin/packages/py-basemap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,8 +22,7 @@ class PyBasemap(PythonPackage): depends_on('py-setuptools', type=('build', 'run')) depends_on('py-numpy', type=('build', 'run')) depends_on('py-matplotlib', type=('build', 'run')) - depends_on('py-pyproj@:1.99', type=('build', 'run'), when='@:1.2.0') - depends_on('py-pyproj', type=('build', 'run')) + depends_on('py-pyproj@:1.99', type=('build', 'run')) depends_on('py-pyshp', type=('build', 'run')) depends_on('pil', type=('build', 'run')) depends_on('geos') @@ -34,8 +33,8 @@ class PyBasemap(PythonPackage): else: return 'https://downloads.sourceforge.net/project/matplotlib/matplotlib-toolkits/basemap-{0}/basemap-{0}.tar.gz'.format(version) - def setup_environment(self, spack_env, run_env): - spack_env.set('GEOS_DIR', self.spec['geos'].prefix) + def setup_build_environment(self, env): + env.set('GEOS_DIR', self.spec['geos'].prefix) def install(self, spec, prefix): """Install everything from build directory.""" diff --git a/var/spack/repos/builtin/packages/py-bcbio-gff/package.py b/var/spack/repos/builtin/packages/py-bcbio-gff/package.py index f5ee74a636..68e6abd7a3 100644 --- a/var/spack/repos/builtin/packages/py-bcbio-gff/package.py +++ b/var/spack/repos/builtin/packages/py-bcbio-gff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-bcrypt/package.py b/var/spack/repos/builtin/packages/py-bcrypt/package.py new file mode 100644 index 0000000000..1b64063991 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-bcrypt/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyBcrypt(PythonPackage): + """Modern password hashing for your software and your servers""" + + homepage = "https://github.com/pyca/bcrypt/" + url = "https://github.com/pyca/bcrypt/archive/3.1.4.tar.gz" + + version('3.1.4', sha256='ca122a2cdcdffb0fd04f9dfe3493766f298bef02dea2f190f35ea6fdee222b96') + + depends_on('py-setuptools', type='build') + depends_on('py-cffi@1.1:', type=('build', 'run')) + depends_on('py-six@1.4.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py index 8a9febcdae..5544150207 100644 --- a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py +++ b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-billiard/package.py b/var/spack/repos/builtin/packages/py-billiard/package.py new file mode 100644 index 0000000000..d70e0b676e --- /dev/null +++ b/var/spack/repos/builtin/packages/py-billiard/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyBilliard(PythonPackage): + """Python multiprocessing fork with improvements and bugfixes""" + + homepage = "https://pypi.org/project/billiard/" + url = "https://pypi.io/packages/source/b/billiard/billiard-3.5.0.5.tar.gz" + + version('3.6.1.0', sha256='b8809c74f648dfe69b973c8e660bcec00603758c9db8ba89d7719f88d5f01f26') + version('3.6.0.0', sha256='756bf323f250db8bf88462cd042c992ba60d8f5e07fc5636c24ba7d6f4261d84') + version('3.5.0.5', sha256='42d9a227401ac4fba892918bba0a0c409def5435c4b483267ebfe821afaaba0e') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-bintrees/package.py b/var/spack/repos/builtin/packages/py-bintrees/package.py index 196d94fca3..b832d60d87 100644 --- a/var/spack/repos/builtin/packages/py-bintrees/package.py +++ b/var/spack/repos/builtin/packages/py-bintrees/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-binwalk/package.py b/var/spack/repos/builtin/packages/py-binwalk/package.py index da9a351936..fce4309425 100644 --- a/var/spack/repos/builtin/packages/py-binwalk/package.py +++ b/var/spack/repos/builtin/packages/py-binwalk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-biom-format/package.py b/var/spack/repos/builtin/packages/py-biom-format/package.py index b316ff2ab0..fae9305010 100644 --- a/var/spack/repos/builtin/packages/py-biom-format/package.py +++ b/var/spack/repos/builtin/packages/py-biom-format/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-biomine/package.py b/var/spack/repos/builtin/packages/py-biomine/package.py index dad9ad3790..8326bf8e99 100644 --- a/var/spack/repos/builtin/packages/py-biomine/package.py +++ b/var/spack/repos/builtin/packages/py-biomine/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-biopython/package.py b/var/spack/repos/builtin/packages/py-biopython/package.py index e9789eb1d3..df5694de42 100644 --- a/var/spack/repos/builtin/packages/py-biopython/package.py +++ b/var/spack/repos/builtin/packages/py-biopython/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-bitarray/package.py b/var/spack/repos/builtin/packages/py-bitarray/package.py index 87763f26e4..e0efb22763 100644 --- a/var/spack/repos/builtin/packages/py-bitarray/package.py +++ b/var/spack/repos/builtin/packages/py-bitarray/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-bitstring/package.py b/var/spack/repos/builtin/packages/py-bitstring/package.py index 049584cfe6..7d96b435dd 100644 --- a/var/spack/repos/builtin/packages/py-bitstring/package.py +++ b/var/spack/repos/builtin/packages/py-bitstring/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-black/package.py b/var/spack/repos/builtin/packages/py-black/package.py index 33ab98b455..913b2592c8 100644 --- a/var/spack/repos/builtin/packages/py-black/package.py +++ b/var/spack/repos/builtin/packages/py-black/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,9 +12,10 @@ class PyBlack(PythonPackage): speed, determinism, and freedom from pycodestyle nagging about formatting. """ - homepage = "https://github.com/ambv/black" + homepage = "https://github.com/psf/black" url = "https://pypi.io/packages/source/b/black/black-18.9b0.tar.gz" + version('19.3b0', sha256='68950ffd4d9169716bcb8719a56c07a2f4485354fec061cdd5910aa07369731c') version('18.9b0', sha256='e030a9a28f542debc08acceb273f228ac422798e5215ba2a791a6ddeaaca22a5') depends_on('python@3.6.0:') diff --git a/var/spack/repos/builtin/packages/py-bleach/package.py b/var/spack/repos/builtin/packages/py-bleach/package.py index 97cff7caac..bf01b9f223 100644 --- a/var/spack/repos/builtin/packages/py-bleach/package.py +++ b/var/spack/repos/builtin/packages/py-bleach/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-blessed/package.py b/var/spack/repos/builtin/packages/py-blessed/package.py index 5f5f7f0fdc..45b5b3b84c 100644 --- a/var/spack/repos/builtin/packages/py-blessed/package.py +++ b/var/spack/repos/builtin/packages/py-blessed/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-blessings/package.py b/var/spack/repos/builtin/packages/py-blessings/package.py index 5d69833a8e..9f563b308e 100644 --- a/var/spack/repos/builtin/packages/py-blessings/package.py +++ b/var/spack/repos/builtin/packages/py-blessings/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-blinker/package.py b/var/spack/repos/builtin/packages/py-blinker/package.py index 5777204f52..dd77fedbe0 100644 --- a/var/spack/repos/builtin/packages/py-blinker/package.py +++ b/var/spack/repos/builtin/packages/py-blinker/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-bokeh/package.py b/var/spack/repos/builtin/packages/py-bokeh/package.py index 1f8ad21519..7497efc23b 100644 --- a/var/spack/repos/builtin/packages/py-bokeh/package.py +++ b/var/spack/repos/builtin/packages/py-bokeh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-boltons/package.py b/var/spack/repos/builtin/packages/py-boltons/package.py index b8d33c6cf7..3ecf04e2c1 100644 --- a/var/spack/repos/builtin/packages/py-boltons/package.py +++ b/var/spack/repos/builtin/packages/py-boltons/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-boto3/package.py b/var/spack/repos/builtin/packages/py-boto3/package.py index d76ee27abf..e31d3b8110 100644 --- a/var/spack/repos/builtin/packages/py-boto3/package.py +++ b/var/spack/repos/builtin/packages/py-boto3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,16 +10,20 @@ class PyBoto3(PythonPackage): """The AWS SDK for Python.""" homepage = "https://github.com/boto/boto3" - url = "https://pypi.io/packages/source/b/boto3/boto3-1.9.169.tar.gz" + url = "https://pypi.io/packages/source/b/boto3/boto3-1.10.44.tar.gz" import_modules = [ 'boto3', 'boto3.s3', 'boto3.resources', 'boto3.dynamodb', 'boto3.docs', 'boto3.ec2' ] + version('1.10.44', sha256='adc0c0269bd65967fd528d7cd826304f381d40d94f2bf2b09f58167e5ac05d86') + version('1.10.38', sha256='6cdb063b2ae5ac7b93ded6b6b17e3da1325b32232d5ff56e6800018d4786bba6') version('1.9.169', sha256='9d8bd0ca309b01265793b7e8d7b88c1df439737d77c8725988f0277bbf58d169') depends_on('py-setuptools', type='build') - depends_on('py-botocore@1.12.169:1.12.999', type=('build', 'run')) + depends_on('py-botocore@1.13.44:1.13.999', when='@1.10.44', type=('build', 'run')) + depends_on('py-botocore@1.13.38:1.13.999', when='@1.10.38', type=('build', 'run')) + depends_on('py-botocore@1.12.169:1.12.999', when='@1.9.169', type=('build', 'run')) depends_on('py-jmespath@0.7.1:0.999', type=('build', 'run')) depends_on('py-s3transfer@0.2.0:0.2.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-botocore/package.py b/var/spack/repos/builtin/packages/py-botocore/package.py index 16877560a2..7b05bf0c72 100644 --- a/var/spack/repos/builtin/packages/py-botocore/package.py +++ b/var/spack/repos/builtin/packages/py-botocore/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,15 +10,17 @@ class PyBotocore(PythonPackage): """Low-level, data-driven core of boto 3.""" homepage = "https://github.com/boto/botocore" - url = "https://pypi.io/packages/source/b/botocore/botocore-1.12.169.tar.gz" + url = "https://pypi.io/packages/source/b/botocore/botocore-1.13.44.tar.gz" import_modules = ['botocore'] + version('1.13.44', sha256='a4409008c32a3305b9c469c5cc92edb5b79d6fcbf6f56fe126886b545f0a4f3f') + version('1.13.38', sha256='15766a367f39dba9de3c6296aaa7da31030f08a0117fd12685e7df682d8acee2') version('1.12.169', sha256='25b44c3253b5ed1c9093efb57ffca440c5099a2d62fa793e8b6c52e72f54b01e') depends_on('py-setuptools', type='build') depends_on('py-jmespath@0.7.1:0.999', type=('build', 'run')) - depends_on('py-docutils@0.10:', type=('build', 'run')) + depends_on('py-docutils@0.10:0.15', type=('build', 'run')) depends_on('py-ordereddict@1.1', type=('build', 'run'), when='^python@2.6.0:2.6.999') depends_on('py-simplejson@3.3.0', type=('build', 'run'), when='^python@2.6.0:2.6.999') depends_on('py-python-dateutil@2.1:2.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py index f1b246cb2f..8870b3197c 100644 --- a/var/spack/repos/builtin/packages/py-bottleneck/package.py +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-breakseq2/package.py b/var/spack/repos/builtin/packages/py-breakseq2/package.py index 4a4e72911f..9c295e7023 100644 --- a/var/spack/repos/builtin/packages/py-breakseq2/package.py +++ b/var/spack/repos/builtin/packages/py-breakseq2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-breathe/package.py b/var/spack/repos/builtin/packages/py-breathe/package.py index 24174992f7..107f55f97c 100644 --- a/var/spack/repos/builtin/packages/py-breathe/package.py +++ b/var/spack/repos/builtin/packages/py-breathe/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-brian/package.py b/var/spack/repos/builtin/packages/py-brian/package.py index f00c3ea6e5..770c19340f 100644 --- a/var/spack/repos/builtin/packages/py-brian/package.py +++ b/var/spack/repos/builtin/packages/py-brian/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-brian2/package.py b/var/spack/repos/builtin/packages/py-brian2/package.py index 5ebb9f85bc..0e7a7bf31d 100644 --- a/var/spack/repos/builtin/packages/py-brian2/package.py +++ b/var/spack/repos/builtin/packages/py-brian2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,20 +10,23 @@ class PyBrian2(PythonPackage): """A clock-driven simulator for spiking neural networks""" homepage = "http://www.briansimulator.org" - url = "https://pypi.io/packages/source/B/Brian2/Brian2-2.0.1.tar.gz" - - version('2.0.1', sha256='195d8ced0d20e9069917776948f92aa70b7457bbc6b5222b8199654402ee1153') - version('2.0rc3', sha256='05f347f5fa6b25d1ce5ec152a2407bbce033599eb6664f32f5331946eb3c7d66') - - variant('doc', default=False, description='Build the documentation') - - # depends on py-setuptools@6: for windows, if spack targets windows, - # this will need to be added here - depends_on('py-setuptools', type='build') - depends_on('py-numpy@1.8.2:', type=('build', 'run')) - depends_on('py-sympy@0.7.6:', type=('build', 'run')) - depends_on('py-pyparsing', type=('build', 'run')) - depends_on('py-jinja2@2.7:', type=('build', 'run')) - depends_on('py-cpuinfo@0.1.6:', type=('build', 'run')) - depends_on('py-sphinx@1.4.2:', type=('build', 'run'), when='+docs') - depends_on('py-nosetests@1.0:', type='test') + url = "https://pypi.io/packages/source/B/Brian2/Brian2-2.2.2.1.tar.gz" + + version('2.2.2.1', sha256='02075f66d42fd243fc5e28e1add8862709ae9fdabaffb69858e6d7f684a91525') + version('2.0.1', sha256='195d8ced0d20e9069917776948f92aa70b7457bbc6b5222b8199654402ee1153') + version('2.0rc3', sha256='05f347f5fa6b25d1ce5ec152a2407bbce033599eb6664f32f5331946eb3c7d66') + + variant('docs', default=False, description='Build the documentation') + + depends_on('python@2.7:', type=('build', 'run')) + depends_on('py-numpy@1.10:', type=('build', 'run')) + depends_on('py-cython@0.29:', type=('build', 'run')) + depends_on('py-sympy@0.7.6:1.0,1.1.1:', type=('build', 'run')) + depends_on('py-pyparsing', type=('build', 'run')) + depends_on('py-jinja2@2.7:', type=('build', 'run')) + depends_on('py-setuptools@21:', type=('build', 'run')) + depends_on('py-sphinx@1.5:', type=('build', 'run'), when='+docs') + depends_on('py-nose@1.0:', type='test') + + def build_args(self, spec, prefix): + return ['--with-cython'] diff --git a/var/spack/repos/builtin/packages/py-brotlipy/package.py b/var/spack/repos/builtin/packages/py-brotlipy/package.py index 82f63e7764..e83bcafea0 100644 --- a/var/spack/repos/builtin/packages/py-brotlipy/package.py +++ b/var/spack/repos/builtin/packages/py-brotlipy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-bsddb3/package.py b/var/spack/repos/builtin/packages/py-bsddb3/package.py index 842ad1b9f1..9dcff4735c 100644 --- a/var/spack/repos/builtin/packages/py-bsddb3/package.py +++ b/var/spack/repos/builtin/packages/py-bsddb3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-bx-python/package.py b/var/spack/repos/builtin/packages/py-bx-python/package.py index 77fcace1eb..ee4dfff7fc 100644 --- a/var/spack/repos/builtin/packages/py-bx-python/package.py +++ b/var/spack/repos/builtin/packages/py-bx-python/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-bz2file/package.py b/var/spack/repos/builtin/packages/py-bz2file/package.py index 908df4dc7c..796e08250f 100644 --- a/var/spack/repos/builtin/packages/py-bz2file/package.py +++ b/var/spack/repos/builtin/packages/py-bz2file/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cached-property/package.py b/var/spack/repos/builtin/packages/py-cached-property/package.py new file mode 100644 index 0000000000..96dada29d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cached-property/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyCachedProperty(PythonPackage): + """A decorator for caching properties in classes.""" + + homepage = "https://pypi.org/project/cached-property/" + url = "https://pypi.io/packages/source/c/cached-property/cached-property-1.5.1.tar.gz" + + version('1.5.1', sha256="9217a59f14a5682da7c4b8829deadbfc194ac22e9908ccf7c8820234e80a1504") + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-cachetools/package.py b/var/spack/repos/builtin/packages/py-cachetools/package.py index 1a2db35d23..a35b423504 100644 --- a/var/spack/repos/builtin/packages/py-cachetools/package.py +++ b/var/spack/repos/builtin/packages/py-cachetools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cairocffi/package.py b/var/spack/repos/builtin/packages/py-cairocffi/package.py index ccc9b83ef1..d4cf1ca37c 100644 --- a/var/spack/repos/builtin/packages/py-cairocffi/package.py +++ b/var/spack/repos/builtin/packages/py-cairocffi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cartopy/package.py b/var/spack/repos/builtin/packages/py-cartopy/package.py index b00c71645c..feb7d8eba7 100644 --- a/var/spack/repos/builtin/packages/py-cartopy/package.py +++ b/var/spack/repos/builtin/packages/py-cartopy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,7 @@ class PyCartopy(PythonPackage): homepage = "http://scitools.org.uk/cartopy/" url = "https://github.com/SciTools/cartopy/archive/v0.16.0.tar.gz" + version('0.17.0', sha256='137642e63952404ec0841fa0333ad14c58fbbf19cca2a5ac6a38498c4b4998fb') version('0.16.0', sha256='cadf62434492c965220b37f0548bc58180466ad6894a1db57dbc51cd43467e5c') depends_on('py-setuptools@0.7.2:', type='build') @@ -21,17 +22,24 @@ class PyCartopy(PythonPackage): depends_on('py-pyshp@1.1.4:', type=('build', 'run')) depends_on('py-six@1.3.0:', type=('build', 'run')) depends_on('geos@3.3.3:') - depends_on('proj@4.9.0:5') + depends_on('proj@4.9.0:5', when='@0.16.0') + depends_on('proj@4.9:', when='@0.17.0') + + variant('epsg', default=True, description='Add support for epsg.io') + variant('ows', default=True, description='Add support for Open Geospatial Consortium (OGC) web service') + variant('plotting', default=True, description='Add plotting functionality') # optional dependecies - depends_on('py-matplotlib@1.5.1:', type=('build', 'run')) - depends_on('gdal@1.10.0:+python', type=('build', 'run')) - depends_on('py-pillow@1.7.8:', type=('build', 'run')) - depends_on('py-pyepsg@0.2.0:', type=('build', 'run')) - depends_on('py-scipy@0.10:', type=('build', 'run')) - depends_on('py-owslib@0.8.11:', type=('build', 'run')) + depends_on('py-matplotlib@1.5.1:', type=('build', 'run'), when='+plotting') + depends_on('gdal@1.10.0:+python', type=('build', 'run'), when='+plotting') + depends_on('py-pillow@1.7.8:', type=('build', 'run'), when='+ows') + depends_on('py-pillow@1.7.8:', type=('build', 'run'), when='+plotting') + depends_on('py-pyepsg@0.2.0:', type=('build', 'run'), when='+epsg') + depends_on('py-scipy@0.10:', type=('build', 'run'), when='+plotting') + depends_on('py-owslib@0.8.11:', type=('build', 'run'), when='+ows') # testing dependencies + depends_on('py-filelock', type='test') depends_on('py-mock@1.0.1', type='test') depends_on('py-pytest@3.0.0:', type='test') @@ -41,4 +49,8 @@ class PyCartopy(PythonPackage): args = ['-I{0}'.format(spec['proj'].prefix.include), '-L{0}'.format(spec['proj'].prefix.lib) ] + + if spec.satisfies('@0.17.0 ^proj@6'): + args.append('-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H') + return args diff --git a/var/spack/repos/builtin/packages/py-cclib/package.py b/var/spack/repos/builtin/packages/py-cclib/package.py index 98b7c315da..c7801a86a0 100644 --- a/var/spack/repos/builtin/packages/py-cclib/package.py +++ b/var/spack/repos/builtin/packages/py-cclib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cdat-lite/package.py b/var/spack/repos/builtin/packages/py-cdat-lite/package.py index facb14a43f..db51d6e3ec 100644 --- a/var/spack/repos/builtin/packages/py-cdat-lite/package.py +++ b/var/spack/repos/builtin/packages/py-cdat-lite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,7 +17,7 @@ class PyCdatLite(PythonPackage): version('6.0.1', sha256='092ae4ff1fb03dee00096e8dd595b769b422759ce972d96525950adf8e1c9374') - depends_on("netcdf") + depends_on("netcdf-c") depends_on("python@2.5:2.8", type=('build', 'run')) depends_on("py-numpy", type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-cdo/package.py b/var/spack/repos/builtin/packages/py-cdo/package.py index d61cb0ff0c..674900d87d 100644 --- a/var/spack/repos/builtin/packages/py-cdo/package.py +++ b/var/spack/repos/builtin/packages/py-cdo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cdsapi/package.py b/var/spack/repos/builtin/packages/py-cdsapi/package.py index aa0d412de5..7d5ed6c865 100644 --- a/var/spack/repos/builtin/packages/py-cdsapi/package.py +++ b/var/spack/repos/builtin/packages/py-cdsapi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-celery/package.py b/var/spack/repos/builtin/packages/py-celery/package.py new file mode 100644 index 0000000000..69189209f3 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-celery/package.py @@ -0,0 +1,57 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyCelery(PythonPackage): + """Celery - Distributed Task Queue.""" + + homepage = "https://pypi.org/project/celery/" + url = "https://pypi.io/packages/source/c/celery/celery-4.2.1.tar.gz" + + version('4.3.0', sha256='4c4532aa683f170f40bd76f928b70bc06ff171a959e06e71bf35f2f9d6031ef9') + + variant('redis', default=False, description="Use redis transport") + # 'auth', + # 'cassandra', + # 'django', + # 'elasticsearch', + # 'memcache', + # 'pymemcache', + # 'couchbase', + # 'arangodb', + # 'eventlet', + # 'rabbitmq' + # 'gevent', + # 'msgpack', + # 'yaml', + # 'sqs', + # 'couchdb', + # 'riak', + # 'zookeeper', + # 'solar', + # 'sqlalchemy', + # 'azureblockblob', + # 'librabbitmq', + # 'pyro', + # 'slmq', + # 'tblib', + # 'consul', + # 'dynamodb', + # 'mongodb', + # 'cosmosdbsql', + # 's3', + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + + depends_on('py-setuptools', type=('build', 'run')) + + depends_on('py-redis@3.2.0:', when='+redis', type=('build', 'run')) + + depends_on('py-pytz@2019.3:', type=('build', 'run')) + depends_on('py-billiard@3.6.0:3.999', type=('build', 'run')) + depends_on('py-kombu@4.4.0:4.999', type=('build', 'run')) + depends_on('py-vine@1.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-certifi/package.py b/var/spack/repos/builtin/packages/py-certifi/package.py index e93c088631..68a1b9c4a9 100644 --- a/var/spack/repos/builtin/packages/py-certifi/package.py +++ b/var/spack/repos/builtin/packages/py-certifi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-certipy/package.py b/var/spack/repos/builtin/packages/py-certipy/package.py index 7bbf223d90..1fe73e8dc7 100644 --- a/var/spack/repos/builtin/packages/py-certipy/package.py +++ b/var/spack/repos/builtin/packages/py-certipy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cf-units/package.py b/var/spack/repos/builtin/packages/py-cf-units/package.py index aaa2505d10..07f062dca9 100644 --- a/var/spack/repos/builtin/packages/py-cf-units/package.py +++ b/var/spack/repos/builtin/packages/py-cf-units/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,4 +26,4 @@ class PyCfUnits(PythonPackage): depends_on('py-numpy', type=('build', 'run')) depends_on('py-antlr4-python3-runtime', type=('build', 'run')) depends_on('py-pytest-runner', type=('build')) - depends_on('udunits2') + depends_on('udunits') diff --git a/var/spack/repos/builtin/packages/py-cffi/package.py b/var/spack/repos/builtin/packages/py-cffi/package.py index e61aa14c67..3035ce295f 100644 --- a/var/spack/repos/builtin/packages/py-cffi/package.py +++ b/var/spack/repos/builtin/packages/py-cffi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cfgv/package.py b/var/spack/repos/builtin/packages/py-cfgv/package.py new file mode 100644 index 0000000000..a9465eb0fc --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cfgv/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyCfgv(PythonPackage): + """Validate configuration and produce human readable error messages.""" + + homepage = "https://github.com/asottile/cfgv/" + url = "https://pypi.io/packages/source/c/cfgv/cfgv-2.0.1.tar.gz" + + version('2.0.1', sha256='edb387943b665bf9c434f717bf630fa78aecd53d5900d2e05da6ad6048553144') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cftime/package.py b/var/spack/repos/builtin/packages/py-cftime/package.py index 6f2a0ddb77..284284391a 100644 --- a/var/spack/repos/builtin/packages/py-cftime/package.py +++ b/var/spack/repos/builtin/packages/py-cftime/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-chai/package.py b/var/spack/repos/builtin/packages/py-chai/package.py new file mode 100644 index 0000000000..f2e7ff7f54 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-chai/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyChai(PythonPackage): + """Chai - Python Mocking Made Easy""" + + homepage = "https://github.com/agoragames/chai" + url = "https://pypi.io/packages/source/c/chai/chai-1.1.2.tar.gz" + + version('1.1.2', sha256='ff8d2b6855f660cd23cd5ec79bd10264d39f24f6235773331b48e7fcd637d6cc') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-chardet/package.py b/var/spack/repos/builtin/packages/py-chardet/package.py index d8d640d3ac..d9360bd277 100644 --- a/var/spack/repos/builtin/packages/py-chardet/package.py +++ b/var/spack/repos/builtin/packages/py-chardet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-checkm-genome/package.py b/var/spack/repos/builtin/packages/py-checkm-genome/package.py index 2b99071d4a..cc1bee25c9 100644 --- a/var/spack/repos/builtin/packages/py-checkm-genome/package.py +++ b/var/spack/repos/builtin/packages/py-checkm-genome/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cheetah/package.py b/var/spack/repos/builtin/packages/py-cheetah/package.py index aaf1a3a45d..d150293c56 100644 --- a/var/spack/repos/builtin/packages/py-cheetah/package.py +++ b/var/spack/repos/builtin/packages/py-cheetah/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cheroot/package.py b/var/spack/repos/builtin/packages/py-cheroot/package.py new file mode 100644 index 0000000000..0732907fbd --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cheroot/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyCheroot(PythonPackage): + """ Highly-optimized, pure-python HTTP server """ + + homepage = "https://cheroot.cherrypy.org/" + url = "https://pypi.io/packages/source/c/cheroot/cheroot-6.5.5.tar.gz" + + version( + '6.5.5', sha256='f6a85e005adb5bc5f3a92b998ff0e48795d4d98a0fbb7edde47a7513d4100601') + + depends_on('py-setuptools', type='build') + depends_on('py-setuptools-scm@1.15.0:', type='build') + depends_on('py-setuptools-scm-git-archive@1.0:', type='build') + depends_on('py-more-itertools@2.6:', type=('build', 'run')) + depends_on('py-six@1.11.0:', type=('build', 'run')) + depends_on('py-backports-functools-lru-cache', type=('build', 'run')) + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cherrypy/package.py b/var/spack/repos/builtin/packages/py-cherrypy/package.py new file mode 100644 index 0000000000..848d185303 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cherrypy/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyCherrypy(PythonPackage): + """CherryPy is a pythonic, object-oriented HTTP framework.""" + + homepage = "https://cherrypy.org/" + url = "https://pypi.io/packages/source/C/CherryPy/CherryPy-18.1.1.tar.gz" + + version('18.1.1', sha256='6585c19b5e4faffa3613b5bf02c6a27dcc4c69a30d302aba819639a2af6fa48b') + + depends_on('py-setuptools', type='build') + depends_on('py-setuptools-scm', type='build') + depends_on('py-more-itertools', type=('build', 'run')) + depends_on('py-zc-lockfile', type=('build', 'run')) + depends_on('py-cheroot@6.2.4:', type=('build', 'run')) + depends_on('py-portend@2.1.1:', type=('build', 'run')) + depends_on('python@3.5:', when='@18.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cinema-lib/package.py b/var/spack/repos/builtin/packages/py-cinema-lib/package.py new file mode 100644 index 0000000000..8034e9c7a1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cinema-lib/package.py @@ -0,0 +1,41 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyCinemaLib(PythonPackage): + """cinema_lib is a set of tools and library for interacting with a + Cinema database (currently Spec A and Spec D) through Python and + the command line tool, cinema.""" + + homepage = "https://cinemascience.github.io/" + url = "https://github.com/cinemascience/cinema_lib/archive/1.2.1.tar.gz" + git = "https://github.com/cinemascience/cinema_lib.git" + + maintainers = ['EthanS94'] + + version('master', branch='master') + version('1.2.1', sha256='13c6c7b3df7dae3e05c2f44009b7c149841f604b7c51f36067bbcea9e2d088eb') + version('1.2.0', sha256='f76b55517b7cfe7311d953426e08ce364b2e7e1cf84699828c229dd068ee3a08') + version('1.1.1', sha256='90001554b0f3207d57da9fcab768732449d89a9d5bf54cfe0928a76649caebe8') + version('1.1.0', sha256='2bd1787106643fd533e899a7e1b0f57f3933cde8c907e762f38ca95ac10316fd') + version('1.0.2', sha256='3ebe52546e1325bd23732cd171146dbb2a9e0c25ac616224bf6f8fff9e8d48b1') + version('1.0.1', sha256='5c2d220aa1dc28aec18f73c5cf0c4be3c834fffa0580e85b07050ff46364095d') + version('1.0.0', sha256='9e2967fd22f1b1324ca2579df6501d0bfbc5fb142ca41c7a02f9b7d109767d3c') + version('ECPMilestone201806', sha256='dfb7b1d0e3d8d1865814622879ddb019c2a16efb947201832a56a98186ff46ce') + + variant('image', default=True, + description='Enable image-processing algorithms from scikit-image') + variant('opencv', default=False, + description='Enable computer vision algorithms from OpenCV') + + depends_on('python@3.6:', type=('build', 'run')) + depends_on('py-numpy@1.13:', when='+image', type=('build', 'run')) + depends_on('py-numpy@1.13:', when='+opencv', type=('build', 'run')) + depends_on('py-scikit-image@0.13.1:', when='+image', + type=('build', 'run')) + depends_on('opencv@3.4:+python', when='+opencv', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-click-plugins/package.py b/var/spack/repos/builtin/packages/py-click-plugins/package.py index bb94c4af5f..33ec97c648 100644 --- a/var/spack/repos/builtin/packages/py-click-plugins/package.py +++ b/var/spack/repos/builtin/packages/py-click-plugins/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-click/package.py b/var/spack/repos/builtin/packages/py-click/package.py index 70f58ed077..6e19441d39 100644 --- a/var/spack/repos/builtin/packages/py-click/package.py +++ b/var/spack/repos/builtin/packages/py-click/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cligj/package.py b/var/spack/repos/builtin/packages/py-cligj/package.py index 72a8d507c0..f35a0ef68f 100644 --- a/var/spack/repos/builtin/packages/py-cligj/package.py +++ b/var/spack/repos/builtin/packages/py-cligj/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-clipboard/package.py b/var/spack/repos/builtin/packages/py-clipboard/package.py index f047eb1cc4..b80f58d098 100644 --- a/var/spack/repos/builtin/packages/py-clipboard/package.py +++ b/var/spack/repos/builtin/packages/py-clipboard/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cloudpickle/package.py b/var/spack/repos/builtin/packages/py-cloudpickle/package.py index 1be2b8d35f..ff1e459e09 100644 --- a/var/spack/repos/builtin/packages/py-cloudpickle/package.py +++ b/var/spack/repos/builtin/packages/py-cloudpickle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-codecov/package.py b/var/spack/repos/builtin/packages/py-codecov/package.py index 0415ceccae..f824ad329d 100644 --- a/var/spack/repos/builtin/packages/py-codecov/package.py +++ b/var/spack/repos/builtin/packages/py-codecov/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cogent/package.py b/var/spack/repos/builtin/packages/py-cogent/package.py index 62b13b4aff..8605e05bea 100644 --- a/var/spack/repos/builtin/packages/py-cogent/package.py +++ b/var/spack/repos/builtin/packages/py-cogent/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,7 @@ class PyCogent(PythonPackage): url = "https://pypi.io/packages/source/c/cogent/cogent-1.9.tar.gz" version('1.9', sha256='57d8c58e0273ffe4f2b907874f9b49dadfd0600f5507b7666369f4e44d56ce14') - version('1.5.3', url="https://pypi.io/packages/source/c/cogent/cogent-1.5.3.tgz", + version('1.5.3', url="https://pypi.io/packages/source/c/cogent/cogent-1.5.3.tgz", sha256='1215ac219070b7b2207b0b47b4388510f3e30ccd88160aa9f02f25d24bcbcd95') variant('matplotlib', default=False, description="graphs related to codon usage") @@ -30,5 +30,5 @@ class PyCogent(PythonPackage): depends_on('py-pymysql', when='+mysql', type=('build', 'run')) depends_on('py-cython@0.17.1:', type='build') - def setup_environment(self, spack_env, run_env): - spack_env.set('DONT_USE_PYREX', '1') + def setup_build_environment(self, env): + env.set('DONT_USE_PYREX', '1') diff --git a/var/spack/repos/builtin/packages/py-colorama/package.py b/var/spack/repos/builtin/packages/py-colorama/package.py index 073279d838..be101dc938 100644 --- a/var/spack/repos/builtin/packages/py-colorama/package.py +++ b/var/spack/repos/builtin/packages/py-colorama/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,8 @@ class PyColorama(PythonPackage): homepage = "https://github.com/tartley/colorama" url = "https://pypi.io/packages/source/c/colorama/colorama-0.3.7.tar.gz" + version('0.4.1', sha256='05eed71e2e327246ad6b38c540c4a3117230b19679b875190486ddd2d721422d') version('0.3.7', sha256='e043c8d32527607223652021ff648fbb394d5e19cba9f1a698670b338c9d782b') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-coloredlogs/package.py b/var/spack/repos/builtin/packages/py-coloredlogs/package.py new file mode 100644 index 0000000000..58caed8c1b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-coloredlogs/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyColoredlogs(PythonPackage): + """Colored terminal output for Python's logging module""" + + homepage = "https://pypi.org/project/coloredlogs/" + url = "https://pypi.io/packages/source/c/coloredlogs/coloredlogs-10.0.tar.gz" + + version('10.0', sha256='b869a2dda3fa88154b9dd850e27828d8755bfab5a838a1c97fbc850c6e377c36') + + depends_on('py-setuptools', type='build') + depends_on('py-humanfriendly@4.7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-colorlog/package.py b/var/spack/repos/builtin/packages/py-colorlog/package.py index 5a51f77ad8..7eb42c2976 100644 --- a/var/spack/repos/builtin/packages/py-colorlog/package.py +++ b/var/spack/repos/builtin/packages/py-colorlog/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-colormath/package.py b/var/spack/repos/builtin/packages/py-colormath/package.py index 676360334d..b190cdd418 100644 --- a/var/spack/repos/builtin/packages/py-colormath/package.py +++ b/var/spack/repos/builtin/packages/py-colormath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-colorpy/package.py b/var/spack/repos/builtin/packages/py-colorpy/package.py index 672badc0c5..da11077eaf 100644 --- a/var/spack/repos/builtin/packages/py-colorpy/package.py +++ b/var/spack/repos/builtin/packages/py-colorpy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-configobj/package.py b/var/spack/repos/builtin/packages/py-configobj/package.py index ef92a59475..6b8521405d 100644 --- a/var/spack/repos/builtin/packages/py-configobj/package.py +++ b/var/spack/repos/builtin/packages/py-configobj/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-configparser/package.py b/var/spack/repos/builtin/packages/py-configparser/package.py index a7804645ef..7a4109552c 100644 --- a/var/spack/repos/builtin/packages/py-configparser/package.py +++ b/var/spack/repos/builtin/packages/py-configparser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-contextlib2/package.py b/var/spack/repos/builtin/packages/py-contextlib2/package.py index edf31e99f3..c4409c8497 100644 --- a/var/spack/repos/builtin/packages/py-contextlib2/package.py +++ b/var/spack/repos/builtin/packages/py-contextlib2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-convertdate/package.py b/var/spack/repos/builtin/packages/py-convertdate/package.py new file mode 100644 index 0000000000..b75b839ad0 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-convertdate/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyConvertdate(PythonPackage): + """Converts between Gregorian dates and other calendar + systems.Calendars included: Baha'i, French Republican, Hebrew, + Indian Civil, Islamic, ISO, Julian, Mayan and Persian.""" + + homepage = "https://github.com/fitnr/convertdate/" + url = "https://pypi.io/packages/source/c/convertdate/convertdate-2.2.0.tar.gz" + + version('2.2.0', sha256='9d2b0cd8d5382d2458d4cfa59665abba398a9e9bfd3a01c6f61b7b47768d28bf') + + depends_on('py-setuptools', type='build') + depends_on('py-pytz@2014.10:2019.13', type=('build', 'run')) + depends_on('py-pymeeus@0.3.6:1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-counter/package.py b/var/spack/repos/builtin/packages/py-counter/package.py index 566c646219..f751818caa 100644 --- a/var/spack/repos/builtin/packages/py-counter/package.py +++ b/var/spack/repos/builtin/packages/py-counter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cov-core/package.py b/var/spack/repos/builtin/packages/py-cov-core/package.py index 08489d723b..8ecc781755 100644 --- a/var/spack/repos/builtin/packages/py-cov-core/package.py +++ b/var/spack/repos/builtin/packages/py-cov-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-coverage/package.py b/var/spack/repos/builtin/packages/py-coverage/package.py index fa1c7a9b81..8459b94699 100644 --- a/var/spack/repos/builtin/packages/py-coverage/package.py +++ b/var/spack/repos/builtin/packages/py-coverage/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-crispresso/package.py b/var/spack/repos/builtin/packages/py-crispresso/package.py index eaab99b35a..fb46dca86a 100644 --- a/var/spack/repos/builtin/packages/py-crispresso/package.py +++ b/var/spack/repos/builtin/packages/py-crispresso/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-crossmap/package.py b/var/spack/repos/builtin/packages/py-crossmap/package.py index 5810a820c9..13261f80c6 100644 --- a/var/spack/repos/builtin/packages/py-crossmap/package.py +++ b/var/spack/repos/builtin/packages/py-crossmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cryptography/package.py b/var/spack/repos/builtin/packages/py-cryptography/package.py index 2a3c99ffc6..ad6ac9d2d0 100644 --- a/var/spack/repos/builtin/packages/py-cryptography/package.py +++ b/var/spack/repos/builtin/packages/py-cryptography/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cssselect/package.py b/var/spack/repos/builtin/packages/py-cssselect/package.py new file mode 100644 index 0000000000..6eec358501 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cssselect/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyCssselect(PythonPackage): + """Python-cssselect parses CSS3 Selectors and translate them to XPath 1.0 + expressions. Such expressions can be used in lxml or another XPath engine + to find the matching elements in an XML or HTML document.""" + + homepage = "https://github.com/scrapy/cssselect" + url = "https://github.com/scrapy/cssselect/archive/v1.1.0.tar.gz" + + version('1.1.0', sha256='dde8c1d4a2c82de6889a3af1c1adbce1a6f3ec08b07a854d873f3f3da92960af') + version('1.0.3', sha256='203d9691c42c13cffe26a2f8fc714977882fcf54a6df82c8eda3371f6beaecdb') + version('1.0.2', sha256='ee16bbb99b0a1f593ed4cd822f20bffefa4a4676d19d7dd1f231b4c1cc1cc1e2') + version('1.0.1', sha256='cdfa17ab5dc8818209f310a930b18d3035a4585ddd2c179e833036e2dde511c6') + version('1.0.0', sha256='2f757203e03aedcc1b31a452cf2752728b843351b7819ea2d4cd9ef38df7b324') diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py index f4e2ce67e7..217a5174f7 100644 --- a/var/spack/repos/builtin/packages/py-csvkit/package.py +++ b/var/spack/repos/builtin/packages/py-csvkit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,13 +13,20 @@ class PyCsvkit(PythonPackage): homepage = 'http://csvkit.rtfd.org/' url = "https://pypi.io/packages/source/c/csvkit/csvkit-0.9.1.tar.gz" + version('1.0.4', sha256='1353a383531bee191820edfb88418c13dfe1cdfa9dd3dc46f431c05cd2a260a0') version('0.9.1', sha256='92f8b8647becb5cb1dccb3af92a13a4e85702d42ba465ce8447881fb38c9f93a') - depends_on('py-setuptools', type='build') + depends_on('py-setuptools', type=('build', 'run')) + depends_on('py-six@1.6.1:', type=('build', 'run')) + depends_on('py-argparse@1.2.1:', type=('build', 'run'), when='^python@:2.6') + depends_on('py-ordereddict@1.1:', type=('build', 'run'), when='^python@:2.6') + depends_on('py-simplejson@3.6.3:', type=('build', 'run'), when='^python@:2.6') depends_on('py-python-dateutil@2.2', type=('build', 'run'), when='@0.9.1') - depends_on('py-python-dateutil', type=('build', 'run'), when='@0.9.2:') - depends_on('py-dbf@0.94.003', type=('build', 'run')) - depends_on('py-xlrd', type=('build', 'run')) - depends_on('py-sqlalchemy', type=('build', 'run')) - depends_on('py-six', type=('build', 'run')) - depends_on('py-openpyxl@2.2.0-b1', type=('build', 'run')) + depends_on('py-dbf@0.94.003', type=('build', 'run'), when='@0.9.1') + depends_on('py-xlrd@0.7.1:', type=('build', 'run'), when='@0.9.1') + depends_on('py-sqlalchemy@0.6.6:', type=('build', 'run'), when='@0.9.1') + depends_on('py-openpyxl@2.2.0-b1', type=('build', 'run'), when='@0.9.1') + depends_on('py-agate@1.6.1:', type=('build', 'run'), when='@1:') + depends_on('py-agate-excel@0.2.2:', type=('build', 'run'), when='@1:') + depends_on('py-agate-dbf@0.2.0:', type=('build', 'run'), when='@1:') + depends_on('py-agate-sql@0.5.3:', type=('build', 'run'), when='@1:') diff --git a/var/spack/repos/builtin/packages/py-current/package.py b/var/spack/repos/builtin/packages/py-current/package.py index 7b3c28abe2..3604d3ca14 100644 --- a/var/spack/repos/builtin/packages/py-current/package.py +++ b/var/spack/repos/builtin/packages/py-current/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cutadapt/package.py b/var/spack/repos/builtin/packages/py-cutadapt/package.py index 167a2b2175..2a5213fd2f 100644 --- a/var/spack/repos/builtin/packages/py-cutadapt/package.py +++ b/var/spack/repos/builtin/packages/py-cutadapt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cvxopt/package.py b/var/spack/repos/builtin/packages/py-cvxopt/package.py index b12dcf4c87..1f031de484 100644 --- a/var/spack/repos/builtin/packages/py-cvxopt/package.py +++ b/var/spack/repos/builtin/packages/py-cvxopt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -37,85 +37,77 @@ class PyCvxopt(PythonPackage): # depends_on('mosek@8:', when='+mosek') depends_on('dsdp@5.8:', when='+dsdp') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec # BLAS/LAPACK Libraries # Default names of BLAS and LAPACK libraries - spack_env.set('CVXOPT_BLAS_LIB', ';'.join(spec['blas'].libs.names)) - spack_env.set('CVXOPT_LAPACK_LIB', ';'.join(spec['lapack'].libs.names)) + env.set('CVXOPT_BLAS_LIB', ';'.join(spec['blas'].libs.names)) + env.set('CVXOPT_LAPACK_LIB', ';'.join(spec['lapack'].libs.names)) # Directory containing BLAS and LAPACK libraries - spack_env.set('CVXOPT_BLAS_LIB_DIR', spec['blas'].libs.directories[0]) + env.set('CVXOPT_BLAS_LIB_DIR', spec['blas'].libs.directories[0]) # SuiteSparse Libraries # Directory containing SuiteSparse libraries - spack_env.set('CVXOPT_SUITESPARSE_LIB_DIR', - spec['suite-sparse'].libs.directories[0]) + env.set('CVXOPT_SUITESPARSE_LIB_DIR', + spec['suite-sparse'].libs.directories[0]) # Directory containing SuiteSparse header files - spack_env.set('CVXOPT_SUITESPARSE_INC_DIR', - spec['suite-sparse'].headers.directories[0]) + env.set('CVXOPT_SUITESPARSE_INC_DIR', + spec['suite-sparse'].headers.directories[0]) # GSL Libraries if '+gsl' in spec: - spack_env.set('CVXOPT_BUILD_GSL', 1) + env.set('CVXOPT_BUILD_GSL', 1) # Directory containing libgsl - spack_env.set('CVXOPT_GSL_LIB_DIR', - spec['gsl'].libs.directories[0]) + env.set('CVXOPT_GSL_LIB_DIR', spec['gsl'].libs.directories[0]) # Directory containing the GSL header files - spack_env.set('CVXOPT_GSL_INC_DIR', - spec['gsl'].headers.directories[0]) + env.set('CVXOPT_GSL_INC_DIR', spec['gsl'].headers.directories[0]) else: - spack_env.set('CVXOPT_BUILD_GSL', 0) + env.set('CVXOPT_BUILD_GSL', 0) # FFTW Libraries if '+fftw' in spec: - spack_env.set('CVXOPT_BUILD_FFTW', 1) + env.set('CVXOPT_BUILD_FFTW', 1) # Directory containing libfftw3 - spack_env.set('CVXOPT_FFTW_LIB_DIR', - spec['fftw'].libs.directories[0]) + env.set('CVXOPT_FFTW_LIB_DIR', spec['fftw'].libs.directories[0]) # Directory containing fftw.h - spack_env.set('CVXOPT_FFTW_INC_DIR', - spec['fftw'].headers.directories[0]) + env.set('CVXOPT_FFTW_INC_DIR', spec['fftw'].headers.directories[0]) else: - spack_env.set('CVXOPT_BUILD_FFTW', 0) + env.set('CVXOPT_BUILD_FFTW', 0) # GLPK Libraries if '+glpk' in spec: - spack_env.set('CVXOPT_BUILD_GLPK', 1) + env.set('CVXOPT_BUILD_GLPK', 1) # Directory containing libglpk - spack_env.set('CVXOPT_GLPK_LIB_DIR', - spec['glpk'].libs.directories[0]) + env.set('CVXOPT_GLPK_LIB_DIR', spec['glpk'].libs.directories[0]) # Directory containing glpk.h - spack_env.set('CVXOPT_GLPK_INC_DIR', - spec['glpk'].headers.directories[0]) + env.set('CVXOPT_GLPK_INC_DIR', spec['glpk'].headers.directories[0]) else: - spack_env.set('CVXOPT_BUILD_GLPK', 0) + env.set('CVXOPT_BUILD_GLPK', 0) # DSDP Libraries if '+dsdp' in spec: - spack_env.set('CVXOPT_BUILD_DSDP', 1) + env.set('CVXOPT_BUILD_DSDP', 1) # Directory containing libdsdp - spack_env.set('CVXOPT_DSDP_LIB_DIR', - spec['dsdp'].libs.directories[0]) + env.set('CVXOPT_DSDP_LIB_DIR', spec['dsdp'].libs.directories[0]) # Directory containing dsdp5.h - spack_env.set('CVXOPT_DSDP_INC_DIR', - spec['dsdp'].headers.directories[0]) + env.set('CVXOPT_DSDP_INC_DIR', spec['dsdp'].headers.directories[0]) @run_after('install') @on_package_attributes(run_tests=True) diff --git a/var/spack/repos/builtin/packages/py-cvxpy/package.py b/var/spack/repos/builtin/packages/py-cvxpy/package.py new file mode 100644 index 0000000000..68b82e8a59 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cvxpy/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyCvxpy(PythonPackage): + """Convex optimization, for everyone.""" + + homepage = "https://www.cvxpy.org/index.html" + url = "https://www.pypi.io/packages/source/c/cvxpy/cvxpy-1.0.25.tar.gz" + + version('1.0.25', sha256='8535529ddb807067b0d59661dce1d9a6ddb2a218398a38ea7772328ad8a6ea13') + + depends_on('py-setuptools', type='build') + depends_on('py-nose', type='test') + + depends_on('py-numpy@1.15:', type=('build', 'run')) + depends_on('py-scipy@1.1.0:', type=('build', 'run')) + depends_on('py-ecos@2:', type=('build', 'run')) + depends_on('py-scs@1.1.3:', type=('build', 'run')) + depends_on('py-osqp@0.4.1', type=('build', 'run')) + + depends_on('py-multiprocess', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cycler/package.py b/var/spack/repos/builtin/packages/py-cycler/package.py index 9af98be2b4..9deebea972 100644 --- a/var/spack/repos/builtin/packages/py-cycler/package.py +++ b/var/spack/repos/builtin/packages/py-cycler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py index c65733652d..34a0d30a70 100644 --- a/var/spack/repos/builtin/packages/py-cython/package.py +++ b/var/spack/repos/builtin/packages/py-cython/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class PyCython(PythonPackage): """The Cython compiler for writing C extensions for the Python language.""" homepage = "https://pypi.python.org/pypi/cython" - url = "https://pypi.io/packages/source/c/cython/Cython-0.29.13.tar.gz" + url = "https://pypi.io/packages/source/c/cython/Cython-0.29.14.tar.gz" import_modules = [ 'cython', 'Cython', 'Cython.Build', 'Cython.Compiler', @@ -20,6 +20,7 @@ class PyCython(PythonPackage): 'Cython.Tempita', 'pyximport', ] + version('0.29.14', sha256='e4d6bb8703d0319eb04b7319b12ea41580df44fd84d83ccda13ea463c6801414') version('0.29.13', sha256='c29d069a4a30f472482343c866f7486731ad638ef9af92bfe5fca9c7323d638e') version('0.29.7', sha256='55d081162191b7c11c7bfcb7c68e913827dfd5de6ecdbab1b99dab190586c1e8') version('0.29.5', sha256='9d5290d749099a8e446422adfb0aa2142c711284800fb1eb70f595101e32cbf1') diff --git a/var/spack/repos/builtin/packages/py-dask/package.py b/var/spack/repos/builtin/packages/py-dask/package.py index 3e83bd08f3..6b44f935af 100644 --- a/var/spack/repos/builtin/packages/py-dask/package.py +++ b/var/spack/repos/builtin/packages/py-dask/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-dataclasses/package.py b/var/spack/repos/builtin/packages/py-dataclasses/package.py new file mode 100644 index 0000000000..c79947953d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-dataclasses/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyDataclasses(PythonPackage): + """A backport of the dataclasses module for Python 3.6""" + + homepage = "https://github.com/ericvsmith/dataclasses" + url = "https://pypi.io/packages/source/d/dataclasses/dataclasses-0.7.tar.gz" + + version('0.7', sha256='494a6dcae3b8bcf80848eea2ef64c0cc5cd307ffc263e17cdf42f3e5420808e6') + + depends_on('python@3.6.00:3.6.99', type=('build', 'run')) + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-dateparser/package.py b/var/spack/repos/builtin/packages/py-dateparser/package.py new file mode 100644 index 0000000000..5d233e6377 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-dateparser/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyDateparser(PythonPackage): + """dateparser -- python parser for human readable dates""" + + homepage = "https://github.com/scrapinghub/dateparser" + url = "https://pypi.io/packages/source/d/dateparser/dateparser-0.7.2.tar.gz" + + version('0.7.2', sha256='e1eac8ef28de69a554d5fcdb60b172d526d61924b1a40afbbb08df459a36006b') + + variant('calendars', default=True, description='Add calendar libraries') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-python-dateutil@2.7.5:', type=('build', 'run')) + depends_on('py-pytz', type=('build', 'run')) + depends_on('py-regex', type=('build', 'run')) + depends_on('py-tzlocal', type=('build', 'run')) + depends_on('py-umalqurra', type=('build', 'run'), when='+calendars') + depends_on('py-ruamel-yaml', type=('build', 'run'), when='+calendars') + depends_on('py-convertdate', type=('build', 'run'), when='+calendars') + depends_on('py-jdatetime', type=('build', 'run'), when='+calendars') + depends_on('py-mock', type='test') + depends_on('py-nose', type='test') + depends_on('py-parameterized', type='test') + depends_on('py-six', type='test') + depends_on('py-coverage', type='test') diff --git a/var/spack/repos/builtin/packages/py-dbf/package.py b/var/spack/repos/builtin/packages/py-dbf/package.py index f460fb4824..d5d2f3b5e7 100644 --- a/var/spack/repos/builtin/packages/py-dbf/package.py +++ b/var/spack/repos/builtin/packages/py-dbf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-dbfread/package.py b/var/spack/repos/builtin/packages/py-dbfread/package.py new file mode 100644 index 0000000000..338382d127 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-dbfread/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyDbfread(PythonPackage): + """DBF is a file format used by databases such dBase, Visual FoxPro, and + FoxBase+. This library reads DBF files and returns the data as native + Python data types for further processing. It is primarily intended for + batch jobs and one-off scripts.""" + + homepage = "https://dbfread.readthedocs.io/en/latest/" + url = "https://pypi.io/packages/source/d/dbfread/dbfread-2.0.7.tar.gz" + + version('2.0.7', sha256='07c8a9af06ffad3f6f03e8fe91ad7d2733e31a26d2b72c4dd4cfbae07ee3b73d') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py index 7902a3074e..9294dd5c49 100644 --- a/var/spack/repos/builtin/packages/py-decorator/package.py +++ b/var/spack/repos/builtin/packages/py-decorator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-deeptools/package.py b/var/spack/repos/builtin/packages/py-deeptools/package.py index 6c65bb1158..35103a5e5d 100644 --- a/var/spack/repos/builtin/packages/py-deeptools/package.py +++ b/var/spack/repos/builtin/packages/py-deeptools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-deeptoolsintervals/package.py b/var/spack/repos/builtin/packages/py-deeptoolsintervals/package.py index bff5b81f69..09e5a32a58 100644 --- a/var/spack/repos/builtin/packages/py-deeptoolsintervals/package.py +++ b/var/spack/repos/builtin/packages/py-deeptoolsintervals/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-defusedxml/package.py b/var/spack/repos/builtin/packages/py-defusedxml/package.py index 972c45e627..659d458ba5 100644 --- a/var/spack/repos/builtin/packages/py-defusedxml/package.py +++ b/var/spack/repos/builtin/packages/py-defusedxml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-dendropy/package.py b/var/spack/repos/builtin/packages/py-dendropy/package.py index 03ded6579e..aa58be0d77 100644 --- a/var/spack/repos/builtin/packages/py-dendropy/package.py +++ b/var/spack/repos/builtin/packages/py-dendropy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-deprecation/package.py b/var/spack/repos/builtin/packages/py-deprecation/package.py new file mode 100644 index 0000000000..2128e78233 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-deprecation/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyDeprecation(PythonPackage): + """The deprecation library provides a deprecated decorator and a + fail_if_not_removed decorator for your tests. """ + + homepage = "http://deprecation.readthedocs.io/" + url = "https://pypi.io/packages/source/d/deprecation/deprecation-2.0.7.tar.gz" + + version('2.0.7', sha256='c0392f676a6146f0238db5744d73e786a43510d54033f80994ef2f4c9df192ed') + + depends_on('py-setuptools', type='build') + depends_on('py-packaging', type='build') diff --git a/var/spack/repos/builtin/packages/py-descartes/package.py b/var/spack/repos/builtin/packages/py-descartes/package.py index f47b7846ae..fb834d07c1 100644 --- a/var/spack/repos/builtin/packages/py-descartes/package.py +++ b/var/spack/repos/builtin/packages/py-descartes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-dill/package.py b/var/spack/repos/builtin/packages/py-dill/package.py index 49bac9470e..9c19f73822 100644 --- a/var/spack/repos/builtin/packages/py-dill/package.py +++ b/var/spack/repos/builtin/packages/py-dill/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,8 +10,9 @@ class PyDill(PythonPackage): """Serialize all of python """ homepage = "https://github.com/uqfoundation/dill" - url = "https://pypi.io/packages/source/d/dill/dill-0.2.6.zip" + url = "https://pypi.io/packages/source/d/dill/dill-0.2.7.tar.gz" + version('0.2.7', sha256='ddda0107e68e4eb1772a9f434f62a513c080c7171bd0dd6fb65d992788509812') version('0.2.6', sha256='6c1ccca68be483fa8c66e85a89ffc850206c26373aa77a97b83d8d0994e7f1fd') version('0.2.5', sha256='e82b3db7b9d962911c9c2d5cf2bb4a04f43933f505a624fb7dc5f68b949f0a5c') version('0.2.4', sha256='db68929eef0e886055d6bcd86f830141c1f653ddbf5d081c086e9d1c45efb334') @@ -23,3 +24,14 @@ class PyDill(PythonPackage): depends_on('python@2.5:2.8,3.1:') depends_on('py-setuptools@0.6:', type='build') + + def url_for_version(self, version): + url = "https://pypi.io/packages/source/d/dill/" + + if version >= Version('0.2.7'): + url += 'dill-{0}.tar.gz' + else: + url += 'dill-{0}.zip' + + url = url.format(version) + return url diff --git a/var/spack/repos/builtin/packages/py-discover/package.py b/var/spack/repos/builtin/packages/py-discover/package.py index d891f38215..8512294724 100644 --- a/var/spack/repos/builtin/packages/py-discover/package.py +++ b/var/spack/repos/builtin/packages/py-discover/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-dlcpar/package.py b/var/spack/repos/builtin/packages/py-dlcpar/package.py index e3fe23f15a..53f8aa5547 100644 --- a/var/spack/repos/builtin/packages/py-dlcpar/package.py +++ b/var/spack/repos/builtin/packages/py-dlcpar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-dnaio/package.py b/var/spack/repos/builtin/packages/py-dnaio/package.py index f67e6acf00..3429d458cf 100644 --- a/var/spack/repos/builtin/packages/py-dnaio/package.py +++ b/var/spack/repos/builtin/packages/py-dnaio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,6 @@ class PyDnaio(PythonPackage): version('0.3', sha256='47e4449affad0981978fe986684fc0d9c39736f05a157f6cf80e54dae0a92638') - depends_on('python@3.4:', type=('build', 'run')) + depends_on('python@3.4:', type=('build', 'run')) depends_on('py-setuptools', type=('build', 'run')) depends_on('py-xopen@0.8.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-docopt/package.py b/var/spack/repos/builtin/packages/py-docopt/package.py index 217b95cb8f..ce0dcd40ad 100644 --- a/var/spack/repos/builtin/packages/py-docopt/package.py +++ b/var/spack/repos/builtin/packages/py-docopt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-docutils-stubs/package.py b/var/spack/repos/builtin/packages/py-docutils-stubs/package.py index 81ddf8e97c..02c7f99d47 100644 --- a/var/spack/repos/builtin/packages/py-docutils-stubs/package.py +++ b/var/spack/repos/builtin/packages/py-docutils-stubs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-docutils/package.py b/var/spack/repos/builtin/packages/py-docutils/package.py index 93d8a0bd7f..573ecc6bae 100644 --- a/var/spack/repos/builtin/packages/py-docutils/package.py +++ b/var/spack/repos/builtin/packages/py-docutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-doxypy/package.py b/var/spack/repos/builtin/packages/py-doxypy/package.py index 2c4c791175..103ac0488f 100644 --- a/var/spack/repos/builtin/packages/py-doxypy/package.py +++ b/var/spack/repos/builtin/packages/py-doxypy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-doxypypy/package.py b/var/spack/repos/builtin/packages/py-doxypypy/package.py index cb2b719ca9..e28970409e 100644 --- a/var/spack/repos/builtin/packages/py-doxypypy/package.py +++ b/var/spack/repos/builtin/packages/py-doxypypy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-dryscrape/package.py b/var/spack/repos/builtin/packages/py-dryscrape/package.py index 3f56b291cf..8aa002bf7b 100644 --- a/var/spack/repos/builtin/packages/py-dryscrape/package.py +++ b/var/spack/repos/builtin/packages/py-dryscrape/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-dxchange/package.py b/var/spack/repos/builtin/packages/py-dxchange/package.py index fb1cd4a565..be0a23916c 100644 --- a/var/spack/repos/builtin/packages/py-dxchange/package.py +++ b/var/spack/repos/builtin/packages/py-dxchange/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-dxfile/package.py b/var/spack/repos/builtin/packages/py-dxfile/package.py index 7dc3ad7ae3..aa7eac9d91 100644 --- a/var/spack/repos/builtin/packages/py-dxfile/package.py +++ b/var/spack/repos/builtin/packages/py-dxfile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-earthengine-api/package.py b/var/spack/repos/builtin/packages/py-earthengine-api/package.py index afcbb7d5f2..6125d918b6 100644 --- a/var/spack/repos/builtin/packages/py-earthengine-api/package.py +++ b/var/spack/repos/builtin/packages/py-earthengine-api/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py b/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py index 29325ea39d..dcc295c63e 100644 --- a/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py +++ b/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py b/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py index 6f7c61e583..83c55889b5 100644 --- a/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py +++ b/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-easybuild-framework/package.py b/var/spack/repos/builtin/packages/py-easybuild-framework/package.py index 290f584cd1..9096f62708 100644 --- a/var/spack/repos/builtin/packages/py-easybuild-framework/package.py +++ b/var/spack/repos/builtin/packages/py-easybuild-framework/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ecdsa/package.py b/var/spack/repos/builtin/packages/py-ecdsa/package.py index b9266a4112..18d6d7eddb 100644 --- a/var/spack/repos/builtin/packages/py-ecdsa/package.py +++ b/var/spack/repos/builtin/packages/py-ecdsa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ecos/package.py b/var/spack/repos/builtin/packages/py-ecos/package.py new file mode 100644 index 0000000000..84e3bcd9eb --- /dev/null +++ b/var/spack/repos/builtin/packages/py-ecos/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyEcos(PythonPackage): + """This is the Python package for ECOS: Embedded Cone Solver.""" + + homepage = "https://github.com/embotech/ecos" + url = "https://www.pypi.io/packages/source/e/ecos/ecos-2.0.7.post1.tar.gz" + + version('2.0.7.post1', sha256='83e90f42b3f32e2a93f255c3cfad2da78dbd859119e93844c45d2fca20bdc758') + + depends_on('py-setuptools', type='build') + depends_on('py-nose', type='test') + depends_on('py-numpy@1.6:', type=('build', 'run')) + depends_on('py-scipy@0.9:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-edffile/package.py b/var/spack/repos/builtin/packages/py-edffile/package.py index ae541be117..ab4a9f9ed9 100644 --- a/var/spack/repos/builtin/packages/py-edffile/package.py +++ b/var/spack/repos/builtin/packages/py-edffile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-editdistance/package.py b/var/spack/repos/builtin/packages/py-editdistance/package.py index 559b948ce5..ccedeef495 100644 --- a/var/spack/repos/builtin/packages/py-editdistance/package.py +++ b/var/spack/repos/builtin/packages/py-editdistance/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-elasticsearch/package.py b/var/spack/repos/builtin/packages/py-elasticsearch/package.py index 8603e47c56..f0199ea97d 100644 --- a/var/spack/repos/builtin/packages/py-elasticsearch/package.py +++ b/var/spack/repos/builtin/packages/py-elasticsearch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-elephant/package.py b/var/spack/repos/builtin/packages/py-elephant/package.py index 56098dc4b8..7d2477ef40 100644 --- a/var/spack/repos/builtin/packages/py-elephant/package.py +++ b/var/spack/repos/builtin/packages/py-elephant/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-emcee/package.py b/var/spack/repos/builtin/packages/py-emcee/package.py index 1c26322598..093a662b2b 100644 --- a/var/spack/repos/builtin/packages/py-emcee/package.py +++ b/var/spack/repos/builtin/packages/py-emcee/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-empy/package.py b/var/spack/repos/builtin/packages/py-empy/package.py index 801dab3600..54b1bd759a 100644 --- a/var/spack/repos/builtin/packages/py-empy/package.py +++ b/var/spack/repos/builtin/packages/py-empy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-entrypoints/package.py b/var/spack/repos/builtin/packages/py-entrypoints/package.py index 0ea816d3f8..84bc7c20f4 100644 --- a/var/spack/repos/builtin/packages/py-entrypoints/package.py +++ b/var/spack/repos/builtin/packages/py-entrypoints/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-enum34/package.py b/var/spack/repos/builtin/packages/py-enum34/package.py index ee2d3e2ac6..7bcdf462b3 100644 --- a/var/spack/repos/builtin/packages/py-enum34/package.py +++ b/var/spack/repos/builtin/packages/py-enum34/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,12 +9,16 @@ from spack import * class PyEnum34(PythonPackage): """Python 3.4 Enum backported to 3.3, 3.2, 3.1, 2.7, 2.6, 2.5, and 2.4.""" - homepage = "https://pypi.python.org/pypi/enum34" + homepage = "https://bitbucket.org/stoneleaf/enum34/src" url = "https://pypi.io/packages/source/e/enum34/enum34-1.1.6.tar.gz" version('1.1.6', sha256='8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1') - depends_on('python') - conflicts('python@3.4:') + # enum34 is a backport of the enum library from Python 3.4. It is not + # intended to be used with Python 3.4+. In fact, it won't build at all + # for Python 3.6+, as new constructs were added to the builtin enum + # library that aren't present in enum34. See: + # https://bitbucket.org/stoneleaf/enum34/issues/19 + depends_on('python@:3.5', type=('build', 'run')) depends_on('py-ordereddict', when='^python@:2.6', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-epydoc/package.py b/var/spack/repos/builtin/packages/py-epydoc/package.py index 1cd9f83a01..cfd14fa4eb 100644 --- a/var/spack/repos/builtin/packages/py-epydoc/package.py +++ b/var/spack/repos/builtin/packages/py-epydoc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-espresso/package.py b/var/spack/repos/builtin/packages/py-espresso/package.py index d238ed591b..4891b8c53e 100644 --- a/var/spack/repos/builtin/packages/py-espresso/package.py +++ b/var/spack/repos/builtin/packages/py-espresso/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-espressopp/package.py b/var/spack/repos/builtin/packages/py-espressopp/package.py index 95bf54a8e9..a4524da78e 100644 --- a/var/spack/repos/builtin/packages/py-espressopp/package.py +++ b/var/spack/repos/builtin/packages/py-espressopp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,7 +14,7 @@ class PyEspressopp(CMakePackage): atomistic or bead-spring models as they are used in soft matter research """ homepage = "https://espressopp.github.io" - url = "https://github.com/espressopp/espressopp/tarball/v1.9.4.1" + url = "https://github.com/espressopp/espressopp/tarball/v2.0.2" git = "https://github.com/espressopp/espressopp.git" version('develop', branch='master') diff --git a/var/spack/repos/builtin/packages/py-et-xmlfile/package.py b/var/spack/repos/builtin/packages/py-et-xmlfile/package.py index 59594033eb..49c508e32b 100644 --- a/var/spack/repos/builtin/packages/py-et-xmlfile/package.py +++ b/var/spack/repos/builtin/packages/py-et-xmlfile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-eventlet/package.py b/var/spack/repos/builtin/packages/py-eventlet/package.py index a0e20e15e6..fa7f734348 100644 --- a/var/spack/repos/builtin/packages/py-eventlet/package.py +++ b/var/spack/repos/builtin/packages/py-eventlet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-execnet/package.py b/var/spack/repos/builtin/packages/py-execnet/package.py index 5b70292a2a..96c26f7717 100644 --- a/var/spack/repos/builtin/packages/py-execnet/package.py +++ b/var/spack/repos/builtin/packages/py-execnet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-exodus/package.py b/var/spack/repos/builtin/packages/py-exodus-bundler/package.py index 5794a146a6..b14570f54b 100644 --- a/var/spack/repos/builtin/packages/py-exodus/package.py +++ b/var/spack/repos/builtin/packages/py-exodus-bundler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PyExodus(PythonPackage): +class PyExodusBundler(PythonPackage): """Exodus is a tool that makes it easy to successfully relocate Linux ELF binaries from one system to another.""" diff --git a/var/spack/repos/builtin/packages/py-extras/package.py b/var/spack/repos/builtin/packages/py-extras/package.py new file mode 100644 index 0000000000..5705b0dfe6 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-extras/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyExtras(PythonPackage): + """Useful extra bits for Python - things that shold be in the standard + library.""" + + homepage = "https://github.com/testing-cabal/extras" + url = "https://pypi.io/packages/source/e/extras/extras-1.0.0.tar.gz" + + version('1.0.0', sha256='132e36de10b9c91d5d4cc620160a476e0468a88f16c9431817a6729611a81b4e') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-fallocate/package.py b/var/spack/repos/builtin/packages/py-fallocate/package.py index a5cc3354c6..0e0a442f2b 100644 --- a/var/spack/repos/builtin/packages/py-fallocate/package.py +++ b/var/spack/repos/builtin/packages/py-fallocate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-fastaindex/package.py b/var/spack/repos/builtin/packages/py-fastaindex/package.py index 47e896d2a4..8b37fd3a4e 100644 --- a/var/spack/repos/builtin/packages/py-fastaindex/package.py +++ b/var/spack/repos/builtin/packages/py-fastaindex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-fastcache/package.py b/var/spack/repos/builtin/packages/py-fastcache/package.py index 95883a4044..bd58a14702 100644 --- a/var/spack/repos/builtin/packages/py-fastcache/package.py +++ b/var/spack/repos/builtin/packages/py-fastcache/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-fasteners/package.py b/var/spack/repos/builtin/packages/py-fasteners/package.py index 0a5299ea7f..685b1dca0e 100644 --- a/var/spack/repos/builtin/packages/py-fasteners/package.py +++ b/var/spack/repos/builtin/packages/py-fasteners/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-faststructure/package.py b/var/spack/repos/builtin/packages/py-faststructure/package.py index 100f8adc05..60e123738f 100644 --- a/var/spack/repos/builtin/packages/py-faststructure/package.py +++ b/var/spack/repos/builtin/packages/py-faststructure/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-filelock/package.py b/var/spack/repos/builtin/packages/py-filelock/package.py index b82459a256..37aea08701 100644 --- a/var/spack/repos/builtin/packages/py-filelock/package.py +++ b/var/spack/repos/builtin/packages/py-filelock/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,15 +12,14 @@ class PyFilelock(PythonPackage): inter-process communication""" homepage = "https://github.com/benediktschmitt/py-filelock" - url = "https://github.com/benediktschmitt/py-filelock/archive/v3.0.4.tar.gz" + url = "https://pypi.io/packages/source/f/filelock/filelock-3.0.4.tar.gz" - version('3.0.4', sha256='8521523f3eafb7bbbdd0a5a7a15ddb8076ea6f106385bbfc4c9d055db2585214') - version('3.0.3', sha256='8e1b1ad91de70e091de381ab8705b37e41d240c211d8d888dcf1d0e31d6274bb') - version('3.0.1', sha256='533107ab60de691030b7e90105ab38c8b0d60d52de382fe5302819cba95561f8') - version('3.0.0', sha256='f41bed24b280b2fd11b2f12fecdfd2a21e5f9babc4e89929b316946288fa195c') - version('2.0.13', sha256='85e2a001693c2995854e42783a8c11994d143f8ba9c92d31f573476a22a5b3b3') - version('2.0.12', sha256='3b67cddd8c405c27b9118a1383d5257b5b6e066d3a9a30ab03d42b4dc6828cbb') - version('2.0.11', sha256='97c36de6e0c2eaed6638a9575a96d176e4ec2820b888f3da3194bbb852f86c5e') - version('2.0.10', sha256='f15d99cfa3e89072d7709bf3b5d354cf1c9096cffdb1127c4dbff1ca4a89cb84') - version('2.0.9', sha256='86d8e95afe77bc92a94c2e0db2b452c067b453b017fd78edfbb679b199dadbd5') - version('2.0.8', sha256='4f69474338ebf6ead2e0c2e91c5f94a25af8125d307f539db10886a19e2e2628') + version('3.0.4', sha256='011327d4ed939693a5b28c0fdf2fd9bda1f68614c1d6d0643a89382ce9843a71') + version('3.0.3', sha256='7d8a86350736aa0efea0730e6a7f774195cbb1c2d61134c15f6be576399e87ff') + version('3.0.0', sha256='b3ad481724adfb2280773edd95ce501e497e88fa4489c6e41e637ab3fd9a456c') + version('2.0.13', sha256='d05079e7d7cae7576e192749d3461999ca6b0843d35b0f79f1fa956b0f6fc7d8') + version('2.0.12', sha256='eb4314a9a032707a914b037433ce866d4ed363fce8605d45f0c9d2cd6ac52f98') + version('2.0.11', sha256='e9e370efe86c30b19a2c8c36dd9fcce8e5ce294ef4ed6ac86664b666eaf852ca') + version('2.0.10', sha256='c73bf706d8a0c5722de0b745495fed9cda0e46c0eabb44eb18ee3f00520fa85f') + version('2.0.9', sha256='0f91dce339c9f25d6f2e0733a17e4f9a47b139dffda52619a0e61e013e5c6782') + version('2.0.8', sha256='7e48e4906de3c9a5d64d8f235eb3ae1050dfefa63fd65eaf318cc915c935212b') diff --git a/var/spack/repos/builtin/packages/py-filemagic/package.py b/var/spack/repos/builtin/packages/py-filemagic/package.py index 7238ac1bc0..8d425dfb37 100644 --- a/var/spack/repos/builtin/packages/py-filemagic/package.py +++ b/var/spack/repos/builtin/packages/py-filemagic/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-fiona/package.py b/var/spack/repos/builtin/packages/py-fiona/package.py index f5ab1b5791..b6ad22a9a7 100644 --- a/var/spack/repos/builtin/packages/py-fiona/package.py +++ b/var/spack/repos/builtin/packages/py-fiona/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-fiscalyear/package.py b/var/spack/repos/builtin/packages/py-fiscalyear/package.py index c4ffdbdbe6..407caa7ce5 100644 --- a/var/spack/repos/builtin/packages/py-fiscalyear/package.py +++ b/var/spack/repos/builtin/packages/py-fiscalyear/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,17 +13,19 @@ class PyFiscalyear(PythonPackage): the fiscal year and fiscal quarter of a date or datetime object.""" homepage = "https://github.com/adamjstewart/fiscalyear" - url = "https://pypi.io/packages/source/f/fiscalyear/fiscalyear-0.1.0.tar.gz" + url = "https://pypi.io/packages/source/f/fiscalyear/fiscalyear-0.2.0.tar.gz" git = "https://github.com/adamjstewart/fiscalyear.git" maintainers = ['adamjstewart'] import_modules = ['fiscalyear'] version('master', branch='master') + version('0.2.0', sha256='f513616aeb03046406c56d7c69cd9e26f6a12963c71c1410cc3d4532a5bfee71') version('0.1.0', sha256='3fde4a12eeb72da446beb487e078adf1223a92d130520e589b82d7d1509701a2') - depends_on('python@2.5:') + depends_on('python@2.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-pytest', type='test') depends_on('py-pytest-runner', type='test') + depends_on('py-pytest-mock', type='test') diff --git a/var/spack/repos/builtin/packages/py-fixtures/package.py b/var/spack/repos/builtin/packages/py-fixtures/package.py new file mode 100644 index 0000000000..2cc0362c4e --- /dev/null +++ b/var/spack/repos/builtin/packages/py-fixtures/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyFixtures(PythonPackage): + """Fixtures, reusable state for writing clean tests and more.""" + + homepage = "https://launchpad.net/python-fixtures" + url = "https://pypi.io/packages/source/f/fixtures/fixtures-3.0.0.tar.gz" + + version('3.0.0', sha256='fcf0d60234f1544da717a9738325812de1f42c2fa085e2d9252d8fff5712b2ef') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-flake8-import-order/package.py b/var/spack/repos/builtin/packages/py-flake8-import-order/package.py index 453b5ef380..a93236e60f 100644 --- a/var/spack/repos/builtin/packages/py-flake8-import-order/package.py +++ b/var/spack/repos/builtin/packages/py-flake8-import-order/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py b/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py index 3c3292d09b..8de1f37505 100644 --- a/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py +++ b/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-flake8/package.py b/var/spack/repos/builtin/packages/py-flake8/package.py index e447b91b86..462758ddf4 100644 --- a/var/spack/repos/builtin/packages/py-flake8/package.py +++ b/var/spack/repos/builtin/packages/py-flake8/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-flask-compress/package.py b/var/spack/repos/builtin/packages/py-flask-compress/package.py index 27914ccd82..c8a2f4ea06 100644 --- a/var/spack/repos/builtin/packages/py-flask-compress/package.py +++ b/var/spack/repos/builtin/packages/py-flask-compress/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-flask-socketio/package.py b/var/spack/repos/builtin/packages/py-flask-socketio/package.py index b2a99926bf..5a31755694 100644 --- a/var/spack/repos/builtin/packages/py-flask-socketio/package.py +++ b/var/spack/repos/builtin/packages/py-flask-socketio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-flask/package.py b/var/spack/repos/builtin/packages/py-flask/package.py index b2b68ec05f..befe505743 100644 --- a/var/spack/repos/builtin/packages/py-flask/package.py +++ b/var/spack/repos/builtin/packages/py-flask/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-flexx/package.py b/var/spack/repos/builtin/packages/py-flexx/package.py index 965986549c..127c97f1ad 100644 --- a/var/spack/repos/builtin/packages/py-flexx/package.py +++ b/var/spack/repos/builtin/packages/py-flexx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-flye/package.py b/var/spack/repos/builtin/packages/py-flye/package.py index 03705a7a3a..db3804e11d 100644 --- a/var/spack/repos/builtin/packages/py-flye/package.py +++ b/var/spack/repos/builtin/packages/py-flye/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,7 +28,7 @@ class PyFlye(PythonPackage): conflicts('%clang@:3.2', msg=msg) # Requires Apple Clang 5.0+ but no way to specify that right now - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if self.spec.target.family == 'aarch64': - spack_env.set('arm_neon', '1') - spack_env.set('aarch64', '1') + env.set('arm_neon', '1') + env.set('aarch64', '1') diff --git a/var/spack/repos/builtin/packages/py-fn/package.py b/var/spack/repos/builtin/packages/py-fn-py/package.py index 95cf3d4adf..bc8e2f85a0 100644 --- a/var/spack/repos/builtin/packages/py-fn/package.py +++ b/var/spack/repos/builtin/packages/py-fn-py/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PyFn(PythonPackage): +class PyFnPy(PythonPackage): """Functional programming in Python: implementation of missing features to enjoy FP.""" diff --git a/var/spack/repos/builtin/packages/py-fortranformat/package.py b/var/spack/repos/builtin/packages/py-fortranformat/package.py index c5241a7208..d193494b6a 100644 --- a/var/spack/repos/builtin/packages/py-fortranformat/package.py +++ b/var/spack/repos/builtin/packages/py-fortranformat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-fparser/package.py b/var/spack/repos/builtin/packages/py-fparser/package.py index b88ed73845..e83f4b78ac 100644 --- a/var/spack/repos/builtin/packages/py-fparser/package.py +++ b/var/spack/repos/builtin/packages/py-fparser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-freezegun/package.py b/var/spack/repos/builtin/packages/py-freezegun/package.py index 30008e4cc6..3329c975bc 100644 --- a/var/spack/repos/builtin/packages/py-freezegun/package.py +++ b/var/spack/repos/builtin/packages/py-freezegun/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-fsspec/package.py b/var/spack/repos/builtin/packages/py-fsspec/package.py index 7d7372f66a..6302fff6d7 100644 --- a/var/spack/repos/builtin/packages/py-fsspec/package.py +++ b/var/spack/repos/builtin/packages/py-fsspec/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,9 +10,9 @@ class PyFsspec(PythonPackage): """A specification for pythonic filesystems.""" homepage = "https://github.com/intake/filesystem_spec" - url = "https://github.com/intake/filesystem_spec/archive/0.4.4.tar.gz" + url = "https://pypi.io/packages/source/f/fsspec/fsspec-0.4.4.tar.gz" - version('0.4.4', sha256='27dfc3dab37d5c037683c7a3eaf7acd8b24ee56e4ce3edb14af54bdb43973d43') + version('0.4.4', sha256='97697a46e8bf8be34461c2520d6fc4bfca0ed749b22bb2b7c21939fd450a7d63') depends_on('python@3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-funcsigs/package.py b/var/spack/repos/builtin/packages/py-funcsigs/package.py index 935b31bbc2..ec53173d15 100644 --- a/var/spack/repos/builtin/packages/py-funcsigs/package.py +++ b/var/spack/repos/builtin/packages/py-funcsigs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-functools32/package.py b/var/spack/repos/builtin/packages/py-functools32/package.py index 9662cbea44..bcec6385a8 100644 --- a/var/spack/repos/builtin/packages/py-functools32/package.py +++ b/var/spack/repos/builtin/packages/py-functools32/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-fusepy/package.py b/var/spack/repos/builtin/packages/py-fusepy/package.py new file mode 100644 index 0000000000..7ca452b538 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-fusepy/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyFusepy(PythonPackage): + """Fusepy is a Python module that provides a simple interface to FUSE and + MacFUSE. It's just one file and is implemented using ctypes.""" + + homepage = "https://github.com/fusepy/fusepy" + url = "https://github.com/fusepy/fusepy/archive/v2.0.4.tar.gz" + + version('2.0.4', sha256='802610ab25ad04fc9ef34d024a0abe41cdcaff6a2cb8b2fb92cdda0057c09d1f') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-future/package.py b/var/spack/repos/builtin/packages/py-future/package.py index 0394a0bd01..10f80d4a0c 100644 --- a/var/spack/repos/builtin/packages/py-future/package.py +++ b/var/spack/repos/builtin/packages/py-future/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-futures/package.py b/var/spack/repos/builtin/packages/py-futures/package.py index 4ed3f59416..699e36f7ea 100644 --- a/var/spack/repos/builtin/packages/py-futures/package.py +++ b/var/spack/repos/builtin/packages/py-futures/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-fypp/package.py b/var/spack/repos/builtin/packages/py-fypp/package.py index 6617ce417d..e28f8b5250 100644 --- a/var/spack/repos/builtin/packages/py-fypp/package.py +++ b/var/spack/repos/builtin/packages/py-fypp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-gast/package.py b/var/spack/repos/builtin/packages/py-gast/package.py index 086bb7af8b..c7730e1e28 100644 --- a/var/spack/repos/builtin/packages/py-gast/package.py +++ b/var/spack/repos/builtin/packages/py-gast/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ class PyGast(PythonPackage): url = "https://pypi.io/packages/source/g/gast/gast-0.3.2.tar.gz" version('0.3.2', sha256='5c7617f1f6c8b8b426819642b16b9016727ddaecd16af9a07753e537eba8a3a5') + version('0.2.2', sha256='fe939df4583692f0512161ec1c880e0a10e71e6a232da045ab8edd3756fbadf0') + version('0.2.0', sha256='7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930') depends_on('py-setuptools', type='build') - depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-gdbgui/package.py b/var/spack/repos/builtin/packages/py-gdbgui/package.py index 1142c14fb3..272d375cd3 100644 --- a/var/spack/repos/builtin/packages/py-gdbgui/package.py +++ b/var/spack/repos/builtin/packages/py-gdbgui/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-gdc-client/package.py b/var/spack/repos/builtin/packages/py-gdc-client/package.py index b7acabbb5c..37bae78010 100644 --- a/var/spack/repos/builtin/packages/py-gdc-client/package.py +++ b/var/spack/repos/builtin/packages/py-gdc-client/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-gee-asset-manager/package.py b/var/spack/repos/builtin/packages/py-gee-asset-manager/package.py index 3107692ab3..f32108bccd 100644 --- a/var/spack/repos/builtin/packages/py-gee-asset-manager/package.py +++ b/var/spack/repos/builtin/packages/py-gee-asset-manager/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-geeadd/package.py b/var/spack/repos/builtin/packages/py-geeadd/package.py index aa748ccbfd..78c260243b 100644 --- a/var/spack/repos/builtin/packages/py-geeadd/package.py +++ b/var/spack/repos/builtin/packages/py-geeadd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-geeup/package.py b/var/spack/repos/builtin/packages/py-geeup/package.py index 6e66dc2ffb..6ac2cc37d0 100644 --- a/var/spack/repos/builtin/packages/py-geeup/package.py +++ b/var/spack/repos/builtin/packages/py-geeup/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-genders/package.py b/var/spack/repos/builtin/packages/py-genders/package.py index 13df2acdc3..33452991fd 100644 --- a/var/spack/repos/builtin/packages/py-genders/package.py +++ b/var/spack/repos/builtin/packages/py-genders/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-genshi/package.py b/var/spack/repos/builtin/packages/py-genshi/package.py index 082ca12d1a..e43cf5d6e1 100644 --- a/var/spack/repos/builtin/packages/py-genshi/package.py +++ b/var/spack/repos/builtin/packages/py-genshi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-gensim/package.py b/var/spack/repos/builtin/packages/py-gensim/package.py index 48e0f09efc..06eaacfe94 100644 --- a/var/spack/repos/builtin/packages/py-gensim/package.py +++ b/var/spack/repos/builtin/packages/py-gensim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-geoalchemy2/package.py b/var/spack/repos/builtin/packages/py-geoalchemy2/package.py index ad5c5a4591..dad20c8e16 100644 --- a/var/spack/repos/builtin/packages/py-geoalchemy2/package.py +++ b/var/spack/repos/builtin/packages/py-geoalchemy2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-geopandas/package.py b/var/spack/repos/builtin/packages/py-geopandas/package.py index e08c386e09..3373e961e5 100644 --- a/var/spack/repos/builtin/packages/py-geopandas/package.py +++ b/var/spack/repos/builtin/packages/py-geopandas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-gevent/package.py b/var/spack/repos/builtin/packages/py-gevent/package.py index 66587fbee4..e1f28b445b 100644 --- a/var/spack/repos/builtin/packages/py-gevent/package.py +++ b/var/spack/repos/builtin/packages/py-gevent/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-gf256/package.py b/var/spack/repos/builtin/packages/py-gf256/package.py new file mode 100644 index 0000000000..9527477a3f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-gf256/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyGf256(PythonPackage): + """GF256 is an implementation of GF(2**8). This Galois Field allows you + to perform finite field arithmetic on byte sized integers.""" + + homepage = "https://github.com/DasIch/gf256/" + url = "https://github.com/DasIch/gf256/archive/0.2.0.tar.gz" + + version('0.2.0', sha256='75966f57674d957fba361b4d41a19ea0989dd55532ca7df1797b1d5c5a67ad71') + + depends_on('py-setuptools', type='build') + depends_on('py-cffi@1.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-git-review/package.py b/var/spack/repos/builtin/packages/py-git-review/package.py index 38d860e86f..b68538eaac 100644 --- a/var/spack/repos/builtin/packages/py-git-review/package.py +++ b/var/spack/repos/builtin/packages/py-git-review/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,5 +23,5 @@ class PyGitReview(PythonPackage): depends_on('git', type=('run')) depends_on('tk', type=('run')) - def setup_environment(self, spack_env, run_env): - run_env.set('PBR_VERSION', str(self.spec.version)) + def setup_run_environment(self, env): + env.set('PBR_VERSION', str(self.spec.version)) diff --git a/var/spack/repos/builtin/packages/py-gnuplot/package.py b/var/spack/repos/builtin/packages/py-gnuplot/package.py index 719d2fd01c..38e5522370 100644 --- a/var/spack/repos/builtin/packages/py-gnuplot/package.py +++ b/var/spack/repos/builtin/packages/py-gnuplot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-goatools/package.py b/var/spack/repos/builtin/packages/py-goatools/package.py index 10a3ed7a4a..863e329169 100644 --- a/var/spack/repos/builtin/packages/py-goatools/package.py +++ b/var/spack/repos/builtin/packages/py-goatools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-google-api-core/package.py b/var/spack/repos/builtin/packages/py-google-api-core/package.py index c659c3b640..f8ca4ea2b5 100644 --- a/var/spack/repos/builtin/packages/py-google-api-core/package.py +++ b/var/spack/repos/builtin/packages/py-google-api-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-google-api-python-client/package.py b/var/spack/repos/builtin/packages/py-google-api-python-client/package.py index 1a00ce83c7..5e85f7181c 100644 --- a/var/spack/repos/builtin/packages/py-google-api-python-client/package.py +++ b/var/spack/repos/builtin/packages/py-google-api-python-client/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-google-auth-httplib2/package.py b/var/spack/repos/builtin/packages/py-google-auth-httplib2/package.py index b081dcd8e3..ab4c3c7e72 100644 --- a/var/spack/repos/builtin/packages/py-google-auth-httplib2/package.py +++ b/var/spack/repos/builtin/packages/py-google-auth-httplib2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-google-auth/package.py b/var/spack/repos/builtin/packages/py-google-auth/package.py index f7f94412ee..1bf19bdb08 100644 --- a/var/spack/repos/builtin/packages/py-google-auth/package.py +++ b/var/spack/repos/builtin/packages/py-google-auth/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-google-cloud-core/package.py b/var/spack/repos/builtin/packages/py-google-cloud-core/package.py index d29abbf439..d32a1dbf15 100644 --- a/var/spack/repos/builtin/packages/py-google-cloud-core/package.py +++ b/var/spack/repos/builtin/packages/py-google-cloud-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-google-cloud-storage/package.py b/var/spack/repos/builtin/packages/py-google-cloud-storage/package.py index 8a54d19958..d89b32b0d4 100644 --- a/var/spack/repos/builtin/packages/py-google-cloud-storage/package.py +++ b/var/spack/repos/builtin/packages/py-google-cloud-storage/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-google-pasta/package.py b/var/spack/repos/builtin/packages/py-google-pasta/package.py new file mode 100644 index 0000000000..ee19406005 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-google-pasta/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyGooglePasta(PythonPackage): + """pasta is an AST-based Python refactoring library.""" + + homepage = "https://github.com/google/pasta" + url = "https://pypi.io/packages/source/g/google-pasta/google-pasta-0.1.8.tar.gz" + + version('0.1.8', sha256='713813a9f7d6589e5defdaf21e80e4392eb124662f8bd829acd51a4f8735c0cb') + + depends_on('py-setuptools', type='build') + depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-google-resumable-media/package.py b/var/spack/repos/builtin/packages/py-google-resumable-media/package.py index b913582884..ea84fc077a 100644 --- a/var/spack/repos/builtin/packages/py-google-resumable-media/package.py +++ b/var/spack/repos/builtin/packages/py-google-resumable-media/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-googleapis-common-protos/package.py b/var/spack/repos/builtin/packages/py-googleapis-common-protos/package.py index f11d9f9eef..ce116afc5c 100644 --- a/var/spack/repos/builtin/packages/py-googleapis-common-protos/package.py +++ b/var/spack/repos/builtin/packages/py-googleapis-common-protos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-gpaw/package.py b/var/spack/repos/builtin/packages/py-gpaw/package.py index f17f740f3d..5474f1e84d 100644 --- a/var/spack/repos/builtin/packages/py-gpaw/package.py +++ b/var/spack/repos/builtin/packages/py-gpaw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-graphviz/package.py b/var/spack/repos/builtin/packages/py-graphviz/package.py index 6cbe0ec74a..da4fbe17b0 100644 --- a/var/spack/repos/builtin/packages/py-graphviz/package.py +++ b/var/spack/repos/builtin/packages/py-graphviz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-greenlet/package.py b/var/spack/repos/builtin/packages/py-greenlet/package.py index d37e061254..cda196c519 100644 --- a/var/spack/repos/builtin/packages/py-greenlet/package.py +++ b/var/spack/repos/builtin/packages/py-greenlet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-grequests/package.py b/var/spack/repos/builtin/packages/py-grequests/package.py index 2bd721c64a..53b804bd6f 100644 --- a/var/spack/repos/builtin/packages/py-grequests/package.py +++ b/var/spack/repos/builtin/packages/py-grequests/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-griddataformats/package.py b/var/spack/repos/builtin/packages/py-griddataformats/package.py index e91aec673c..f7c8584ac0 100644 --- a/var/spack/repos/builtin/packages/py-griddataformats/package.py +++ b/var/spack/repos/builtin/packages/py-griddataformats/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,8 +13,10 @@ class PyGriddataformats(PythonPackage): data again.""" homepage = "http://www.mdanalysis.org/GridDataFormats" - url = "https://pypi.io/packages/source/G/GridDataFormats/GridDataFormats-0.3.3.tar.gz" + url = "https://pypi.io/packages/source/G/GridDataFormats/GridDataFormats-0.5.0.tar.gz" + version('0.5.0', sha256='f317ed60708de22d1b2a76ce89a00f722d903291b1055ff1018d441870c39d69') + version('0.4.1', sha256='b362662c2dc475e2a3895fe044eaaa9a707bd660fd109a63dac84a47236690a3') version('0.3.3', sha256='938f0efcb3bc2f58ec85048b933942da8a52c134170acc97cb095f09d3698fbd') depends_on('python@2.7:') diff --git a/var/spack/repos/builtin/packages/py-grpcio/package.py b/var/spack/repos/builtin/packages/py-grpcio/package.py new file mode 100644 index 0000000000..bdda7c85e3 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-grpcio/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyGrpcio(PythonPackage): + """HTTP/2-based RPC framework.""" + + homepage = "https://grpc.io/" + url = "https://pypi.io/packages/source/g/grpcio/grpcio-1.25.0.tar.gz" + + version('1.25.0', sha256='c948c034d8997526011960db54f512756fb0b4be1b81140a15b4ef094c6594a4') + + depends_on('py-setuptools', type='build') + depends_on('py-six@1.5.2:', type=('build', 'run')) + depends_on('py-futures@2.2.0:', when='^python@:3.1', type=('build', 'run')) + depends_on('py-enum34@1.0.4:', when='^python@:3.3', type=('build', 'run')) + depends_on('py-cython@0.23:', type='build') + depends_on('openssl') + depends_on('zlib') + depends_on('c-ares') + + def setup_build_environment(self, env): + env.set('GRPC_PYTHON_BUILD_WITH_CYTHON', True) + env.set('GRPC_PYTHON_BUILD_SYSTEM_OPENSSL', True) + env.set('GRPC_PYTHON_BUILD_SYSTEM_ZLIB', True) + env.set('GRPC_PYTHON_BUILD_SYSTEM_CARES', True) diff --git a/var/spack/repos/builtin/packages/py-guidata/package.py b/var/spack/repos/builtin/packages/py-guidata/package.py index c3b2f96cca..40ddc445b2 100644 --- a/var/spack/repos/builtin/packages/py-guidata/package.py +++ b/var/spack/repos/builtin/packages/py-guidata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-guiqwt/package.py b/var/spack/repos/builtin/packages/py-guiqwt/package.py index b7ca220b12..84a983473d 100644 --- a/var/spack/repos/builtin/packages/py-guiqwt/package.py +++ b/var/spack/repos/builtin/packages/py-guiqwt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-h5glance/package.py b/var/spack/repos/builtin/packages/py-h5glance/package.py index 5e44903573..93a1be4028 100644 --- a/var/spack/repos/builtin/packages/py-h5glance/package.py +++ b/var/spack/repos/builtin/packages/py-h5glance/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,4 +19,4 @@ class PyH5glance(PythonPackage): depends_on('python@3.5:', type=('build', 'run')) depends_on('py-h5py', type=('build', 'run')) - depends_on('py-python-htmlgen', type='run') + depends_on('py-htmlgen', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index d3c67a813e..d09fc71505 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-h5sh/package.py b/var/spack/repos/builtin/packages/py-h5sh/package.py new file mode 100644 index 0000000000..a85c123475 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-h5sh/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyH5sh(PythonPackage): + """Shell-like environment for HDF5.""" + + homepage = "https://pypi.python.org/pypi/h5sh" + url = "https://github.com/sethrj/h5sh/archive/v0.1.1.tar.gz" + + maintainers = ['sethrj'] + + version('0.1.1', sha256='111989d8200d1da8e150aee637a907e524ca0f98d5005a55587cba0d94d9c4a0') + + depends_on('py-setuptools', type=('build', 'run')) + depends_on('py-h5py', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-prompt-toolkit@2:', type=('build', 'run')) + depends_on('py-pygments', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) + depends_on('py-pytest', type='test') diff --git a/var/spack/repos/builtin/packages/py-hacking/package.py b/var/spack/repos/builtin/packages/py-hacking/package.py new file mode 100644 index 0000000000..dae3f8b281 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-hacking/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyHacking(PythonPackage): + """OpenStack Hacking Guideline Enforcement.""" + + homepage = "https://docs.openstack.org/hacking/latest/" + url = "https://pypi.io/packages/source/h/hacking/hacking-1.1.0.tar.gz" + + import_modules = ['hacking'] + + version('1.1.0', sha256='23a306f3a1070a4469a603886ba709780f02ae7e0f1fc7061e5c6fb203828fee') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-hdfs/package.py b/var/spack/repos/builtin/packages/py-hdfs/package.py index 994d60af31..599a00fad8 100644 --- a/var/spack/repos/builtin/packages/py-hdfs/package.py +++ b/var/spack/repos/builtin/packages/py-hdfs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-hepdata-validator/package.py b/var/spack/repos/builtin/packages/py-hepdata-validator/package.py index 6df139ea42..ca4daefff5 100644 --- a/var/spack/repos/builtin/packages/py-hepdata-validator/package.py +++ b/var/spack/repos/builtin/packages/py-hepdata-validator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-hpccm/package.py b/var/spack/repos/builtin/packages/py-hpccm/package.py index fee945d1ed..db041ef65a 100644 --- a/var/spack/repos/builtin/packages/py-hpccm/package.py +++ b/var/spack/repos/builtin/packages/py-hpccm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,9 +11,9 @@ class PyHpccm(PythonPackage): tool to make it easier to generate container specification files.""" homepage = "https://github.com/NVIDIA/hpc-container-maker" - url = "https://github.com/NVIDIA/hpc-container-maker/archive/v19.2.0.tar.gz" + url = "https://pypi.io/packages/source/h/hpccm/hpccm-19.2.0.tar.gz" - version('19.2.0', sha256='99eb0f48cfbdfb29815aed8bcd0fa8c5a857fd912a2bb9658b217b0712ca4af5') + version('19.2.0', sha256='c60eec914a802b0a76596cfd5fdf7122d3f8665fcef06ef928323f5dfb5219a6') depends_on('py-setuptools', type=('build', 'run')) depends_on('py-enum34', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-html2text/package.py b/var/spack/repos/builtin/packages/py-html2text/package.py index 5d01275747..69895a7361 100644 --- a/var/spack/repos/builtin/packages/py-html2text/package.py +++ b/var/spack/repos/builtin/packages/py-html2text/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-html5lib/package.py b/var/spack/repos/builtin/packages/py-html5lib/package.py index 2e9181ef4f..e9e8b485ab 100644 --- a/var/spack/repos/builtin/packages/py-html5lib/package.py +++ b/var/spack/repos/builtin/packages/py-html5lib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-htmlgen/package.py b/var/spack/repos/builtin/packages/py-htmlgen/package.py index 546991b9ee..b15fe69769 100644 --- a/var/spack/repos/builtin/packages/py-python-htmlgen/package.py +++ b/var/spack/repos/builtin/packages/py-htmlgen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,7 +7,7 @@ from spack import * -class PyPythonHtmlgen(PythonPackage): +class PyHtmlgen(PythonPackage): """Library to generate HTML from classes. """ @@ -16,9 +16,7 @@ class PyPythonHtmlgen(PythonPackage): version('1.2.2', sha256='9dc60e10511f0fd13014659514c6c333498c21779173deb585cd4964ea667770') - conflicts('python@3.0:3.3.99') - + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') - # dependencies for tests + depends_on('py-asserts@0.8.0:0.8.999', type='test') depends_on('py-typing', type='test') - depends_on('py-python-asserts', type='test') diff --git a/var/spack/repos/builtin/packages/py-htseq/package.py b/var/spack/repos/builtin/packages/py-htseq/package.py index f5a33d4129..693c12840c 100644 --- a/var/spack/repos/builtin/packages/py-htseq/package.py +++ b/var/spack/repos/builtin/packages/py-htseq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-httpbin/package.py b/var/spack/repos/builtin/packages/py-httpbin/package.py index 7c3078ed09..815f748885 100644 --- a/var/spack/repos/builtin/packages/py-httpbin/package.py +++ b/var/spack/repos/builtin/packages/py-httpbin/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-httplib2/package.py b/var/spack/repos/builtin/packages/py-httplib2/package.py index 93b8c5833d..73877056ac 100644 --- a/var/spack/repos/builtin/packages/py-httplib2/package.py +++ b/var/spack/repos/builtin/packages/py-httplib2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-humanfriendly/package.py b/var/spack/repos/builtin/packages/py-humanfriendly/package.py new file mode 100644 index 0000000000..a1b63e8233 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-humanfriendly/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class PyHumanfriendly(PythonPackage): + """Human friendly output for text interfaces using Python""" + + homepage = "https://pypi.org/project/humanfriendly/" + url = "https://files.pythonhosted.org/packages/26/71/e7daf57e819a70228568ff5395fdbc4de81b63067b93167e07825fcf0bcf/humanfriendly-4.18.tar.gz" + + version('4.18', sha256='33ee8ceb63f1db61cce8b5c800c531e1a61023ac5488ccde2ba574a85be00a85') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-humanize/package.py b/var/spack/repos/builtin/packages/py-humanize/package.py index 17129e1ee8..c83200de00 100644 --- a/var/spack/repos/builtin/packages/py-humanize/package.py +++ b/var/spack/repos/builtin/packages/py-humanize/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-hvac/package.py b/var/spack/repos/builtin/packages/py-hvac/package.py new file mode 100644 index 0000000000..968fef45e6 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-hvac/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyHvac(PythonPackage): + """HashiCorp Vault API client""" + + homepage = "https://github.com/hvac/hvac/" + url = "https://github.com/hvac/hvac/archive/v0.2.17.tar.gz" + + version('0.9.6', sha256='ff60972edc512c73ac4811e91bcffccdb99f0d8975c0b41e44a4c79d73c711af') + version('0.9.5', sha256='3e4af2d84833b8f61c9c3351d4a9799bf8e8e4344d0ad4e162609a7379961a16') + version('0.9.4', sha256='ebb14b9a5b347c4f0b4dcea59f435dcc190d8ccb4cb9a20e5daf260af6509dd6') + version('0.9.3', sha256='cac16bc089be9966f1fe5c108fb966949dc5bb4348cc1f5f54ebd8511c410ed4') + version('0.2.17', sha256='a767be25fcb1165f4b28da3312a0bd196d1101c53c60fb99f899ff6c7b9aaa78') + + depends_on('py-setuptools', type='build') + depends_on('py-requests@2.7.0:', type=('build', 'run')) + depends_on('py-requests@2.21.0:', type=('build', 'run'), when='@0.9.3:') + depends_on('py-six@1.5.0:', type=('build', 'run'), when='@0.9.6:') diff --git a/var/spack/repos/builtin/packages/py-hypothesis/package.py b/var/spack/repos/builtin/packages/py-hypothesis/package.py index 2820ddcd7e..2bd02545e4 100644 --- a/var/spack/repos/builtin/packages/py-hypothesis/package.py +++ b/var/spack/repos/builtin/packages/py-hypothesis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,9 +21,12 @@ class PyHypothesis(PythonPackage): # TODO: Add missing dependency required to import hypothesis.extra.django version('4.41.2', sha256='6847df3ffb4aa52798621dd007e6b61dbcf2d76c30ba37dc2699720e2c734b7a') + version('4.24.3', sha256='fd90a319f409f34a173156ca704d6c0c6c0bb30a2e43dbf26aced2c75569e5d5') version('4.7.2', sha256='87944c6379f77634474b88abbf1e5ed5fe966637cc926131eda5e2af5b54a608') version('3.7.0', sha256='0fea49d08f2d5884f014151a5af6fb48d862f6ad567ffc4a2e84abf2f186c423') depends_on('py-setuptools', type='build') - depends_on('py-attrs@19.2.0:', type=('build', 'run')) + depends_on('py-attrs@19.2.0:', when='@4.38.2:', type=('build', 'run')) + depends_on('py-attrs@16.0.0:', when='@3.44.22:', type=('build', 'run')) + depends_on('py-attrs', when='@3.28.0:', type=('build', 'run')) depends_on('py-enum34', type=('build', 'run'), when='^python@:2') diff --git a/var/spack/repos/builtin/packages/py-ics/package.py b/var/spack/repos/builtin/packages/py-ics/package.py new file mode 100644 index 0000000000..7c91e2c5ff --- /dev/null +++ b/var/spack/repos/builtin/packages/py-ics/package.py @@ -0,0 +1,39 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyIcs(PythonPackage): + """Ics.py : iCalendar for Humans + + Ics.py is a pythonic and easy iCalendar library. Its goals are to + read and write ics data in a developer friendly way. + + iCalendar is a widely-used and useful format but not user friendly. + Ics.py is there to give you the ability of creating and reading + this format without any knowledge of it. + + It should be able to parse every calendar that respects the + rfc5545 and maybe some more. It also outputs rfc compliant + calendars. + + iCalendar (file extension .ics) is used by Google Calendar, Apple + Calendar, Android and many more. + + Ics.py is available for Python>=3.6 and is Apache2 Licensed. + """ + + homepage = "https://github.com/C4ptainCrunch/ics.py" + url = "https://github.com/C4ptainCrunch/ics.py/archive/v0.6.tar.gz" + + version('0.6', sha256='4947263136202d0489d4f5e5c7175dfd2db5d3508b8b003ddeaef96347f68830') + + depends_on('python@3.6:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-python-dateutil', type=('build', 'run')) + depends_on('py-arrow@0.11:0.14.99', type=('build', 'run')) + depends_on('py-six@1.5:', type=('build', 'run')) + depends_on('py-tatsu@4.2:', type=('build', 'run'), when='@0.6:') diff --git a/var/spack/repos/builtin/packages/py-identify/package.py b/var/spack/repos/builtin/packages/py-identify/package.py new file mode 100644 index 0000000000..3ffafe94d7 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-identify/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyIdentify(PythonPackage): + """File identification library for Python. + + Given a file (or some information about a file), return a set of + standardized tags identifying what the file is.""" + + homepage = "https://github.com/chriskuehl/identify" + url = "https://pypi.io/packages/source/i/identify/identify-1.4.7.tar.gz" + + version('1.4.7', sha256='d8919589bd2a5f99c66302fec0ef9027b12ae150b0b0213999ad3f695fc7296e') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-idna/package.py b/var/spack/repos/builtin/packages/py-idna/package.py index 2685080056..95498e38a6 100644 --- a/var/spack/repos/builtin/packages/py-idna/package.py +++ b/var/spack/repos/builtin/packages/py-idna/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-illumina-utils/package.py b/var/spack/repos/builtin/packages/py-illumina-utils/package.py index 711ab6af88..081b14163a 100644 --- a/var/spack/repos/builtin/packages/py-illumina-utils/package.py +++ b/var/spack/repos/builtin/packages/py-illumina-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-imageio/package.py b/var/spack/repos/builtin/packages/py-imageio/package.py index e39965b574..12111352d4 100644 --- a/var/spack/repos/builtin/packages/py-imageio/package.py +++ b/var/spack/repos/builtin/packages/py-imageio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-imagesize/package.py b/var/spack/repos/builtin/packages/py-imagesize/package.py index 994535b0aa..e9f2033413 100644 --- a/var/spack/repos/builtin/packages/py-imagesize/package.py +++ b/var/spack/repos/builtin/packages/py-imagesize/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-iminuit/package.py b/var/spack/repos/builtin/packages/py-iminuit/package.py index 48109815b1..f9531d640b 100644 --- a/var/spack/repos/builtin/packages/py-iminuit/package.py +++ b/var/spack/repos/builtin/packages/py-iminuit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-importlib-metadata/package.py b/var/spack/repos/builtin/packages/py-importlib-metadata/package.py index b456fe128f..cd65b09ce0 100644 --- a/var/spack/repos/builtin/packages/py-importlib-metadata/package.py +++ b/var/spack/repos/builtin/packages/py-importlib-metadata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,17 +9,19 @@ from spack import * class PyImportlibMetadata(PythonPackage): """Read metadata from Python packages.""" - homepage = "http://importlib-metadata.readthedocs.io/" - url = "https://pypi.io/packages/source/i/importlib_metadata/importlib_metadata-0.23.tar.gz" + homepage = "https://importlib-metadata.readthedocs.io/" + url = "https://pypi.io/packages/source/i/importlib_metadata/importlib_metadata-1.2.0.tar.gz" - version('0.23', sha256='aa18d7378b00b40847790e7c27e11673d7fed219354109d0e7b9e5b25dc3ad26') - version('0.19', sha256='23d3d873e008a513952355379d93cbcab874c58f4f034ff657c7a87422fa64e8') + version('1.2.0', sha256='41e688146d000891f32b1669e8573c57e39e5060e7f5f647aa617cd9a9568278') + version('0.23', sha256='aa18d7378b00b40847790e7c27e11673d7fed219354109d0e7b9e5b25dc3ad26') + version('0.19', sha256='23d3d873e008a513952355379d93cbcab874c58f4f034ff657c7a87422fa64e8') - depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-setuptools-scm', type='build') depends_on('py-zipp@0.5:', type=('build', 'run')) - depends_on('py-pathlib2', when='^python@:3.4', type=('build', 'run')) - depends_on('py-contextlib2', when='^python@:2.8', type=('build', 'run')) - depends_on('py-configparser@3.5:', when='^python@:2.8', type=('build', 'run')) + depends_on('py-pathlib2', when='^python@:2', type=('build', 'run')) + depends_on('py-contextlib2', when='^python@:2', type=('build', 'run')) + depends_on('py-configparser@3.5:', when='^python@:2', type=('build', 'run')) + depends_on('py-importlib-resources', when='^python@:3.6', type='test') depends_on('py-packaging', type='test') diff --git a/var/spack/repos/builtin/packages/py-importlib-resources/package.py b/var/spack/repos/builtin/packages/py-importlib-resources/package.py new file mode 100644 index 0000000000..4c0a6e1243 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-importlib-resources/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyImportlibResources(PythonPackage): + """Read resources from Python packages""" + + homepage = "https://pypi.org/project/importlib_resources/" + url = "https://pypi.io/packages/source/i/importlib_resources/importlib_resources-1.0.2.tar.gz" + + version('1.0.2', sha256='d3279fd0f6f847cced9f7acc19bd3e5df54d34f93a2e7bb5f238f81545787078') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + + depends_on('py-setuptools', type='build') + depends_on('py-wheel', type='build') + depends_on('py-pathlib2', when='^python@:2', type=('build', 'run')) + depends_on('py-typing', when='^python@:3.4', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-importlib/package.py b/var/spack/repos/builtin/packages/py-importlib/package.py index f799406507..723eb00c05 100644 --- a/var/spack/repos/builtin/packages/py-importlib/package.py +++ b/var/spack/repos/builtin/packages/py-importlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-iniparse/package.py b/var/spack/repos/builtin/packages/py-iniparse/package.py index 131ab55029..f8083f0c5f 100644 --- a/var/spack/repos/builtin/packages/py-iniparse/package.py +++ b/var/spack/repos/builtin/packages/py-iniparse/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-intervaltree/package.py b/var/spack/repos/builtin/packages/py-intervaltree/package.py new file mode 100644 index 0000000000..f5d4501dd7 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-intervaltree/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyIntervaltree(PythonPackage): + """Editable interval tree data structure for Python 2 and 3.""" + + homepage = "https://github.com/chaimleib/intervaltree" + url = "https://github.com/chaimleib/intervaltree/archive/3.0.2.tar.gz" + + version('3.0.2', sha256='e8ab75b66077f2e5fb85ac56cb6df834689edb048d38601d53d8867cce3b77d1') + + depends_on('py-sortedcontainers@2:2.999', type=('build', 'run')) + depends_on('py-pytest', type='test') + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-invoke/package.py b/var/spack/repos/builtin/packages/py-invoke/package.py index 3bc3bbae16..28a4bcd2b1 100644 --- a/var/spack/repos/builtin/packages/py-invoke/package.py +++ b/var/spack/repos/builtin/packages/py-invoke/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ipaddress/package.py b/var/spack/repos/builtin/packages/py-ipaddress/package.py index e2aff6fd1d..357fb78d95 100644 --- a/var/spack/repos/builtin/packages/py-ipaddress/package.py +++ b/var/spack/repos/builtin/packages/py-ipaddress/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,8 +11,9 @@ class PyIpaddress(PythonPackage): """Python 3.3's ipaddress for older Python versions""" homepage = "https://github.com/phihag/ipaddress" - url = "https://pypi.io/packages/source/i/ipaddress/ipaddress-1.0.18.tar.gz" + url = "https://pypi.io/packages/source/i/ipaddress/ipaddress-1.0.23.tar.gz" + version('1.0.23', sha256='b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2') version('1.0.18', sha256='5d8534c8e185f2d8a1fda1ef73f2c8f4b23264e8e30063feeb9511d492a413e1') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-ipdb/package.py b/var/spack/repos/builtin/packages/py-ipdb/package.py index bb99a117f6..81c4bfb705 100644 --- a/var/spack/repos/builtin/packages/py-ipdb/package.py +++ b/var/spack/repos/builtin/packages/py-ipdb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ipykernel/package.py b/var/spack/repos/builtin/packages/py-ipykernel/package.py index d38f9ea52e..21c210f5d1 100644 --- a/var/spack/repos/builtin/packages/py-ipykernel/package.py +++ b/var/spack/repos/builtin/packages/py-ipykernel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ipython-genutils/package.py b/var/spack/repos/builtin/packages/py-ipython-genutils/package.py index a5a31973e0..b6a5d66085 100644 --- a/var/spack/repos/builtin/packages/py-ipython-genutils/package.py +++ b/var/spack/repos/builtin/packages/py-ipython-genutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ipython/package.py b/var/spack/repos/builtin/packages/py-ipython/package.py index 0b13d59860..2e2cfc6966 100644 --- a/var/spack/repos/builtin/packages/py-ipython/package.py +++ b/var/spack/repos/builtin/packages/py-ipython/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ipywidgets/package.py b/var/spack/repos/builtin/packages/py-ipywidgets/package.py index d5c066b14b..e8a8bfa258 100644 --- a/var/spack/repos/builtin/packages/py-ipywidgets/package.py +++ b/var/spack/repos/builtin/packages/py-ipywidgets/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-isodate/package.py b/var/spack/repos/builtin/packages/py-isodate/package.py new file mode 100644 index 0000000000..bac6f2b44d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-isodate/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyIsodate(PythonPackage): + """This module implements ISO 8601 date, time and duration parsing. The + implementation follows ISO8601:2004 standard, and implements only date/time + representations mentioned in the standard. If something is not mentioned + there, then it is treated as non existent, and not as an allowed option.""" + + homepage = "https://github.com/gweis/isodate/" + url = "https://pypi.io/packages/source/i/isodate/isodate-0.6.0.tar.gz" + + version('0.6.0', sha256='2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8') + + depends_on('py-setuptools', type='build') + depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-isort/package.py b/var/spack/repos/builtin/packages/py-isort/package.py index 1ba594611e..bdb7d6eb05 100644 --- a/var/spack/repos/builtin/packages/py-isort/package.py +++ b/var/spack/repos/builtin/packages/py-isort/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-itsdangerous/package.py b/var/spack/repos/builtin/packages/py-itsdangerous/package.py index e92393d176..27278a879a 100644 --- a/var/spack/repos/builtin/packages/py-itsdangerous/package.py +++ b/var/spack/repos/builtin/packages/py-itsdangerous/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-jaraco-functools/package.py b/var/spack/repos/builtin/packages/py-jaraco-functools/package.py new file mode 100644 index 0000000000..4b8af85094 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-jaraco-functools/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyJaracoFunctools(PythonPackage): + """Functools like those found in stdlib""" + + homepage = "https://github.com/jaraco/jaraco.functools" + url = "https://pypi.io/packages/source/j/jaraco.functools/jaraco.functools-2.0.tar.gz" + + version( + '2.0', sha256='35ba944f52b1a7beee8843a5aa6752d1d5b79893eeb7770ea98be6b637bf9345') + + depends_on('py-setuptools', type='build') + depends_on('py-setuptools-scm@1.15.0:', type='build') + depends_on('py-backports-functools-lru-cache@1.0.3:', + when='^python@:2', type=('build', 'run')) + depends_on('py-more-itertools', type=('build', 'run')) + depends_on('python@2.7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jdatetime/package.py b/var/spack/repos/builtin/packages/py-jdatetime/package.py new file mode 100644 index 0000000000..1efdc373a5 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-jdatetime/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyJdatetime(PythonPackage): + """jdatetime is Jalali implementation of Python's datetime module""" + + homepage = "https://github.com/slashmili/python-jalali" + url = "https://pypi.io/packages/source/j/jdatetime/jdatetime-3.6.2.tar.gz" + + version('3.6.2', sha256='a589e35f0dab89283c1a3de9d70ed6cf657932aaed8e8ce1b0e5801aaab1da67') diff --git a/var/spack/repos/builtin/packages/py-jdcal/package.py b/var/spack/repos/builtin/packages/py-jdcal/package.py index 1d3d1eff06..06e1eba505 100644 --- a/var/spack/repos/builtin/packages/py-jdcal/package.py +++ b/var/spack/repos/builtin/packages/py-jdcal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-jedi/package.py b/var/spack/repos/builtin/packages/py-jedi/package.py index 7c9c220895..2c95433aa3 100644 --- a/var/spack/repos/builtin/packages/py-jedi/package.py +++ b/var/spack/repos/builtin/packages/py-jedi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-jellyfish/package.py b/var/spack/repos/builtin/packages/py-jellyfish/package.py new file mode 100644 index 0000000000..6316162289 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-jellyfish/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyJellyfish(PythonPackage): + """a library for doing approximate and phonetic matching of strings.""" + + homepage = "https://pypi.org/project/jellyfish/" + url = "https://pypi.io/packages/source/j/jellyfish/jellyfish-0.6.1.tar.gz" + + version('0.6.1', sha256='5104e45a2b804b48a46a92a5e6d6e86830fe60ae83b1da32c867402c8f4c2094') + version('0.5.6', sha256='887a9a49d0caee913a883c3e7eb185f6260ebe2137562365be422d1316bd39c9') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-jinja2/package.py b/var/spack/repos/builtin/packages/py-jinja2/package.py index b0daeaa1af..dd9f8fee2a 100644 --- a/var/spack/repos/builtin/packages/py-jinja2/package.py +++ b/var/spack/repos/builtin/packages/py-jinja2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-jmespath/package.py b/var/spack/repos/builtin/packages/py-jmespath/package.py index 43727153f4..ed5da676f2 100644 --- a/var/spack/repos/builtin/packages/py-jmespath/package.py +++ b/var/spack/repos/builtin/packages/py-jmespath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-joblib/package.py b/var/spack/repos/builtin/packages/py-joblib/package.py index bf77972969..43ea04ed99 100644 --- a/var/spack/repos/builtin/packages/py-joblib/package.py +++ b/var/spack/repos/builtin/packages/py-joblib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,6 +19,7 @@ class PyJoblib(PythonPackage): version('0.14.0', sha256='6fcc57aacb4e89451fd449e9412687c51817c3f48662c3d8f38ba3f8a0a193ff') version('0.13.2', sha256='315d6b19643ec4afd4c41c671f9f2d65ea9d787da093487a81ead7b0bac94524') + version('0.11', sha256='7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085') version('0.10.3', sha256='29b2965a9efbc90a5fe66a389ae35ac5b5b0c1feabfc7cab7fd5d19f429a071d') version('0.10.2', sha256='3123553bdad83b143428033537c9e1939caf4a4d8813dade6a2246948c94494b') version('0.10.0', sha256='49b3a0ba956eaa2f077e1ebd230b3c8d7b98afc67520207ada20a4d8b8efd071') diff --git a/var/spack/repos/builtin/packages/py-jplephem/package.py b/var/spack/repos/builtin/packages/py-jplephem/package.py index 5f8f563d4d..fb4456d800 100644 --- a/var/spack/repos/builtin/packages/py-jplephem/package.py +++ b/var/spack/repos/builtin/packages/py-jplephem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-jprops/package.py b/var/spack/repos/builtin/packages/py-jprops/package.py index fd0fe0c4ae..16fed619dd 100644 --- a/var/spack/repos/builtin/packages/py-jprops/package.py +++ b/var/spack/repos/builtin/packages/py-jprops/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-jpype/package.py b/var/spack/repos/builtin/packages/py-jpype1/package.py index f8292f4132..7b1424efcb 100644 --- a/var/spack/repos/builtin/packages/py-jpype/package.py +++ b/var/spack/repos/builtin/packages/py-jpype1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PyJpype(PythonPackage): +class PyJpype1(PythonPackage): """JPype is an effort to allow python programs full access to java class libraries.""" diff --git a/var/spack/repos/builtin/packages/py-jsonpatch/package.py b/var/spack/repos/builtin/packages/py-jsonpatch/package.py index b9e60c9a88..eab7421ffb 100644 --- a/var/spack/repos/builtin/packages/py-jsonpatch/package.py +++ b/var/spack/repos/builtin/packages/py-jsonpatch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,9 +10,9 @@ class PyJsonpatch(PythonPackage): """Library to apply JSON Patches according to RFC 6902""" homepage = "https://github.com/stefankoegl/python-json-patch" - url = "https://github.com/stefankoegl/python-json-patch/archive/v1.23.tar.gz" + url = "https://pypi.io/packages/source/j/jsonpatch/jsonpatch-1.23.tar.gz" - version('1.23', sha256='0af03651204ea3049bc4aedaa42b591e134a4ee16e421f9c5f3ac4e9092885ad') + version('1.23', sha256='49f29cab70e9068db3b1dc6b656cbe2ee4edf7dfe9bf5a0055f17a4b6804a4b9') depends_on('py-setuptools', type='build') depends_on('py-jsonpointer@1.9', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jsonpointer/package.py b/var/spack/repos/builtin/packages/py-jsonpointer/package.py index 9e33b53b0d..a9307fd3f6 100644 --- a/var/spack/repos/builtin/packages/py-jsonpointer/package.py +++ b/var/spack/repos/builtin/packages/py-jsonpointer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,8 +10,8 @@ class PyJsonpointer(PythonPackage): """Library to resolve JSON Pointers according to RFC 6901""" homepage = "https://github.com/stefankoegl/python-json-pointer" - url = "https://github.com/stefankoegl/python-json-pointer/archive/v2.0.tar.gz" + url = "https://pypi.io/packages/source/j/jsonpointer/jsonpointer-2.0.tar.gz" - version('2.0', sha256='9594b7574a3216c9994181e9db7566a5cafb4ab24956e554f2dba1bb39edecb2') + version('2.0', sha256='c192ba86648e05fdae4f08a17ec25180a9aef5008d973407b581798a83975362') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-jsonschema/package.py b/var/spack/repos/builtin/packages/py-jsonschema/package.py index 51d0e17ffc..815decdbb2 100644 --- a/var/spack/repos/builtin/packages/py-jsonschema/package.py +++ b/var/spack/repos/builtin/packages/py-jsonschema/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-junit-xml/package.py b/var/spack/repos/builtin/packages/py-junit-xml/package.py index bbdaf9a41b..7d59fe205c 100644 --- a/var/spack/repos/builtin/packages/py-junit-xml/package.py +++ b/var/spack/repos/builtin/packages/py-junit-xml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-jupyter-client/package.py b/var/spack/repos/builtin/packages/py-jupyter-client/package.py index 1b69aa1e4e..8224c0f617 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-client/package.py +++ b/var/spack/repos/builtin/packages/py-jupyter-client/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,7 @@ class PyJupyterClient(PythonPackage): homepage = "https://github.com/jupyter/jupyter_client" url = "https://github.com/jupyter/jupyter_client/archive/4.4.0.tar.gz" + version('5.3.4', sha256='2af6f0e0e4d88009b11103490bea0bfb405c1c470e226c2b7b17c10e5dda9734') version('4.4.0', sha256='2fda7fe1af35f0b4a77c4a2fd4ee38ac3666ed7f4d92a5b6ff8aaf764c38e199') version('4.3.0', sha256='90b6ea3ced910ed94c5d558373490a81b33c672d877c1ffdc76b281e3216f1f6') version('4.2.2', sha256='bf3e8ea4c44f07dbe2991e41031f6dab242734be424f4d40b72cc58a12c7d2ca') @@ -21,7 +22,11 @@ class PyJupyterClient(PythonPackage): version('4.1.0', sha256='ecf76a159381ec9880fd2c31388c6983b1d855f92f0292cf0667a90dd63f51c0') version('4.0.0', sha256='33b15abb1307d8d3716b0d3b5d07aa22fdfbbf65a9f1aedf478a274a6adc11c0') - depends_on('python@2.7:2.8,3.3:') + depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.5:', type=('build', 'run'), when='@5:') depends_on('py-traitlets', type=('build', 'run')) depends_on('py-jupyter-core', type=('build', 'run')) - depends_on('py-zmq@13:', type=('build', 'run')) + depends_on('py-pyzmq@13:', type=('build', 'run')) + depends_on('py-python-dateutil@2.1:', type=('build', 'run'), when='@5:') + depends_on('py-tornado@4.1:', type=('build', 'run'), when='@5:') + depends_on('py-setuptools', type='build', when='@5:') diff --git a/var/spack/repos/builtin/packages/py-jupyter-console/package.py b/var/spack/repos/builtin/packages/py-jupyter-console/package.py index 89aecd40cc..990c8a4f7b 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-console/package.py +++ b/var/spack/repos/builtin/packages/py-jupyter-console/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-jupyter-core/package.py b/var/spack/repos/builtin/packages/py-jupyter-core/package.py index 109eddef3d..fbdc376b2b 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-core/package.py +++ b/var/spack/repos/builtin/packages/py-jupyter-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,19 +10,21 @@ class PyJupyterCore(PythonPackage): """Core Jupyter functionality""" homepage = "http://jupyter-core.readthedocs.io/" - url = "https://github.com/jupyter/jupyter_core/archive/4.2.0.tar.gz" + url = "https://pypi.io/packages/source/j/jupyter-core/jupyter_core-4.6.0.tar.gz" - version('4.4.0', sha256='a3c693cb4cd1251f887f034eba4b74e5ad1beab5baef43cc3ae9387450e72367') - version('4.2.0', sha256='ca2db4bc44b870ad9039bfdcad81bb0466e6bf0e6e2e03626815977ee73dc7a7') - version('4.1.1', sha256='1908dd9eceb8994c1f0b1bb81c20a52dbb01692e4f1fdf5d12e04846b94eb05c') - version('4.1.0', sha256='80b78d215399760f4678cc1512118257543e17b48316254d1e1dbddfafa2dffc') - version('4.0.6', sha256='76d9f95eec679d1ce8a07fba4e373bda3b17ca89e3b03ee6186a7dbdc117d7e8') - version('4.0.5', sha256='783c2be522010db9dd0ff54c28fcdf31afe73a5f7d956eb89ddce2c48f381548') - version('4.0.4', sha256='ee81c1e2c67afe0b9c1097043f76063b452670fc63377ab4656ce1b2826cd166') - version('4.0.3', sha256='5ecc177e8c711a410f857adc65f8413b06ea1f2fa2330559a723d6c1981852f8') - version('4.0.2', sha256='ad2f537aacaa9978b37ac5d39d9bd582d2a9dfc104b3d289b88687c1c5a0ece0') - version('4.0.1', sha256='faa3878b286f63d1853aec3e4b80e2a7299f580a9acebd4a1cafa36b264ec0a3') - version('4.0', sha256='2b491a5da687ffab4e5702e37d3cb8b6b184cd46520cae9c459bdb1fd144f026') + version('4.6.0', sha256='85103cee6548992780912c1a0a9ec2583a4a18f1ef79a248ec0db4446500bce3') + version('4.4.0', sha256='ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7') + version('4.2.0', sha256='44ec837a53bebf4e937112d3f9ccf31fee4f8db3e406dd0dd4f0378a354bed9c') + version('4.1.1', sha256='ae0e69435258126466c86cd989e465a9c334c50107ef4f257decc8693650bf4c') + version('4.1.0', sha256='146af0679c33c56db4b85b785f3dacd933ffaca97e7d2d56ff577a5485c2bd13') + version('4.0.6', sha256='96a68a3b1d018ff7776270b26b7cb0cfd7a18a53ef2061421daff435707d198c') + version('4.0.5', sha256='9f6581b827f56cfa1771d7b1bd8ecc1274afa7f6e3e1046b7e0d4e05d52bf6e8') + version('4.0.4', sha256='fcf45478025f34174943993947f51a41ad871ac998a14bf1cb87d8eb61e75c6d') + version('4.0.3', sha256='12258d8c593c53bb08e09f3da63a418d7cb5b5852b3d0ffa29639402f56dcbdb') + version('4.0.2', sha256='13a46b3c493ac63bd75048d6d2142cfc44258bc6c260d96c506f0214fcd78a70') + version('4.0.1', sha256='7c165f7de7a063596f8be1bcfc86e9ba6897e38baf24e8510514690963600122') + version('4.0.0', sha256='9025208cdfc40718c7e3ab62b5e17aacf68e3fc66e34ff21fe032d553620122a') - depends_on('python@2.7:2.8,3.3:') + depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) + depends_on('py-setuptools', when='@4.5.0:', type='build') depends_on('py-traitlets', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jupyter/package.py b/var/spack/repos/builtin/packages/py-jupyter/package.py new file mode 100644 index 0000000000..4c6f0d9a07 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-jupyter/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyJupyter(PythonPackage): + """Jupyter metapackage. Install all the Jupyter components in one go.""" + + homepage = "https://jupyter.org/" + url = "https://pypi.io/packages/source/j/jupyter/jupyter-1.0.0.tar.gz" + + version('1.0.0', sha256='d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f') + + depends_on('py-notebook', type=('build', 'run')) + depends_on('py-qtconsole', type=('build', 'run')) + depends_on('py-jupyter-console', type=('build', 'run')) + depends_on('py-nbconvert', type=('build', 'run')) + depends_on('py-ipykernel', type=('build', 'run')) + depends_on('py-ipywidgets', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jupyterhub/package.py b/var/spack/repos/builtin/packages/py-jupyterhub/package.py index 2b3e39a389..3e95b7496f 100644 --- a/var/spack/repos/builtin/packages/py-jupyterhub/package.py +++ b/var/spack/repos/builtin/packages/py-jupyterhub/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,5 +31,5 @@ class PyJupyterhub(PythonPackage): depends_on('py-oauthlib@3.0:', when='@1.0.0:', type=('build', 'run')) depends_on('py-python-oauth2@1.0:', when='@:9.4', type=('build', 'run')) depends_on('py-pamela', type=('build', 'run')) - depends_on('py-jupyter-notebook', type=('build', 'run')) + depends_on('py-notebook', type=('build', 'run')) depends_on('py-prometheus-client@0.0.21:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-keras-applications/package.py b/var/spack/repos/builtin/packages/py-keras-applications/package.py index 321c48688a..a26a4e8a26 100644 --- a/var/spack/repos/builtin/packages/py-keras-applications/package.py +++ b/var/spack/repos/builtin/packages/py-keras-applications/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-keras-preprocessing/package.py b/var/spack/repos/builtin/packages/py-keras-preprocessing/package.py index 18f8edb434..f9a5499612 100644 --- a/var/spack/repos/builtin/packages/py-keras-preprocessing/package.py +++ b/var/spack/repos/builtin/packages/py-keras-preprocessing/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-keras/package.py b/var/spack/repos/builtin/packages/py-keras/package.py index 1daab3c5d3..fc9eeaa8a4 100644 --- a/var/spack/repos/builtin/packages/py-keras/package.py +++ b/var/spack/repos/builtin/packages/py-keras/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-kitchen/package.py b/var/spack/repos/builtin/packages/py-kitchen/package.py index 29503f43c8..0e8683d5d8 100644 --- a/var/spack/repos/builtin/packages/py-kitchen/package.py +++ b/var/spack/repos/builtin/packages/py-kitchen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-kiwisolver/package.py b/var/spack/repos/builtin/packages/py-kiwisolver/package.py index fb8509f1db..ebf05e6702 100644 --- a/var/spack/repos/builtin/packages/py-kiwisolver/package.py +++ b/var/spack/repos/builtin/packages/py-kiwisolver/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-kmodes/package.py b/var/spack/repos/builtin/packages/py-kmodes/package.py index b90a2c7746..a3bbe8ea75 100644 --- a/var/spack/repos/builtin/packages/py-kmodes/package.py +++ b/var/spack/repos/builtin/packages/py-kmodes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-kombu/package.py b/var/spack/repos/builtin/packages/py-kombu/package.py new file mode 100644 index 0000000000..732b6e02b4 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-kombu/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyKombu(PythonPackage): + """Messaging library for Python.""" + + homepage = "https://pypi.org/project/kombu/" + url = "https://pypi.io/packages/source/k/kombu/kombu-4.3.0.tar.gz" + + version('4.6.6', sha256='1760b54b1d15a547c9a26d3598a1c8cdaf2436386ac1f5561934bc8a3cbbbd86') + version('4.5.0', sha256='389ba09e03b15b55b1a7371a441c894fd8121d174f5583bbbca032b9ea8c9edd') + version('4.3.0', sha256='529df9e0ecc0bad9fc2b376c3ce4796c41b482cf697b78b71aea6ebe7ca353c8') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + + depends_on('py-setuptools', type='build') + depends_on('py-amqp@2.5.2:2.5.999', type=('build', 'run')) + depends_on('py-importlib-metadata@0.18:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-lark-parser/package.py b/var/spack/repos/builtin/packages/py-lark-parser/package.py index 3772f52f7b..d84e320f1f 100644 --- a/var/spack/repos/builtin/packages/py-lark-parser/package.py +++ b/var/spack/repos/builtin/packages/py-lark-parser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-latexcodec/package.py b/var/spack/repos/builtin/packages/py-latexcodec/package.py index b61bc629be..d379022142 100644 --- a/var/spack/repos/builtin/packages/py-latexcodec/package.py +++ b/var/spack/repos/builtin/packages/py-latexcodec/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py b/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py index f4d4c288bb..606dc00136 100644 --- a/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py +++ b/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-lazy-property/package.py b/var/spack/repos/builtin/packages/py-lazy-property/package.py index 8c36f09269..b6acd6a82e 100644 --- a/var/spack/repos/builtin/packages/py-lazy-property/package.py +++ b/var/spack/repos/builtin/packages/py-lazy-property/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-lazy/package.py b/var/spack/repos/builtin/packages/py-lazy/package.py index 9d5bdb5a3d..d8f2a46022 100644 --- a/var/spack/repos/builtin/packages/py-lazy/package.py +++ b/var/spack/repos/builtin/packages/py-lazy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-lazyarray/package.py b/var/spack/repos/builtin/packages/py-lazyarray/package.py index 254a59361c..cc9e68f8f3 100644 --- a/var/spack/repos/builtin/packages/py-lazyarray/package.py +++ b/var/spack/repos/builtin/packages/py-lazyarray/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-leather/package.py b/var/spack/repos/builtin/packages/py-leather/package.py new file mode 100644 index 0000000000..96aecebd96 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-leather/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyLeather(PythonPackage): + """Leather is the Python charting library for those who need charts now and + don't care if they're perfect.""" + + homepage = "https://leather.readthedocs.io/en/stable/" + url = "https://pypi.io/packages/source/l/leather/leather-0.3.3.tar.gz" + + version('0.3.3', sha256='076d1603b5281488285718ce1a5ce78cf1027fe1e76adf9c548caf83c519b988') + + depends_on('py-setuptools', type='build') + depends_on('py-six@1.6.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-libconf/package.py b/var/spack/repos/builtin/packages/py-libconf/package.py index c57a654428..4cfeb251da 100644 --- a/var/spack/repos/builtin/packages/py-libconf/package.py +++ b/var/spack/repos/builtin/packages/py-libconf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-libensemble/package.py b/var/spack/repos/builtin/packages/py-libensemble/package.py index ed752518d3..67fc1bbc18 100644 --- a/var/spack/repos/builtin/packages/py-libensemble/package.py +++ b/var/spack/repos/builtin/packages/py-libensemble/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,10 +11,11 @@ class PyLibensemble(PythonPackage): """Library for managing ensemble-like collections of computations.""" homepage = "https://libensemble.readthedocs.io" - url = "https://pypi.io/packages/source/l/libensemble/libensemble-0.5.2.tar.gz" + url = "https://pypi.io/packages/source/l/libensemble/libensemble-0.6.0.tar.gz" git = "https://github.com/Libensemble/libensemble.git" version('develop', branch='develop') + version('0.6.0', sha256='3f6a926d3868da53835ed93fc2e2a047b368dacb648c7608ee3a66debcee4d38') version('0.5.2', sha256='3e36c29a4a2adc0984ecfcc998cb5bb8a2cdfbe7a1ae92f7b35b06e41d21b889') version('0.5.1', sha256='522e0cc086a3ed75a101b704c0fe01eae07f2684bd8d6da7bdfe9371d3187362') version('0.5.0', sha256='c4623171dee049bfaa38a9c433609299a56b1afb774db8b71321247bc7556b8f') diff --git a/var/spack/repos/builtin/packages/py-ligo-segments/package.py b/var/spack/repos/builtin/packages/py-ligo-segments/package.py index e81c6d6068..aacb0affc5 100644 --- a/var/spack/repos/builtin/packages/py-ligo-segments/package.py +++ b/var/spack/repos/builtin/packages/py-ligo-segments/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-line-profiler/package.py b/var/spack/repos/builtin/packages/py-line-profiler/package.py index c06a8968ea..c252dca53f 100644 --- a/var/spack/repos/builtin/packages/py-line-profiler/package.py +++ b/var/spack/repos/builtin/packages/py-line-profiler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,8 +24,11 @@ class PyLineProfiler(PythonPackage): # See https://github.com/rkern/line_profiler/issues/166 @run_before('build') - @when('^python@3.7:') def fix_cython(self): + # TODO: Replace the check with a `@when('^python@3.7:')` decorator once + # https://github.com/spack/spack/issues/12736 is resolved + if not self.spec.satisfies("^python@3.7:"): + return cython = self.spec['py-cython'].command for root, _, files in os.walk('.'): for fn in files: diff --git a/var/spack/repos/builtin/packages/py-linecache2/package.py b/var/spack/repos/builtin/packages/py-linecache2/package.py index e23bc0d20b..b490059705 100644 --- a/var/spack/repos/builtin/packages/py-linecache2/package.py +++ b/var/spack/repos/builtin/packages/py-linecache2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-lit/package.py b/var/spack/repos/builtin/packages/py-lit/package.py index cfade2e9a3..b09f8cb956 100644 --- a/var/spack/repos/builtin/packages/py-lit/package.py +++ b/var/spack/repos/builtin/packages/py-lit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-llvmlite/package.py b/var/spack/repos/builtin/packages/py-llvmlite/package.py index e9d075ab2e..ad5e401963 100644 --- a/var/spack/repos/builtin/packages/py-llvmlite/package.py +++ b/var/spack/repos/builtin/packages/py-llvmlite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,7 @@ class PyLlvmlite(PythonPackage): homepage = "http://llvmlite.readthedocs.io/en/latest/index.html" url = "https://pypi.io/packages/source/l/llvmlite/llvmlite-0.23.0.tar.gz" + version('0.29.0', sha256='3adb0d4c9a17ad3dca82c7e88118babd61eeee0ee985ce31fa43ec27aa98c963') version('0.27.1', sha256='48a1c3ae69fd8920cba153bfed8a46ac46474bc706a2100226df4abffe0000ab') version('0.26.0', sha256='13e84fe6ebb0667233074b429fd44955f309dead3161ec89d9169145dbad2ebf') version('0.25.0', sha256='fd64def9a51dd7dc61913a7a08eeba5b9785522740bec5a7c5995b2a90525025') @@ -21,7 +22,10 @@ class PyLlvmlite(PythonPackage): depends_on('py-setuptools', type='build') depends_on('python@2.6:2.8,3.4:', type=('build', 'run')) depends_on('py-enum34', type=('build', 'run'), when='^python@:3.3.99') - depends_on('llvm@7.0:7.99', when='@0.27.0:') + + # llvmlite compatibility information taken from https://github.com/numba/llvmlite#compatibility + depends_on('llvm@7.0:8.0.99', when='@0.29.0:') + depends_on('llvm@7.0:7.99', when='@0.27.0:0.28.99') depends_on('llvm@6.0:6.99', when='@0.23.0:0.26.99') depends_on('llvm@4.0:4.99', when='@0.17.0:0.20.99') depends_on('binutils', type='build') diff --git a/var/spack/repos/builtin/packages/py-lmfit/package.py b/var/spack/repos/builtin/packages/py-lmfit/package.py index 3da5e6c0c0..4c798622b0 100644 --- a/var/spack/repos/builtin/packages/py-lmfit/package.py +++ b/var/spack/repos/builtin/packages/py-lmfit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-localcider/package.py b/var/spack/repos/builtin/packages/py-localcider/package.py index e72dd898f6..7603a6045d 100644 --- a/var/spack/repos/builtin/packages/py-localcider/package.py +++ b/var/spack/repos/builtin/packages/py-localcider/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-locket/package.py b/var/spack/repos/builtin/packages/py-locket/package.py index de7ea76325..2ef69b2992 100644 --- a/var/spack/repos/builtin/packages/py-locket/package.py +++ b/var/spack/repos/builtin/packages/py-locket/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-lockfile/package.py b/var/spack/repos/builtin/packages/py-lockfile/package.py index 674bba7cdb..95b5289b89 100644 --- a/var/spack/repos/builtin/packages/py-lockfile/package.py +++ b/var/spack/repos/builtin/packages/py-lockfile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-logilab-common/package.py b/var/spack/repos/builtin/packages/py-logilab-common/package.py index 548050f166..6dd556f1c3 100644 --- a/var/spack/repos/builtin/packages/py-logilab-common/package.py +++ b/var/spack/repos/builtin/packages/py-logilab-common/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-lrudict/package.py b/var/spack/repos/builtin/packages/py-lru-dict/package.py index 79c3550219..aa31ec491e 100644 --- a/var/spack/repos/builtin/packages/py-lrudict/package.py +++ b/var/spack/repos/builtin/packages/py-lru-dict/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,13 @@ from spack import * -class PyLrudict(PythonPackage): - """ A fast LRU cache""" +class PyLruDict(PythonPackage): + """A fast LRU cache""" homepage = "https://github.com/amitdev/lru-dict" url = "https://pypi.io/packages/source/l/lru-dict/lru-dict-1.1.6.tar.gz" version('1.1.6', sha256='365457660e3d05b76f1aba3e0f7fedbfcd6528e97c5115a351ddd0db488354cc') - depends_on('python@2.7:') + depends_on('python@2.7:', type=('build', 'run')) depends_on('py-setuptools', type=('build')) diff --git a/var/spack/repos/builtin/packages/py-lscsoft-glue/package.py b/var/spack/repos/builtin/packages/py-lscsoft-glue/package.py index 3770ee668f..f746285d3a 100644 --- a/var/spack/repos/builtin/packages/py-lscsoft-glue/package.py +++ b/var/spack/repos/builtin/packages/py-lscsoft-glue/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-luigi/package.py b/var/spack/repos/builtin/packages/py-luigi/package.py index 5c90a9a87c..18adbff049 100644 --- a/var/spack/repos/builtin/packages/py-luigi/package.py +++ b/var/spack/repos/builtin/packages/py-luigi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,4 +20,4 @@ class PyLuigi(PythonPackage): depends_on('py-python-daemon@:2.1', type=('build', 'run')) depends_on('py-python-dateutil@2.7.5', when='@2.8.3:', type=('build', 'run')) - depends_on('py-test@3.3.0:', type='test') + depends_on('py-pytest@3.3.0:', type='test') diff --git a/var/spack/repos/builtin/packages/py-lxml/package.py b/var/spack/repos/builtin/packages/py-lxml/package.py index 86dcd9181b..cdb82cafef 100644 --- a/var/spack/repos/builtin/packages/py-lxml/package.py +++ b/var/spack/repos/builtin/packages/py-lxml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-lzstring/package.py b/var/spack/repos/builtin/packages/py-lzstring/package.py index 7a1fe90847..33eb630918 100644 --- a/var/spack/repos/builtin/packages/py-lzstring/package.py +++ b/var/spack/repos/builtin/packages/py-lzstring/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-m2r/package.py b/var/spack/repos/builtin/packages/py-m2r/package.py index 31b9c60b4b..a107f6d18e 100644 --- a/var/spack/repos/builtin/packages/py-m2r/package.py +++ b/var/spack/repos/builtin/packages/py-m2r/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-macholib/package.py b/var/spack/repos/builtin/packages/py-macholib/package.py index 4f730733c8..702ea07e0b 100644 --- a/var/spack/repos/builtin/packages/py-macholib/package.py +++ b/var/spack/repos/builtin/packages/py-macholib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class PyMacholib(PythonPackage): """Python package for Mach-O header analysis and editing""" homepage = "https://pypi.python.org/pypi/macholib" - url = "https://pypi.io/packages/source/m/macholib/macholib-1.8.tar.gz" + url = "https://pypi.io/packages/source/m/macholib/macholib-1.11.tar.gz" version('1.11', 'c4180ffc6f909bf8db6cd81cff4b6f601d575568f4d5dee148c830e9851eb9db') diff --git a/var/spack/repos/builtin/packages/py-machotools/package.py b/var/spack/repos/builtin/packages/py-machotools/package.py index 4d69883206..a0b4337892 100644 --- a/var/spack/repos/builtin/packages/py-machotools/package.py +++ b/var/spack/repos/builtin/packages/py-machotools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-macs2/package.py b/var/spack/repos/builtin/packages/py-macs2/package.py index 9e2e4f3d3f..c20463b6e9 100644 --- a/var/spack/repos/builtin/packages/py-macs2/package.py +++ b/var/spack/repos/builtin/packages/py-macs2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-maestrowf/package.py b/var/spack/repos/builtin/packages/py-maestrowf/package.py index 66e766536f..5fdefea272 100644 --- a/var/spack/repos/builtin/packages/py-maestrowf/package.py +++ b/var/spack/repos/builtin/packages/py-maestrowf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,10 +11,22 @@ class PyMaestrowf(PythonPackage): simulation studies.""" homepage = "https://github.com/LLNL/maestrowf/" - url = "https://github.com/LLNL/maestrowf/archive/v1.1.2.tar.gz" + url = "https://github.com/LLNL/maestrowf/archive/v1.1.6.tar.gz" + git = "https://github.com/LLNL/maestrowf/" maintainers = ['FrankD412'] + # git branches + version('develop', branch='develop') + version('master', branch='master') + + # Pre-release candidates + version('1.1.5dev', sha256='eb3d6f31c233e2cde3b84e15c657002b83ff43d4d6b218b33d023a4f527b9e08') + version('1.1.4dev1.0', sha256='67f59eed6fa69fc71b88a0a769de9f080300497d3c30d3a0893eabd0702bc48e') + version('1.1.4dev1.1', sha256='c8612b5423b44f11e2a7c4fbc31eb741013245870512ee2dbf7367024517528f') + + # pypi releases + version('1.1.6', sha256='27a4ab9072c5b5e2edf91c192d9fe67f040dd45be7f3e44fd9a998ce4cb1e92d', preferred=True) version('1.1.4', sha256='2cb0fa6f6281d8618ac79217ea5f4fd8cb24955c4315e873657f96b815f171d5') version('1.1.2', sha256='ebb45bff54625435bc9f2462e1bdc3b5bdc4d943378c53e7810c11836794c5e0') version('1.1.1', sha256='a476ad4b40846d7b7f9540d6413df1b42eb655735e8d3c6c07e0baa68e20a8bb') diff --git a/var/spack/repos/builtin/packages/py-mako/package.py b/var/spack/repos/builtin/packages/py-mako/package.py index 3221f8711f..b60dd8d184 100644 --- a/var/spack/repos/builtin/packages/py-mako/package.py +++ b/var/spack/repos/builtin/packages/py-mako/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-markdown/package.py b/var/spack/repos/builtin/packages/py-markdown/package.py index 6d6b6a49c1..665d94dee4 100644 --- a/var/spack/repos/builtin/packages/py-markdown/package.py +++ b/var/spack/repos/builtin/packages/py-markdown/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-markupsafe/package.py b/var/spack/repos/builtin/packages/py-markupsafe/package.py index d962c3615a..f334d03cee 100644 --- a/var/spack/repos/builtin/packages/py-markupsafe/package.py +++ b/var/spack/repos/builtin/packages/py-markupsafe/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index a53c2c892b..6ef54f981d 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,7 +14,7 @@ class PyMatplotlib(PythonPackage): environments across platforms.""" homepage = "https://pypi.python.org/pypi/matplotlib" - url = "https://pypi.io/packages/source/m/matplotlib/matplotlib-3.1.1.tar.gz" + url = "https://pypi.io/packages/source/m/matplotlib/matplotlib-3.1.3.tar.gz" maintainers = ['adamjstewart'] @@ -28,9 +28,12 @@ class PyMatplotlib(PythonPackage): 'matplotlib.testing.jpl_units' ] + version('3.1.3', sha256='db3121f12fb9b99f105d1413aebaeb3d943f269f3d262b45586d12765866f0c6') + version('3.1.2', sha256='8e8e2c2fe3d873108735c6ee9884e6f36f467df4a143136209cff303b183bada') version('3.1.1', sha256='1febd22afe1489b13c6749ea059d392c03261b2950d1d45c17e3aed812080c93') version('3.0.2', sha256='c94b792af431f6adb6859eb218137acd9a35f4f7442cea57e4a59c54751c36af') version('3.0.0', sha256='b4e2333c98a7c2c1ff6eb930cd2b57d4b818de5437c5048802096b32f66e65f9') + version('2.2.5', sha256='a3037a840cd9dfdc2df9fee8af8f76ca82bfab173c0f9468193ca7a89a2b60ea') version('2.2.3', sha256='7355bf757ecacd5f0ac9dd9523c8e1a1103faadf8d33c22664178e17533f8ce5') version('2.2.2', sha256='4dc7ef528aad21f22be85e95725234c5178c0f938e2228ca76640e5e84d8cde8') version('2.0.2', sha256='0ffbc44faa34a8b1704bc108c451ecf87988f900ef7ce757b8e2e84383121ff1') @@ -85,35 +88,35 @@ class PyMatplotlib(PythonPackage): depends_on('py-subprocess32', type=('build', 'run'), when='^python@:2.7') depends_on('py-functools32', type=('build', 'run'), when='@:2.0.999 ^python@2.7') depends_on('py-backports-functools-lru-cache', type=('build', 'run'), - when='@2.1.0:2.999.999') + when='@2.1.0:2.999.999 ^python@:2') depends_on('py-six@1.9.0:', type=('build', 'run'), when='@:2') # Optional backend dependencies - depends_on('tk@8.3:8.5,8.6.2:', when='backend=tkagg') - depends_on('tk@8.3:8.5,8.6.2:', when='backend=tkcairo') - depends_on('python+tkinter', when='backend=tkagg') - depends_on('python+tkinter', when='backend=tkcairo') - depends_on('py-pyqt4@4.6:', when='backend=qt4agg') # or py-pyside@1.0.3: - depends_on('py-pyqt4@4.6:', when='backend=qt4cairo') # or py-pyside@1.0.3: - depends_on('py-pyqt5', when='backend=qt5agg') - depends_on('py-pyqt5', when='backend=qt5cairo') - depends_on('py-pygobject', when='backend=gtk3agg') - depends_on('py-pygobject', when='backend=gtk3cairo') - depends_on('py-wxpython@4:', when='backend=wx') - depends_on('py-wxpython@4:', when='backend=wxagg') - depends_on('py-wxpython@4:', when='backend=wxcairo') - depends_on('py-cairocffi@0.8:', when='backend=gtk3cairo') - depends_on('py-cairocffi@0.8:', when='backend=qt4cairo') - depends_on('py-cairocffi@0.8:', when='backend=qt5cairo') - depends_on('py-cairocffi@0.8:', when='backend=tkcairo') - depends_on('py-cairocffi@0.8:', when='backend=wxcairo') - depends_on('py-cairocffi@0.8:', when='backend=cairo') - depends_on('py-tornado', when='backend=webagg') + depends_on('tk@8.3:8.5,8.6.2:', when='backend=tkagg', type='run') + depends_on('tk@8.3:8.5,8.6.2:', when='backend=tkcairo', type='run') + depends_on('python+tkinter', when='backend=tkagg', type='run') + depends_on('python+tkinter', when='backend=tkcairo', type='run') + depends_on('py-pyqt4@4.6:', when='backend=qt4agg', type='run') # or py-pyside@1.0.3: + depends_on('py-pyqt4@4.6:', when='backend=qt4cairo', type='run') # or py-pyside@1.0.3: + depends_on('py-pyqt5', when='backend=qt5agg', type='run') + depends_on('py-pyqt5', when='backend=qt5cairo', type='run') + depends_on('py-pygobject', when='backend=gtk3agg', type='run') + depends_on('py-pygobject', when='backend=gtk3cairo', type='run') + depends_on('py-wxpython@4:', when='backend=wx', type='run') + depends_on('py-wxpython@4:', when='backend=wxagg', type='run') + depends_on('py-wxpython@4:', when='backend=wxcairo', type='run') + depends_on('py-cairocffi@0.8:', when='backend=gtk3cairo', type='run') + depends_on('py-cairocffi@0.8:', when='backend=qt4cairo', type='run') + depends_on('py-cairocffi@0.8:', when='backend=qt5cairo', type='run') + depends_on('py-cairocffi@0.8:', when='backend=tkcairo', type='run') + depends_on('py-cairocffi@0.8:', when='backend=wxcairo', type='run') + depends_on('py-cairocffi@0.8:', when='backend=cairo', type='run') + depends_on('py-tornado', when='backend=webagg', type='run') # Optional dependencies depends_on('ffmpeg', when='+movies') # depends_on('libav', when='+movies') - depends_on('image-magick', when='+animation') + depends_on('imagemagick', when='+animation') depends_on('py-pillow@3.4:', when='+image', type=('build', 'run')) depends_on('texlive', when='+latex', type='run') depends_on('ghostscript@0.9:', when='+latex', type='run') diff --git a/var/spack/repos/builtin/packages/py-mccabe/package.py b/var/spack/repos/builtin/packages/py-mccabe/package.py index 82ff0dc819..cd4c0df089 100644 --- a/var/spack/repos/builtin/packages/py-mccabe/package.py +++ b/var/spack/repos/builtin/packages/py-mccabe/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mdanalysis/package.py b/var/spack/repos/builtin/packages/py-mdanalysis/package.py index 6d0ad83f18..a419dff426 100644 --- a/var/spack/repos/builtin/packages/py-mdanalysis/package.py +++ b/var/spack/repos/builtin/packages/py-mdanalysis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mechanize/package.py b/var/spack/repos/builtin/packages/py-mechanize/package.py index 9c019c73ee..06ae015836 100644 --- a/var/spack/repos/builtin/packages/py-mechanize/package.py +++ b/var/spack/repos/builtin/packages/py-mechanize/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-memory-profiler/package.py b/var/spack/repos/builtin/packages/py-memory-profiler/package.py index 97aea2dd13..9d6af1c9bb 100644 --- a/var/spack/repos/builtin/packages/py-memory-profiler/package.py +++ b/var/spack/repos/builtin/packages/py-memory-profiler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-merlin/package.py b/var/spack/repos/builtin/packages/py-merlin/package.py index 9260f82d5c..7ae05a8014 100644 --- a/var/spack/repos/builtin/packages/py-merlin/package.py +++ b/var/spack/repos/builtin/packages/py-merlin/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-merlinwf/package.py b/var/spack/repos/builtin/packages/py-merlinwf/package.py new file mode 100644 index 0000000000..2082e77997 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-merlinwf/package.py @@ -0,0 +1,38 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyMerlinwf(PythonPackage): + """Merlin Workflow for HPC.""" + + homepage = "https://github.com/LLNL/merlin" + url = "https://pypi.io/packages/source/m/merlinwf/merlinwf-1.2.3.tar.gz" + git = "https://github.com/LLNL/merlin.git" + + version('1.2.3', sha256='6b13a315f3e8e2894ea05d9cc072639f02eaf71ae0fdbd2bafebd1c20c8470ab') + version('1.1.1', sha256='306055a987e42a79ce348a3f9d71293ed8a9b7f5909c26b6fd233d6a176fff6d') + version('1.0.5', sha256='d66f50eac84ff9d7aa484f2d9655dc60f0352196d333284d81b6623a6f0aa180') + version('master', branch='master') + version('develop', branch='develop') + + depends_on('python@3.6:', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) + + depends_on('py-pytest', type='test') + + depends_on('py-cached-property', type=('build', 'run')) + depends_on('py-celery@4.3.0:+redis', type=('build', 'run')) + depends_on('py-coloredlogs@10.0:', type=('build', 'run')) + depends_on('py-cryptography', type=('build', 'run')) + depends_on('py-importlib-resources', when="^python@3.0:3.6.99", type=('build', 'run')) + depends_on('py-maestrowf@1.1.7dev0:', when="@1.2.0:", type=('build', 'run')) + depends_on('py-maestrowf@1.1.6:', when="@:1.1.99", type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-parse', type=('build', 'run')) + depends_on('py-psutil@5.1.0:', type=('build', 'run')) + depends_on('py-pyyaml@5.1.2:', type=('build', 'run')) + depends_on('py-tabulate', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-metasv/package.py b/var/spack/repos/builtin/packages/py-metasv/package.py index 02681d704a..f9b81e4209 100644 --- a/var/spack/repos/builtin/packages/py-metasv/package.py +++ b/var/spack/repos/builtin/packages/py-metasv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-methylcode/package.py b/var/spack/repos/builtin/packages/py-methylcode/package.py index 512d1f2d01..698588600a 100644 --- a/var/spack/repos/builtin/packages/py-methylcode/package.py +++ b/var/spack/repos/builtin/packages/py-methylcode/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,15 +11,13 @@ class PyMethylcode(PythonPackage): reads and outputs per-base methylation data. """ homepage = "https://github.com/brentp/methylcode" - url = "https://github.com/brentp/methylcode/archive/master.zip" + git = "https://github.com/brentp/methylcode.git" - version('1.0.0', sha256='30f707a690a887e3161c8debba3c322bd313865df40212275b02203c52a416ae') + version('master', branch='master') - depends_on('python@2.7.0:2.7.999') - depends_on('py-six') - depends_on('py-setuptools') + depends_on('python@2.6:2.8', type=('build', 'run')) + depends_on('py-setuptools', type='build') depends_on('py-numpy') - depends_on('py-pyparsing') depends_on('py-pyfasta') depends_on('py-bsddb3') depends_on('bowtie') diff --git a/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py b/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py index 10aa6de90d..80f444c207 100644 --- a/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py +++ b/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-misopy/package.py b/var/spack/repos/builtin/packages/py-misopy/package.py index 93a2df8086..d55896c680 100644 --- a/var/spack/repos/builtin/packages/py-misopy/package.py +++ b/var/spack/repos/builtin/packages/py-misopy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mistune/package.py b/var/spack/repos/builtin/packages/py-mistune/package.py index 5abb62288e..f500e469d9 100644 --- a/var/spack/repos/builtin/packages/py-mistune/package.py +++ b/var/spack/repos/builtin/packages/py-mistune/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,14 @@ class PyMistune(PythonPackage): homepage = "http://mistune.readthedocs.org/en/latest/" url = "https://github.com/lepture/mistune/archive/v0.7.1.tar.gz" + version('0.8.4', sha256='a1443771ea9ed7268a0cb3cf31462604ae148938ba32070bd5c54545f8f36a5d') + version('0.8.3', sha256='666c93fc10cb0aa924a373898a709eba4d43f4e453264a4c7396878ec8145a4a') + version('0.8.2', sha256='997c6d723350093760ccd48b722344b3330a5f947dec264e129160b85037784e') + version('0.8.1', sha256='77ae24a5accfd62d23f945d7e6598392194f8ca6ef1bd70ddc81e151ac3eb1fe') + version('0.8', sha256='f479dc2ceac7d593231e77448cb5cf7194fdbebad1d88fcdb78eacac1c042f6e') + version('0.7.4', sha256='5030d5e3e0ec90fbdaed0f52d3c756ffb30e4ab46c3de159c97482c09569abcb') + version('0.7.3', sha256='c4f391e61d3b5e8fbb112669a5c6960fb04b71b61d35f0f09a201809545b1676') + version('0.7.2', sha256='a3fe17dfad99bd353485879a5c05827dd2932219da8b078212a21797f6cdbf0b') version('0.7.1', sha256='d6684534174caa30e0169e106a7152aee14507796a610b76be9fe9b335b18410') version('0.7', sha256='9b2cac8053d21dde5f2b3edb01948dac8ee5c3a85eeeeb6913c3ddf2f773c7b6') version('0.6', sha256='c2d976c06c099edb525b8ac3745f3d3b5c49af6189edb6de390ddf9c248913cf') diff --git a/var/spack/repos/builtin/packages/py-mlxtend/package.py b/var/spack/repos/builtin/packages/py-mlxtend/package.py index eefd78ae71..3fb1aef151 100644 --- a/var/spack/repos/builtin/packages/py-mlxtend/package.py +++ b/var/spack/repos/builtin/packages/py-mlxtend/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mo-pack/package.py b/var/spack/repos/builtin/packages/py-mo-pack/package.py index 0d4bee45f7..c880d5d584 100644 --- a/var/spack/repos/builtin/packages/py-mo-pack/package.py +++ b/var/spack/repos/builtin/packages/py-mo-pack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mock/package.py b/var/spack/repos/builtin/packages/py-mock/package.py index 90fecff01e..1f35d26020 100644 --- a/var/spack/repos/builtin/packages/py-mock/package.py +++ b/var/spack/repos/builtin/packages/py-mock/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-modred/package.py b/var/spack/repos/builtin/packages/py-modred/package.py index dc408e764a..e4715365c7 100644 --- a/var/spack/repos/builtin/packages/py-modred/package.py +++ b/var/spack/repos/builtin/packages/py-modred/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-moltemplate/package.py b/var/spack/repos/builtin/packages/py-moltemplate/package.py index 7d05b4cc69..ea2fed2e4f 100644 --- a/var/spack/repos/builtin/packages/py-moltemplate/package.py +++ b/var/spack/repos/builtin/packages/py-moltemplate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mongo/package.py b/var/spack/repos/builtin/packages/py-mongo/package.py deleted file mode 100644 index 117c59cf70..0000000000 --- a/var/spack/repos/builtin/packages/py-mongo/package.py +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class PyMongo(PythonPackage): - """Python driver for MongoDB <http://www.mongodb.org>""" - - homepage = "http://github.com/mongodb/mongo-python-driver" - url = "https://pypi.io/packages/source/p/pymongo/pymongo-3.6.0.tar.gz" - - version('3.6.0', sha256='c6de26d1e171cdc449745b82f1addbc873d105b8e7335097da991c0fc664a4a8') - version('3.3.0', sha256='3d45302fc2622fabf34356ba274c69df41285bac71bbd229f1587283b851b91e') - - depends_on('python@2.6:2.8,3.3:') - - depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-monotonic/package.py b/var/spack/repos/builtin/packages/py-monotonic/package.py index 08afbabbe1..fec3f99f96 100644 --- a/var/spack/repos/builtin/packages/py-monotonic/package.py +++ b/var/spack/repos/builtin/packages/py-monotonic/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-monty/package.py b/var/spack/repos/builtin/packages/py-monty/package.py index 7b6ceedff7..8b4d406242 100644 --- a/var/spack/repos/builtin/packages/py-monty/package.py +++ b/var/spack/repos/builtin/packages/py-monty/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-more-itertools/package.py b/var/spack/repos/builtin/packages/py-more-itertools/package.py index 2989bc3843..57c684585e 100644 --- a/var/spack/repos/builtin/packages/py-more-itertools/package.py +++ b/var/spack/repos/builtin/packages/py-more-itertools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py index 86b176081c..c4ce8b3a98 100644 --- a/var/spack/repos/builtin/packages/py-mpi4py/package.py +++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,19 +13,20 @@ class PyMpi4py(PythonPackage): standard MPI-2 C++ bindings. """ homepage = "https://pypi.python.org/pypi/mpi4py" - url = "https://pypi.io/packages/source/m/mpi4py/mpi4py-3.0.0.tar.gz" + url = "https://pypi.io/packages/source/m/mpi4py/mpi4py-3.0.3.tar.gz" git = "https://github.com/mpi4py/mpi4py.git" version('develop', branch='master') + version('3.0.3', sha256='012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f') version('3.0.1', sha256='6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851') version('3.0.0', sha256='b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7') version('2.0.0', sha256='6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81') version('1.3.1', sha256='e7bd2044aaac5a6ea87a87b2ecc73b310bb6efe5026031e33067ea3c2efc3507') - depends_on('python@2.7:2.8,3.3:') + depends_on('python@2.6:2.7.99,3.2:') depends_on('py-setuptools', type='build') depends_on('mpi') - depends_on('py-cython', when='@develop', type='build') + depends_on('py-cython@0.22.0:', when='@develop', type='build') def build_args(self, spec, prefix): return ['--mpicc=%s -shared' % spec['mpi'].mpicc] diff --git a/var/spack/repos/builtin/packages/py-mpld3/package.py b/var/spack/repos/builtin/packages/py-mpld3/package.py index 3d63ceec54..9b5ba868cf 100644 --- a/var/spack/repos/builtin/packages/py-mpld3/package.py +++ b/var/spack/repos/builtin/packages/py-mpld3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mpmath/package.py b/var/spack/repos/builtin/packages/py-mpmath/package.py index 218c53f7e4..c6c4e02646 100644 --- a/var/spack/repos/builtin/packages/py-mpmath/package.py +++ b/var/spack/repos/builtin/packages/py-mpmath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-msgpack/package.py b/var/spack/repos/builtin/packages/py-msgpack/package.py new file mode 100644 index 0000000000..0c05cf5d34 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-msgpack/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyMsgpack(PythonPackage): + """MessagePack (de)serializer.""" + + homepage = "https://msgpack.org/" + url = "https://pypi.io/packages/source/m/msgpack/msgpack-0.6.2.tar.gz" + + version('0.6.2', sha256='ea3c2f859346fcd55fc46e96885301d9c2f7a36d453f5d8f2967840efa1e1830') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-multi-key-dict/package.py b/var/spack/repos/builtin/packages/py-multi-key-dict/package.py index ddf59628f9..d30777b9ef 100644 --- a/var/spack/repos/builtin/packages/py-multi-key-dict/package.py +++ b/var/spack/repos/builtin/packages/py-multi-key-dict/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-multiprocess/package.py b/var/spack/repos/builtin/packages/py-multiprocess/package.py index 086b002391..beaa083061 100644 --- a/var/spack/repos/builtin/packages/py-multiprocess/package.py +++ b/var/spack/repos/builtin/packages/py-multiprocess/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-multiqc/package.py b/var/spack/repos/builtin/packages/py-multiqc/package.py index 52d2a2bcbc..a1ab08fae8 100644 --- a/var/spack/repos/builtin/packages/py-multiqc/package.py +++ b/var/spack/repos/builtin/packages/py-multiqc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,5 +31,6 @@ class PyMultiqc(PythonPackage): depends_on('py-pyyaml', type=('build', 'run')) depends_on('py-simplejson', type=('build', 'run')) depends_on('py-requests', type=('build', 'run'), when='@1.5:') - depends_on('py-enum34', type=('build', 'run'), when='@1.5:') + depends_on('py-enum34', type=('build', 'run'), when='@1.4:1.5 ^python@:3.3') + depends_on('py-enum34', type=('build', 'run'), when='@1.3') depends_on('py-markdown', type=('build', 'run'), when='@1.5:') diff --git a/var/spack/repos/builtin/packages/py-munch/package.py b/var/spack/repos/builtin/packages/py-munch/package.py index 560fdfb801..9360e01efb 100644 --- a/var/spack/repos/builtin/packages/py-munch/package.py +++ b/var/spack/repos/builtin/packages/py-munch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mx/package.py b/var/spack/repos/builtin/packages/py-mx/package.py index 0428d38410..6dfdddc487 100644 --- a/var/spack/repos/builtin/packages/py-mx/package.py +++ b/var/spack/repos/builtin/packages/py-mx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-myhdl/package.py b/var/spack/repos/builtin/packages/py-myhdl/package.py index ca6cb5a1e0..98056266b8 100644 --- a/var/spack/repos/builtin/packages/py-myhdl/package.py +++ b/var/spack/repos/builtin/packages/py-myhdl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mypy-extensions/package.py b/var/spack/repos/builtin/packages/py-mypy-extensions/package.py index f0ee060789..4a31b6816b 100644 --- a/var/spack/repos/builtin/packages/py-mypy-extensions/package.py +++ b/var/spack/repos/builtin/packages/py-mypy-extensions/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mypy/package.py b/var/spack/repos/builtin/packages/py-mypy/package.py index 887964fe5b..b8cde685dc 100644 --- a/var/spack/repos/builtin/packages/py-mypy/package.py +++ b/var/spack/repos/builtin/packages/py-mypy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mysql-connector/package.py b/var/spack/repos/builtin/packages/py-mysql-connector-python/package.py index e3e04280c4..2ebd16a459 100644 --- a/var/spack/repos/builtin/packages/py-mysql-connector/package.py +++ b/var/spack/repos/builtin/packages/py-mysql-connector-python/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PyMysqlConnector(PythonPackage): +class PyMysqlConnectorPython(PythonPackage): """MySQL Connector/Python is implementing the MySQL Client/Server protocol completely in Python. No MySQL libraries are needed, and no compilation is necessary to run this Python DB API v2.0 diff --git a/var/spack/repos/builtin/packages/py-mysql-connector/single-version.patch b/var/spack/repos/builtin/packages/py-mysql-connector-python/single-version.patch index 27cf5e5d22..27cf5e5d22 100644 --- a/var/spack/repos/builtin/packages/py-mysql-connector/single-version.patch +++ b/var/spack/repos/builtin/packages/py-mysql-connector-python/single-version.patch diff --git a/var/spack/repos/builtin/packages/py-mysqlclient/package.py b/var/spack/repos/builtin/packages/py-mysqlclient/package.py index 779a34eef5..d1e6ef37a8 100644 --- a/var/spack/repos/builtin/packages/py-mysqlclient/package.py +++ b/var/spack/repos/builtin/packages/py-mysqlclient/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-mysqldb1/package.py b/var/spack/repos/builtin/packages/py-mysqldb1/package.py index 28966f890a..daa13088f6 100644 --- a/var/spack/repos/builtin/packages/py-mysqldb1/package.py +++ b/var/spack/repos/builtin/packages/py-mysqldb1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-natsort/package.py b/var/spack/repos/builtin/packages/py-natsort/package.py index c171847962..32358db64f 100644 --- a/var/spack/repos/builtin/packages/py-natsort/package.py +++ b/var/spack/repos/builtin/packages/py-natsort/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-nbconvert/package.py b/var/spack/repos/builtin/packages/py-nbconvert/package.py index 0634c6b5d0..419deb7b1c 100644 --- a/var/spack/repos/builtin/packages/py-nbconvert/package.py +++ b/var/spack/repos/builtin/packages/py-nbconvert/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,21 +13,37 @@ class PyNbconvert(PythonPackage): homepage = "https://github.com/jupyter/nbconvert" url = "https://github.com/jupyter/nbconvert/archive/4.2.0.tar.gz" + version('5.6.0', sha256='21a69fe5756a3af8e76dcc105217cc3bea4d8f23dbff5727d9fd1e4388b53beb') version('4.2.0', sha256='32394be5a20f39f99fabfb9b2f2625df17f1c2a6699182ca41598e98e7cc9610') version('4.1.0', sha256='459f23381411fd1ff9ec5ed71fcd56b8c080d97b3a1e47dae1c5c391f9a47266') version('4.0.0', sha256='00e25eeca90523ba6b774b289073631ef5ac65bb2de9774e9b7f29604516265c') - depends_on('py-pycurl', type='build') - depends_on('python@2.7:2.8,3.3:') - depends_on('py-mistune', type=('build', 'run')) + variant('execute', default=True, description='Include jupyter-client') + variant('serve', default=True, description='Include a webserver') + + depends_on('py-pycurl', type='build', when='^python@2.7:2.8') + depends_on('py-setuptools', type='build', when='@5:') + depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.5:', type=('build', 'run'), when='@5:') + depends_on('py-mistune@0.8.1:1.999', type=('build', 'run')) depends_on('py-jinja2', type=('build', 'run')) + depends_on('py-jinja2@2.4:', type=('build', 'run'), when='@5:') depends_on('py-pygments', type=('build', 'run')) depends_on('py-traitlets', type=('build', 'run')) + depends_on('py-traitlets@4.2:', type=('build', 'run'), when='@5:') depends_on('py-jupyter-core', type=('build', 'run')) depends_on('py-nbformat', type=('build', 'run')) + depends_on('py-nbformat@4.4.0:', type=('build', 'run'), when='@5:') depends_on('py-entrypoints', type=('build', 'run')) - depends_on('py-tornado', type=('build', 'run')) - depends_on('py-jupyter-client', type=('build', 'run')) + depends_on('py-entrypoints@0.2.2:', type=('build', 'run'), when='@5:') + depends_on('py-tornado@4.0:', type=('build', 'run'), when='+serve') + depends_on('py-jupyter-client', type=('build', 'run'), when='+execute') + depends_on('py-jupyter-client@4.2:', type=('build', 'run'), when='@5.2.1:+execute') + depends_on('py-jupyter-client@5.3.1:', type=('build', 'run'), when='@5.6.0:+execute') + depends_on('py-defusedxml', type=('build', 'run'), when='@5:') + depends_on('py-testpath', type=('build', 'run'), when='@5:') + depends_on('py-bleach', type=('build', 'run'), when='@5:') + depends_on('py-pandocfilters@1.4.1:', type=('build', 'run'), when='@5:') def patch(self): # We bundle this with the spack package so that the installer diff --git a/var/spack/repos/builtin/packages/py-nbformat/package.py b/var/spack/repos/builtin/packages/py-nbformat/package.py index 4bb931e6af..0648ee19df 100644 --- a/var/spack/repos/builtin/packages/py-nbformat/package.py +++ b/var/spack/repos/builtin/packages/py-nbformat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-nc-time-axis/package.py b/var/spack/repos/builtin/packages/py-nc-time-axis/package.py index bfa2e8c3ad..0703e25af7 100644 --- a/var/spack/repos/builtin/packages/py-nc-time-axis/package.py +++ b/var/spack/repos/builtin/packages/py-nc-time-axis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-neo/package.py b/var/spack/repos/builtin/packages/py-neo/package.py index 8375b69839..9015a53edf 100644 --- a/var/spack/repos/builtin/packages/py-neo/package.py +++ b/var/spack/repos/builtin/packages/py-neo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-nestle/package.py b/var/spack/repos/builtin/packages/py-nestle/package.py index 8b2fb69a7e..941e5b0234 100644 --- a/var/spack/repos/builtin/packages/py-nestle/package.py +++ b/var/spack/repos/builtin/packages/py-nestle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-netcdf4/package.py b/var/spack/repos/builtin/packages/py-netcdf4/package.py index ef9bbafad1..a9dd01db2c 100644 --- a/var/spack/repos/builtin/packages/py-netcdf4/package.py +++ b/var/spack/repos/builtin/packages/py-netcdf4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,15 +22,15 @@ class PyNetcdf4(PythonPackage): depends_on('py-numpy@1.7:', type=('build', 'run')) depends_on('py-cftime', type=('build', 'run')) - depends_on('netcdf') + depends_on('netcdf-c') depends_on('hdf5@1.8.0:+hl') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): """Ensure installed netcdf and hdf5 libraries are used""" # Explicitly set these variables so setup.py won't erroneously pick up # system versions - spack_env.set('USE_SETUPCFG', '0') - spack_env.set('HDF5_INCDIR', self.spec['hdf5'].prefix.include) - spack_env.set('HDF5_LIBDIR', self.spec['hdf5'].prefix.lib) - spack_env.set('NETCDF4_INCDIR', self.spec['netcdf'].prefix.include) - spack_env.set('NETCDF4_LIBDIR', self.spec['netcdf'].prefix.lib) + env.set('USE_SETUPCFG', '0') + env.set('HDF5_INCDIR', self.spec['hdf5'].prefix.include) + env.set('HDF5_LIBDIR', self.spec['hdf5'].prefix.lib) + env.set('NETCDF4_INCDIR', self.spec['netcdf-c'].prefix.include) + env.set('NETCDF4_LIBDIR', self.spec['netcdf-c'].prefix.lib) diff --git a/var/spack/repos/builtin/packages/py-netifaces/package.py b/var/spack/repos/builtin/packages/py-netifaces/package.py index 56736539c1..08d8200904 100644 --- a/var/spack/repos/builtin/packages/py-netifaces/package.py +++ b/var/spack/repos/builtin/packages/py-netifaces/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py index 678e7644ee..da616eefd4 100644 --- a/var/spack/repos/builtin/packages/py-networkx/package.py +++ b/var/spack/repos/builtin/packages/py-networkx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-nodeenv/package.py b/var/spack/repos/builtin/packages/py-nodeenv/package.py new file mode 100644 index 0000000000..03120dd227 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-nodeenv/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyNodeenv(PythonPackage): + """Node.js virtual environment""" + + homepage = "https://github.com/ekalinin/nodeenv" + url = "https://pypi.io/packages/source/n/nodeenv/nodeenv-1.3.3.tar.gz" + + version('1.3.3', sha256='ad8259494cf1c9034539f6cced78a1da4840a4b157e23640bc4a0c0546b0cb7a') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-nose-cov/package.py b/var/spack/repos/builtin/packages/py-nose-cov/package.py new file mode 100644 index 0000000000..88431ff9e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-nose-cov/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyNoseCov(PythonPackage): + """This plugin produces coverage reports.""" + + homepage = "http://bitbucket.org/memedough/nose-cov/overview" + url = "https://pypi.io/packages/source/n/nose-cov/nose-cov-1.6.tar.gz" + + version('1.6', sha256='8bec0335598f1cc69e3262cc50d7678c1a6010fa44625ce343c4ec1500774412') + + depends_on('py-setuptools', type='build') + depends_on('py-nose@0.11.4:', type=('build', 'run')) + depends_on('py-cov-core@1.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index a87ef5305a..fcafc521c7 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-nose2/package.py b/var/spack/repos/builtin/packages/py-nose2/package.py index 880d1fe42f..510fbd8850 100644 --- a/var/spack/repos/builtin/packages/py-nose2/package.py +++ b/var/spack/repos/builtin/packages/py-nose2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-nosexcover/package.py b/var/spack/repos/builtin/packages/py-nosexcover/package.py index 4707104398..c92b5f9d77 100644 --- a/var/spack/repos/builtin/packages/py-nosexcover/package.py +++ b/var/spack/repos/builtin/packages/py-nosexcover/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py b/var/spack/repos/builtin/packages/py-notebook/package.py index 55c2f0f256..d02c39f1e2 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py +++ b/var/spack/repos/builtin/packages/py-notebook/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,14 @@ from spack import * -class PyJupyterNotebook(PythonPackage): +class PyNotebook(PythonPackage): """Jupyter Interactive Notebook""" homepage = "https://github.com/jupyter/notebook" url = "https://pypi.io/packages/source/n/notebook/notebook-4.2.3.tar.gz" + version('6.0.1', sha256='660976fe4fe45c7aa55e04bf4bccb9f9566749ff637e9020af3422f9921f9a5d') + version('5.7.8', sha256='573e0ae650c5d76b18b6e564ba6d21bf321d00847de1d215b418acb64f056eb8') version('4.2.3', sha256='39a9603d3fe88b60de2903680c965cf643acf2c16fb2c6bac1d905e1042b5851') version('4.2.2', sha256='418ba230c9b2e7e739940cae9fb4625e10a63f038e9c95cf1a9b7a244256ba38') version('4.2.1', sha256='a49de524dabb99f214bdf2a58f26c7892650251a23a3669c6492fb180492e197') @@ -21,19 +23,29 @@ class PyJupyterNotebook(PythonPackage): version('4.0.4', sha256='a57852514bce1b1cf41fa0311f6cf894960cf68b083b55e6c408316b598d5648') version('4.0.2', sha256='8478d7e2ab474855b0ff841f693983388af8662d3af1adcb861acb900274f22a') - variant('terminal', default=False, description="Enable terminal functionality") - - depends_on('python@2.7:2.8,3.3:') + depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) + depends_on('python@3.5:', type=('build', 'run'), when='@6:') + depends_on('py-setuptools', type='build', when='@5:') depends_on('py-jinja2', type=('build', 'run')) - depends_on('py-tornado@4:', type=('build', 'run')) + depends_on('py-tornado@4.0:6.999', type=('build', 'run'), when='@:5.7.4') + depends_on('py-tornado@4.1:6.999', type=('build', 'run'), when='@5.7.5:6.0.1') depends_on('py-ipython-genutils', type=('build', 'run')) depends_on('py-traitlets', type=('build', 'run')) + depends_on('py-traitlets@4.2.1:', type=('build', 'run'), when='@5:') depends_on('py-jupyter-core', type=('build', 'run')) + depends_on('py-jupyter-core@4.4.0:', type=('build', 'run'), when='@5.7.0:') depends_on('py-jupyter-client', type=('build', 'run')) - depends_on('py-jupyter-console', type=('build', 'run')) + depends_on('py-jupyter-client@5.2.0:', type=('build', 'run'), when='@5.7.0:') depends_on('py-nbformat', type=('build', 'run')) depends_on('py-nbconvert', type=('build', 'run')) depends_on('py-ipykernel', type=('build', 'run')) - depends_on('py-ipykernel@5.1.0:', when='@4.2.0:', type=('build', 'run')) - depends_on('py-terminado@0.3.3:', when="+terminal", type=('build', 'run')) + depends_on('py-ipykernel@5.1.0:', when='@4.2.0: ^python@3.3:', type=('build', 'run')) + depends_on('py-ipykernel@:5.0.0', when='@4.2.0: ^python@:2.8', type=('build', 'run')) depends_on('py-ipywidgets', when="+terminal", type=('build', 'run')) + depends_on('py-prometheus-client', type=('build', 'run'), when='@5.7.0:') + depends_on('py-terminado@0.3.3:', type=('build', 'run'), when='@:5.7.0') + depends_on('py-terminado@0.8.1:', type=('build', 'run'), when='@5.7.0:') + depends_on('py-send2trash', type=('build', 'run'), when='@6:') + depends_on('py-pyzmq@17:', type=('build', 'run'), when='@6:') + depends_on('py-traitlets@4.2.1:', type=('build', 'run'), when='@6:') + depends_on('py-ipaddress', type=('build', 'run'), when='@5.7.0: ^python@:2.8') diff --git a/var/spack/repos/builtin/packages/py-numba/package.py b/var/spack/repos/builtin/packages/py-numba/package.py index efad3b2a17..a6f4175e07 100644 --- a/var/spack/repos/builtin/packages/py-numba/package.py +++ b/var/spack/repos/builtin/packages/py-numba/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,7 +27,7 @@ class PyNumba(PythonPackage): depends_on('py-llvmlite@0.25:', type=('build', 'run'), when='@0.40.1:') depends_on('py-llvmlite@0.20:0.25', type=('build', 'run'), when='@0.35.1') - depends_on('py-argparse', type=('build', 'run')) + depends_on('py-argparse', type=('build', 'run'), when='^python@:2.6') depends_on('py-funcsigs', type=('build', 'run'), when='^python@:3.3.99') depends_on('py-singledispatch', type=('build', 'run'), when='^python@:3.3.99') diff --git a/var/spack/repos/builtin/packages/py-numcodecs/package.py b/var/spack/repos/builtin/packages/py-numcodecs/package.py new file mode 100644 index 0000000000..2fd992447e --- /dev/null +++ b/var/spack/repos/builtin/packages/py-numcodecs/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyNumcodecs(PythonPackage): + """Numcodecs is a Python package providing buffer compression and + transformation codecs for use in data storage and communication + applications. + """ + + homepage = "https://github.com/zarr-developers/numcodecs" + url = "https://pypi.io/packages/source/n/numcodecs/numcodecs-0.6.4.tar.gz" + + version('0.6.4', sha256='ef4843d5db4d074e607e9b85156835c10d006afc10e175bda62ff5412fca6e4d') + + variant('msgpack', default=False, description='Codec to encode data as msgpacked bytes.') + + depends_on('py-setuptools@18.0:', type='build') + depends_on('py-setuptools-scm@1.5.4:', type=('build', 'run')) + depends_on('py-numpy@1.7:', type=('build', 'run')) + depends_on('py-msgpack', type=('build', 'run'), when='+msgpack') diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py index 062c7d6d4f..21fd4bf81a 100644 --- a/var/spack/repos/builtin/packages/py-numexpr/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-numexpr3/package.py b/var/spack/repos/builtin/packages/py-numexpr3/package.py index 50a023c4af..f58baaf3f9 100644 --- a/var/spack/repos/builtin/packages/py-numexpr3/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,7 +20,7 @@ class PyNumexpr3(PythonPackage): homepage = "https://github.com/pydata/numexpr/tree/numexpr-3.0" url = "https://pypi.io/packages/source/n/numexpr3/numexpr3-3.0.1a1.tar.gz" - version('3.0.1.a1', sha256sum='de06f1b4206704b5bc19ea09b5c94350b97c211c26bc866f275252a8461b87e6') + version('3.0.1a1', sha256='de06f1b4206704b5bc19ea09b5c94350b97c211c26bc866f275252a8461b87e6') # TODO: Add CMake build system for better control of passing flags related # to CPU ISA. diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index e1ca99d749..c685a6fb4c 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -1,10 +1,11 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * import platform +import subprocess class PyNumpy(PythonPackage): @@ -14,8 +15,9 @@ class PyNumpy(PythonPackage): Fortran code, and useful linear algebra, Fourier transform, and random number capabilities""" - homepage = "http://www.numpy.org/" - url = "https://pypi.io/packages/source/n/numpy/numpy-1.17.3.zip" + homepage = "https://numpy.org/" + url = "https://pypi.io/packages/source/n/numpy/numpy-1.18.1.zip" + git = "https://github.com/numpy/numpy.git" maintainers = ['adamjstewart'] install_time_test_callbacks = ['install_test', 'import_module_test'] @@ -27,10 +29,16 @@ class PyNumpy(PythonPackage): 'numpy.distutils.command', 'numpy.distutils.fcompiler' ] + version('master', branch='master') + version('1.18.1', sha256='b6ff59cee96b454516e47e7721098e6ceebef435e3e21ac2d6c3b8b02628eb77') + version('1.18.0', sha256='a9d72d9abaf65628f0f31bbb573b7d9304e43b1e6bbae43149c17737a42764c4') + version('1.17.5', sha256='16507ba6617f62ae3c6ab1725ae6f550331025d4d9a369b83f6d5a470446c342') + version('1.17.4', sha256='f58913e9227400f1395c7b800503ebfdb0772f1c33ff8cb4d6451c06cabdf316') version('1.17.3', sha256='a0678793096205a4d784bd99f32803ba8100f639cf3b932dc63b21621390ea7e') version('1.17.2', sha256='73615d3edc84dd7c4aeb212fa3748fb83217e00d201875a47327f55363cef2df') version('1.17.1', sha256='f11331530f0eff69a758d62c2461cd98cdc2eae0147279d8fc86e0464eb7e8ca') version('1.17.0', sha256='951fefe2fb73f84c620bec4e001e80a80ddaa1b84dce244ded7f1e0cbe0ed34a') + version('1.16.6', sha256='e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff') version('1.16.5', sha256='8bb452d94e964b312205b0de1238dd7209da452343653ab214b5d681780e7a0c') version('1.16.4', sha256='7242be12a58fec245ee9734e625964b97cf7e3f2f7d016603f9e56660ce479c7') version('1.16.3', sha256='78a6f89da87eeb48014ec652a65c4ffde370c036d780a995edaeb121d3625621') @@ -71,6 +79,9 @@ class PyNumpy(PythonPackage): depends_on('python@2.7:2.8,3.5:', type=('build', 'run'), when='@1.16:') depends_on('python@3.5:', type=('build', 'run'), when='@1.17:') depends_on('py-setuptools', type='build') + # Check pyproject.toml for updates to the required cython version + depends_on('py-cython@0.29.13:', when='@1.18.0:', type='build') + depends_on('py-cython@0.29.14:', when='@1.18.1:', type='build') depends_on('blas', when='+blas') depends_on('lapack', when='+lapack') @@ -88,6 +99,28 @@ class PyNumpy(PythonPackage): # -std=c99 at least required, old versions of GCC default to -std=c90 if self.spec.satisfies('%gcc@:5.1') and name == 'cflags': flags.append(self.compiler.c99_flag) + # Check gcc version in use by intel compiler + # This will essentially check the system gcc compiler unless a gcc + # module is already loaded. + if self.spec.satisfies('%intel') and name == 'cflags': + p1 = subprocess.Popen( + [self.compiler.cc, '-v'], + stderr=subprocess.PIPE + ) + p2 = subprocess.Popen( + ['grep', 'compatibility'], + stdin=p1.stderr, + stdout=subprocess.PIPE + ) + p1.stderr.close() + out, err = p2.communicate() + gcc_version = Version(out.split()[5].decode('utf-8')) + if gcc_version < Version('4.8'): + raise InstallError('The GCC version that the Intel compiler ' + 'uses must be >= 4.8. The GCC in use is ' + '{0}'.format(gcc_version)) + if gcc_version <= Version('5.1'): + flags.append(self.compiler.c99_flag) return (flags, None, None) @run_before('build') diff --git a/var/spack/repos/builtin/packages/py-numpydoc/package.py b/var/spack/repos/builtin/packages/py-numpydoc/package.py index bd9607c7c4..cef8a2f7d2 100644 --- a/var/spack/repos/builtin/packages/py-numpydoc/package.py +++ b/var/spack/repos/builtin/packages/py-numpydoc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-oauth2client/package.py b/var/spack/repos/builtin/packages/py-oauth2client/package.py index 901605c411..2b05c982fc 100644 --- a/var/spack/repos/builtin/packages/py-oauth2client/package.py +++ b/var/spack/repos/builtin/packages/py-oauth2client/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-oauthlib/package.py b/var/spack/repos/builtin/packages/py-oauthlib/package.py index cc818163ec..659b272901 100644 --- a/var/spack/repos/builtin/packages/py-oauthlib/package.py +++ b/var/spack/repos/builtin/packages/py-oauthlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-olefile/package.py b/var/spack/repos/builtin/packages/py-olefile/package.py index 44f256319f..4e9826b18b 100644 --- a/var/spack/repos/builtin/packages/py-olefile/package.py +++ b/var/spack/repos/builtin/packages/py-olefile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-onnx/package.py b/var/spack/repos/builtin/packages/py-onnx/package.py index 861edc2203..fd6d6b0b6d 100644 --- a/var/spack/repos/builtin/packages/py-onnx/package.py +++ b/var/spack/repos/builtin/packages/py-onnx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py b/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py index fbbd3e22a3..9c71274e60 100644 --- a/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py +++ b/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-openpmd-validator/package.py b/var/spack/repos/builtin/packages/py-openpmd-validator/package.py index 4018c8419f..3da15810d5 100644 --- a/var/spack/repos/builtin/packages/py-openpmd-validator/package.py +++ b/var/spack/repos/builtin/packages/py-openpmd-validator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py index 75411cd5ff..b846002800 100644 --- a/var/spack/repos/builtin/packages/py-openpyxl/package.py +++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-openslide-python/package.py b/var/spack/repos/builtin/packages/py-openslide-python/package.py index ff1632a150..a3e0e2c1d2 100644 --- a/var/spack/repos/builtin/packages/py-openslide-python/package.py +++ b/var/spack/repos/builtin/packages/py-openslide-python/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-opentuner/package.py b/var/spack/repos/builtin/packages/py-opentuner/package.py index 5c34fbfab7..5efd8039f3 100644 --- a/var/spack/repos/builtin/packages/py-opentuner/package.py +++ b/var/spack/repos/builtin/packages/py-opentuner/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,7 +18,7 @@ class PyOpentuner(PythonPackage): depends_on('python@2.7:2.8', type=('build', 'run')) depends_on('py-argparse@1.2.1:', type=('build', 'run')) - depends_on('py-fn@0.2.12:', type=('build', 'run')) + depends_on('py-fn-py@0.2.12:', type=('build', 'run')) depends_on('py-numpy@1.8.0:', type=('build', 'run')) depends_on('py-pysqlite@2.6.3:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-opppy/package.py b/var/spack/repos/builtin/packages/py-opppy/package.py index b6edea8226..6e512b12c6 100644 --- a/var/spack/repos/builtin/packages/py-opppy/package.py +++ b/var/spack/repos/builtin/packages/py-opppy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,16 +12,17 @@ class PyOpppy(PythonPackage): output and dump files generated by scientific software packages.""" homepage = "https://github.com/lanl/opppy" - url = "https://github.com/lanl/OPPPY/archive/OPPPY-0_1_1.tar.gz" + url = "https://github.com/lanl/OPPPY/archive/opppy-0_1_2.tar.gz" git = "https://github.com/lanl/opppy.git" version('master', branch='master') + version('0_1_2', sha256='ef3795d3164fa0aa7ea7da7e223d6d0a48d2960aefd03a7d90cdb8b8f480cd4c') version('0_1_1', sha256='505c023853e75552abc65de9777a125ecb6a99a1cb4e605a4f702af837e3168b') depends_on('py-setuptools', type=('build', 'run')) depends_on('py-numpy@1.6:', type=('build', 'run')) depends_on('python@3:', type=('build', 'run')) - depends_on('py-argparse', type=('build', 'run')) + depends_on('py-argparse', type=('build', 'run'), when='^python@:2.6') depends_on('py-scipy', type=('build', 'run')) depends_on('py-matplotlib', type=('build', 'run')) depends_on('py-sphinx', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-opt-einsum/package.py b/var/spack/repos/builtin/packages/py-opt-einsum/package.py new file mode 100644 index 0000000000..4de5712076 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-opt-einsum/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyOptEinsum(PythonPackage): + """Optimized Einsum: A tensor contraction order optimizer.""" + + homepage = "https://github.com/dgasmith/opt_einsum" + url = "https://pypi.io/packages/source/o/opt_einsum/opt_einsum-3.1.0.tar.gz" + + version('3.1.0', sha256='edfada4b1d0b3b782ace8bc14e80618ff629abf53143e1e6bbf9bd00b11ece77') + + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-numpy@1.7:', type=('build', 'run')) + depends_on('py-pytest', type='test') + depends_on('py-pytest-cov', type='test') + depends_on('py-pytest-pep8', type='test') diff --git a/var/spack/repos/builtin/packages/py-ordereddict/package.py b/var/spack/repos/builtin/packages/py-ordereddict/package.py index 4e40791d62..afba6ee6f3 100644 --- a/var/spack/repos/builtin/packages/py-ordereddict/package.py +++ b/var/spack/repos/builtin/packages/py-ordereddict/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-oset/package.py b/var/spack/repos/builtin/packages/py-oset/package.py index 225d7a62ca..9dfb7c47db 100644 --- a/var/spack/repos/builtin/packages/py-oset/package.py +++ b/var/spack/repos/builtin/packages/py-oset/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-osqp/package.py b/var/spack/repos/builtin/packages/py-osqp/package.py new file mode 100644 index 0000000000..1bec5cdf49 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-osqp/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyOsqp(PythonPackage): + """OSQP: The Operator Splitting QP Solver""" + + homepage = "https://osqp.org/" + url = "https://pypi.io/packages/source/o/osqp/osqp-0.6.1.tar.gz" + + version('0.6.1', sha256='47b17996526d6ecdf35cfaead6e3e05d34bc2ad48bcb743153cefe555ecc0e8c') + + depends_on('cmake', type='build') + depends_on('py-setuptools', type='build') + depends_on('py-numpy@1.7:', type=('build', 'run')) + depends_on('py-scipy@0.13.2:', type=('build', 'run')) + depends_on('py-future', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-overpy/package.py b/var/spack/repos/builtin/packages/py-overpy/package.py index cd83009ee0..24b3186e17 100644 --- a/var/spack/repos/builtin/packages/py-overpy/package.py +++ b/var/spack/repos/builtin/packages/py-overpy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-owslib/package.py b/var/spack/repos/builtin/packages/py-owslib/package.py index 3d0a8adc99..7f90a62ee1 100644 --- a/var/spack/repos/builtin/packages/py-owslib/package.py +++ b/var/spack/repos/builtin/packages/py-owslib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-packaging/package.py b/var/spack/repos/builtin/packages/py-packaging/package.py index 8137fb84ea..466d3f787f 100644 --- a/var/spack/repos/builtin/packages/py-packaging/package.py +++ b/var/spack/repos/builtin/packages/py-packaging/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-palettable/package.py b/var/spack/repos/builtin/packages/py-palettable/package.py index 1646f6dfb7..716c9842e5 100644 --- a/var/spack/repos/builtin/packages/py-palettable/package.py +++ b/var/spack/repos/builtin/packages/py-palettable/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pamela/package.py b/var/spack/repos/builtin/packages/py-pamela/package.py index 28ad7d47ef..58312ce3c3 100644 --- a/var/spack/repos/builtin/packages/py-pamela/package.py +++ b/var/spack/repos/builtin/packages/py-pamela/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 8a604a339f..2403197c9e 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pandocfilters/package.py b/var/spack/repos/builtin/packages/py-pandocfilters/package.py new file mode 100644 index 0000000000..168a2363f3 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pandocfilters/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPandocfilters(PythonPackage): + """A python module for writing pandoc filters""" + + homepage = "https://github.com/jgm/pandocfilters" + url = "https://pypi.io/packages/source/p/pandocfilters/pandocfilters-1.4.2.tar.gz" + + version('1.4.2', sha256='b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9') diff --git a/var/spack/repos/builtin/packages/py-parameterized/package.py b/var/spack/repos/builtin/packages/py-parameterized/package.py new file mode 100644 index 0000000000..ff68c38080 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-parameterized/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyParameterized(PythonPackage): + """Parameterized testing with any Python test framework.""" + + homepage = "https://github.com/wolever/parameterized" + url = "https://pypi.io/packages/source/p/parameterized/parameterized-0.7.1.tar.gz" + + version('0.7.1', sha256='6a94dbea30c6abde99fd4c2f2042c1bf7f980e48908bf92ead62394f93cf57ed') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-paramiko/package.py b/var/spack/repos/builtin/packages/py-paramiko/package.py index a5f68cf46b..043b04ed5e 100644 --- a/var/spack/repos/builtin/packages/py-paramiko/package.py +++ b/var/spack/repos/builtin/packages/py-paramiko/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-parse/package.py b/var/spack/repos/builtin/packages/py-parse/package.py new file mode 100644 index 0000000000..1e337c8b22 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-parse/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyParse(PythonPackage): + """parse() is the opposite of format()""" + + homepage = "https://pypi.org/project/parse/" + url = "https://pypi.io/packages/source/p/parse/parse-1.11.1.tar.gz" + + version('1.12.1', sha256='a5fca7000c6588d77bc65c28f3f21bfce03b5e44daa8f9f07c17fe364990d717') + version('1.11.1', sha256='870dd675c1ee8951db3e29b81ebe44fd131e3eb8c03a79483a58ea574f3145c2') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-parsedatetime/package.py b/var/spack/repos/builtin/packages/py-parsedatetime/package.py new file mode 100644 index 0000000000..afb8db85bb --- /dev/null +++ b/var/spack/repos/builtin/packages/py-parsedatetime/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyParsedatetime(PythonPackage): + """Parse human-readable date/time strings.""" + + homepage = "https://github.com/bear/parsedatetime" + url = "https://pypi.io/packages/source/p/parsedatetime/parsedatetime-2.5.tar.gz" + + version('2.5', sha256='d2e9ddb1e463de871d32088a3f3cea3dc8282b1b2800e081bd0ef86900451667') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-partd/package.py b/var/spack/repos/builtin/packages/py-partd/package.py index e40968871f..616f960f23 100644 --- a/var/spack/repos/builtin/packages/py-partd/package.py +++ b/var/spack/repos/builtin/packages/py-partd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-path-py/package.py b/var/spack/repos/builtin/packages/py-path-py/package.py index 428c668acd..6d578b2d8b 100644 --- a/var/spack/repos/builtin/packages/py-path-py/package.py +++ b/var/spack/repos/builtin/packages/py-path-py/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pathlib/package.py b/var/spack/repos/builtin/packages/py-pathlib/package.py index b6b0c9095d..a0676b0494 100644 --- a/var/spack/repos/builtin/packages/py-pathlib/package.py +++ b/var/spack/repos/builtin/packages/py-pathlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pathlib2/package.py b/var/spack/repos/builtin/packages/py-pathlib2/package.py index 25a852d1f4..b1759bb188 100644 --- a/var/spack/repos/builtin/packages/py-pathlib2/package.py +++ b/var/spack/repos/builtin/packages/py-pathlib2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pathos/package.py b/var/spack/repos/builtin/packages/py-pathos/package.py index 73930a0303..e4b2bc6c4f 100644 --- a/var/spack/repos/builtin/packages/py-pathos/package.py +++ b/var/spack/repos/builtin/packages/py-pathos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,14 +10,25 @@ class PyPathos(PythonPackage): """Parallel graph management and execution in heterogeneous computing """ homepage = "https://github.com/uqfoundation/pathos" - url = "https://pypi.io/packages/source/p/pathos/pathos-0.2.0.zip" + url = "https://pypi.io/packages/source/p/pathos/pathos-0.2.3.tar.gz" + version('0.2.3', sha256='954c5b0a8b257c375e35d311c65fa62a210a3d65269195557de38418ac9f61f9') version('0.2.0', sha256='2f4e67e7914c95fb0cce766bab173eb2c5860ee420108fa183099557ac2e50e9') depends_on('python@2.6:2.8,3.1:') depends_on('py-setuptools@0.6:', type='build') - depends_on('py-multiprocess@0.70.4:', type=('build', 'run')) - depends_on('py-pox@0.2.2:', type=('build', 'run')) - depends_on('py-ppft@1.6.4.5:', type=('build', 'run')) - depends_on('py-dill@0.2.5:', type=('build', 'run')) + depends_on('py-multiprocess@0.70.7:', type=('build', 'run')) + depends_on('py-pox@0.2.5:', type=('build', 'run')) + depends_on('py-ppft@1.6.4.9:', type=('build', 'run')) + depends_on('py-dill@0.2.9:', type=('build', 'run')) + + def url_for_version(self, version): + url = self.url.rsplit('/', 1)[0] + if version >= Version('0.2.2'): + url += '/pathos-{0}.tar.gz' + else: + url += '/pathos-{0}.zip' + + url = url.format(version) + return url diff --git a/var/spack/repos/builtin/packages/py-pathspec/package.py b/var/spack/repos/builtin/packages/py-pathspec/package.py index 75de04f4a5..fdf65b9484 100644 --- a/var/spack/repos/builtin/packages/py-pathspec/package.py +++ b/var/spack/repos/builtin/packages/py-pathspec/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-patsy/package.py b/var/spack/repos/builtin/packages/py-patsy/package.py index d5e744d1d0..eb20c74049 100644 --- a/var/spack/repos/builtin/packages/py-patsy/package.py +++ b/var/spack/repos/builtin/packages/py-patsy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,6 +11,8 @@ class PyPatsy(PythonPackage): homepage = "https://github.com/pydata/patsy" url = "https://pypi.io/packages/source/p/patsy/patsy-0.4.1.zip" + version('0.5.1', sha256='f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991', + url="https://pypi.io/packages/source/p/patsy/patsy-0.5.1.tar.gz") version('0.4.1', sha256='dc1cc280045b0e6e50c04706fd1e26d2a00ea400aa112f88e8142f88b0b7d3d4') variant('splines', default=False, description="Offers spline related functions") diff --git a/var/spack/repos/builtin/packages/py-pauvre/package.py b/var/spack/repos/builtin/packages/py-pauvre/package.py index 24f0f6c0ad..679e6c0034 100644 --- a/var/spack/repos/builtin/packages/py-pauvre/package.py +++ b/var/spack/repos/builtin/packages/py-pauvre/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pbr/package.py b/var/spack/repos/builtin/packages/py-pbr/package.py index be84096ed6..ae5661c37f 100644 --- a/var/spack/repos/builtin/packages/py-pbr/package.py +++ b/var/spack/repos/builtin/packages/py-pbr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pep8-naming/package.py b/var/spack/repos/builtin/packages/py-pep8-naming/package.py index 3783fa2afa..ed123b773d 100644 --- a/var/spack/repos/builtin/packages/py-pep8-naming/package.py +++ b/var/spack/repos/builtin/packages/py-pep8-naming/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pep8/package.py b/var/spack/repos/builtin/packages/py-pep8/package.py new file mode 100644 index 0000000000..d1eaa13470 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pep8/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPep8(PythonPackage): + """Python style guide checker (deprecated, use py-pycodestyle instead).""" + + homepage = "https://pep8.readthedocs.org/" + url = "https://pypi.io/packages/source/p/pep8/pep8-1.7.1.tar.gz" + + import_modules = ['pep8'] + + version('1.7.1', sha256='fe249b52e20498e59e0b5c5256aa52ee99fc295b26ec9eaa85776ffdb9fe6374') + + depends_on('py-setuptools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-performance/package.py b/var/spack/repos/builtin/packages/py-performance/package.py index 9abc3c4d48..41c12556d3 100644 --- a/var/spack/repos/builtin/packages/py-performance/package.py +++ b/var/spack/repos/builtin/packages/py-performance/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,4 +22,4 @@ class PyPerformance(PythonPackage): depends_on('py-setuptools', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) - depends_on('py-perf', type=('build', 'run')) + depends_on('py-pyperf', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-periodictable/package.py b/var/spack/repos/builtin/packages/py-periodictable/package.py index 0e26034757..253a808c0b 100644 --- a/var/spack/repos/builtin/packages/py-periodictable/package.py +++ b/var/spack/repos/builtin/packages/py-periodictable/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-petsc4py/package.py b/var/spack/repos/builtin/packages/py-petsc4py/package.py index b2626f5378..cd14745f36 100644 --- a/var/spack/repos/builtin/packages/py-petsc4py/package.py +++ b/var/spack/repos/builtin/packages/py-petsc4py/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pexpect/package.py b/var/spack/repos/builtin/packages/py-pexpect/package.py index 0c9e08dc2a..fd5d7d5d96 100644 --- a/var/spack/repos/builtin/packages/py-pexpect/package.py +++ b/var/spack/repos/builtin/packages/py-pexpect/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-phonopy/package.py b/var/spack/repos/builtin/packages/py-phonopy/package.py index 6b3202df4a..f297faf44d 100644 --- a/var/spack/repos/builtin/packages/py-phonopy/package.py +++ b/var/spack/repos/builtin/packages/py-phonopy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pickleshare/package.py b/var/spack/repos/builtin/packages/py-pickleshare/package.py index c8a9a61e44..f48b5cc200 100644 --- a/var/spack/repos/builtin/packages/py-pickleshare/package.py +++ b/var/spack/repos/builtin/packages/py-pickleshare/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-picrust/package.py b/var/spack/repos/builtin/packages/py-picrust/package.py index 49984aa324..e346e5b012 100644 --- a/var/spack/repos/builtin/packages/py-picrust/package.py +++ b/var/spack/repos/builtin/packages/py-picrust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pil/package.py b/var/spack/repos/builtin/packages/py-pil/package.py index a5bd284d88..c248c9207f 100644 --- a/var/spack/repos/builtin/packages/py-pil/package.py +++ b/var/spack/repos/builtin/packages/py-pil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py index 50c16e1175..36d99f2c01 100644 --- a/var/spack/repos/builtin/packages/py-pillow/package.py +++ b/var/spack/repos/builtin/packages/py-pillow/package.py @@ -1,10 +1,9 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * -import sys class PyPillow(PythonPackage): @@ -14,8 +13,14 @@ class PyPillow(PythonPackage): capabilities.""" homepage = "https://python-pillow.org/" - url = "https://pypi.io/packages/source/P/Pillow/Pillow-6.2.0.tar.gz" + url = "https://pypi.io/packages/source/P/Pillow/Pillow-7.0.0.tar.gz" + maintainers = ['adamjstewart'] + import_modules = ['PIL'] + + version('7.0.0', sha256='4d9ed9a64095e031435af120d3c910148067087541131e82b3e8db302f4c8946') + version('6.2.2', sha256='db9ff0c251ed066d367f53b64827cc9e18ccea001b986d08c265e53625dab950') + version('6.2.1', sha256='bf4e972a88f8841d8fdc6db1a75e0f8d763e66e3754b03006cbc3854d89f1cb1') version('6.2.0', sha256='4548236844327a718ce3bb182ab32a16fa2050c61e334e959f554cac052fb0df') version('5.4.1', sha256='5233664eadfa342c639b9b9977190d64ad7aca4edc51a966394d7e08e7f38a9f') version('5.1.0', sha256='cee9bc75bff455d317b6947081df0824a8f118de2786dc3d74a3503fd631f4ef') @@ -25,80 +30,86 @@ class PyPillow(PythonPackage): provides('pil') # These defaults correspond to Pillow defaults - variant('tiff', default=False, description='Access to TIFF files') - variant('freetype', default=False, description='Font related services') + # https://pillow.readthedocs.io/en/stable/installation.html#external-libraries + variant('tiff', default=False, description='Compressed TIFF functionality') + variant('freetype', default=False, description='Type related services') variant('lcms', default=False, description='Color management') - variant('jpeg2000', default=False, description='Provide JPEG 2000 functionality') + variant('webp', default=False, description='WebP format') + variant('webpmux', default=False, description='WebP metadata') + variant('jpeg2000', default=False, description='JPEG 2000 functionality') # Spack does not (yet) support these modes of building - # variant('webp', default=False, description='Provide the WebP format') - # variant('webpmux', default=False, - # description='WebP metadata, relies on WebP support') # variant('imagequant', default=False, - # description='Provide improved color quantization') + # description='Improved color quantization') # Required dependencies - depends_on('binutils', type='build', when=sys.platform != 'darwin') - depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('python@2.6:2.8,3.2:', when='@3:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.3:', when='@4:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.4:', when='@5:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.5:', when='@6:', type=('build', 'run')) + depends_on('python@3.5:', when='@7:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('jpeg') depends_on('zlib') + depends_on('jpeg') + depends_on('py-pytest', type='test') + depends_on('py-pytest-runner', type='test') # Optional dependencies depends_on('libtiff', when='+tiff') depends_on('freetype', when='+freetype') - depends_on('lcms', when='+lcms') + depends_on('lcms@2:', when='+lcms') + depends_on('libwebp', when='+webp') + depends_on('libwebp+libwebpmux+libwebpdemux', when='+webpmux') depends_on('openjpeg', when='+jpeg2000') + depends_on('imagemagick', type='test') # Spack does not (yet) support these modes of building - # depends_on('webp', when='+webp') - # depends_on('webpmux', when='+webpmux') - # depends_on('imagequant', when='+imagequant') + # depends_on('libimagequant', when='+imagequant') + + conflicts('+webpmux', when='~webp', msg='Webpmux relies on WebP support') phases = ['build_ext', 'install'] def patch(self): - """Patch setup.py to provide lib and include directories + """Patch setup.py to provide library and include directories for dependencies.""" - spec = self.spec - setup = FileFilter('setup.py') + library_dirs = [] + include_dirs = [] + for dep in self.spec.dependencies(deptype='link'): + query = self.spec[dep.name] + library_dirs.extend(query.libs.directories) + include_dirs.extend(query.headers.directories) - setup.filter('JPEG_ROOT = None', - 'JPEG_ROOT=("{0}","{1}")'.format( - spec['jpeg'].libs.directories[0], - spec['jpeg'].prefix.include)) - setup.filter('ZLIB_ROOT = None', - 'ZLIB_ROOT = ("{0}", "{1}")'.format( - spec['zlib'].prefix.lib, - spec['zlib'].prefix.include)) - if '+tiff' in spec: - setup.filter('TIFF_ROOT = None', - 'TIFF_ROOT = ("{0}", "{1}")'.format( - spec['libtiff'].prefix.lib, - spec['libtiff'].prefix.include)) - if '+freetype' in spec: - setup.filter('FREETYPE_ROOT = None', - 'FREETYPE_ROOT = ("{0}", "{1}")'.format( - spec['freetype'].prefix.lib, - spec['freetype'].prefix.include)) - if '+lcms' in spec: - setup.filter('LCMS_ROOT = None', - 'LCMS_ROOT = ("{0}", "{1}")'.format( - spec['lcms'].prefix.lib, - spec['lcms'].prefix.include)) - if '+jpeg2000' in spec: - setup.filter('JPEG2K_ROOT = None', - 'JPEG2K_ROOT = ("{0}", "{1}")'.format( - spec['openjpeg'].prefix.lib, - spec['openjpeg'].prefix.include)) - - def build_ext_args(self, spec, prefix): - def variant_to_flag(variant): - able = 'enable' if '+{0}'.format(variant) in spec else 'disable' - return '--{0}-{1}'.format(able, variant) - - variants = ['jpeg', 'zlib', 'tiff', 'freetype', 'lcms', 'jpeg2000'] - args = list(map(variant_to_flag, variants)) - args.extend(['--rpath=%s' % ":".join(self.rpath)]) - return args + setup = FileFilter('setup.py') + setup.filter('library_dirs = []', + 'library_dirs = {0}'.format(library_dirs), string=True) + setup.filter('include_dirs = []', + 'include_dirs = {0}'.format(include_dirs), string=True) + + def variant_to_cfg(setup): + able = 'enable' if '+' + variant in self.spec else 'disable' + return '{0}-{1}=1\n'.format(able, variant) + + with open('setup.cfg', 'a') as setup: + # Default backend + setup.write('[build_ext]\n') + setup.write('enable-zlib=1\n') + setup.write('enable-jpeg=1\n') + variants = ['tiff', 'freetype', 'lcms', 'webp', + 'webpmux', 'jpeg2000'] + for variant in variants: + setup.write(variant_to_cfg(setup)) + + # Spack does not (yet) support these modes of building + setup.write('disable-imagequant=1\n') + + setup.write('rpath={0}\n'.format(':'.join(self.rpath))) + setup.write('[install]\n') + + # Tests need to be re-added since `phases` was overridden + run_after('build_ext')( + PythonPackage._run_default_build_time_test_callbacks) + run_after('install')( + PythonPackage._run_default_install_time_test_callbacks) + run_after('install')(PythonPackage.sanity_check_prefix) diff --git a/var/spack/repos/builtin/packages/py-pint/package.py b/var/spack/repos/builtin/packages/py-pint/package.py index 4466111348..6287cc76bd 100644 --- a/var/spack/repos/builtin/packages/py-pint/package.py +++ b/var/spack/repos/builtin/packages/py-pint/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pip/package.py b/var/spack/repos/builtin/packages/py-pip/package.py index 24883e0712..d9104ec4f9 100644 --- a/var/spack/repos/builtin/packages/py-pip/package.py +++ b/var/spack/repos/builtin/packages/py-pip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pipits/package.py b/var/spack/repos/builtin/packages/py-pipits/package.py index 666e738cfc..f1a4067f8d 100644 --- a/var/spack/repos/builtin/packages/py-pipits/package.py +++ b/var/spack/repos/builtin/packages/py-pipits/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -57,15 +57,15 @@ class PyPipits(PythonPackage): install_tree(join_path(self.stage.source_path, 'refdb'), self.prefix.refdb) - def setup_environment(self, spack_env, run_env): - run_env.set('PIPITS_UNITE_REFERENCE_DATA_CHIMERA', join_path( - self.prefix, 'refdb', - 'uchime_reference_dataset_01.01.2016', - 'uchime_reference_dataset_01.01.2016.fasta')) - run_env.set('PIPITS_UNITE_RETRAINED_DIR', - self.prefix.refdb.UNITE_retrained) - run_env.set('PIPITS_WARCUP_RETRAINED_DIR', - self.prefix.refdb.warcup_retrained_V2) - run_env.set('PIPITS_RDP_CLASSIFIER_JAR', join_path( - self.spec['rdp-classifier'].prefix.bin, - 'classifier.jar')) + def setup_run_environment(self, env): + env.set('PIPITS_UNITE_REFERENCE_DATA_CHIMERA', join_path( + self.prefix, 'refdb', + 'uchime_reference_dataset_01.01.2016', + 'uchime_reference_dataset_01.01.2016.fasta')) + env.set('PIPITS_UNITE_RETRAINED_DIR', + self.prefix.refdb.UNITE_retrained) + env.set('PIPITS_WARCUP_RETRAINED_DIR', + self.prefix.refdb.warcup_retrained_V2) + env.set('PIPITS_RDP_CLASSIFIER_JAR', join_path( + self.spec['rdp-classifier'].prefix.bin, + 'classifier.jar')) diff --git a/var/spack/repos/builtin/packages/py-pispino/package.py b/var/spack/repos/builtin/packages/py-pispino/package.py index bcb3c04e38..c216c220a5 100644 --- a/var/spack/repos/builtin/packages/py-pispino/package.py +++ b/var/spack/repos/builtin/packages/py-pispino/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pkgconfig/package.py b/var/spack/repos/builtin/packages/py-pkgconfig/package.py index d1d0ab004a..f519422138 100644 --- a/var/spack/repos/builtin/packages/py-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/py-pkgconfig/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,11 +12,13 @@ class PyPkgconfig(PythonPackage): homepage = "http://github.com/matze/pkgconfig" url = "https://pypi.io/packages/source/p/pkgconfig/pkgconfig-1.2.2.tar.gz" + version('1.5.1', sha256='97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f') version('1.4.0', sha256='048c3b457da7b6f686b647ab10bf09e2250e4c50acfe6f215398a8b5e6fcdb52') version('1.2.2', sha256='3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa') - depends_on('python@2.6:') - depends_on('py-setuptools', type='build') + depends_on('python@2.6:2.8,3.3:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.3:', when='@1.5:', type=('build', 'run')) + depends_on('py-setuptools', when='@:1.4', type=('build', 'run')) depends_on('pkgconfig', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pkginfo/package.py b/var/spack/repos/builtin/packages/py-pkginfo/package.py index bca33619dd..f8f323fc80 100644 --- a/var/spack/repos/builtin/packages/py-pkginfo/package.py +++ b/var/spack/repos/builtin/packages/py-pkginfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-planar/package.py b/var/spack/repos/builtin/packages/py-planar/package.py index 8b8d284b28..b01737828f 100644 --- a/var/spack/repos/builtin/packages/py-planar/package.py +++ b/var/spack/repos/builtin/packages/py-planar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-plotly/package.py b/var/spack/repos/builtin/packages/py-plotly/package.py index cd315180ed..72a0727be5 100644 --- a/var/spack/repos/builtin/packages/py-plotly/package.py +++ b/var/spack/repos/builtin/packages/py-plotly/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,9 +10,9 @@ class PyPlotly(PythonPackage): """An interactive, browser-based graphing library for Python""" homepage = "https://plot.ly/python/" - url = "https://github.com/plotly/plotly.py/archive/v2.2.0.tar.gz" + url = "https://pypi.io/packages/source/p/plotly/plotly-2.2.0.tar.gz" - version('2.2.0', sha256='dad2a49fe355dddb6ae159e96c10ac22413a33cbac513b4dbf3791e63ec33c1f') + version('2.2.0', sha256='ca668911ffb4d11fed6d7fbb12236f8ecc6a7209db192326bcb64bdb41451a58') depends_on('py-setuptools', type='build') depends_on('py-requests@2.3.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pluggy/package.py b/var/spack/repos/builtin/packages/py-pluggy/package.py index 8e9dd50cf3..1e2fb3f2bd 100644 --- a/var/spack/repos/builtin/packages/py-pluggy/package.py +++ b/var/spack/repos/builtin/packages/py-pluggy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ply/package.py b/var/spack/repos/builtin/packages/py-ply/package.py index 8c2b20c67b..6149a4f9de 100644 --- a/var/spack/repos/builtin/packages/py-ply/package.py +++ b/var/spack/repos/builtin/packages/py-ply/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pmw/package.py b/var/spack/repos/builtin/packages/py-pmw/package.py index 33b1d2e680..3ccc11fef4 100644 --- a/var/spack/repos/builtin/packages/py-pmw/package.py +++ b/var/spack/repos/builtin/packages/py-pmw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-portend/package.py b/var/spack/repos/builtin/packages/py-portend/package.py new file mode 100644 index 0000000000..b039fb06aa --- /dev/null +++ b/var/spack/repos/builtin/packages/py-portend/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPortend(PythonPackage): + """TCP port monitoring and discovery """ + + homepage = "https://github.com/jaraco/portend" + url = "https://pypi.io/packages/source/p/portend/portend-2.5.tar.gz" + + version( + '2.5', sha256='19dc27bfb3c72471bd30a235a4d5fbefef8a7e31cab367744b5d87a205e7bfd9') + + depends_on('py-setuptools', type='build') + depends_on('py-setuptools-scm@1.15.0:', type='build') + depends_on('py-tempora@1.8:', type=('run', 'build')) + depends_on('python@2.7:', type=('run', 'build')) diff --git a/var/spack/repos/builtin/packages/py-poster/package.py b/var/spack/repos/builtin/packages/py-poster/package.py index d7952fe6cb..a5fde5f22d 100644 --- a/var/spack/repos/builtin/packages/py-poster/package.py +++ b/var/spack/repos/builtin/packages/py-poster/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pox/package.py b/var/spack/repos/builtin/packages/py-pox/package.py index d0c3f99810..5ab43df6b4 100644 --- a/var/spack/repos/builtin/packages/py-pox/package.py +++ b/var/spack/repos/builtin/packages/py-pox/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,8 +10,9 @@ class PyPox(PythonPackage): """Utilities for filesystem exploration and automated builds.""" homepage = "https://github.com/uqfoundation/pox" - url = "https://pypi.io/packages/source/p/pox/pox-0.2.3.zip" + url = "https://pypi.io/packages/source/p/pox/pox-0.2.5.tar.gz" + version('0.2.5', sha256='2b53fbdf02596240483dc2cb94f94cc21252ad1b1858c7b1c151afeec9022cc8') version('0.2.3', sha256='d3e8167a1ebe08ae56262a0b9359118d90bc4648cd284b5d10ae240343100a75') version('0.2.2', sha256='c0b88e59ef0e4f2fa4839e11bf90d2c32d6ceb5abaf01f0c8138f7558e6f87c1') version('0.2.1', sha256='580bf731fee233c58eac0974011b5bf0698efb7337b0a1696d289043b4fcd7f4') @@ -19,3 +20,13 @@ class PyPox(PythonPackage): depends_on('python@2.5:2.8,3.1:') depends_on('py-setuptools@0.6:', type='build') + + def url_for_version(self, version): + url = "https://pypi.io/packages/source/p/pox/" + if version >= Version('0.2.4'): + url += 'pox-{0}.tar.gz' + else: + url += 'pox-{0}.zip' + + url = url.format(version) + return url diff --git a/var/spack/repos/builtin/packages/py-ppft/package.py b/var/spack/repos/builtin/packages/py-ppft/package.py index 49fa256cdc..810d61c315 100644 --- a/var/spack/repos/builtin/packages/py-ppft/package.py +++ b/var/spack/repos/builtin/packages/py-ppft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,8 +10,9 @@ class PyPpft(PythonPackage): """Distributed and parallel python """ homepage = "https://github.com/uqfoundation/ppft" - url = "https://pypi.io/packages/source/p/ppft/ppft-1.6.4.7.1.zip" + url = "https://pypi.io/packages/source/p/ppft/ppft-1.6.4.9.tar.gz" + version('1.6.4.9', sha256='5537b00afb7b247da0f59cc57ee5680178be61c8b2e21b5a0672b70a3d247791') version('1.6.4.7.1', sha256='f94b26491b4a36adc975fc51dba7568089a24756007a3a4ef3414a98d7337651') version('1.6.4.6', sha256='92d09061f5425634c43dbf99c5558f2cf2a2e1e351929f8da7e85f4649c11095') version('1.6.4.5', sha256='d47da9d2e553848b75727ce7c510f9e149965d5c68f9fc56c774a7c6a3d18214') @@ -21,3 +22,13 @@ class PyPpft(PythonPackage): depends_on('py-setuptools@0.6:', type='build') depends_on('py-six@1.7.3:', type=('build', 'run')) depends_on('py-dill@0.2.6:', type=('build', 'run')) + + def url_for_version(self, version): + url = "https://pypi.io/packages/source/p/ppft/" + if version >= Version('1.6.4.8'): + url += 'ppft-{0}.tar.gz' + else: + url += 'ppft-{0}.zip' + + url = url.format(version) + return url diff --git a/var/spack/repos/builtin/packages/py-pre-commit/package.py b/var/spack/repos/builtin/packages/py-pre-commit/package.py new file mode 100644 index 0000000000..5a6c381118 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pre-commit/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPreCommit(PythonPackage): + """A framework for managing and maintaining multi-language pre-commit + hooks.""" + + homepage = "https://github.com/pre-commit/pre-commit" + url = "https://pypi.io/packages/source/p/pre_commit/pre_commit-1.20.0.tar.gz" + + version('1.20.0', sha256='9f152687127ec90642a2cc3e4d9e1e6240c4eb153615cb02aa1ad41d331cbb6e') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-aspy-yaml', type=('build', 'run')) + depends_on('py-cfgv@2.0.0:', type=('build', 'run')) + depends_on('py-identify@1.0.0:', type=('build', 'run')) + depends_on('py-nodeenv@0.11.1:', type=('build', 'run')) + depends_on('py-pyyaml', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) + depends_on('py-toml', type=('build', 'run')) + depends_on('py-virtualenv@15.2:', type=('build', 'run')) + depends_on('py-futures', type=('build', 'run'), when='^python@:3.1.99') + depends_on('py-importlib-metadata', type=('build', 'run'), when='^python@:3.7.99') + depends_on('py-importlib-resources', type=('build', 'run'), when='^python@:3.6.99') diff --git a/var/spack/repos/builtin/packages/py-prettytable/package.py b/var/spack/repos/builtin/packages/py-prettytable/package.py index f4aecdd8a1..b2969b6e1f 100644 --- a/var/spack/repos/builtin/packages/py-prettytable/package.py +++ b/var/spack/repos/builtin/packages/py-prettytable/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-progress/package.py b/var/spack/repos/builtin/packages/py-progress/package.py index c1ef6a6dda..3ae16e5e59 100644 --- a/var/spack/repos/builtin/packages/py-progress/package.py +++ b/var/spack/repos/builtin/packages/py-progress/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-progressbar2/package.py b/var/spack/repos/builtin/packages/py-progressbar2/package.py index 91a8217f60..31f2688a57 100644 --- a/var/spack/repos/builtin/packages/py-progressbar2/package.py +++ b/var/spack/repos/builtin/packages/py-progressbar2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-projectq/package.py b/var/spack/repos/builtin/packages/py-projectq/package.py index 8c1dfe4cc7..d22a51584f 100644 --- a/var/spack/repos/builtin/packages/py-projectq/package.py +++ b/var/spack/repos/builtin/packages/py-projectq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-prometheus-client/package.py b/var/spack/repos/builtin/packages/py-prometheus-client/package.py index a89649b967..92fb9665ab 100644 --- a/var/spack/repos/builtin/packages/py-prometheus-client/package.py +++ b/var/spack/repos/builtin/packages/py-prometheus-client/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py b/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py index 212fa469f5..90a1b72098 100644 --- a/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py +++ b/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-protobuf/package.py b/var/spack/repos/builtin/packages/py-protobuf/package.py index edab6e1524..c2f1efd2f9 100644 --- a/var/spack/repos/builtin/packages/py-protobuf/package.py +++ b/var/spack/repos/builtin/packages/py-protobuf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,25 +15,47 @@ class PyProtobuf(PythonPackage): and using a variety of languages.""" homepage = 'https://developers.google.com/protocol-buffers/' - url = 'https://pypi.io/packages/source/p/protobuf/protobuf-3.0.0b2.tar.gz' + url = 'https://pypi.io/packages/source/p/protobuf/protobuf-3.11.0.tar.gz' variant('cpp', default=False, description='Enable the cpp implementation') - version('3.7.1', sha256='21e395d7959551e759d604940a115c51c6347d90a475c9baf471a1a86b5604a9') - version('3.6.1', sha256='1489b376b0f364bcc6f89519718c057eb191d7ad6f1b395ffd93d1aa45587811') - version('3.5.2.post1', sha256='3b60685732bd0cbdc802dfcb6071efbcf5d927ce3127c13c33ea1a8efae3aa76') - version('3.5.2', sha256='09879a295fd7234e523b62066223b128c5a8a88f682e3aff62fb115e4a0d8be0') - version('3.5.1', sha256='95b78959572de7d7fafa3acb718ed71f482932ddddddbd29ba8319c10639d863') + version('3.11.2', sha256='3d7a7d8d20b4e7a8f63f62de2d192cfd8b7a53c56caba7ece95367ca2b80c574') + version('3.11.1', sha256='aecdf12ef6dc7fd91713a6da93a86c2f2a8fe54840a3b1670853a2b7402e77c9') + version('3.11.0', sha256='97b08853b9bb71512ed52381f05cf2d4179f4234825b505d8f8d2bb9d9429939') + version('3.10.0', sha256='db83b5c12c0cd30150bb568e6feb2435c49ce4e68fe2d7b903113f0e221e58fe') + version('3.9.2', sha256='843f498e98ad1469ad54ecb4a7ccf48605a1c5d2bd26ae799c7a2cddab4a37ec') + version('3.9.1', sha256='d831b047bd69becaf64019a47179eb22118a50dd008340655266a906c69c6417') + version('3.7.1', sha256='21e395d7959551e759d604940a115c51c6347d90a475c9baf471a1a86b5604a9') + version('3.6.1', sha256='1489b376b0f364bcc6f89519718c057eb191d7ad6f1b395ffd93d1aa45587811') + version('3.6.0', sha256='a37836aa47d1b81c2db1a6b7a5e79926062b5d76bd962115a0e615551be2b48d') + version('3.5.2', sha256='09879a295fd7234e523b62066223b128c5a8a88f682e3aff62fb115e4a0d8be0') + version('3.5.1', sha256='95b78959572de7d7fafa3acb718ed71f482932ddddddbd29ba8319c10639d863') + version('3.4.0', sha256='ef02609ef445987976a3a26bff77119c518e0915c96661c3a3b17856d0ef6374') + version('3.3.0', sha256='1cbcee2c45773f57cb6de7ee0eceb97f92b9b69c0178305509b162c0160c1f04') + version('3.1.0', sha256='0bc10bfd00a9614fae58c86c21fbcf339790e48accf6d45f098034de985f5405', + url='https://github.com/protocolbuffers/protobuf/releases/download/v3.1.0/protobuf-python-3.1.0.tar.gz') + version('3.0.0', sha256='ecc40bc30f1183b418fe0ec0c90bc3b53fa1707c4205ee278c6b90479e5b6ff5') version('3.0.0b2', sha256='d5b560bbc4b7d97cc2455c05cad9299d9db02d7bd11193b05684e3a86303c229') - version('2.6.1', sha256='8faca1fb462ee1be58d00f5efb4ca4f64bde92187fe61fde32615bbee7b3e745') - version('2.5.0', sha256='58292c459598c9297258bf57acc055f701c727f0154a86af8c0947dde37d8172') - version('2.4.1', sha256='df30b98acb6ef892da8b4776175510cff2131908fd0526b6bad960c55a830a1b') - version('2.3.0', sha256='374bb047874a506507912c3717d0ce62affbaa9a22bcb494d63d60326a0867b5') + version('3.0.0a3', sha256='b61622de5048415bfd3f2d812ad64606438ac9e25009ae84191405fe58e522c1') + version('2.6.1', sha256='8faca1fb462ee1be58d00f5efb4ca4f64bde92187fe61fde32615bbee7b3e745') + version('2.5.0', sha256='58292c459598c9297258bf57acc055f701c727f0154a86af8c0947dde37d8172') + version('2.4.1', sha256='df30b98acb6ef892da8b4776175510cff2131908fd0526b6bad960c55a830a1b') + version('2.3.0', sha256='374bb047874a506507912c3717d0ce62affbaa9a22bcb494d63d60326a0867b5') - depends_on('py-setuptools', type='build') + depends_on('py-setuptools', type=('build', 'run')) + depends_on('py-six@1.9:', when='@3:', type=('build', 'run')) + depends_on('py-ordereddict', when='@3: ^python@:2', type=('build', 'run')) + depends_on('py-unittest2', when='@3: ^python@:2', type=('build', 'run')) depends_on('protobuf', when='+cpp') + @property + def build_directory(self): + if self.spec.satisfies('@3.1.0'): + return 'python' + else: + return '.' + @when('+cpp') def build_args(self, spec, prefix): return ['--cpp_implementation'] diff --git a/var/spack/repos/builtin/packages/py-psutil/package.py b/var/spack/repos/builtin/packages/py-psutil/package.py index 6c3720bc62..be282f141f 100644 --- a/var/spack/repos/builtin/packages/py-psutil/package.py +++ b/var/spack/repos/builtin/packages/py-psutil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-psyclone/package.py b/var/spack/repos/builtin/packages/py-psyclone/package.py index fc51370f18..0a1510677c 100644 --- a/var/spack/repos/builtin/packages/py-psyclone/package.py +++ b/var/spack/repos/builtin/packages/py-psyclone/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -38,6 +38,6 @@ class PyPsyclone(PythonPackage): with working_dir('src'): Executable('py.test')() - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Allow testing with installed executables: - spack_env.prepend_path('PATH', self.prefix.bin) + env.prepend_path('PATH', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/py-psycopg2/package.py b/var/spack/repos/builtin/packages/py-psycopg2/package.py index 0483c794af..5e95e42f4c 100644 --- a/var/spack/repos/builtin/packages/py-psycopg2/package.py +++ b/var/spack/repos/builtin/packages/py-psycopg2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ptyprocess/package.py b/var/spack/repos/builtin/packages/py-ptyprocess/package.py index c0734d41cb..d95e1f7107 100644 --- a/var/spack/repos/builtin/packages/py-ptyprocess/package.py +++ b/var/spack/repos/builtin/packages/py-ptyprocess/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pudb/package.py b/var/spack/repos/builtin/packages/py-pudb/package.py index 4826be0031..4d7b43b7f0 100644 --- a/var/spack/repos/builtin/packages/py-pudb/package.py +++ b/var/spack/repos/builtin/packages/py-pudb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-cpuinfo/package.py b/var/spack/repos/builtin/packages/py-py-cpuinfo/package.py index e9f4db3142..9e56235f18 100644 --- a/var/spack/repos/builtin/packages/py-cpuinfo/package.py +++ b/var/spack/repos/builtin/packages/py-py-cpuinfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PyCpuinfo(PythonPackage): +class PyPyCpuinfo(PythonPackage): """Get CPU info with pure Python 2 & 3""" homepage = "https://github.com/workhorsy/py-cpuinfo" diff --git a/var/spack/repos/builtin/packages/py-py/package.py b/var/spack/repos/builtin/packages/py-py/package.py index 1d6bb4ec45..2cb000a846 100644 --- a/var/spack/repos/builtin/packages/py-py/package.py +++ b/var/spack/repos/builtin/packages/py-py/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-py2bit/package.py b/var/spack/repos/builtin/packages/py-py2bit/package.py index ca0c7fd0ca..7df420e00d 100644 --- a/var/spack/repos/builtin/packages/py-py2bit/package.py +++ b/var/spack/repos/builtin/packages/py-py2bit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-py2cairo/package.py b/var/spack/repos/builtin/packages/py-py2cairo/package.py index 10d22b74b8..1427c7e45c 100644 --- a/var/spack/repos/builtin/packages/py-py2cairo/package.py +++ b/var/spack/repos/builtin/packages/py-py2cairo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py index 573b84be1b..ef4ed46cd5 100644 --- a/var/spack/repos/builtin/packages/py-py2neo/package.py +++ b/var/spack/repos/builtin/packages/py-py2neo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-py4j/package.py b/var/spack/repos/builtin/packages/py-py4j/package.py index 45ad5dfb37..db51d6eb90 100644 --- a/var/spack/repos/builtin/packages/py-py4j/package.py +++ b/var/spack/repos/builtin/packages/py-py4j/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyani/package.py b/var/spack/repos/builtin/packages/py-pyani/package.py index a5a0f12faa..afa5fdf640 100644 --- a/var/spack/repos/builtin/packages/py-pyani/package.py +++ b/var/spack/repos/builtin/packages/py-pyani/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyarrow/package.py b/var/spack/repos/builtin/packages/py-pyarrow/package.py index faa27b1052..ed10482145 100644 --- a/var/spack/repos/builtin/packages/py-pyarrow/package.py +++ b/var/spack/repos/builtin/packages/py-pyarrow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,8 +13,9 @@ class PyPyarrow(PythonPackage): """ homepage = "http://arrow.apache.org" - url = "https://pypi.org/packages/source/p/pyarrow/pyarrow-0.9.0.tar.gz" + url = 'https://pypi.org/packages/source/p/pyarrow/pyarrow-0.15.1.tar.gz' + version('0.15.1', sha256='7ad074690ba38313067bf3bbda1258966d38e2037c035d08b9ffe3cce07747a5') version('0.12.1', sha256='10db6e486c918c3af999d0114a22d92770687e3a6607ea3f14e6748854824c2a') version('0.11.0', sha256='07a6fd71c5d7440f2c42383dd2c5daa12d7f0a012f1e88288ed08a247032aead') version('0.9.0', sha256='7db8ce2f0eff5a00d6da918ce9f9cfec265e13f8a119b4adb1595e5b19fd6242') @@ -24,9 +25,19 @@ class PyPyarrow(PythonPackage): depends_on('cmake@3.0.0:', type='build') depends_on('pkgconfig', type='build') depends_on('py-setuptools', type='build') + depends_on('py-setuptools-scm', type='build', when='@0.15.0:') depends_on('py-cython', type='build') - - for v in ('@0.9.0', '@0.11.0', '@0.12.1'): + depends_on('py-cython@0.29:', type='build', when='@0.15.0:') + depends_on('py-pytest', type='test', when='@0.15.0:') + depends_on('py-pandas', type='test', when='@0.15.0:') + depends_on('py-hypothesis', type='test', when='@0.15.0:') + depends_on('py-pathlib2', type='test', when='@0.15.0: ^python@:3.3.99') + depends_on('py-numpy@1.14:', type=('build', 'run'), when='@0.15.0:') + depends_on('py-six@1.0.0:', type=('build', 'run'), when='@0.15.0:') + depends_on('py-futures', type=('build', 'run'), when='@0.15.0:^python@:3.1.99') + depends_on('py-enum34@1.1.6:', type=('build', 'run'), when='@0.15.0:^python@:3.3.99') + + for v in ('@0.9.0', '@0.11.0', '@0.12.1', '@0.15.1'): depends_on('arrow+python' + v, when=v) depends_on('arrow+parquet+python' + v, when='+parquet' + v) diff --git a/var/spack/repos/builtin/packages/py-pyasn1-modules/package.py b/var/spack/repos/builtin/packages/py-pyasn1-modules/package.py index 33b1cc145b..649d0e367e 100644 --- a/var/spack/repos/builtin/packages/py-pyasn1-modules/package.py +++ b/var/spack/repos/builtin/packages/py-pyasn1-modules/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,7 +15,9 @@ class PyPyasn1Modules(PythonPackage): url = "https://pypi.io/packages/source/p/pyasn1-modules/pyasn1-modules-0.2.6.tar.gz" version('0.2.6', sha256='43c17a83c155229839cc5c6b868e8d0c6041dba149789b6d6e28801c64821722') + version('0.2.5', sha256='ef721f68f7951fab9b0404d42590f479e30d9005daccb1699b0a51bb4177db96') depends_on('python@2.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('py-pyasn1@0.4.6:0.4.999', type=('build', 'run')) + depends_on('py-pyasn1@0.4.6:0.4.999', type=('build', 'run'), when='@0.2.6') + depends_on('py-pyasn1@0.4.1:0.4.999', type=('build', 'run'), when='@0.2.5') diff --git a/var/spack/repos/builtin/packages/py-pyasn1/package.py b/var/spack/repos/builtin/packages/py-pyasn1/package.py index acfab10948..3d4d9ab3a3 100644 --- a/var/spack/repos/builtin/packages/py-pyasn1/package.py +++ b/var/spack/repos/builtin/packages/py-pyasn1/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pybedtools/package.py b/var/spack/repos/builtin/packages/py-pybedtools/package.py index a0bab2d445..fc8e0fe7c7 100644 --- a/var/spack/repos/builtin/packages/py-pybedtools/package.py +++ b/var/spack/repos/builtin/packages/py-pybedtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pybigwig/package.py b/var/spack/repos/builtin/packages/py-pybigwig/package.py index c44fb88395..41f6ee7ffa 100644 --- a/var/spack/repos/builtin/packages/py-pybigwig/package.py +++ b/var/spack/repos/builtin/packages/py-pybigwig/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pybind11/package.py b/var/spack/repos/builtin/packages/py-pybind11/package.py index ac4b684450..cda6cada32 100644 --- a/var/spack/repos/builtin/packages/py-pybind11/package.py +++ b/var/spack/repos/builtin/packages/py-pybind11/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,6 +8,7 @@ from spack import * class PyPybind11(CMakePackage): """pybind11 -- Seamless operability between C++11 and Python. + pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. Its goals and syntax are similar to the excellent Boost.Python @@ -18,9 +19,11 @@ class PyPybind11(CMakePackage): homepage = "https://pybind11.readthedocs.io" url = "https://github.com/pybind/pybind11/archive/v2.1.0.tar.gz" git = "https://github.com/pybind/pybind11.git" + maintainers = ['ax3l'] - version('develop', branch='master') + version('master', branch='master') + version('2.4.3', sha256='1eed57bc6863190e35637290f97a20c81cfe4d9090ac0a24f3bbf08f265eb71d') version('2.3.0', sha256='0f34838f2c8024a6765168227ba587b3687729ebf03dc912f88ff75c7aa9cfe8') version('2.2.4', sha256='b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e') version('2.2.3', sha256='3a3b7b651afab1c5ba557f4c37d785a522b8030dfc765da26adc2ecd1de940ea') @@ -50,10 +53,30 @@ class PyPybind11(CMakePackage): ] return args - def setup_environment(self, spack_env, run_env): - spack_env.set('PYBIND11_USE_CMAKE', 1) + def setup_build_environment(self, env): + env.set('PYBIND11_USE_CMAKE', 1) + + def patch(self): + """ see https://github.com/spack/spack/issues/13559 """ + filter_file('import sys', + 'import sys; return "{0}"'.format(self.prefix.include), + 'pybind11/__init__.py', + string=True) def install(self, spec, prefix): super(PyPybind11, self).install(spec, prefix) setup_py('install', '--single-version-externally-managed', '--root=/', '--prefix={0}'.format(prefix)) + + @run_after('install') + @on_package_attributes(run_tests=True) + def test(self): + with working_dir('spack-test', create=True): + # test include helper points to right location + python = self.spec['python'].command + inc = python( + '-c', + 'import pybind11 as py; ' + + self.spec['python'].package.print_string('py.get_include()'), + output=str) + assert inc.strip() == str(self.prefix.include) diff --git a/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py b/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py index 0cffded42f..ba93a2a994 100644 --- a/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py +++ b/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pybtex/package.py b/var/spack/repos/builtin/packages/py-pybtex/package.py index 5b39a3a766..56bfb42a50 100644 --- a/var/spack/repos/builtin/packages/py-pybtex/package.py +++ b/var/spack/repos/builtin/packages/py-pybtex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pycairo/package.py b/var/spack/repos/builtin/packages/py-pycairo/package.py index 106a5babd5..7a373609cd 100644 --- a/var/spack/repos/builtin/packages/py-pycairo/package.py +++ b/var/spack/repos/builtin/packages/py-pycairo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pycares/package.py b/var/spack/repos/builtin/packages/py-pycares/package.py index 13322bd144..c782f719b4 100644 --- a/var/spack/repos/builtin/packages/py-pycares/package.py +++ b/var/spack/repos/builtin/packages/py-pycares/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pycbc/package.py b/var/spack/repos/builtin/packages/py-pycbc/package.py index ae24350952..69513c2a64 100644 --- a/var/spack/repos/builtin/packages/py-pycbc/package.py +++ b/var/spack/repos/builtin/packages/py-pycbc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pychecker/package.py b/var/spack/repos/builtin/packages/py-pychecker/package.py index a8c535293c..04e06a50fc 100644 --- a/var/spack/repos/builtin/packages/py-pychecker/package.py +++ b/var/spack/repos/builtin/packages/py-pychecker/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pycmd/package.py b/var/spack/repos/builtin/packages/py-pycmd/package.py new file mode 100644 index 0000000000..791852e95b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pycmd/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPycmd(PythonPackage): + """pycmd is a collection of command line tools for helping with Python + development.""" + + homepage = "https://pypi.org/project/pycmd/" + url = "https://pypi.io/packages/source/p/pycmd/pycmd-1.2.tar.gz" + + version('1.2', sha256='adc1976c0106919e9338db20102b91009256dcfec924a66928d7297026f72477') + + depends_on('py-py@1.4.9:', type=('build', 'run')) + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pycodestyle/package.py b/var/spack/repos/builtin/packages/py-pycodestyle/package.py index bba9848748..6f9da670f8 100644 --- a/var/spack/repos/builtin/packages/py-pycodestyle/package.py +++ b/var/spack/repos/builtin/packages/py-pycodestyle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pycparser/package.py b/var/spack/repos/builtin/packages/py-pycparser/package.py index d82b4e3c86..9e74d9b06e 100644 --- a/var/spack/repos/builtin/packages/py-pycparser/package.py +++ b/var/spack/repos/builtin/packages/py-pycparser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pycrypto/package.py b/var/spack/repos/builtin/packages/py-pycrypto/package.py index d79fb549c9..4de3bca71f 100644 --- a/var/spack/repos/builtin/packages/py-pycrypto/package.py +++ b/var/spack/repos/builtin/packages/py-pycrypto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pycuda/package.py b/var/spack/repos/builtin/packages/py-pycuda/package.py index b67b7397b4..a5f2153d9d 100644 --- a/var/spack/repos/builtin/packages/py-pycuda/package.py +++ b/var/spack/repos/builtin/packages/py-pycuda/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pycurl/package.py b/var/spack/repos/builtin/packages/py-pycurl/package.py index fa8c22fd79..ba23c5238a 100644 --- a/var/spack/repos/builtin/packages/py-pycurl/package.py +++ b/var/spack/repos/builtin/packages/py-pycurl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pydatalog/package.py b/var/spack/repos/builtin/packages/py-pydatalog/package.py index 398baf3113..41b6a26993 100644 --- a/var/spack/repos/builtin/packages/py-pydatalog/package.py +++ b/var/spack/repos/builtin/packages/py-pydatalog/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pydispatcher/package.py b/var/spack/repos/builtin/packages/py-pydispatcher/package.py index 77eaf09aca..8cb0218bd9 100644 --- a/var/spack/repos/builtin/packages/py-pydispatcher/package.py +++ b/var/spack/repos/builtin/packages/py-pydispatcher/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pydot/package.py b/var/spack/repos/builtin/packages/py-pydot/package.py index 8f42147fe1..a9989cdeab 100644 --- a/var/spack/repos/builtin/packages/py-pydot/package.py +++ b/var/spack/repos/builtin/packages/py-pydot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pydot2/package.py b/var/spack/repos/builtin/packages/py-pydot2/package.py index 483e3fe690..9894d47659 100644 --- a/var/spack/repos/builtin/packages/py-pydot2/package.py +++ b/var/spack/repos/builtin/packages/py-pydot2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pydotplus/package.py b/var/spack/repos/builtin/packages/py-pydotplus/package.py index 6cdfae682c..07370cbc1c 100644 --- a/var/spack/repos/builtin/packages/py-pydotplus/package.py +++ b/var/spack/repos/builtin/packages/py-pydotplus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pydv/package.py b/var/spack/repos/builtin/packages/py-pydv/package.py index 2da0b177f5..147b6374a6 100644 --- a/var/spack/repos/builtin/packages/py-pydv/package.py +++ b/var/spack/repos/builtin/packages/py-pydv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyelftools/package.py b/var/spack/repos/builtin/packages/py-pyelftools/package.py index e9a02af8e4..a69d0a2e7e 100644 --- a/var/spack/repos/builtin/packages/py-pyelftools/package.py +++ b/var/spack/repos/builtin/packages/py-pyelftools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyepsg/package.py b/var/spack/repos/builtin/packages/py-pyepsg/package.py index bdcc59d171..2b0ecd21a4 100644 --- a/var/spack/repos/builtin/packages/py-pyepsg/package.py +++ b/var/spack/repos/builtin/packages/py-pyepsg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyfaidx/package.py b/var/spack/repos/builtin/packages/py-pyfaidx/package.py index 75d39166ea..22740a4f83 100644 --- a/var/spack/repos/builtin/packages/py-pyfaidx/package.py +++ b/var/spack/repos/builtin/packages/py-pyfaidx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyfasta/package.py b/var/spack/repos/builtin/packages/py-pyfasta/package.py index eafd6777fd..961bc0f75e 100644 --- a/var/spack/repos/builtin/packages/py-pyfasta/package.py +++ b/var/spack/repos/builtin/packages/py-pyfasta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyfftw/package.py b/var/spack/repos/builtin/packages/py-pyfftw/package.py index 98e0cbc30c..f021516857 100644 --- a/var/spack/repos/builtin/packages/py-pyfftw/package.py +++ b/var/spack/repos/builtin/packages/py-pyfftw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyflakes/package.py b/var/spack/repos/builtin/packages/py-pyflakes/package.py index 4176626812..156db2f0da 100644 --- a/var/spack/repos/builtin/packages/py-pyflakes/package.py +++ b/var/spack/repos/builtin/packages/py-pyflakes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pygdal/package.py b/var/spack/repos/builtin/packages/py-pygdal/package.py index 356ea54e0d..2374e9cb19 100644 --- a/var/spack/repos/builtin/packages/py-pygdal/package.py +++ b/var/spack/repos/builtin/packages/py-pygdal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,6 +22,8 @@ class PyPygdal(PythonPackage): version('3.0.1.5', sha256='1222f69fe5e6b632d0d2a42d3acb8fac80fb4577c05e01969d8cd5548192ccaa') version('2.4.2.5', sha256='73386683c0b10ab43b6d64257fca2ba812f53ec61b268de8811565fd9ae9bacd') + version('2.4.1.6', sha256='5d1af98ad09f59e34e3b332cf20630b532b33c7120295aaaabbccebf58a11aa4') + version('2.4.0.6', sha256='728d11f3ecae0cd3493cd27dab599a0b6184f5504cc172d49400d88ea2b24a9c') version('1.11.5.3', sha256='746d13b73a284446a1b604772f869789eabfe6e69dee463f537da27845b29fa7') version('1.11.4.3', sha256='99d4b0c94d57ae50592924faaa65cc6a0c0892d83764e9f24ef9270c3a4b111a') @@ -29,5 +31,7 @@ class PyPygdal(PythonPackage): depends_on('py-numpy@1.0.0:', type=('build', 'run')) depends_on('gdal@3.0.1', type=('build', 'link', 'run'), when='@3.0.1.5') depends_on('gdal@2.4.2', type=('build', 'link', 'run'), when='@2.4.2.5') + depends_on('gdal@2.4.1', type=('build', 'link', 'run'), when='@2.4.1.6') + depends_on('gdal@2.4.0', type=('build', 'link', 'run'), when='@2.4.0.6') depends_on('gdal@1.11.5', type=('build', 'link', 'run'), when='@1.11.5.3') depends_on('gdal@1.11.4', type=('build', 'link', 'run'), when='@1.11.4.3') diff --git a/var/spack/repos/builtin/packages/py-pygdbmi/package.py b/var/spack/repos/builtin/packages/py-pygdbmi/package.py index cb7d59bfd0..98f45a564d 100644 --- a/var/spack/repos/builtin/packages/py-pygdbmi/package.py +++ b/var/spack/repos/builtin/packages/py-pygdbmi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-git2/package.py b/var/spack/repos/builtin/packages/py-pygit2/package.py index a4c6404ef1..b90652fa33 100644 --- a/var/spack/repos/builtin/packages/py-git2/package.py +++ b/var/spack/repos/builtin/packages/py-pygit2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PyGit2(PythonPackage): +class PyPygit2(PythonPackage): """Pygit2 is a set of Python bindings to the libgit2 shared library, libgit2 implements the core of Git. """ @@ -24,8 +24,8 @@ class PyGit2(PythonPackage): depends_on('py-six', type=('build', 'run')) depends_on('py-cffi', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec # http://www.pygit2.org/install.html - spack_env.set('LIBGIT2', spec['libgit2'].prefix) - spack_env.set('LIBGIT2_LIB', spec['libgit2'].prefix.lib) + env.set('LIBGIT2', spec['libgit2'].prefix) + env.set('LIBGIT2_LIB', spec['libgit2'].prefix.lib) diff --git a/var/spack/repos/builtin/packages/py-pyglet/package.py b/var/spack/repos/builtin/packages/py-pyglet/package.py index 2266726ade..ff01b7f2d6 100644 --- a/var/spack/repos/builtin/packages/py-pyglet/package.py +++ b/var/spack/repos/builtin/packages/py-pyglet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pygments/package.py b/var/spack/repos/builtin/packages/py-pygments/package.py index 3391dbec81..c5da704ac0 100644 --- a/var/spack/repos/builtin/packages/py-pygments/package.py +++ b/var/spack/repos/builtin/packages/py-pygments/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pygobject/package.py b/var/spack/repos/builtin/packages/py-pygobject/package.py index 2bcfbc22b3..66dcb74371 100644 --- a/var/spack/repos/builtin/packages/py-pygobject/package.py +++ b/var/spack/repos/builtin/packages/py-pygobject/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pygpu/package.py b/var/spack/repos/builtin/packages/py-pygpu/package.py index 3675482b08..49dc42eede 100644 --- a/var/spack/repos/builtin/packages/py-pygpu/package.py +++ b/var/spack/repos/builtin/packages/py-pygpu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,4 +28,4 @@ class PyPygpu(PythonPackage): depends_on('py-nose', type=('build', 'run')) depends_on('py-numpy', type=('build', 'run')) depends_on('py-mako', type=('build', 'run')) - depends_on('libcheck') + depends_on('check') diff --git a/var/spack/repos/builtin/packages/py-pygresql/package.py b/var/spack/repos/builtin/packages/py-pygresql/package.py index 9a532cb47c..9db0bc7d20 100644 --- a/var/spack/repos/builtin/packages/py-pygresql/package.py +++ b/var/spack/repos/builtin/packages/py-pygresql/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pygtk/package.py b/var/spack/repos/builtin/packages/py-pygtk/package.py index a94d19f1e1..661661a39e 100644 --- a/var/spack/repos/builtin/packages/py-pygtk/package.py +++ b/var/spack/repos/builtin/packages/py-pygtk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyinstrument-cext/package.py b/var/spack/repos/builtin/packages/py-pyinstrument-cext/package.py new file mode 100644 index 0000000000..4eb2f799c1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pyinstrument-cext/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPyinstrumentCext(PythonPackage): + """A CPython extension supporting pyinstrument.""" + + homepage = "https://github.com/joerick/pyinstrument_cext" + url = "https://pypi.io/packages/source/p/pyinstrument_cext/pyinstrument_cext-0.2.2.tar.gz" + + version('0.2.2', sha256='f29e25f71d74c0415ca9310e5567fff0f5d29f4240a09a885abf8b0eed71cc5b') + + depends_on('py-setuptools', type='build') + depends_on('py-nose', type='test') diff --git a/var/spack/repos/builtin/packages/py-pyinstrument/package.py b/var/spack/repos/builtin/packages/py-pyinstrument/package.py new file mode 100644 index 0000000000..5f8cc15286 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pyinstrument/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPyinstrument(PythonPackage): + """Call stack profiler for Python. Shows you why your code is slow!""" + + homepage = "https://github.com/joerick/pyinstrument" + url = "https://github.com/joerick/pyinstrument/archive/v3.1.0.tar.gz" + + version('3.1.0', sha256='02319607daf65110e246085f5e2ee111f565f213eed1991229f2d58e9a7657a5') + + depends_on('py-setuptools', type='build') + depends_on('py-pytest-runner', type='build') + depends_on('npm', type='build') + depends_on('py-pyinstrument-cext@0.2.2:', type=('build', 'run')) + depends_on('py-pytest', type='test') diff --git a/var/spack/repos/builtin/packages/py-pyjwt/package.py b/var/spack/repos/builtin/packages/py-pyjwt/package.py index eaa8babb53..70ee8da737 100644 --- a/var/spack/repos/builtin/packages/py-pyjwt/package.py +++ b/var/spack/repos/builtin/packages/py-pyjwt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyke/package.py b/var/spack/repos/builtin/packages/py-pyke/package.py index e003dbc981..634e109e20 100644 --- a/var/spack/repos/builtin/packages/py-pyke/package.py +++ b/var/spack/repos/builtin/packages/py-pyke/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,8 +13,8 @@ class PyPyke(PythonPackage): """ homepage = "http://sourceforge.net/projects/pyke" - url = "https://downloads.sourceforge.net/pyke/pyke3-1.1.1.zip" + url = "https://sourceforge.net/projects/pyke/files/pyke/1.1.1/pyke-1.1.1.zip" - version('1.1.1', sha256='b877b390e70a2eacc01d97c3a992fde947276afc2798ca3ac6c6f74c796cb6dc') + version('1.1.1', sha256='b0b294f435c6e6d2d4a80badf57d92cb66814dfe21e644a521901209e6a3f8ae') - depends_on('python@3:') + depends_on('python@3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pykml/package.py b/var/spack/repos/builtin/packages/py-pykml/package.py index 1729813317..bfa1359ebf 100644 --- a/var/spack/repos/builtin/packages/py-pykml/package.py +++ b/var/spack/repos/builtin/packages/py-pykml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pykwalify/package.py b/var/spack/repos/builtin/packages/py-pykwalify/package.py index ceb4a815cd..0ab872d561 100644 --- a/var/spack/repos/builtin/packages/py-pykwalify/package.py +++ b/var/spack/repos/builtin/packages/py-pykwalify/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyliblzma/package.py b/var/spack/repos/builtin/packages/py-pyliblzma/package.py index 0d1af1c864..5630768af5 100644 --- a/var/spack/repos/builtin/packages/py-pyliblzma/package.py +++ b/var/spack/repos/builtin/packages/py-pyliblzma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pylint/package.py b/var/spack/repos/builtin/packages/py-pylint/package.py index 01e14ba11e..37ac870657 100644 --- a/var/spack/repos/builtin/packages/py-pylint/package.py +++ b/var/spack/repos/builtin/packages/py-pylint/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pymatgen/package.py b/var/spack/repos/builtin/packages/py-pymatgen/package.py index 78c62422f0..5da5c1bee3 100644 --- a/var/spack/repos/builtin/packages/py-pymatgen/package.py +++ b/var/spack/repos/builtin/packages/py-pymatgen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pymeeus/package.py b/var/spack/repos/builtin/packages/py-pymeeus/package.py new file mode 100644 index 0000000000..7dc522bd51 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pymeeus/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPymeeus(PythonPackage): + """Library of astronomical algorithms in Python.""" + + homepage = "https://github.com/architest/pymeeus" + url = "https://pypi.io/packages/source/P/PyMeeus/PyMeeus-0.3.6.tar.gz" + + version('0.3.6', sha256='1f1ba0682e1b5c6b0cd6432c966e8bc8acc31737ea6f0ae79917a2189a98bb87') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyminifier/package.py b/var/spack/repos/builtin/packages/py-pyminifier/package.py index dd83e74421..edff48c36c 100644 --- a/var/spack/repos/builtin/packages/py-pyminifier/package.py +++ b/var/spack/repos/builtin/packages/py-pyminifier/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pymol/package.py b/var/spack/repos/builtin/packages/py-pymol/package.py index c85f380d24..158985aaeb 100644 --- a/var/spack/repos/builtin/packages/py-pymol/package.py +++ b/var/spack/repos/builtin/packages/py-pymol/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,20 +13,19 @@ class PyPymol(PythonPackage): movies. Open Source PyMOL is free to everyone!""" homepage = "https://pymol.org" - url = "https://sourceforge.net/projects/pymol/files/pymol/2/pymol-v2.1.0.tar.bz2" + url = "https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz" - version('2.1.0', sha256='7ae8ebb899533d691a67c1ec731b00518dea456ab3e258aa052a65c24b63eae2') + version('2.3.0', sha256='62aa21fafd1db805c876f89466e47513809f8198395e1f00a5f5cc40d6f40ed0') depends_on('python+tkinter', type=('build', 'run')) - depends_on('tcl') - depends_on('tk') - depends_on('py-pmw') - depends_on('gl') - depends_on('glu') + depends_on('freetype', type=('build', 'run')) depends_on('glew') - depends_on('libpng') - depends_on('freetype') - depends_on('libxml2') - depends_on('msgpack-c') - depends_on('py-pyqt4', type=('build', 'run')) - depends_on('freeglut') + depends_on('glm') + depends_on('freeglut', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('tcsh', type=('build', 'run')) + depends_on('py-pyqt5', type=('build', 'run')) + depends_on('py-pmw', type=('build', 'run')) + + depends_on('libmmtf-cpp', type=('build')) + depends_on('msgpack-c', type=('build')) diff --git a/var/spack/repos/builtin/packages/py-pymongo/package.py b/var/spack/repos/builtin/packages/py-pymongo/package.py index 8e28001e4c..41e13d305f 100644 --- a/var/spack/repos/builtin/packages/py-pymongo/package.py +++ b/var/spack/repos/builtin/packages/py-pymongo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,6 +19,8 @@ class PyPymongo(PythonPackage): url = "https://pypi.io/packages/source/p/pymongo/pymongo-3.9.0.tar.gz" version('3.9.0', sha256='4249c6ba45587b959292a727532826c5032d59171f923f7f823788f413c2a5a3') + version('3.6.0', sha256='c6de26d1e171cdc449745b82f1addbc873d105b8e7335097da991c0fc664a4a8') + version('3.3.0', sha256='3d45302fc2622fabf34356ba274c69df41285bac71bbd229f1587283b851b91e') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pymorph/package.py b/var/spack/repos/builtin/packages/py-pymorph/package.py index 40702c48e3..5ef91f7f3f 100644 --- a/var/spack/repos/builtin/packages/py-pymorph/package.py +++ b/var/spack/repos/builtin/packages/py-pymorph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pympler/package.py b/var/spack/repos/builtin/packages/py-pympler/package.py index c525133a8f..0aa7d03986 100644 --- a/var/spack/repos/builtin/packages/py-pympler/package.py +++ b/var/spack/repos/builtin/packages/py-pympler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pymysql/package.py b/var/spack/repos/builtin/packages/py-pymysql/package.py index 282229289d..96f23fa088 100644 --- a/var/spack/repos/builtin/packages/py-pymysql/package.py +++ b/var/spack/repos/builtin/packages/py-pymysql/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pynio/package.py b/var/spack/repos/builtin/packages/py-pynio/package.py index d6d4076554..3f24c7165f 100644 --- a/var/spack/repos/builtin/packages/py-pynio/package.py +++ b/var/spack/repos/builtin/packages/py-pynio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,7 +27,7 @@ class PyPynio(PythonPackage): # Spack does not currently have netcdf below 4.x, and 3.x is a # fundamentally different format. So, currently this is only providing # support for netcdf4. - depends_on('netcdf@3.6.0:') + depends_on('netcdf-c@3.6.0:') # Turning on the hdf (i.e. hdf4) dependency causes it not to build, with # compile errors that (weirdly) relate to the declarations of HDF5. @@ -50,22 +50,22 @@ class PyPynio(PythonPackage): depends_on('py-numpy', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): """ These environment variables are how the setup.py knows which options to turn on, and how to find them. """ - spack_env.set('F2CLIBS', 'gfortran') - spack_env.set('HAS_NETCDF4', '1') - spack_env.set('NETCDF4_PREFIX', self.spec['netcdf'].prefix) + env.set('F2CLIBS', 'gfortran') + env.set('HAS_NETCDF4', '1') + env.set('NETCDF4_PREFIX', self.spec['netcdf-c'].prefix) if '+hdf5' in self.spec: - spack_env.set('HAS_HDF5', '1') - spack_env.set('HDF5_PREFIX', self.spec['hdf5'].prefix) + env.set('HAS_HDF5', '1') + env.set('HDF5_PREFIX', self.spec['hdf5'].prefix) if '+gdal' in self.spec: - spack_env.set('HAS_GDAL', '1') - spack_env.set('GDAL_PREFIX', self.spec['gdal'].prefix) + env.set('HAS_GDAL', '1') + env.set('GDAL_PREFIX', self.spec['gdal'].prefix) # This one is trouble - see comments above. # if '+hdf4' in self.spec: -# spack_env.set('HAS_HDF4', '1') -# spack_env.set('HDF4_PREFIX', self.spec['hdf'].prefix) +# env.set('HAS_HDF4', '1') +# env.set('HDF4_PREFIX', self.spec['hdf'].prefix) diff --git a/var/spack/repos/builtin/packages/py-pynn/package.py b/var/spack/repos/builtin/packages/py-pynn/package.py index 4e09d56dbd..12304f9c9c 100644 --- a/var/spack/repos/builtin/packages/py-pynn/package.py +++ b/var/spack/repos/builtin/packages/py-pynn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyodbc/package.py b/var/spack/repos/builtin/packages/py-pyodbc/package.py index 473000c471..68a83caf2c 100644 --- a/var/spack/repos/builtin/packages/py-pyodbc/package.py +++ b/var/spack/repos/builtin/packages/py-pyodbc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyomo/package.py b/var/spack/repos/builtin/packages/py-pyomo/package.py index c39491f633..c56f5b9d77 100644 --- a/var/spack/repos/builtin/packages/py-pyomo/package.py +++ b/var/spack/repos/builtin/packages/py-pyomo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyopenssl/package.py b/var/spack/repos/builtin/packages/py-pyopenssl/package.py index c829e00852..70e0c86c72 100644 --- a/var/spack/repos/builtin/packages/py-pyopenssl/package.py +++ b/var/spack/repos/builtin/packages/py-pyopenssl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pypar/package.py b/var/spack/repos/builtin/packages/py-pypar/package.py index 6cd04aca09..b8ead69dbb 100644 --- a/var/spack/repos/builtin/packages/py-pypar/package.py +++ b/var/spack/repos/builtin/packages/py-pypar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyparsing/package.py b/var/spack/repos/builtin/packages/py-pyparsing/package.py index cdf415e3b2..009831901d 100644 --- a/var/spack/repos/builtin/packages/py-pyparsing/package.py +++ b/var/spack/repos/builtin/packages/py-pyparsing/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pypeflow/package.py b/var/spack/repos/builtin/packages/py-pypeflow/package.py index 0f2167cd9e..225ad550fa 100644 --- a/var/spack/repos/builtin/packages/py-pypeflow/package.py +++ b/var/spack/repos/builtin/packages/py-pypeflow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyperclip/package.py b/var/spack/repos/builtin/packages/py-pyperclip/package.py index 98853bef11..441f5fca3a 100644 --- a/var/spack/repos/builtin/packages/py-pyperclip/package.py +++ b/var/spack/repos/builtin/packages/py-pyperclip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-perf/package.py b/var/spack/repos/builtin/packages/py-pyperf/package.py index 2d2c025691..435e1d8255 100644 --- a/var/spack/repos/builtin/packages/py-perf/package.py +++ b/var/spack/repos/builtin/packages/py-pyperf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PyPerf(PythonPackage): +class PyPyperf(PythonPackage): """The Python perf module is a toolkit to write, run and analyze benchmarks. """ @@ -14,6 +14,8 @@ class PyPerf(PythonPackage): homepage = "https://pypi.python.org/pypi/pyperf" url = "https://github.com/vstinner/pyperf/archive/1.5.1.tar.gz" + version('1.6.1', sha256='fbe793f6f2e036ab4dcca105b5c5aa34fd331dd881e7a3e158e5e218c63cfc32') + version('1.6.0', sha256='7af7b9cfd9d26548ab7127f8e51791357ecd78cda46aad5b2d9664a70fc58878') version('1.5.1', sha256='9c271862bc2911be8eb01031a4a86cbc3f5bb615971514383802d3dcf46f18ed') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyprof2html/package.py b/var/spack/repos/builtin/packages/py-pyprof2html/package.py index 4d33e96d31..1ed3728834 100644 --- a/var/spack/repos/builtin/packages/py-pyprof2html/package.py +++ b/var/spack/repos/builtin/packages/py-pyprof2html/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyproj/package.py b/var/spack/repos/builtin/packages/py-pyproj/package.py index 143cf0f39b..8c66ff3aca 100644 --- a/var/spack/repos/builtin/packages/py-pyproj/package.py +++ b/var/spack/repos/builtin/packages/py-pyproj/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,5 +30,5 @@ class PyPyproj(PythonPackage): depends_on('proj@6.1:', when='@2.2:') depends_on('proj@6.0:', when='@2.0:') - def setup_environment(self, spack_env, run_env): - spack_env.set('PROJ_DIR', self.spec['proj'].prefix) + def setup_build_environment(self, env): + env.set('PROJ_DIR', self.spec['proj'].prefix) diff --git a/var/spack/repos/builtin/packages/py-pyqi/package.py b/var/spack/repos/builtin/packages/py-pyqi/package.py index 2b4b7ce36c..9cca0d591b 100644 --- a/var/spack/repos/builtin/packages/py-pyqi/package.py +++ b/var/spack/repos/builtin/packages/py-pyqi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyqt4/package.py b/var/spack/repos/builtin/packages/py-pyqt4/package.py index b13eaba22b..c0e3ae1085 100644 --- a/var/spack/repos/builtin/packages/py-pyqt4/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt4/package.py @@ -1,9 +1,10 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import os class PyPyqt4(SIPPackage): @@ -28,16 +29,73 @@ class PyPyqt4(SIPPackage): version('4.11.3', sha256='853780dcdbe2e6ba785d703d059b096e1fc49369d3e8d41a060be874b8745686', url='http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-4.11.3/PyQt-x11-gpl-4.11.3.tar.gz') + variant('qsci', default=False, description='Build with QScintilla python bindings') + # Supposedly can also be built with Qt 5 compatibility layer depends_on('qt@:4') + depends_on('qscintilla', when='+qsci') + + # For building Qscintilla python bindings + resource(name='qscintilla', + url='https://www.riverbankcomputing.com/static/Downloads/QScintilla/2.10.2/QScintilla_gpl-2.10.2.tar.gz', + sha256='14b31d20717eed95ea9bea4cd16e5e1b72cee7ebac647cba878e0f6db6a65ed0', + destination='spack-resource-qscintilla', + when='^qscintilla@2.10.2' + ) # https://www.riverbankcomputing.com/static/Docs/PyQt4/installation.html def configure_file(self): return 'configure-ng.py' def configure_args(self): - return [ + args = [ '--pyuic4-interpreter', self.spec['python'].command.path, '--sipdir', self.prefix.share.sip.PyQt4, - '--stubsdir', join_path(site_packages_dir, 'PyQt4'), + '--stubsdir', join_path(site_packages_dir, 'PyQt4') ] + if '+qsci' in self.spec: + args.extend(['--qsci-api-destdir', self.prefix.share.qsci]) + return args + + @run_after('install') + def make_qsci(self): + if '+qsci' in self.spec: + rsrc_py_path = os.path.join( + self.stage.source_path, + 'spack-resource-qscintilla/QScintilla_gpl-' + + str(self.spec['qscintilla'].version), 'Python') + with working_dir(rsrc_py_path): + pydir = join_path(site_packages_dir, 'PyQt4') + python = self.spec['python'].command + python('configure.py', + '--sip=' + self.prefix.bin.sip, + '--qsci-incdir=' + + self.spec['qscintilla'].prefix.include, + '--qsci-libdir=' + self.spec['qscintilla'].prefix.lib, + '--qsci-sipdir=' + self.prefix.share.sip.PyQt4, + '--apidir=' + self.prefix.share.qsci, + '--destdir=' + pydir, + '--pyqt-sipdir=' + self.prefix.share.sip.PyQt4, + '--sip-incdir=' + python_include_dir, + '--stubsdir=' + pydir) + + # Fix build errors + # "QAbstractScrollArea: No such file or directory" + # "qprinter.h: No such file or directory" + # ".../Qsci.so: undefined symbol: _ZTI10Qsci...." + qscipro = FileFilter('Qsci/Qsci.pro') + link_qscilibs = 'LIBS += -L' + self.prefix.lib +\ + ' -lqscintilla2_qt4' + qscipro.filter('TEMPLATE = lib', + 'TEMPLATE = lib\nQT += widgets' + + '\nQT += printsupport\n' + link_qscilibs) + + make() + + # Fix installation prefixes + makefile = FileFilter('Makefile') + makefile.filter(r'\$\(INSTALL_ROOT\)', '') + makefile = FileFilter('Qsci/Makefile') + makefile.filter(r'\$\(INSTALL_ROOT\)', '') + + make('install') diff --git a/var/spack/repos/builtin/packages/py-pyqt5/package.py b/var/spack/repos/builtin/packages/py-pyqt5/package.py index 0ec76b16c9..b186a13ad2 100644 --- a/var/spack/repos/builtin/packages/py-pyqt5/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt5/package.py @@ -1,9 +1,10 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import os class PyPyqt5(SIPPackage): @@ -27,16 +28,74 @@ class PyPyqt5(SIPPackage): version('5.13.0', sha256='0cdbffe5135926527b61cc3692dd301cd0328dd87eeaf1313e610787c46faff9') + variant('qsci', default=False, description='Build with QScintilla python bindings') + # Without opengl support, I got the following error: # sip: QOpenGLFramebufferObject is undefined depends_on('qt@5:+opengl') depends_on('python@2.6:', type=('build', 'run')) depends_on('py-enum34', type=('build', 'run'), when='^python@:3.3') + depends_on('qscintilla', when='+qsci') + + # For building Qscintilla python bindings + resource(name='qscintilla', + url='https://www.riverbankcomputing.com/static/Downloads/QScintilla/2.10.2/QScintilla_gpl-2.10.2.tar.gz', + sha256='14b31d20717eed95ea9bea4cd16e5e1b72cee7ebac647cba878e0f6db6a65ed0', + destination='spack-resource-qscintilla', + when='^qscintilla@2.10.2' + ) + # https://www.riverbankcomputing.com/static/Docs/PyQt5/installation.html def configure_args(self): - return [ + args = [ '--pyuic5-interpreter', self.spec['python'].command.path, '--sipdir', self.prefix.share.sip.PyQt5, '--stubsdir', join_path(site_packages_dir, 'PyQt5'), ] + if '+qsci' in self.spec: + args.extend(['--qsci-api-destdir', self.prefix.share.qsci]) + return args + + @run_after('install') + def make_qsci(self): + if '+qsci' in self.spec: + rsrc_py_path = os.path.join( + self.stage.source_path, + 'spack-resource-qscintilla/QScintilla_gpl-' + + str(self.spec['qscintilla'].version), 'Python') + with working_dir(rsrc_py_path): + pydir = join_path(site_packages_dir, 'PyQt5') + python = self.spec['python'].command + python('configure.py', '--pyqt=PyQt5', + '--sip=' + self.prefix.bin.sip, + '--qsci-incdir=' + + self.spec['qscintilla'].prefix.include, + '--qsci-libdir=' + self.spec['qscintilla'].prefix.lib, + '--qsci-sipdir=' + self.prefix.share.sip.PyQt5, + '--apidir=' + self.prefix.share.qsci, + '--destdir=' + pydir, + '--pyqt-sipdir=' + self.prefix.share.sip.PyQt5, + '--sip-incdir=' + python_include_dir, + '--stubsdir=' + pydir) + + # Fix build errors + # "QAbstractScrollArea: No such file or directory" + # "qprinter.h: No such file or directory" + # ".../Qsci.so: undefined symbol: _ZTI10Qsci...." + qscipro = FileFilter('Qsci/Qsci.pro') + link_qscilibs = 'LIBS += -L' + self.prefix.lib +\ + ' -lqscintilla2_qt5' + qscipro.filter('TEMPLATE = lib', + 'TEMPLATE = lib\nQT += widgets' + + '\nQT += printsupport\n' + link_qscilibs) + + make() + + # Fix installation prefixes + makefile = FileFilter('Makefile') + makefile.filter(r'\$\(INSTALL_ROOT\)', '') + makefile = FileFilter('Qsci/Makefile') + makefile.filter(r'\$\(INSTALL_ROOT\)', '') + + make('install') diff --git a/var/spack/repos/builtin/packages/py-pyrad/package.py b/var/spack/repos/builtin/packages/py-pyrad/package.py index 6ecbd7c4d7..cb16b4296d 100644 --- a/var/spack/repos/builtin/packages/py-pyrad/package.py +++ b/var/spack/repos/builtin/packages/py-pyrad/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyrosar/package.py b/var/spack/repos/builtin/packages/py-pyrosar/package.py index 0c62dc7bd0..b0af64b270 100644 --- a/var/spack/repos/builtin/packages/py-pyrosar/package.py +++ b/var/spack/repos/builtin/packages/py-pyrosar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pysam/package.py b/var/spack/repos/builtin/packages/py-pysam/package.py index 1cac32702a..38a2a26b40 100644 --- a/var/spack/repos/builtin/packages/py-pysam/package.py +++ b/var/spack/repos/builtin/packages/py-pysam/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyscaf/package.py b/var/spack/repos/builtin/packages/py-pyscaf/package.py index a64f870e94..53a9adfc56 100644 --- a/var/spack/repos/builtin/packages/py-pyscaf/package.py +++ b/var/spack/repos/builtin/packages/py-pyscaf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyserial/package.py b/var/spack/repos/builtin/packages/py-pyserial/package.py index e5074b0e19..07534b8c6b 100644 --- a/var/spack/repos/builtin/packages/py-pyserial/package.py +++ b/var/spack/repos/builtin/packages/py-pyserial/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyshp/package.py b/var/spack/repos/builtin/packages/py-pyshp/package.py index 20bc7e2545..c4374c8f0e 100644 --- a/var/spack/repos/builtin/packages/py-pyshp/package.py +++ b/var/spack/repos/builtin/packages/py-pyshp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyside/package.py b/var/spack/repos/builtin/packages/py-pyside/package.py index bd4f622d9b..f6c86506c1 100644 --- a/var/spack/repos/builtin/packages/py-pyside/package.py +++ b/var/spack/repos/builtin/packages/py-pyside/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -42,6 +42,17 @@ class PyPyside(PythonPackage): rpath.append(os.path.join( self.prefix, pypkg.site_packages_dir, 'PySide')) + # Fix subprocess.mswindows check for Python 3.5 + # https://github.com/pyside/pyside-setup/pull/55 + filter_file( + '^if subprocess.mswindows:', + 'mswindows = (sys.platform == "win32")\r\nif mswindows:', + "popenasync.py") + filter_file( + '^ if subprocess.mswindows:', + ' if mswindows:', + "popenasync.py") + # Add Spack's standard CMake args to the sub-builds. # They're called BY setup.py so we have to patch it. filter_file( diff --git a/var/spack/repos/builtin/packages/py-pyside2/package.py b/var/spack/repos/builtin/packages/py-pyside2/package.py new file mode 100644 index 0000000000..69828029bf --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pyside2/package.py @@ -0,0 +1,53 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPyside2(PythonPackage): + """Python bindings for Qt.""" + homepage = "https://pypi.org/project/PySide2/" + url = "https://code.qt.io/pyside/pyside-setup.git" + git = "https://code.qt.io/pyside/pyside-setup.git" + + # More recent versions of PySide2 (for Qt5) have been taken under + # the offical Qt umbrella. For more information, see: + # http://wiki.qt.io/Qt_for_Python_Development_Getting_Started + + version('develop', tag='dev') + version('5.13.2', tag='v5.13.2', submodules=True) + version('5.13.1', tag='v5.13.1', submodules=True) + version('5.13.0', tag='v5.13.0', submodules=True) + version('5.12.5', tag='v5.12.5', submodules=True) + + variant('doc', default=False, description='Enables the generation of html and man page documentation') + + depends_on('python@2.7:2.7.99,3.5.0:3.5.99,3.6.1:', type=('build', 'run')) + + depends_on('cmake@3.1:', type='build') + depends_on('llvm@6:', type='build') + depends_on('py-setuptools', type='build') + depends_on('py-wheel', type='build') + depends_on('qt@5.11:+opengl', type=('build', 'run')) + + depends_on('graphviz', when='+doc', type='build') + depends_on('libxml2@2.6.32:', when='+doc', type='build') + depends_on('libxslt@1.1.19:', when='+doc', type='build') + depends_on('py-sphinx', when='+doc', type='build') + + def build_args(self, spec, prefix): + args = [ + '--parallel={0}'.format(make_jobs), + '--ignore-git', + '--qmake={0}'.format(spec['qt'].prefix.bin.qmake) + ] + if self.run_tests: + args.append('--build-tests') + return args + + @run_after('build') + def build_docs(self): + if '+doc' in self.spec: + make('apidoc') diff --git a/var/spack/repos/builtin/packages/py-pysmartdl/package.py b/var/spack/repos/builtin/packages/py-pysmartdl/package.py index 032dc0cbbb..16ba79f983 100644 --- a/var/spack/repos/builtin/packages/py-pysmartdl/package.py +++ b/var/spack/repos/builtin/packages/py-pysmartdl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pysocks/package.py b/var/spack/repos/builtin/packages/py-pysocks/package.py index 32e781b2c0..200902f536 100644 --- a/var/spack/repos/builtin/packages/py-pysocks/package.py +++ b/var/spack/repos/builtin/packages/py-pysocks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyspark/package.py b/var/spack/repos/builtin/packages/py-pyspark/package.py index 4aafdde2d7..15285d3c30 100644 --- a/var/spack/repos/builtin/packages/py-pyspark/package.py +++ b/var/spack/repos/builtin/packages/py-pyspark/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pysqlite/package.py b/var/spack/repos/builtin/packages/py-pysqlite/package.py index 48f41cedb9..a624f47dd6 100644 --- a/var/spack/repos/builtin/packages/py-pysqlite/package.py +++ b/var/spack/repos/builtin/packages/py-pysqlite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytailf/package.py b/var/spack/repos/builtin/packages/py-pytailf/package.py index 4d94fced0e..0b08866c12 100644 --- a/var/spack/repos/builtin/packages/py-pytailf/package.py +++ b/var/spack/repos/builtin/packages/py-pytailf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytest-cache/package.py b/var/spack/repos/builtin/packages/py-pytest-cache/package.py index 6094911d4f..c74cd44384 100644 --- a/var/spack/repos/builtin/packages/py-pytest-cache/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-cache/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,5 +17,5 @@ class PyPytestCache(PythonPackage): version('1.0', sha256='be7468edd4d3d83f1e844959fd6e3fd28e77a481440a7118d430130ea31b07a9') depends_on('py-setuptools', type='build') - depends_on('py-pytest@2.2.0:2.7.3', type=('build', 'run')) + depends_on('py-pytest@2.2:', type=('build', 'run')) depends_on('py-execnet@1.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pytest-cov/package.py b/var/spack/repos/builtin/packages/py-pytest-cov/package.py index 91a9d5be46..154547cda9 100644 --- a/var/spack/repos/builtin/packages/py-pytest-cov/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-cov/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytest-flake8/package.py b/var/spack/repos/builtin/packages/py-pytest-flake8/package.py index bdd6b9af89..108196f7cc 100644 --- a/var/spack/repos/builtin/packages/py-pytest-flake8/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-flake8/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytest-forked/package.py b/var/spack/repos/builtin/packages/py-pytest-forked/package.py index ac70de0148..9fe5556428 100644 --- a/var/spack/repos/builtin/packages/py-pytest-forked/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-forked/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py b/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py index 8d5cf50250..5e270bf4df 100644 --- a/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytest-isort/package.py b/var/spack/repos/builtin/packages/py-pytest-isort/package.py index e07fd1b80f..d55b9550e2 100644 --- a/var/spack/repos/builtin/packages/py-pytest-isort/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-isort/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytest-mock/package.py b/var/spack/repos/builtin/packages/py-pytest-mock/package.py index 32c89a10ba..e5a3240d99 100644 --- a/var/spack/repos/builtin/packages/py-pytest-mock/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-mock/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytest-mypy/package.py b/var/spack/repos/builtin/packages/py-pytest-mypy/package.py new file mode 100644 index 0000000000..1f7cc82af8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pytest-mypy/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPytestMypy(PythonPackage): + """Mypy static type checker plugin for Pytest.""" + + homepage = "https://github.com/dbader/pytest-mypy" + url = "https://pypi.io/packages/source/p/pytest-mypy/pytest-mypy-0.4.2.tar.gz" + + version('0.4.2', sha256='5a5338cecff17f005b181546a13e282761754b481225df37f33d37f86ac5b304') + + depends_on('python@3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-pytest@2.8:', when='^python@3.5:', type=('build', 'run')) + depends_on('py-pytest@2.8:4.6', when='^python@:3.4', type=('build', 'run')) + depends_on('py-mypy@0.500:0.699', when='^python@:3.4', type=('build', 'run')) + depends_on('py-mypy@0.500:', when='^python@3.5:3.7', type=('build', 'run')) + depends_on('py-mypy@0.700:', when='^python@3.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pytest-pep8/package.py b/var/spack/repos/builtin/packages/py-pytest-pep8/package.py new file mode 100644 index 0000000000..f365a172eb --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pytest-pep8/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPytestPep8(PythonPackage): + """pytest plugin for efficiently checking PEP8 compliance""" + + homepage = "https://bitbucket.org/pytest-dev/pytest-pep8" + url = "https://pypi.io/packages/source/p/pytest-pep8/pytest-pep8-1.0.6.tar.gz" + + import_modules = ['pytest_pep8'] + + version('1.0.6', sha256='032ef7e5fa3ac30f4458c73e05bb67b0f036a8a5cb418a534b3170f89f120318') + + depends_on('py-setuptools', type='build') + depends_on('py-pytest-cache', type=('build', 'run')) + depends_on('py-pytest@2.4.2:', type=('build', 'run')) + depends_on('py-pep8@1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pytest-runner/package.py b/var/spack/repos/builtin/packages/py-pytest-runner/package.py index 415efa0703..d3337bcac9 100644 --- a/var/spack/repos/builtin/packages/py-pytest-runner/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-runner/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytest-xdist/package.py b/var/spack/repos/builtin/packages/py-pytest-xdist/package.py index a35d8995e4..389d7c7689 100644 --- a/var/spack/repos/builtin/packages/py-pytest-xdist/package.py +++ b/var/spack/repos/builtin/packages/py-pytest-xdist/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,11 +13,18 @@ class PyPytestXdist(PythonPackage): url = "https://pypi.io/packages/source/p/pytest-xdist/pytest-xdist-1.30.0.tar.gz" version('1.30.0', sha256='5d1b1d4461518a6023d56dab62fb63670d6f7537f23e2708459a557329accf48') + version('1.29.0', sha256='3489d91516d7847db5eaecff7a2e623dba68984835dbe6cedb05ae126c4fb17f') + version('1.27.0', sha256='a96ed691705882560fa3fc95531fbd4c224896c827f4004817eb2dcac4ba41a2') + version('1.24.0', sha256='8e188d13ce6614c7a678179a76f46231199ffdfe6163de031c17e62ffa256917') + version('1.17.0', sha256='e7e48c111677af23078b1ed23501e493e12c4b6d91657f6884a64e4ce0f14144') version('1.16.0', sha256='42e5a1e5da9d7cff3e74b07f8692598382f95624f234ff7e00a3b1237e0feba2') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-execnet@1.1:', type=('build', 'run')) - depends_on('py-pytest@4.4.0:', type=('build', 'run')) - depends_on('py-pytest-forked', type=('build', 'run')) - depends_on('py-six', type=('build', 'run')) + depends_on('py-pytest@4.4.0:', type=('build', 'run'), when='@1.28.0:') + depends_on('py-pytest@3.6.0:', type=('build', 'run'), when='@1.25.0:1.27.0') + depends_on('py-pytest@3.0.0:', type=('build', 'run'), when='@1.18.0:1.24.0') + depends_on('py-pytest@2.7.0:', type=('build', 'run'), when='@1.16.0:1.17.0') + depends_on('py-pytest-forked', type=('build', 'run'), when='@1.19.0:') + depends_on('py-six', type=('build', 'run'), when='@1.23.0:') diff --git a/var/spack/repos/builtin/packages/py-pytest/package.py b/var/spack/repos/builtin/packages/py-pytest/package.py index 23c1877400..c59d0878ea 100644 --- a/var/spack/repos/builtin/packages/py-pytest/package.py +++ b/var/spack/repos/builtin/packages/py-pytest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pythia/package.py b/var/spack/repos/builtin/packages/py-pythia/package.py index 74ed43fcd6..721d7470fa 100644 --- a/var/spack/repos/builtin/packages/py-pythia/package.py +++ b/var/spack/repos/builtin/packages/py-pythia/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-daemon/package.py b/var/spack/repos/builtin/packages/py-python-daemon/package.py index 95f31f0109..6b70c03234 100644 --- a/var/spack/repos/builtin/packages/py-python-daemon/package.py +++ b/var/spack/repos/builtin/packages/py-python-daemon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-dateutil/package.py b/var/spack/repos/builtin/packages/py-python-dateutil/package.py index 397c4ae085..13e04b4e6e 100644 --- a/var/spack/repos/builtin/packages/py-python-dateutil/package.py +++ b/var/spack/repos/builtin/packages/py-python-dateutil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-editor/package.py b/var/spack/repos/builtin/packages/py-python-editor/package.py index 0a4fada91d..3db92f7a21 100644 --- a/var/spack/repos/builtin/packages/py-python-editor/package.py +++ b/var/spack/repos/builtin/packages/py-python-editor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-engineio/package.py b/var/spack/repos/builtin/packages/py-python-engineio/package.py index 1878e07381..3d6ccca57b 100644 --- a/var/spack/repos/builtin/packages/py-python-engineio/package.py +++ b/var/spack/repos/builtin/packages/py-python-engineio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-gitlab/package.py b/var/spack/repos/builtin/packages/py-python-gitlab/package.py index 50a6783b8d..e89b6e06d1 100644 --- a/var/spack/repos/builtin/packages/py-python-gitlab/package.py +++ b/var/spack/repos/builtin/packages/py-python-gitlab/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-igraph/package.py b/var/spack/repos/builtin/packages/py-python-igraph/package.py index e6f6ccdf20..88da5b0656 100644 --- a/var/spack/repos/builtin/packages/py-igraph/package.py +++ b/var/spack/repos/builtin/packages/py-python-igraph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PyIgraph(PythonPackage): +class PyPythonIgraph(PythonPackage): """igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use.""" diff --git a/var/spack/repos/builtin/packages/py-python-jenkins/package.py b/var/spack/repos/builtin/packages/py-python-jenkins/package.py index cc9836e5ef..601951c90e 100644 --- a/var/spack/repos/builtin/packages/py-python-jenkins/package.py +++ b/var/spack/repos/builtin/packages/py-python-jenkins/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-ldap/package.py b/var/spack/repos/builtin/packages/py-python-ldap/package.py index 002de856e0..e4f8cc1938 100644 --- a/var/spack/repos/builtin/packages/py-python-ldap/package.py +++ b/var/spack/repos/builtin/packages/py-python-ldap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-levenshtein/package.py b/var/spack/repos/builtin/packages/py-python-levenshtein/package.py index ec536420a0..5dc3a4305d 100644 --- a/var/spack/repos/builtin/packages/py-python-levenshtein/package.py +++ b/var/spack/repos/builtin/packages/py-python-levenshtein/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-logstash/package.py b/var/spack/repos/builtin/packages/py-python-logstash/package.py new file mode 100644 index 0000000000..5eb60590d2 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-python-logstash/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythonLogstash(PythonPackage): + """Python logging handler for Logstash.""" + + homepage = "https://github.com/vklochan/python-logstash" + url = "https://pypi.io/packages/source/p/python-logstash/python-logstash-0.4.6.tar.gz" + + version('0.4.6', sha256='10943e5df83f592b4d61b63ad1afff855ccc8c9467f78718f0a59809ba1fe68c') diff --git a/var/spack/repos/builtin/packages/py-python-magic/package.py b/var/spack/repos/builtin/packages/py-python-magic/package.py index 376d601f08..7fe5bab70c 100644 --- a/var/spack/repos/builtin/packages/py-python-magic/package.py +++ b/var/spack/repos/builtin/packages/py-python-magic/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-mapnik/package.py b/var/spack/repos/builtin/packages/py-python-mapnik/package.py index 6d1cf944b0..79e2bc41a6 100644 --- a/var/spack/repos/builtin/packages/py-python-mapnik/package.py +++ b/var/spack/repos/builtin/packages/py-python-mapnik/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,10 +20,12 @@ class PyPythonMapnik(PythonPackage): depends_on('py-setuptools', type='build') depends_on('mapnik', type=('build', 'link', 'run')) depends_on('boost +python+thread') + # py-pycairo is need by mapnik.printing + depends_on('py-pycairo', type=('build', 'run')) # Package can't find boost_python without the following - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Inform the package that boost python library is of form # 'libboost_python27.so' as opposed to 'libboost_python.so' py_ver = str(self.spec['python'].version.up_to(2).joined) - spack_env.set('BOOST_PYTHON_LIB', 'boost_python' + py_ver) + env.set('BOOST_PYTHON_LIB', 'boost_python' + py_ver) diff --git a/var/spack/repos/builtin/packages/py-meep/package.py b/var/spack/repos/builtin/packages/py-python-meep/package.py index 81a219145f..d7e50e8509 100644 --- a/var/spack/repos/builtin/packages/py-meep/package.py +++ b/var/spack/repos/builtin/packages/py-python-meep/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PyMeep(PythonPackage): +class PyPythonMeep(PythonPackage): """Python-meep is a wrapper around libmeep. It allows the scripting of Meep-simulations with Python""" diff --git a/var/spack/repos/builtin/packages/py-python-memcached/package.py b/var/spack/repos/builtin/packages/py-python-memcached/package.py index 13c14d38a6..9347aea117 100644 --- a/var/spack/repos/builtin/packages/py-python-memcached/package.py +++ b/var/spack/repos/builtin/packages/py-python-memcached/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-oauth2/package.py b/var/spack/repos/builtin/packages/py-python-oauth2/package.py index 6c0c723183..1ced77c542 100644 --- a/var/spack/repos/builtin/packages/py-python-oauth2/package.py +++ b/var/spack/repos/builtin/packages/py-python-oauth2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-rapidjson/package.py b/var/spack/repos/builtin/packages/py-python-rapidjson/package.py new file mode 100644 index 0000000000..3715c34b64 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-python-rapidjson/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythonRapidjson(PythonPackage): + """Python wrapper around rapidjson.""" + + homepage = "https://github.com/python-rapidjson/python-rapidjson" + url = "https://pypi.io/packages/source/p/python-rapidjson/python-rapidjson-0.9.1.tar.gz" + + version('0.9.1', sha256='ad80bd7e4bb15d9705227630037a433e2e2a7982b54b51de2ebabdd1611394a1') + + depends_on('python@3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-python-slugify/package.py b/var/spack/repos/builtin/packages/py-python-slugify/package.py new file mode 100644 index 0000000000..506fb66810 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-python-slugify/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythonSlugify(PythonPackage): + """A Python Slugify application that handles Unicode""" + + homepage = "https://github.com/un33k/python-slugify" + url = "https://pypi.io/packages/source/p/python-slugify/python-slugify-4.0.0.tar.gz" + + version('4.0.0', sha256='a8fc3433821140e8f409a9831d13ae5deccd0b033d4744d94b31fea141bdd84c') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-text-unidecode@1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-python-socketio/package.py b/var/spack/repos/builtin/packages/py-python-socketio/package.py index 1065a1473a..dad0618940 100644 --- a/var/spack/repos/builtin/packages/py-python-socketio/package.py +++ b/var/spack/repos/builtin/packages/py-python-socketio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-python-subunit/package.py b/var/spack/repos/builtin/packages/py-python-subunit/package.py new file mode 100644 index 0000000000..e894ae2b71 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-python-subunit/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythonSubunit(PythonPackage): + """Python implementation of subunit test streaming protocol.""" + + homepage = "https://launchpad.net/subunit" + url = "https://pypi.io/packages/source/p/python-subunit/python-subunit-1.3.0.tar.gz" + + version('1.3.0', sha256='9607edbee4c1e5a30ff88549ce8d9feb0b9bcbcb5e55033a9d76e86075465cbb') + + depends_on('py-setuptools', type='build') + depends_on('py-extras', type=('build', 'run')) + depends_on('py-testtools@0.9.34:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-python-utils/package.py b/var/spack/repos/builtin/packages/py-python-utils/package.py index a3e8865eb0..bc6057a078 100644 --- a/var/spack/repos/builtin/packages/py-python-utils/package.py +++ b/var/spack/repos/builtin/packages/py-python-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pythonqwt/package.py b/var/spack/repos/builtin/packages/py-pythonqwt/package.py index 582b3b4570..8de66c15bb 100644 --- a/var/spack/repos/builtin/packages/py-pythonqwt/package.py +++ b/var/spack/repos/builtin/packages/py-pythonqwt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytimeparse/package.py b/var/spack/repos/builtin/packages/py-pytimeparse/package.py new file mode 100644 index 0000000000..ef2a2e8196 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pytimeparse/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPytimeparse(PythonPackage): + """A small Python library to parse various kinds of time expressions.""" + + homepage = "https://github.com/wroberts/pytimeparse" + url = "https://pypi.io/packages/source/p/pytimeparse/pytimeparse-1.1.8.tar.gz" + + version('1.1.8', sha256='e86136477be924d7e670646a98561957e8ca7308d44841e21f5ddea757556a0a') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pytools/package.py b/var/spack/repos/builtin/packages/py-pytools/package.py index 988c29ad0c..95b33b9707 100644 --- a/var/spack/repos/builtin/packages/py-pytools/package.py +++ b/var/spack/repos/builtin/packages/py-pytools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py index 7e42f9af9f..1143d0b5cb 100644 --- a/var/spack/repos/builtin/packages/py-pytz/package.py +++ b/var/spack/repos/builtin/packages/py-pytz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyudev/package.py b/var/spack/repos/builtin/packages/py-pyudev/package.py index 6e2d7dfc3a..700eec6b62 100644 --- a/var/spack/repos/builtin/packages/py-pyudev/package.py +++ b/var/spack/repos/builtin/packages/py-pyudev/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyugrid/package.py b/var/spack/repos/builtin/packages/py-pyugrid/package.py index 5960ae8344..c411460ea6 100644 --- a/var/spack/repos/builtin/packages/py-pyugrid/package.py +++ b/var/spack/repos/builtin/packages/py-pyugrid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyutilib/package.py b/var/spack/repos/builtin/packages/py-pyutilib/package.py index ed620b1626..0fc62c07a4 100644 --- a/var/spack/repos/builtin/packages/py-pyutilib/package.py +++ b/var/spack/repos/builtin/packages/py-pyutilib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyvcf/package.py b/var/spack/repos/builtin/packages/py-pyvcf/package.py index 23b35513c0..f1a3f7201d 100644 --- a/var/spack/repos/builtin/packages/py-pyvcf/package.py +++ b/var/spack/repos/builtin/packages/py-pyvcf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pywavelets/package.py b/var/spack/repos/builtin/packages/py-pywavelets/package.py index d5c459a4e0..f3601473b5 100644 --- a/var/spack/repos/builtin/packages/py-pywavelets/package.py +++ b/var/spack/repos/builtin/packages/py-pywavelets/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py index 980d5fae51..d4059441cc 100644 --- a/var/spack/repos/builtin/packages/py-pyyaml/package.py +++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,8 +8,9 @@ from spack import * class PyPyyaml(PythonPackage): """PyYAML is a YAML parser and emitter for Python.""" + homepage = "http://pyyaml.org/wiki/PyYAML" - url = "http://pyyaml.org/download/pyyaml/PyYAML-5.1.2.tar.gz" + url = "https://pypi.io/packages/source/P/PyYAML/PyYAML-5.1.2.tar.gz" version('5.1.2', sha256='01adf0b6c6f61bd11af6e10ca52b7d4057dd0be0343eb9283c878cf3af56aee4') version('3.13', sha256='3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf') diff --git a/var/spack/repos/builtin/packages/py-zmq/package.py b/var/spack/repos/builtin/packages/py-pyzmq/package.py index 7d2d783a7a..6f62a3bf3e 100644 --- a/var/spack/repos/builtin/packages/py-zmq/package.py +++ b/var/spack/repos/builtin/packages/py-pyzmq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,16 +6,20 @@ from spack import * -class PyZmq(PythonPackage): +class PyPyzmq(PythonPackage): """PyZMQ: Python bindings for zeromq.""" homepage = "https://github.com/zeromq/pyzmq" url = "https://github.com/zeromq/pyzmq/archive/v14.7.0.tar.gz" + version('18.1.0', sha256='32f7618b8104021bc96cbd60be4330bdf37b929e8061dbce362c9f3478a08e21') version('17.1.2', sha256='77a32350440e321466b1748e6063b34a8a73768b62cb674e7d799fbc654b7c45') version('16.0.2', sha256='717dd902c3cf432b1c68e7b299ad028b0de0d0a823858e440b81d5f1baa2b1c1') version('14.7.0', sha256='809a5fcc720d286c840f7f64696e60322b5b2544795a73db626f09b344d16a15') + depends_on('python@2.7:2.8,3.3:', type=('build', 'run'), when='@18:') depends_on('py-cython@0.16:', type=('build', 'run')) + depends_on('py-cython@0.20:', type=('build', 'run'), when='@18:') + # these dependencies might only be needed for pypy depends_on('py-py', type=('build', 'run')) depends_on('py-cffi', type=('build', 'run')) - depends_on('zeromq') + depends_on('libzmq') diff --git a/var/spack/repos/builtin/packages/py-qtawesome/package.py b/var/spack/repos/builtin/packages/py-qtawesome/package.py index 28babe1528..962a74654a 100644 --- a/var/spack/repos/builtin/packages/py-qtawesome/package.py +++ b/var/spack/repos/builtin/packages/py-qtawesome/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-qtconsole/package.py b/var/spack/repos/builtin/packages/py-qtconsole/package.py index fb81aaa70a..434766f72a 100644 --- a/var/spack/repos/builtin/packages/py-qtconsole/package.py +++ b/var/spack/repos/builtin/packages/py-qtconsole/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-qtpy/package.py b/var/spack/repos/builtin/packages/py-qtpy/package.py index 9ee1d42f71..6acb27f6cf 100644 --- a/var/spack/repos/builtin/packages/py-qtpy/package.py +++ b/var/spack/repos/builtin/packages/py-qtpy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,12 +7,22 @@ from spack import * class PyQtpy(PythonPackage): - """QtPy: Abtraction layer for PyQt5/PyQt4/PySide""" + """QtPy: Abtraction layer for PyQt5/PyQt4/PySide/PySide2""" homepage = "https://github.com/spyder-ide/qtpy" url = "https://pypi.io/packages/source/Q/QtPy/QtPy-1.2.1.tar.gz" + version('1.7.1', sha256='e97275750934b3a1f4d8e263f5b889ae817ed36f26867ab0ce52be731ab1ed9e') version('1.2.1', sha256='5803ce31f50b24295e8e600b76cc91d7f2a3140a5a0d526d40226f9ec5e9097d') + apis = ['pyqt5', 'pyqt4', 'pyside2', 'pyside'] + + variant('api', default='pyqt5', description='Default QT API', + values=apis, multi=False) + depends_on('py-setuptools', type='build') - depends_on('py-pyqt4', type=('build', 'run')) + for api in apis: + depends_on('py-' + api, when='+' + api, type='run') + + def setup_run_environment(self, env): + env.set('QT_API', self.spec.variants['api'].value) diff --git a/var/spack/repos/builtin/packages/py-quantities/package.py b/var/spack/repos/builtin/packages/py-quantities/package.py index 2f6e4c24e4..f503eddc1c 100644 --- a/var/spack/repos/builtin/packages/py-quantities/package.py +++ b/var/spack/repos/builtin/packages/py-quantities/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-quast/package.py b/var/spack/repos/builtin/packages/py-quast/package.py index fd232743ac..5f8962ab78 100644 --- a/var/spack/repos/builtin/packages/py-quast/package.py +++ b/var/spack/repos/builtin/packages/py-quast/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-queryablelist/package.py b/var/spack/repos/builtin/packages/py-queryablelist/package.py index beee2e49bc..f69e621e83 100644 --- a/var/spack/repos/builtin/packages/py-queryablelist/package.py +++ b/var/spack/repos/builtin/packages/py-queryablelist/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-radical-utils/package.py b/var/spack/repos/builtin/packages/py-radical-utils/package.py index 0961beaed7..c0c38ecd40 100644 --- a/var/spack/repos/builtin/packages/py-radical-utils/package.py +++ b/var/spack/repos/builtin/packages/py-radical-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ranger-fm/package.py b/var/spack/repos/builtin/packages/py-ranger-fm/package.py new file mode 100644 index 0000000000..92485a649b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-ranger-fm/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +# +from spack import * + + +class PyRangerFm(PythonPackage): + """A VIM-inspired filemanager for the console""" + + homepage = "https://pypi.python.org/pypi/ranger-fm" + url = "https://pypi.io/packages/source/r/ranger-fm/ranger-fm-1.9.2.tar.gz" + git = "https://github.com/ranger/ranger.git" + + version('1.9.2', sha256='0ec62031185ad1f40b9faebd5a2d517c8597019c2eee919e3f1c60ce466d8625') diff --git a/var/spack/repos/builtin/packages/py-ranger/package.py b/var/spack/repos/builtin/packages/py-ranger/package.py deleted file mode 100644 index 2676d51354..0000000000 --- a/var/spack/repos/builtin/packages/py-ranger/package.py +++ /dev/null @@ -1,18 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -# -from spack import * - - -class PyRanger(PythonPackage): - """A VIM-inspired filemanager for the console""" - - homepage = "http://ranger.nongnu.org/" - url = "https://github.com/ranger/ranger/archive/v1.7.2.tar.gz" - - version('1.7.2', sha256='80917c93396e46272b6de63816d925eb708291a9f7a559d49b24c571ea0eeeb3') - - depends_on('python@2.6:') diff --git a/var/spack/repos/builtin/packages/py-rasterio/package.py b/var/spack/repos/builtin/packages/py-rasterio/package.py index 9bd8e04cc4..21f132cc9b 100644 --- a/var/spack/repos/builtin/packages/py-rasterio/package.py +++ b/var/spack/repos/builtin/packages/py-rasterio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ratelim/package.py b/var/spack/repos/builtin/packages/py-ratelim/package.py index f16804bca4..30653282cb 100644 --- a/var/spack/repos/builtin/packages/py-ratelim/package.py +++ b/var/spack/repos/builtin/packages/py-ratelim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-raven/package.py b/var/spack/repos/builtin/packages/py-raven/package.py index 9236d7a5f8..a78fc59f0a 100644 --- a/var/spack/repos/builtin/packages/py-raven/package.py +++ b/var/spack/repos/builtin/packages/py-raven/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-readme-renderer/package.py b/var/spack/repos/builtin/packages/py-readme-renderer/package.py index 925cf96402..edfdfa6d46 100644 --- a/var/spack/repos/builtin/packages/py-readme-renderer/package.py +++ b/var/spack/repos/builtin/packages/py-readme-renderer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-redis/package.py b/var/spack/repos/builtin/packages/py-redis/package.py index fbfc0757e9..c04677a782 100644 --- a/var/spack/repos/builtin/packages/py-redis/package.py +++ b/var/spack/repos/builtin/packages/py-redis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-regex/package.py b/var/spack/repos/builtin/packages/py-regex/package.py index c7a11de731..a6ab78adb7 100644 --- a/var/spack/repos/builtin/packages/py-regex/package.py +++ b/var/spack/repos/builtin/packages/py-regex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,7 @@ class PyRegex(PythonPackage): homepage = "https://pypi.python.org/pypi/regex/" url = "https://pypi.io/packages/source/r/regex/regex-2017.07.11.tar.gz" + version('2019.11.1', sha256='720e34a539a76a1fedcebe4397290604cc2bdf6f81eca44adb9fb2ea071c0c69') version('2017.07.11', sha256='dbda8bdc31a1c85445f1a1b29d04abda46e5c690f8f933a9cc3a85a358969616') - depends_on('py-setuptools', type='build') + depends_on('py-setuptools', type='build', when='@2017.07.11') diff --git a/var/spack/repos/builtin/packages/py-reportlab/package.py b/var/spack/repos/builtin/packages/py-reportlab/package.py index 46c3d8d897..222890124f 100644 --- a/var/spack/repos/builtin/packages/py-reportlab/package.py +++ b/var/spack/repos/builtin/packages/py-reportlab/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-repoze-lru/package.py b/var/spack/repos/builtin/packages/py-repoze-lru/package.py index bc28155e96..ceec2fcb87 100644 --- a/var/spack/repos/builtin/packages/py-repoze-lru/package.py +++ b/var/spack/repos/builtin/packages/py-repoze-lru/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-requests-futures/package.py b/var/spack/repos/builtin/packages/py-requests-futures/package.py index e75fdf4d52..4c79bcf871 100644 --- a/var/spack/repos/builtin/packages/py-requests-futures/package.py +++ b/var/spack/repos/builtin/packages/py-requests-futures/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-requests-mock/package.py b/var/spack/repos/builtin/packages/py-requests-mock/package.py new file mode 100644 index 0000000000..94807b5cbd --- /dev/null +++ b/var/spack/repos/builtin/packages/py-requests-mock/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyRequestsMock(PythonPackage): + """Mock out responses from the requests package.""" + + homepage = "https://requests-mock.readthedocs.io/" + url = "https://pypi.io/packages/source/r/requests-mock/requests-mock-1.7.0.tar.gz" + + import_modules = ['requests_mock'] + + version('1.7.0', sha256='88d3402dd8b3c69a9e4f9d3a73ad11b15920c6efd36bc27bf1f701cf4a8e4646') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-requests-oauthlib/package.py b/var/spack/repos/builtin/packages/py-requests-oauthlib/package.py index 512bdf2b45..6c6a633e47 100644 --- a/var/spack/repos/builtin/packages/py-requests-oauthlib/package.py +++ b/var/spack/repos/builtin/packages/py-requests-oauthlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py index c6e25d373e..e34d1c5a73 100644 --- a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py +++ b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,10 +11,10 @@ class PyRequestsToolbelt(PythonPackage): python-requests""" homepage = "https://toolbelt.readthedocs.org/" - url = "https://github.com/requests/toolbelt/archive/0.9.1.tar.gz" + url = "https://pypi.io/packages/source/r/requests-toolbelt/requests-toolbelt-0.9.1.tar.gz" - version('0.9.1', sha256='c8e68e537e87ae088e3a0eb6d80ed5b7cf5d6df503d0e843e0a5e47283db487b') - version('0.8.0', sha256='f151c07e88148dc05b6f31cc75dfb7a6770968e4a5c8e6690325eed4e79160a1') + version('0.9.1', sha256='968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0') + version('0.8.0', sha256='f6a531936c6fa4c6cfce1b9c10d5c4f498d16528d2a54a22ca00011205a187b5') depends_on('py-setuptools', type='build') depends_on('py-requests@2.0.1:2.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-requests/package.py b/var/spack/repos/builtin/packages/py-requests/package.py index f93ad6d952..5d7249a079 100644 --- a/var/spack/repos/builtin/packages/py-requests/package.py +++ b/var/spack/repos/builtin/packages/py-requests/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-restview/package.py b/var/spack/repos/builtin/packages/py-restview/package.py index 1ea038cfe2..40d2765aec 100644 --- a/var/spack/repos/builtin/packages/py-restview/package.py +++ b/var/spack/repos/builtin/packages/py-restview/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-retrying/package.py b/var/spack/repos/builtin/packages/py-retrying/package.py index 83d09849cf..ef5a7d05ca 100644 --- a/var/spack/repos/builtin/packages/py-retrying/package.py +++ b/var/spack/repos/builtin/packages/py-retrying/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-rnacocktail/package.py b/var/spack/repos/builtin/packages/py-rnacocktail/package.py new file mode 100644 index 0000000000..13c05186e4 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-rnacocktail/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyRnacocktail(PythonPackage): + """RNACocktail: A comprehensive framework + for accurate and efficient RNA-Seq analysis.""" + + homepage = "http://bioinform.github.io/rnacocktail/" + url = "https://github.com/bioinform/rnacocktail/archive/v0.2.2.tar.gz" + + version('0.2.2', sha256='34aa0d1d7bd9d80303fe7dac5acc0519f7c1ed986397692588343d82ce45c7a5') + + depends_on('python@2.7:2.8', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-pybedtools', type=('build', 'run')) + depends_on('py-pysam', type=('build', 'run')) + # Higher version of py-pandas and py-numpy + # depends on python@3: which conflicts with py-rnacocktail + depends_on('py-pandas@:0.24.2', type=('build', 'run')) + depends_on('py-numpy@:1.16.5', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-rope/package.py b/var/spack/repos/builtin/packages/py-rope/package.py index fc47d63933..7ea1eea1fc 100644 --- a/var/spack/repos/builtin/packages/py-rope/package.py +++ b/var/spack/repos/builtin/packages/py-rope/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-rpy2/package.py b/var/spack/repos/builtin/packages/py-rpy2/package.py index 6d5eca5195..d3578c2cc2 100644 --- a/var/spack/repos/builtin/packages/py-rpy2/package.py +++ b/var/spack/repos/builtin/packages/py-rpy2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-rsa/package.py b/var/spack/repos/builtin/packages/py-rsa/package.py index c991be58e7..b3d9cb7a37 100644 --- a/var/spack/repos/builtin/packages/py-rsa/package.py +++ b/var/spack/repos/builtin/packages/py-rsa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-rseqc/package.py b/var/spack/repos/builtin/packages/py-rseqc/package.py index d7e078b29b..1b3ac0a88a 100644 --- a/var/spack/repos/builtin/packages/py-rseqc/package.py +++ b/var/spack/repos/builtin/packages/py-rseqc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-rtree/package.py b/var/spack/repos/builtin/packages/py-rtree/package.py index 4d0db48ecb..1c62efb500 100644 --- a/var/spack/repos/builtin/packages/py-rtree/package.py +++ b/var/spack/repos/builtin/packages/py-rtree/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,9 +16,9 @@ class PyRtree(PythonPackage): depends_on('py-setuptools', type='build') depends_on('libspatialindex') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): lib = self.spec['libspatialindex'].prefix.lib - spack_env.set('SPATIALINDEX_LIBRARY', - join_path(lib, 'libspatialindex.%s' % dso_suffix)) - spack_env.set('SPATIALINDEX_C_LIBRARY', - join_path(lib, 'libspatialindex_c.%s' % dso_suffix)) + env.set('SPATIALINDEX_LIBRARY', + join_path(lib, 'libspatialindex.%s' % dso_suffix)) + env.set('SPATIALINDEX_C_LIBRARY', + join_path(lib, 'libspatialindex_c.%s' % dso_suffix)) diff --git a/var/spack/repos/builtin/packages/py-ruamel-yaml/package.py b/var/spack/repos/builtin/packages/py-ruamel-yaml/package.py index efe5481522..9c3ba76038 100644 --- a/var/spack/repos/builtin/packages/py-ruamel-yaml/package.py +++ b/var/spack/repos/builtin/packages/py-ruamel-yaml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-s3cmd/package.py b/var/spack/repos/builtin/packages/py-s3cmd/package.py new file mode 100644 index 0000000000..469ee29703 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-s3cmd/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyS3cmd(PythonPackage): + """ + S3cmd (s3cmd) is a free command line tool and client for uploading, + retrieving and managing data in Amazon S3 and other cloud storage + service providers that use the S3 protocol, such as Google Cloud + Storage or DreamHost DreamObjects. It is best suited for power + users who are familiar with command line programs. + """ + + homepage = "https://github.com/s3tools/s3cmd" + url = "https://github.com/s3tools/s3cmd/releases/download/v2.0.2/s3cmd-2.0.2.tar.gz" + + version('2.0.2', sha256='9f244c0c10d58d0ccacbba3aa977463e32491bdd9d95109e27b67e4d46c5bd52') + version('2.0.1', sha256='caf09f1473301c442fba6431c983c361c9af8bde503dac0953f0d2f8f2c53c8f') + version('2.0.0', sha256='bf2a50802f1031cba83e99be488965803899d8ab0228c800c833b55c7269cd48') + version('1.6.1', sha256='4675794f84d8744ee3d35873d180f41c7b2116895ccbe2738a9bc552e1cf214e') + version('1.6.0', sha256='04279ee26c661d4b740449460ed93a74ffec91616f685474beea97e930fdfa5c') + version('1.5.2', sha256='ff8a6764e8bdd7ed48a93e51b08222bea33469d248a90b8d25315b023717b42d') + + depends_on('py-setuptools', type='build') + depends_on('python@2.6:+pyexpat', type=('build', 'run')) + depends_on('py-python-dateutil', type=('build', 'run')) + depends_on('py-python-magic', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-s3transfer/package.py b/var/spack/repos/builtin/packages/py-s3transfer/package.py index b2160b3e45..5db6bd28a3 100644 --- a/var/spack/repos/builtin/packages/py-s3transfer/package.py +++ b/var/spack/repos/builtin/packages/py-s3transfer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-saga-python/package.py b/var/spack/repos/builtin/packages/py-saga-python/package.py index 746095fba9..96fb39c3f5 100644 --- a/var/spack/repos/builtin/packages/py-saga-python/package.py +++ b/var/spack/repos/builtin/packages/py-saga-python/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-scandir/package.py b/var/spack/repos/builtin/packages/py-scandir/package.py index 4d4bfb5868..d370328b6e 100644 --- a/var/spack/repos/builtin/packages/py-scandir/package.py +++ b/var/spack/repos/builtin/packages/py-scandir/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-scientificpython/package.py b/var/spack/repos/builtin/packages/py-scientificpython/package.py index aabec4e81c..58a142ccbd 100644 --- a/var/spack/repos/builtin/packages/py-scientificpython/package.py +++ b/var/spack/repos/builtin/packages/py-scientificpython/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-scikit-build/package.py b/var/spack/repos/builtin/packages/py-scikit-build/package.py new file mode 100644 index 0000000000..911a6edf15 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-scikit-build/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyScikitBuild(PythonPackage): + """scikit-build is an improved build system generator for CPython + C/C++/Fortran/Cython extensions. It provides better support for + additional compilers, build systems, cross compilation, and + locating dependencies and their associated build requirements. + + The scikit-build package is fundamentally just glue between + the setuptools Python module and CMake.""" + + homepage = "https://scikit-build.readthedocs.io/en/latest/" + url = "https://github.com/scikit-build/scikit-build/archive/0.10.0.tar.gz" + + maintainers = ['coreyjadams'] + + version('0.10.0', sha256='2beec252813b20327072c15e9d997f15972aedcc6a130d0154979ff0fdb1b010') + + depends_on('py-setuptools@28.0.0:', type=('build', 'run')) + depends_on('py-packaging', type=('build', 'run')) + depends_on('py-wheel@0.29.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py index c60a13477a..c43df31787 100644 --- a/var/spack/repos/builtin/packages/py-scikit-image/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py index 02d85c33cd..d5b47d785b 100644 --- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class PyScikitLearn(PythonPackage): """A set of python modules for machine learning and data mining.""" homepage = "https://pypi.python.org/pypi/scikit-learn" - url = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.21.3.tar.gz" + url = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.22.tar.gz" git = "https://github.com/scikit-learn/scikit-learn.git" maintainers = ['adamjstewart'] @@ -33,6 +33,8 @@ class PyScikitLearn(PythonPackage): ] version('master', branch='master') + version('0.22.1', sha256='51ee25330fc244107588545c70e2f3570cfc4017cff09eed69d6e1d82a212b7d') + version('0.22', sha256='314abf60c073c48a1e95feaae9f3ca47a2139bd77cebb5b877c23a45c9e03012') version('0.21.3', sha256='eb9b8ebf59eddd8b96366428238ab27d05a19e89c5516ce294abc35cea75d003') version('0.21.2', sha256='0aafc312a55ebf58073151b9308761a5fcfa45b7f7730cea4b1f066f824c72db') version('0.21.1', sha256='228d0611e69e5250946f8cd7bbefec75347950f0ca426d0c518db8f06583f660') @@ -79,7 +81,7 @@ class PyScikitLearn(PythonPackage): # https://scikit-learn.org/stable/developers/advanced_installation.html#mac-osx elif self.spec.satisfies('@0.21: %clang platform=darwin +openmp'): env.append_flags( - 'CPPFLAGS', '-Xpreprocessor -fopenmp') + 'CPPFLAGS', self.compiler.openmp_flag) env.append_flags( 'CFLAGS', self.spec['llvm-openmp'].headers.include_flags) env.append_flags( diff --git a/var/spack/repos/builtin/packages/py-scikit-optimize/package.py b/var/spack/repos/builtin/packages/py-scikit-optimize/package.py index ebf4b8ec4c..6f148d5fe1 100644 --- a/var/spack/repos/builtin/packages/py-scikit-optimize/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-optimize/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,11 +22,10 @@ class PyScikitOptimize(PythonPackage): variant('plots', default=True, description='Build with plot support from py-matplotlib') - depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) - depends_on('py-scikit-learn@0.19.0:', type=('build', 'run')) depends_on('py-scipy@0.14.0:', type=('build', 'run')) + depends_on('py-scikit-learn@0.19.1:', type=('build', 'run')) depends_on('py-matplotlib', when='+plots') - depends_on('py-test@3.3.0:', type='test') + depends_on('py-pytest@3.3.0:', type='test') diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index b173be57ea..5cbd2438f7 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,8 +11,8 @@ class PyScipy(PythonPackage): It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.""" - homepage = "http://www.scipy.org/" - url = "https://pypi.io/packages/source/s/scipy/scipy-1.3.1.tar.gz" + homepage = "https://www.scipy.org/" + url = "https://pypi.io/packages/source/s/scipy/scipy-1.4.1.tar.gz" maintainers = ['adamjstewart'] install_time_test_callbacks = ['install_test', 'import_module_test'] @@ -30,30 +30,35 @@ class PyScipy(PythonPackage): 'scipy.sparse.linalg.eigen.lobpcg', 'scipy.special._precompute' ] - version('1.3.1', sha256='2643cfb46d97b7797d1dbdb6f3c23fe3402904e3c90e6facfe6a9b98d808c1b5') - version('1.3.0', sha256='c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a') - version('1.2.2', sha256='a4331e0b8dab1ff75d2c67b5158a8bb9a83c799d7140094dda936d876c7cfbb1') - version('1.2.1', sha256='e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c') - version('1.1.0', sha256='878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1') - version('1.0.0', sha256='87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10') + version('1.4.1', sha256='dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59') + version('1.4.0', sha256='31f7cfa93b01507c935c12b535e24812594002a02a56803d7cd063e9920d25e8') + version('1.3.3', sha256='64bf4e8ae0db2d42b58477817f648d81e77f0b381d0ea4427385bba3f959380a') + version('1.3.2', sha256='a03939b431994289f39373c57bbe452974a7da724ae7f9620a1beee575434da4') + version('1.3.1', sha256='2643cfb46d97b7797d1dbdb6f3c23fe3402904e3c90e6facfe6a9b98d808c1b5') + version('1.3.0', sha256='c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a') + version('1.2.3', sha256='ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57') + version('1.2.2', sha256='a4331e0b8dab1ff75d2c67b5158a8bb9a83c799d7140094dda936d876c7cfbb1') + version('1.2.1', sha256='e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c') + version('1.1.0', sha256='878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1') + version('1.0.0', sha256='87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10') version('0.19.1', sha256='a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6') - version('0.19.0', sha256='4190d34bf9a09626cd42100bbb12e3d96b2daf1a8a3244e991263eb693732122', - url="https://pypi.io/packages/source/s/scipy/scipy-0.19.0.zip") version('0.18.1', sha256='8ab6e9c808bf2fb3e8576cd8cf07226d9cdc18b012c06d9708429a821ac6634e') version('0.17.0', sha256='f600b755fb69437d0f70361f9e560ab4d304b1b66987ed5a28bdd9dd7793e089') version('0.15.1', sha256='a212cbc3b79e9a563aa45fc5c517b3499198bd7eb7e7be1e047568a5f48c259a') version('0.15.0', sha256='0c74e31e08acc8bf9b6ceb9bced73df2ae0cc76003e0366350bc7b26292bf8b1') - depends_on('python@2.6:2.8,3.2:') - depends_on('python@2.7:2.8,3.4:', when='@0.18:') - depends_on('python@3.5:', when='@1.3:') + depends_on('python@2.6:2.8,3.2:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.4:', when='@0.18:', type=('build', 'run')) + depends_on('python@3.5:', when='@1.3:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('py-pytest', type='test') + depends_on('py-pybind11@2.4.0:', when='@1.4.1:', type='build') + depends_on('py-pybind11@2.2.4:', when='@1.4.0:', type='build') depends_on('py-numpy@1.5.1:+blas+lapack', type=('build', 'run')) - depends_on('py-numpy@1.6.2:+blas+lapack', type=('build', 'run'), when='@0.16:') - depends_on('py-numpy@1.7.1:+blas+lapack', type=('build', 'run'), when='@0.18:') - depends_on('py-numpy@1.8.2:+blas+lapack', type=('build', 'run'), when='@0.19:') - depends_on('py-numpy@1.13.3:+blas+lapack', type=('build', 'run'), when='@1.3:') + depends_on('py-numpy@1.6.2:+blas+lapack', when='@0.16:', type=('build', 'run')) + depends_on('py-numpy@1.7.1:+blas+lapack', when='@0.18:', type=('build', 'run')) + depends_on('py-numpy@1.8.2:+blas+lapack', when='@0.19:', type=('build', 'run')) + depends_on('py-numpy@1.13.3:+blas+lapack', when='@1.3:', type=('build', 'run')) + depends_on('py-pytest', type='test') # NOTE: scipy picks up Blas/Lapack from numpy, see # http://www.scipy.org/scipylib/building/linux.html#step-4-build-numpy-1-5-0 diff --git a/var/spack/repos/builtin/packages/py-scoop/package.py b/var/spack/repos/builtin/packages/py-scoop/package.py index b26140c384..2fc309bbd6 100644 --- a/var/spack/repos/builtin/packages/py-scoop/package.py +++ b/var/spack/repos/builtin/packages/py-scoop/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,4 +19,4 @@ class PyScoop(PythonPackage): depends_on('py-setuptools', type='build') depends_on('py-greenlet@0.3.4:', type=('build', 'run')) - depends_on('py-zmq@13.1.0:', type=('build', 'run')) + depends_on('py-pyzmq@13.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-scp/package.py b/var/spack/repos/builtin/packages/py-scp/package.py index 1b8021fadb..85bb112cd4 100644 --- a/var/spack/repos/builtin/packages/py-scp/package.py +++ b/var/spack/repos/builtin/packages/py-scp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-scs/package.py b/var/spack/repos/builtin/packages/py-scs/package.py new file mode 100644 index 0000000000..7715349fb3 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-scs/package.py @@ -0,0 +1,43 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyScs(PythonPackage): + """SCS: splitting conic solver""" + + homepage = "https://github.com/cvxgrp/scs" + url = "https://www.pypi.io/packages/source/s/scs/scs-2.1.1-2.tar.gz" + + version('2.1.1-2', sha256='f816cfe3d4b4cff3ac2b8b96588c5960ddd2a3dc946bda6b09db04e7bc6577f2') + + variant('cuda', default=False, description="Also compile the GPU CUDA version of SCS") + variant('float32', default=False, description="Use 32 bit (single precision) floats, default is 64 bit") + variant('extra_verbose', default=False, description="Extra verbose SCS (for debugging)") + variant('int32', default=False, description="Use 32 bit ints") + variant('blas64', default=False, description="Use 64 bit ints for the blas/lapack libs") + + depends_on('py-setuptools', type='build') + depends_on('py-numpy@1.7:', type=('build', 'run')) + depends_on('py-scipy@0.13.2:', type=('build', 'run')) + + def build_args(self, spec, prefix): + args = [] + if '+cuda' in spec or '+float32' in spec or '+int32' in spec or\ + '+extra_verbose' in spec or '+blas64' in spec: + args = ['--scs'] + if '+cuda' in spec: + args.append('--gpu') + if '+float32' in spec: + args.append('--float') + if '+extra_verbose' in spec: + args.append('--extraverbose') + if '+int32' in spec: + args.append('--int') + if '+blas64' in spec: + args.append('--blas64') + return args diff --git a/var/spack/repos/builtin/packages/py-seaborn/package.py b/var/spack/repos/builtin/packages/py-seaborn/package.py index a4dc90e766..feaf12abb2 100644 --- a/var/spack/repos/builtin/packages/py-seaborn/package.py +++ b/var/spack/repos/builtin/packages/py-seaborn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-selenium/package.py b/var/spack/repos/builtin/packages/py-selenium/package.py index e61113610d..33082ec78f 100644 --- a/var/spack/repos/builtin/packages/py-selenium/package.py +++ b/var/spack/repos/builtin/packages/py-selenium/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-semantic-version/package.py b/var/spack/repos/builtin/packages/py-semantic-version/package.py index 7086d8adb0..d05d902e10 100644 --- a/var/spack/repos/builtin/packages/py-semantic-version/package.py +++ b/var/spack/repos/builtin/packages/py-semantic-version/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-semver/package.py b/var/spack/repos/builtin/packages/py-semver/package.py new file mode 100644 index 0000000000..a73401d254 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-semver/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySemver(PythonPackage): + """A Python module for semantic versioning. + Simplifies comparing versions.""" + + homepage = "https://semver.org/" + url = "https://pypi.io/packages/source/s/semver/semver-2.8.1.tar.gz" + + version('2.8.1', sha256='5b09010a66d9a3837211bb7ae5a20d10ba88f8cb49e92cb139a69ef90d5060d8') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-send2trash/package.py b/var/spack/repos/builtin/packages/py-send2trash/package.py index be38ccf59c..c4882b8e95 100644 --- a/var/spack/repos/builtin/packages/py-send2trash/package.py +++ b/var/spack/repos/builtin/packages/py-send2trash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-setuptools-git/package.py b/var/spack/repos/builtin/packages/py-setuptools-git/package.py index e89d358ca4..fa8a51908e 100644 --- a/var/spack/repos/builtin/packages/py-setuptools-git/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools-git/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-setuptools-scm-git-archive/package.py b/var/spack/repos/builtin/packages/py-setuptools-scm-git-archive/package.py new file mode 100644 index 0000000000..2fb6a9e267 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-setuptools-scm-git-archive/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySetuptoolsScmGitArchive(PythonPackage): + """This is a setuptools_scm plugin that adds support for git archives + (for example the ones GitHub automatically generates).""" + + homepage = "https://github.com/Changaco/setuptools_scm_git_archive/" + url = "https://pypi.io/packages/source/s/setuptools_scm_git_archive/setuptools_scm_git_archive-1.1.tar.gz" + + maintainers = ['marcmengel'] + + version( + '1.1', sha256='6026f61089b73fa1b5ee737e95314f41cb512609b393530385ed281d0b46c062') + version( + '1.0', sha256='52425f905518247c685fc64c5fdba6e1e74443c8562e141c8de56059be0e31da') + + depends_on('py-setuptools', type='build') + depends_on('py-setuptools-scm', type='build') diff --git a/var/spack/repos/builtin/packages/py-setuptools-scm/package.py b/var/spack/repos/builtin/packages/py-setuptools-scm/package.py index 45a8706a95..b91bc3e324 100644 --- a/var/spack/repos/builtin/packages/py-setuptools-scm/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools-scm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 3ac2236f7a..ee47532b1e 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sfepy/package.py b/var/spack/repos/builtin/packages/py-sfepy/package.py index 9d78ff1421..579f11b1b7 100644 --- a/var/spack/repos/builtin/packages/py-sfepy/package.py +++ b/var/spack/repos/builtin/packages/py-sfepy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sgp4/package.py b/var/spack/repos/builtin/packages/py-sgp4/package.py index bbddcb6479..79af5e7112 100644 --- a/var/spack/repos/builtin/packages/py-sgp4/package.py +++ b/var/spack/repos/builtin/packages/py-sgp4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sh/package.py b/var/spack/repos/builtin/packages/py-sh/package.py index 6438d99128..7f8b639fbf 100644 --- a/var/spack/repos/builtin/packages/py-sh/package.py +++ b/var/spack/repos/builtin/packages/py-sh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-shapely/package.py b/var/spack/repos/builtin/packages/py-shapely/package.py index c1809767cf..9edb86674f 100644 --- a/var/spack/repos/builtin/packages/py-shapely/package.py +++ b/var/spack/repos/builtin/packages/py-shapely/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,6 +30,6 @@ class PyShapely(PythonPackage): depends_on('geos@3.3:', when='@1.3:') depends_on('py-pytest', type='test') - def setup_environment(self, spack_env, run_env): - spack_env.set('GEOS_CONFIG', - join_path(self.spec['geos'].prefix.bin, 'geos-config')) + def setup_build_environment(self, env): + env.set('GEOS_CONFIG', + join_path(self.spec['geos'].prefix.bin, 'geos-config')) diff --git a/var/spack/repos/builtin/packages/py-shiboken/package.py b/var/spack/repos/builtin/packages/py-shiboken/package.py index d5ddcbe667..e7403bbfd6 100644 --- a/var/spack/repos/builtin/packages/py-shiboken/package.py +++ b/var/spack/repos/builtin/packages/py-shiboken/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-simplegeneric/package.py b/var/spack/repos/builtin/packages/py-simplegeneric/package.py index faec17ca84..eb92c5d8de 100644 --- a/var/spack/repos/builtin/packages/py-simplegeneric/package.py +++ b/var/spack/repos/builtin/packages/py-simplegeneric/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-simplejson/package.py b/var/spack/repos/builtin/packages/py-simplejson/package.py index 8cae5d59e2..ea8799b75a 100644 --- a/var/spack/repos/builtin/packages/py-simplejson/package.py +++ b/var/spack/repos/builtin/packages/py-simplejson/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-simplekml/package.py b/var/spack/repos/builtin/packages/py-simplekml/package.py index a74a4df04f..23b309f670 100644 --- a/var/spack/repos/builtin/packages/py-simplekml/package.py +++ b/var/spack/repos/builtin/packages/py-simplekml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-singledispatch/package.py b/var/spack/repos/builtin/packages/py-singledispatch/package.py index 2a4d1fdedc..21c91a6465 100644 --- a/var/spack/repos/builtin/packages/py-singledispatch/package.py +++ b/var/spack/repos/builtin/packages/py-singledispatch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sip/package.py b/var/spack/repos/builtin/packages/py-sip/package.py index 997b4f9c01..4b625d8f3f 100644 --- a/var/spack/repos/builtin/packages/py-sip/package.py +++ b/var/spack/repos/builtin/packages/py-sip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py index ce2acc7013..a7a8d32af6 100644 --- a/var/spack/repos/builtin/packages/py-six/package.py +++ b/var/spack/repos/builtin/packages/py-six/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-slepc4py/package.py b/var/spack/repos/builtin/packages/py-slepc4py/package.py index edf21aadf4..4e726c8a9b 100644 --- a/var/spack/repos/builtin/packages/py-slepc4py/package.py +++ b/var/spack/repos/builtin/packages/py-slepc4py/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,10 +10,14 @@ class PySlepc4py(PythonPackage): """This package provides Python bindings for the SLEPc package. """ - homepage = "https://bitbucket.org/slepc/slepc4py" - url = "https://bitbucket.org/slepc/slepc4py/get/3.10.0.tar.gz" - git = "https://bitbucket.org/slepc/slepc4py.git" + homepage = "https://gitlab.com/slepc/slepc4py" + url = "https://gitlab.com/slepc/slepc4py/-/archive/3.12.0/slepc4py-3.12.0.tar.gz" + git = "https://gitlab.com/slepc/slepc4py.git" + maintainers = ['dalcinl', 'joseeroman', 'balay'] + + version('3.12.0', sha256='d8c06953b7d00f529a9a7fd016dfa8efdf1d05995baeea7688d1d59611f424f7') + version('3.11.0', sha256='1e591056beee209f585cd781e5fe88174cd2a61215716a71d9eaaf9411b6a775') version('3.10.0', sha256='6494959f44280d3b80e73978d7a6bf656c9bb04bb3aa395c668c7a58948db1c6') version('3.9.0', sha256='84cab4216268c2cb7d01e7cdbb1204a3c3e13cdfcd7a78ea057095f96f68c3c0') version('3.8.0', sha256='988815b3650b69373be9abbf2355df512dfd200aa74b1785b50a484d6dfee971') @@ -22,6 +26,8 @@ class PySlepc4py(PythonPackage): depends_on('py-setuptools', type='build') depends_on('py-petsc4py', type=('build', 'run')) + depends_on('py-petsc4py@3.12:3.12.99', when='@3.12:3.12.99', type=('build', 'run')) + depends_on('py-petsc4py@3.11:3.11.99', when='@3.11:3.11.99', type=('build', 'run')) depends_on('py-petsc4py@3.10:3.10.99', when='@3.10:3.10.99', type=('build', 'run')) depends_on('py-petsc4py@3.9:3.9.99', when='@3.9:3.9.99', type=('build', 'run')) depends_on('py-petsc4py@3.8:3.8.99', when='@3.8:3.8.99', type=('build', 'run')) @@ -29,6 +35,8 @@ class PySlepc4py(PythonPackage): depends_on('py-petsc4py@3.6:3.6.99', when='@3.6:3.6.99', type=('build', 'run')) depends_on('slepc') + depends_on('slepc@3.12:3.12.99', when='@3.12:3.12.99') + depends_on('slepc@3.11:3.11.99', when='@3.11:3.11.99') depends_on('slepc@3.10:3.10.99', when='@3.10:3.10.99') depends_on('slepc@3.9:3.9.99', when='@3.9:3.9.99') depends_on('slepc@3.8:3.8.99', when='@3.8:3.8.99') diff --git a/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py b/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py index 1233492b11..a04d974aa8 100644 --- a/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py +++ b/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-smart-open/package.py b/var/spack/repos/builtin/packages/py-smart-open/package.py index 483e55a6b4..5def4a84f3 100644 --- a/var/spack/repos/builtin/packages/py-smart-open/package.py +++ b/var/spack/repos/builtin/packages/py-smart-open/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sncosmo/package.py b/var/spack/repos/builtin/packages/py-sncosmo/package.py index 5709d140ff..3108b961cf 100644 --- a/var/spack/repos/builtin/packages/py-sncosmo/package.py +++ b/var/spack/repos/builtin/packages/py-sncosmo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-snowballstemmer/package.py b/var/spack/repos/builtin/packages/py-snowballstemmer/package.py index 20a65a1b45..80af93c40a 100644 --- a/var/spack/repos/builtin/packages/py-snowballstemmer/package.py +++ b/var/spack/repos/builtin/packages/py-snowballstemmer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,4 +18,4 @@ class PySnowballstemmer(PythonPackage): version('2.0.0', sha256='df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52') version('1.2.1', sha256='919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128') - depends_on('py-setuptools', type='build') + depends_on('py-setuptools', when='@2:', type='build') diff --git a/var/spack/repos/builtin/packages/py-snuggs/package.py b/var/spack/repos/builtin/packages/py-snuggs/package.py index 510152b073..8dd4c79b43 100644 --- a/var/spack/repos/builtin/packages/py-snuggs/package.py +++ b/var/spack/repos/builtin/packages/py-snuggs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sortedcontainers/package.py b/var/spack/repos/builtin/packages/py-sortedcontainers/package.py index 57e3938849..33ab9ee443 100644 --- a/var/spack/repos/builtin/packages/py-sortedcontainers/package.py +++ b/var/spack/repos/builtin/packages/py-sortedcontainers/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-soupsieve/package.py b/var/spack/repos/builtin/packages/py-soupsieve/package.py index d850e8b04e..be9d52e208 100644 --- a/var/spack/repos/builtin/packages/py-soupsieve/package.py +++ b/var/spack/repos/builtin/packages/py-soupsieve/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-spatialist/package.py b/var/spack/repos/builtin/packages/py-spatialist/package.py index 4b4e09beb9..e1beee57e5 100644 --- a/var/spack/repos/builtin/packages/py-spatialist/package.py +++ b/var/spack/repos/builtin/packages/py-spatialist/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-spdlog/package.py b/var/spack/repos/builtin/packages/py-spdlog/package.py new file mode 100644 index 0000000000..2e149b6b30 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-spdlog/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySpdlog(PythonPackage): + """The py-spdlog package provides a Python wrapper + to the C++ spdlog library.""" + + homepage = 'https://github.com/bodgergely/spdlog-python' + url = 'https://pypi.io/packages/source/s/spdlog/spdlog-2.0.0.tar.gz' + git = 'https://github.com/bodgergely/spdlog-python.git' + + # NOTE: Righ now py-spdlog works with a git submodule containing a copy + # of spdlog. Ideally we would want to install spdlog ourselves and make + # this package depend on it. There is an issue for that on the py-spdlog + # github repository: https://github.com/bodgergely/spdlog-python/issues/19 + + version('master', branch='master', submodules=True) + version('2.0.0', sha256='b8d3732839850da414a47e91547ee1246f0690cb83f43f11a1fbaec40b7b968c') + + depends_on('py-pybind11@2.2:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-pytest-runner', type='build') + depends_on('py-pytest', type='test') diff --git a/var/spack/repos/builtin/packages/py-spectra/package.py b/var/spack/repos/builtin/packages/py-spectra/package.py index f15d97d9c6..063680bb7c 100644 --- a/var/spack/repos/builtin/packages/py-spectra/package.py +++ b/var/spack/repos/builtin/packages/py-spectra/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-spefile/package.py b/var/spack/repos/builtin/packages/py-spefile/package.py index b6890e30c8..54eec9ff91 100644 --- a/var/spack/repos/builtin/packages/py-spefile/package.py +++ b/var/spack/repos/builtin/packages/py-spefile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-spglib/package.py b/var/spack/repos/builtin/packages/py-spglib/package.py index a258434234..c1b6cf6981 100644 --- a/var/spack/repos/builtin/packages/py-spglib/package.py +++ b/var/spack/repos/builtin/packages/py-spglib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py b/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py index 227d8a7f04..f24af6bbb7 100644 --- a/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py +++ b/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py b/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py index 901faec4b8..45a5e2104a 100644 --- a/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py +++ b/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinx/package.py b/var/spack/repos/builtin/packages/py-sphinx/package.py index 291b064b5d..550b503e6c 100644 --- a/var/spack/repos/builtin/packages/py-sphinx/package.py +++ b/var/spack/repos/builtin/packages/py-sphinx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py b/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py index 0781ea59f3..7538121854 100644 --- a/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,9 +10,9 @@ class PySphinxautomodapi(PythonPackage): """Provides Sphinx directives to autogenerate API documentation pages""" homepage = "https://sphinx-automodapi.readthedocs.io/en/latest/" - url = "https://github.com/astropy/sphinx-automodapi/archive/v0.9.tar.gz" + url = "https://pypi.io/packages/source/s/sphinx-automodapi/sphinx-automodapi-0.9.tar.gz" - version('0.9', sha256='017817812e9266319fdcfcc89ddfbe570935ca87a3bda62d61c8507cf1337aa8') + version('0.9', sha256='71a69e1a7ab8d849f416d7431db854d7b1925f749ba6345bc7d88f288892871d') depends_on('py-setuptools', type='build') depends_on('py-sphinx@1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-applehelp/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-applehelp/package.py index 089ef152cf..25f1a7ce5f 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-applehelp/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-applehelp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py index 48eb4a239c..9ba3dbc720 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-devhelp/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-devhelp/package.py index 244fd13b78..ff90a9a5d4 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-devhelp/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-devhelp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-htmlhelp/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-htmlhelp/package.py index b4c8961d2c..96a51d3113 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-htmlhelp/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-htmlhelp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-issuetracker/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-issuetracker/package.py new file mode 100644 index 0000000000..2197c3080c --- /dev/null +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-issuetracker/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySphinxcontribIssuetracker(PythonPackage): + """Sphinx integration with different issuetrackers.""" + + homepage = "https://sphinxcontrib-issuetracker.readthedocs.org/" + url = "https://pypi.io/packages/source/s/sphinxcontrib-issuetracker/sphinxcontrib-issuetracker-0.11.tar.gz" + + version('0.11', sha256='843753d8b5e989116378ab45ecccb368fb78dc56eaa1554ed25e4fbf22745f4e') + + depends_on('py-setuptools', type='build') + depends_on('py-sphinx@1.1:', type=('build', 'run')) + depends_on('py-requests@1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-jsmath/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-jsmath/package.py index 213dca354d..45ee46bc67 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-jsmath/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-jsmath/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py index 30ec4a0aba..56028f5163 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-qthelp/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-qthelp/package.py index 17c2ba1e95..86a58d456f 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-qthelp/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-qthelp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-serializinghtml/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-serializinghtml/package.py index ba43127222..97b79a8012 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-serializinghtml/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-serializinghtml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py index 4346ec4bff..c5a8f80a5b 100644 --- a/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-spyder/package.py b/var/spack/repos/builtin/packages/py-spyder/package.py index 607a52393b..a6ee780dd6 100644 --- a/var/spack/repos/builtin/packages/py-spyder/package.py +++ b/var/spack/repos/builtin/packages/py-spyder/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -39,6 +39,6 @@ class PySpyder(PythonPackage): # to pick up webkit, but this is the easier solution (see #9207) depends_on('qt+webkit', type=('build', 'run')) depends_on('py-pickleshare', type=('build', 'run')) - depends_on('py-zmq', type=('build', 'run')) + depends_on('py-pyzmq', type=('build', 'run')) depends_on('py-chardet@2.0.0:', type=('build', 'run')) depends_on('py-numpydoc', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-spykeutils/package.py b/var/spack/repos/builtin/packages/py-spykeutils/package.py index 19ee496146..bef3f0589d 100644 --- a/var/spack/repos/builtin/packages/py-spykeutils/package.py +++ b/var/spack/repos/builtin/packages/py-spykeutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py index 7f6512a60a..d951684c5c 100644 --- a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py +++ b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-statsmodels/package.py b/var/spack/repos/builtin/packages/py-statsmodels/package.py index 79f3ae49be..eebc206640 100644 --- a/var/spack/repos/builtin/packages/py-statsmodels/package.py +++ b/var/spack/repos/builtin/packages/py-statsmodels/package.py @@ -1,9 +1,10 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import glob class PyStatsmodels(PythonPackage): @@ -12,19 +13,36 @@ class PyStatsmodels(PythonPackage): homepage = "http://www.statsmodels.org" url = "https://pypi.io/packages/source/s/statsmodels/statsmodels-0.8.0.tar.gz" + version('0.10.1', sha256='320659a80f916c2edf9dfbe83512d9004bb562b72eedb7d9374562038697fa10') version('0.8.0', sha256='26431ab706fbae896db7870a0892743bfbb9f5c83231644692166a31d2d86048') variant('plotting', default=False, description='With matplotlib') + depends_on('python@:3.6', when='@:0.8.0', type=('build', 'run')) + # according to http://www.statsmodels.org/dev/install.html earlier versions # might work. depends_on('py-setuptools@0.6c5:', type='build') - depends_on('py-numpy@1.7.0:', type=('build', 'run')) - depends_on('py-scipy@0.11:', type=('build', 'run')) - depends_on('py-pandas@0.12:', type=('build', 'run')) - depends_on('py-patsy@0.2.1:', type=('build', 'run')) - depends_on('py-cython@0.24:', type=('build', 'run')) - depends_on('py-matplotlib@1.3:', type='run', when='+plotting') - - # TODO: Add a 'test' deptype - # depends_on('py-nose', type='test') + + depends_on('py-numpy@1.7.0:', type=('build', 'run'), when='@0.8.0') + depends_on('py-pandas@0.12:', type=('build', 'run'), when='@0.8.0') + depends_on('py-patsy@0.2.1:', type=('build', 'run'), when='@0.8.0') + depends_on('py-scipy@0.11:', type=('build', 'run'), when='@0.8.0') + depends_on('py-matplotlib@1.3:', type=('build', 'run'), when='@0.8.0 +plotting') + + # patsy@0.5.1 works around a Python change + # https://github.com/statsmodels/statsmodels/issues/5343 and + # https://github.com/pydata/patsy/pull/131 + depends_on('py-numpy', type=('build', 'run'), when='@0.10.1') + depends_on('py-pandas', type=('build', 'run'), when='@0.10.1') + depends_on('py-patsy', type=('build', 'run'), when='@0.10.1') + depends_on('py-scipy@0.5.1:', type=('build', 'run'), when='@0.10.1') + depends_on('py-matplotlib', type=('build', 'run'), when='@0.10.1 +plotting') + + depends_on('py-pytest', type='test') + + def test(self): + dirs = glob.glob("build/lib*") # There can be only one... + with working_dir(dirs[0]): + pytest = which('pytest') + pytest('statsmodels') diff --git a/var/spack/repos/builtin/packages/py-stestr/package.py b/var/spack/repos/builtin/packages/py-stestr/package.py new file mode 100644 index 0000000000..fbc7259d2c --- /dev/null +++ b/var/spack/repos/builtin/packages/py-stestr/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyStestr(PythonPackage): + """A parallel Python test runner built around subunit.""" + + homepage = "https://stestr.readthedocs.io/en/latest/" + url = "https://pypi.io/packages/source/s/stestr/stestr-2.5.1.tar.gz" + + version('2.5.1', sha256='151479fdf2db9f5f492b5285f4696f2d38960639054835dbdcd4c0687122c0fd') + + depends_on('python@2.7:', type=('build', 'run')) + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-stevedore/package.py b/var/spack/repos/builtin/packages/py-stevedore/package.py index 33bad888f9..d57b6f373b 100644 --- a/var/spack/repos/builtin/packages/py-stevedore/package.py +++ b/var/spack/repos/builtin/packages/py-stevedore/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-storm/package.py b/var/spack/repos/builtin/packages/py-storm/package.py index 0e31547293..dae4a9941d 100644 --- a/var/spack/repos/builtin/packages/py-storm/package.py +++ b/var/spack/repos/builtin/packages/py-storm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-stratify/package.py b/var/spack/repos/builtin/packages/py-stratify/package.py index 2323c0f551..bce0899efe 100644 --- a/var/spack/repos/builtin/packages/py-stratify/package.py +++ b/var/spack/repos/builtin/packages/py-stratify/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-subprocess32/package.py b/var/spack/repos/builtin/packages/py-subprocess32/package.py index 728be86016..9c362b30cf 100644 --- a/var/spack/repos/builtin/packages/py-subprocess32/package.py +++ b/var/spack/repos/builtin/packages/py-subprocess32/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,4 +12,7 @@ class PySubprocess32(PythonPackage): homepage = "https://pypi.python.org/pypi/subprocess32" url = "https://pypi.io/packages/source/s/subprocess32/subprocess32-3.2.7.tar.gz" + version('3.5.4', sha256='eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d') version('3.2.7', sha256='1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590') + + depends_on('py-setuptools', type='build', when='@3.5.0:') diff --git a/var/spack/repos/builtin/packages/py-subrosa/package.py b/var/spack/repos/builtin/packages/py-subrosa/package.py new file mode 100644 index 0000000000..19420f3574 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-subrosa/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySubrosa(PythonPackage): + """Subrosa is a Python implementation of Shamir's Secret Sharing. An + algorithm for sharing a secret with a group of people without letting any + individual of the group know the secret.""" + + homepage = "https://github.com/DasIch/subrosa/" + url = "https://github.com/DasIch/subrosa/archive/0.1.0.tar.gz" + + version('0.1.0', sha256='dc8172119a338874afa0bdcba035224c965ff71d2cbceda70b1ed2377aa390ea') + + depends_on('py-setuptools', type='build') + depends_on('py-gf256', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-svgpathtools/package.py b/var/spack/repos/builtin/packages/py-svgpathtools/package.py new file mode 100644 index 0000000000..b4e23be0a7 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-svgpathtools/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PySvgpathtools(PythonPackage): + """A collection of tools for manipulating and analyzing SVG Path objects + and Bezier curves.""" + + homepage = "https://pypi.org/project/svgpathtools/" + url = "https://pypi.io/packages/source/s/svgpathtools/svgpathtools-1.3.3.tar.gz" + + version('1.3.3', sha256='e4b3784ae41b725fbce6a33a8981210967b16d0b557cb5d98c0ed0c81f0f89b9') + + depends_on('py-setuptools', type='build') + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-svgwrite', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-svgwrite/package.py b/var/spack/repos/builtin/packages/py-svgwrite/package.py new file mode 100644 index 0000000000..23373f95e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-svgwrite/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PySvgwrite(PythonPackage): + """A Python library to create SVG drawings.""" + + homepage = "https://pypi.org/project/svgwrite/" + url = "https://pypi.io/packages/source/s/svgwrite/svgwrite-1.1.12.zip" + + version('1.1.12', sha256='968c99f193f34f0fa7f0b3e82f49b93789c7c45cd89ce190480f16020d41ab79') + + depends_on('py-setuptools', type='build') + depends_on('py-pyparsing@2.0.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-symengine/package.py b/var/spack/repos/builtin/packages/py-symengine/package.py index 3e3664f075..c9eb6078f0 100644 --- a/var/spack/repos/builtin/packages/py-symengine/package.py +++ b/var/spack/repos/builtin/packages/py-symengine/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,14 +10,14 @@ class PySymengine(PythonPackage): """Python wrappers for SymEngine, a symbolic manipulation library.""" homepage = "https://github.com/symengine/symengine.py" - url = "https://github.com/symengine/symengine.py/archive/v0.2.0.tar.gz" + url = "https://pypi.io/packages/source/s/symengine/symengine-0.2.0.tar.gz" git = "https://github.com/symengine/symengine.py.git" version('develop', branch='master') - version('0.2.0', sha256='8f6468137baa7f799e047dd0b9149c4017d8d32e755f1e0329209680879c1f8f') + version('0.2.0', sha256='78a14aea7aad5e7cbfb5cabe141581f9bba30e3c319690e5db8ad99fdf2d8885') # Build dependencies - depends_on('python@2.7:2.8,3.3:') + depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-cython@0.19.1:', type='build') depends_on('cmake@2.8.7:', type='build') diff --git a/var/spack/repos/builtin/packages/py-symfit/package.py b/var/spack/repos/builtin/packages/py-symfit/package.py index 6fac0315f3..2124792628 100644 --- a/var/spack/repos/builtin/packages/py-symfit/package.py +++ b/var/spack/repos/builtin/packages/py-symfit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-sympy/package.py b/var/spack/repos/builtin/packages/py-sympy/package.py index ec7b668c5c..7b588cd08c 100644 --- a/var/spack/repos/builtin/packages/py-sympy/package.py +++ b/var/spack/repos/builtin/packages/py-sympy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-syned/package.py b/var/spack/repos/builtin/packages/py-syned/package.py new file mode 100644 index 0000000000..12c1a98343 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-syned/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySyned(PythonPackage): + """A python library to define the components of a synchrotron beamline and + their positions. They can be read/write to json files. It is used by OASYS + as a common tool to define sources and optical systems that are then + exported to the different add-ons.""" + + homepage = "https://github.com/oasys-kit/syned" + git = "https://github.com/oasys-kit/syned.git" + + version('develop', branch='master') + + depends_on('py-numpy') + depends_on('py-scipy') + depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/py-systemd-python/package.py b/var/spack/repos/builtin/packages/py-systemd-python/package.py index e7ef51a145..82a9d44870 100644 --- a/var/spack/repos/builtin/packages/py-systemd-python/package.py +++ b/var/spack/repos/builtin/packages/py-systemd-python/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-tables/package.py b/var/spack/repos/builtin/packages/py-tables/package.py index 2fcb494c6c..8de84b4322 100644 --- a/var/spack/repos/builtin/packages/py-tables/package.py +++ b/var/spack/repos/builtin/packages/py-tables/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,18 +11,18 @@ class PyTables(PythonPackage): efficiently and easily cope with extremely large amounts of data.""" homepage = "http://www.pytables.org/" - url = "https://github.com/PyTables/PyTables/archive/v3.6.0.tar.gz" + url = "https://pypi.io/packages/source/t/tables/tables-3.6.1.tar.gz" import_modules = [ 'tables', 'tables.misc', 'tables.nodes', 'tables.scripts' ] - version('3.6.0', sha256='2dcd077f42b195f48aa00f5a720b79189ea92fba0d16ad35e2881e403ba6914e') - version('3.5.2', sha256='e4fc6f1194f02a8b10ff923e77364fb70710592f620d7de35f4d4e064dc70e91') - version('3.4.4', sha256='c9682c0f35d8175e12bbd38d925bdb606d47b7c8e358ba056a9dbf3b1f183114') - version('3.3.0', sha256='dceb15fef556a2775121bcc695561df4ff0e09248e0ce3a2d58f5244a9f61421') - version('3.2.2', sha256='2626e874caa6b3fcf2bfc28b9dd6a40a3f859c72e19ce0764a60a6d77e350008', - url='https://github.com/PyTables/PyTables/archive/v.3.2.2.tar.gz') + version('3.6.1', sha256='49a972b8a7c27a8a173aeb05f67acb45fe608b64cd8e9fa667c0962a60b71b49') + version('3.6.0', sha256='db3488214864fb313a611fca68bf1c9019afe4e7877be54d0e61c84416603d4d') + version('3.5.2', sha256='b220e32262bab320aa41d33125a7851ff898be97c0de30b456247508e2cc33c2') + version('3.4.4', sha256='bdc5c073712af2a43babd139c4855fc99496bb2c3f3f5d1b4770a985e6f9ce29') + version('3.3.0', sha256='8383ccf02e041a5d55494a09fc5514140b4653055a2732c981b5fd0f7408822c') + version('3.2.2', sha256='3564b351a71ec1737b503b001eb7ceae1f65d5d6e3ffe1ea75aafba10f37fa84') variant('zlib', default=True, description='Support for zlib compression') variant('bzip2', default=False, description='Support for bzip2 compression') diff --git a/var/spack/repos/builtin/packages/py-tabulate/package.py b/var/spack/repos/builtin/packages/py-tabulate/package.py index 17fc9e34f5..4baf18c70d 100644 --- a/var/spack/repos/builtin/packages/py-tabulate/package.py +++ b/var/spack/repos/builtin/packages/py-tabulate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,8 +10,10 @@ class PyTabulate(PythonPackage): """Pretty-print tabular data""" homepage = "https://bitbucket.org/astanin/python-tabulate" - url = "https://pypi.io/packages/source/t/tabulate/tabulate-0.7.7.tar.gz" + url = "https://pypi.io/packages/source/t/tabulate/tabulate-0.8.6.tar.gz" + version('0.8.6', sha256='5470cc6687a091c7042cee89b2946d9235fe9f6d49c193a4ae2ac7bf386737c8') + version('0.8.3', sha256='8af07a39377cee1103a5c8b3330a421c2d99b9141e9cc5ddd2e3263fea416943') version('0.7.7', sha256='83a0b8e17c09f012090a50e1e97ae897300a72b35e0c86c0b53d3bd2ae86d8c6') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-tappy/package.py b/var/spack/repos/builtin/packages/py-tap-py/package.py index 1c97e7a763..e3f453763d 100644 --- a/var/spack/repos/builtin/packages/py-tappy/package.py +++ b/var/spack/repos/builtin/packages/py-tap-py/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,10 +6,10 @@ from spack import * -class PyTappy(PythonPackage): +class PyTapPy(PythonPackage): """Python TAP interface module for unit tests""" + homepage = "https://github.com/mblayman/tappy" - # base https://pypi.python.org/pypi/cffi url = "https://pypi.io/packages/source/t/tap.py/tap.py-1.6.tar.gz" version('1.6', sha256='3ee315567cd1cf444501c405b7f7146ffdb2e630bac58d0840d378a3b9a0dbe4') diff --git a/var/spack/repos/builtin/packages/py-tatsu/package.py b/var/spack/repos/builtin/packages/py-tatsu/package.py new file mode 100644 index 0000000000..8b157932bf --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tatsu/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTatsu(PythonPackage): + """TatSu (the successor to Grako) is a tool that takes grammars in + a variation of EBNF as input, and outputs memoizing (Packrat) PEG + parsers in Python.""" + + homepage = "https://github.com/neogeny/tatsu" + url = "https://pypi.io/packages/source/T/TatSu/TatSu-4.4.0.zip" + + version('4.4.0', sha256='80713413473a009f2081148d0f494884cabaf9d6866b71f2a68a92b6442f343d') + + variant('future_regex', default=True, description='Use regex implementation') + + depends_on('python@3.6:', type=('build', 'run'), when='@4.5:') + depends_on('py-setuptools', type='build') + # part of the standard lib in python@3.7.0, required in the current HEAD + depends_on('py-dataclasses@0.6:', type=('build', 'run'), when='@4.5:^python@:3.6.99') + depends_on('py-pytest-mypy', type='test') + # optional dependency, otherwise falls back to standard implementation + depends_on('py-regex@2018.8:', type=('build', 'run'), when='+future_regex') diff --git a/var/spack/repos/builtin/packages/py-tblib/package.py b/var/spack/repos/builtin/packages/py-tblib/package.py index 253df4e5ae..5234fde4e0 100644 --- a/var/spack/repos/builtin/packages/py-tblib/package.py +++ b/var/spack/repos/builtin/packages/py-tblib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-tempora/package.py b/var/spack/repos/builtin/packages/py-tempora/package.py new file mode 100644 index 0000000000..cb69e148ad --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tempora/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTempora(PythonPackage): + """Objects and routines pertaining to date and time (tempora) """ + + homepage = "https://github.com/jaraco/tempora" + url = "https://pypi.io/packages/source/t/tempora/tempora-1.14.1.tar.gz" + + version('1.14.1', sha256='cb60b1d2b1664104e307f8e5269d7f4acdb077c82e35cd57246ae14a3427d2d6') + + depends_on('py-setuptools', type='build') + depends_on('py-setuptools-scm@1.15.0:', type='build') + depends_on('py-six', type=('build', 'run')) + depends_on('py-pytz', type=('build', 'run')) + depends_on('py-jaraco-functools@1.20:', type=('build', 'run')) + depends_on('python@2.7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-tensorflow-estimator/package.py b/var/spack/repos/builtin/packages/py-tensorflow-estimator/package.py new file mode 100644 index 0000000000..638d011f72 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tensorflow-estimator/package.py @@ -0,0 +1,47 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTensorflowEstimator(Package): + """TensorFlow Estimator is a high-level TensorFlow API that greatly + simplifies machine learning programming.""" + + homepage = "https://github.com/tensorflow/estimator" + url = "https://github.com/tensorflow/estimator/archive/v1.13.0.tar.gz" + + version('2.0.0', sha256='6f4bdf1ab219e1f1cba25d2af097dc820f56479f12a839853d97422fe4d8b465') + version('1.13.0', sha256='a787b150ff436636df723e507019c72a5d6486cfe506886279d380166953f12f', preferred=True) + + extends('python') + + depends_on('py-tensorflow@2.0.0', when='@2.0.0') + depends_on('py-tensorflow@1.13.1', when='@1.13.0') + + depends_on('bazel@0.19.0', type='build') + depends_on('py-pip', type='build') + depends_on('py-funcsigs@1.0.2:', type=('build', 'run')) + + def install(self, spec, prefix): + tmp_path = join_path(env.get('SPACK_TMPDIR', '/tmp/spack'), + 'tf-estimator', + self.module.site_packages_dir[1:]) + mkdirp(tmp_path) + env['TEST_TMPDIR'] = tmp_path + env['HOME'] = tmp_path + + # bazel uses system PYTHONPATH instead of spack paths + bazel('--action_env', 'PYTHONPATH={0}'.format(env['PYTHONPATH']), + '//tensorflow_estimator/tools/pip_package:build_pip_package') + + build_pip_package = Executable(join_path( + 'bazel-bin/tensorflow_estimator/tools', + 'pip_package/build_pip_package')) + build_pip_package(tmp_path) + + pip = Executable('pip') + pip('install', '--prefix={0}'.format(prefix), + '--find-links={0}'.format(tmp_path), 'tensorflow-estimator') diff --git a/var/spack/repos/builtin/packages/py-tensorflow/crosstool.patch b/var/spack/repos/builtin/packages/py-tensorflow/crosstool.patch new file mode 100644 index 0000000000..3583211cab --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tensorflow/crosstool.patch @@ -0,0 +1,21 @@ ++++ tensorflow-1.0.0-rc2/third_party/gpus/crosstool/clang/bin/crosstool_wrapper_driver_is_not_gcc.tpl 2017-02-15 20:40:47.633496842 +0100 +--- tensorflow-1.0.0-rc2/third_party/gpus/crosstool/clang/bin/crosstool_wrapper_driver_is_not_gcc.tpl 2017-02-08 19:32:14.000000000 +0100 +@@ -46,13 +46,13 @@ import sys + import pipes + + # Template values set by cuda_autoconf. +-CPU_COMPILER = ('%{cpu_compiler}') +-GCC_HOST_COMPILER_PATH = ('%{gcc_host_compiler_path}') ++CPU_COMPILER = os.environ['SPACK_CC'] ++GCC_HOST_COMPILER_PATH = CPU_COMPILER + + CURRENT_DIR = os.path.dirname(sys.argv[0]) + NVCC_PATH = CURRENT_DIR + '/../../../cuda/bin/nvcc' +-LLVM_HOST_COMPILER_PATH = ('/usr/bin/gcc') +-PREFIX_DIR = os.path.dirname(GCC_HOST_COMPILER_PATH) ++LLVM_HOST_COMPILER_PATH = os.environ['SPACK_CC'] ++PREFIX_DIR = os.path.dirname(os.environ['SPACK_CC']) + NVCC_VERSION = '%{cuda_version}' + + def Log(s): + diff --git a/var/spack/repos/builtin/packages/py-tensorflow/http_archive.patch b/var/spack/repos/builtin/packages/py-tensorflow/http_archive.patch new file mode 100644 index 0000000000..ea919567c1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tensorflow/http_archive.patch @@ -0,0 +1,57 @@ +diff --git a/WORKSPACE b/WORKSPACE +index 1796182..84b5eab 100644 +--- a/WORKSPACE ++++ b/WORKSPACE +@@ -1,5 +1,7 @@ + workspace(name = "org_tensorflow") + ++load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive", "http_file") ++ + http_archive( + name = "io_bazel_rules_closure", + sha256 = "a38539c5b5c358548e75b44141b4ab637bba7c4dc02b46b1f62a96d6433f56ae", +@@ -30,7 +32,7 @@ android_workspace() + # Please add all new TensorFlow dependencies in workspace.bzl. + tf_workspace() + +-new_http_archive( ++http_archive( + name = "inception_v1", + build_file = "models.BUILD", + sha256 = "7efe12a8363f09bc24d7b7a450304a15655a57a7751929b2c1593a71183bb105", +@@ -40,7 +42,7 @@ new_http_archive( + ], + ) + +-new_http_archive( ++http_archive( + name = "mobile_ssd", + build_file = "models.BUILD", + sha256 = "bddd81ea5c80a97adfac1c9f770e6f55cbafd7cce4d3bbe15fbeb041e6b8f3e8", +@@ -50,7 +52,7 @@ new_http_archive( + ], + ) + +-new_http_archive( ++http_archive( + name = "mobile_multibox", + build_file = "models.BUILD", + sha256 = "859edcddf84dddb974c36c36cfc1f74555148e9c9213dedacf1d6b613ad52b96", +@@ -60,7 +62,7 @@ new_http_archive( + ], + ) + +-new_http_archive( ++http_archive( + name = "stylize", + build_file = "models.BUILD", + sha256 = "3d374a730aef330424a356a8d4f04d8a54277c425e274ecb7d9c83aa912c6bfa", +@@ -70,7 +72,7 @@ new_http_archive( + ], + ) + +-new_http_archive( ++http_archive( + name = "speech_commands", + build_file = "models.BUILD", + sha256 = "c3ec4fea3158eb111f1d932336351edfe8bd515bb6e87aad4f25dbad0a600d0c", diff --git a/var/spack/repos/builtin/packages/py-tensorflow/io_bazel_rules_docker2.patch b/var/spack/repos/builtin/packages/py-tensorflow/io_bazel_rules_docker2.patch new file mode 100644 index 0000000000..5b341e69f1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tensorflow/io_bazel_rules_docker2.patch @@ -0,0 +1,18 @@ +diff --git a/WORKSPACE b/WORKSPACE +index 74ea14d..0b09a6e 100644 +--- a/WORKSPACE ++++ b/WORKSPACE +@@ -34,6 +34,13 @@ load( + + bazel_toolchains_repositories() + ++http_archive( ++ name = "io_bazel_rules_docker", ++ sha256 = "413bb1ec0895a8d3249a01edf24b82fd06af3c8633c9fb833a0cb1d4b234d46d", ++ strip_prefix = "rules_docker-0.12.0", ++ urls = ["https://github.com/bazelbuild/rules_docker/releases/download/v0.12.0/rules_docker-v0.12.0.tar.gz"], ++) ++ + load( + "@io_bazel_rules_docker//repositories:repositories.bzl", + container_repositories = "repositories", diff --git a/var/spack/repos/builtin/packages/py-tensorflow/package.py b/var/spack/repos/builtin/packages/py-tensorflow/package.py new file mode 100644 index 0000000000..d493c32283 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tensorflow/package.py @@ -0,0 +1,711 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +import glob +import os +import sys + + +class PyTensorflow(Package, CudaPackage): + """TensorFlow is an Open Source Software Library for Machine Intelligence + """ + + homepage = "https://www.tensorflow.org" + url = "https://github.com/tensorflow/tensorflow/archive/v2.1.0.tar.gz" + + maintainers = ['adamjstewart'] + import_modules = ['tensorflow'] + + version('2.1.0', sha256='638e541a4981f52c69da4a311815f1e7989bf1d67a41d204511966e1daed14f7') + version('2.0.1', sha256='29197d30923b9670992ee4b9c6161f50c7452e9a4158c720746e846080ac245a') + version('2.0.0', sha256='49b5f0495cd681cbcb5296a4476853d4aea19a43bdd9f179c928a977308a0617') + version('1.15.2', sha256='d95d75d26a298211b5e802842e87fda5b8b14f6ad83719377b391e5fb71b8746') + version('1.15.1', sha256='19b6e72bc8675937f618cede364d7228a71c2eeaffc42801bcefd98dda7ca056') + version('1.15.0', sha256='a5d49c00a175a61da7431a9b289747d62339be9cf37600330ad63b611f7f5dc9') + version('1.14.0', sha256='aa2a6a1daafa3af66807cfe0bc77bfe1144a9a53df9a96bab52e3e575b3047ed') + version('1.13.2', sha256='abe3bf0c47845a628b7df4c57646f41a10ee70f914f1b018a5c761be75e1f1a9') + version('1.13.1', sha256='7cd19978e6bc7edc2c847bce19f95515a742b34ea5e28e4389dade35348f58ed') + version('1.12.3', sha256='b9e5488e84f4a133ed20b18605f0cd6301f11d356bd959712db4e7b9301d0462') + version('1.12.2', sha256='90ffc7cf1df5e4b8385c9108db18d5d5034ec423547c0e167d44f5746a20d06b') + version('1.12.1', sha256='7b559a3ae56322b7a7e4307f45f9fce96022c533a98b32c18bfdff8c5838271d') + version('1.12.0', sha256='3c87b81e37d4ed7f3da6200474fa5e656ffd20d8811068572f43610cae97ca92') + version('1.11.0', sha256='f49ce3f1d04cee854bc9f74fa9696991140b34a2e2447f35f01391b72c8bfa9f') + version('1.10.1', sha256='83092d709800e2d93d4d4b1bcacaeb74f2f328962ed764cb35bbee20402879c6') + version('1.10.0', sha256='ee9cb98d9e0d8106f2f4ed52a38fe89399324af303e1401567e5b64a9f86744b') + version('1.9.0', sha256='ffc3151b06823d57b4a408261ba8efe53601563dfe93af0866751d4f6ca5068c') + version('1.8.0', sha256='47646952590fd213b747247e6870d89bb4a368a95ae3561513d6c76e44f92a75') + version('1.7.1', sha256='3147f8c60d1f30da23a831bcf732e74b935dcee7c62e4b8b85f0f093030b52c8') + version('1.7.0', sha256='c676a96fc8700722816b2b98c85578b2f99fac7a7b2484c9c7f0641484f8d50d') + version('1.6.0', sha256='03cf1423446abbead6bd8c3cf6e6affa7d99746cd119691b012aac9a1795f4fb') + version('1.5.1', sha256='cab2157783905e12a7a3baae3264edfb739dd92d5658019a131fff4b14190240') + version('1.5.0', sha256='0642781c3a3a8c2c4834b91b86aec385f0b2ada7d721571458079478cc5b29c8') + version('1.4.1', sha256='1f75e463318419a1b3ae076d5a92697c1d3a85e8377c946a5510b651ff5c0d60') + version('1.4.0', sha256='8a0ad8d61f8f6c0282c548661994a5ab83ac531bac496c3041dedc1ab021107b') + version('1.3.1', sha256='ded509c209f8a1d390df8a2f44be5b5c29963172b0e0f095304efb59765d0523') + version('1.3.0', sha256='e1af1bb767b57c3416de0d43a5f74d174c42b85231dffd36f3630173534d4307') + version('1.2.1', sha256='f2baf09b1a9a0500907b4d5cb5473070b3ecede06ed6e8d1096873c91922fb9e') + version('1.2.0', sha256='03dbf7548d1fc1c11ed58da5fa68616f795c819f868f43478cbcaa26abed374f') + version('1.1.0', sha256='aad4470f52fa59f54de7b9a2da727429e6755d91d756f245f952698c42a60027') + version('1.0.1', sha256='deea3c65e0703da96d9c3f1162e464c51d37659dd129396af134e9e8f1ea8c05') + version('1.0.0', sha256='db8b3b8f4134b7c9c1b4165492ad5d5bb78889fcd99ffdffc325e97da3e8c677') + version('0.12.0', sha256='13a1d4e98c82eae7e26fe75384de1517d6126f63ba5d302392ec02ac3ae4b1b9') + version('0.11.0', sha256='24242ff696234bb1e58d09d45169b148525ccb706f980a4a92ddd3b82c7546dc') + version('0.10.0', sha256='f32df04e8f7186aaf6723fc5396733b2f6c2fd6fe4a53a54a68b80f3ec855680') + version('0.9.0', sha256='3128c396af19518c642d3e590212291e1d93c5b047472a10cf3245b53adac9c9') + version('0.8.0', sha256='f201ba7fb7609a6416968d4e1920d87d67be693b5bc7d34b6b4a79860a9a8a4e') + version('0.7.1', sha256='ef34121432f7a522cf9f99a56cdd86e370cc5fa3ee31255ca7cb17f36b8dfc0d') + version('0.7.0', sha256='43dd3051f947aa66e6fc09dac2f86a2efe2e019736bbd091c138544b86d717ce') + version('0.6.0', sha256='f86ace45e99053b09749cd55ab79c57274d8c7460ae763c5e808d81ffbc3b657') + + variant('mkl', default=False, description='Build with MKL support') + variant('jemalloc', default=False, description='Build with jemalloc as malloc support') + variant('gcp', default=False, description='Build with Google Cloud Platform support') + variant('hdfs', default=False, description='Build with Hadoop File System support') + variant('aws', default=False, description='Build with Amazon AWS Platform support') + variant('kafka', default=False, description='Build with Apache Kafka Platform support') + variant('ignite', default=False, description='Build with Apache Ignite support') + variant('xla', default=False, description='Build with XLA JIT support') + variant('gdr', default=False, description='Build with GDR support') + variant('verbs', default=False, description='Build with libverbs support') + variant('ngraph', default=False, description='Build with Intel nGraph support') + variant('opencl', default=False, description='Build with OpenCL SYCL support') + variant('computecpp', default=False, description='Build with ComputeCPP support') + variant('rocm', default=False, description='Build with ROCm support') + variant('tensorrt', default=False, description='Build with TensorRT support') + variant('cuda', default=sys.platform != 'darwin', description='Build with CUDA support') + variant('nccl', default=sys.platform.startswith('linux'), description='Enable NVIDIA NCCL support') + variant('mpi', default=False, description='Build with MPI support') + variant('android', default=False, description='Configure for Android builds') + variant('ios', default=False, description='Build with iOS support (macOS only)') + variant('monolithic', default=False, description='Static monolithic build') + variant('numa', default=False, description='Build with NUMA support') + variant('dynamic_kernels', default=False, description='Build kernels into separate shared objects') + + extends('python') + + # TODO: Older versions of TensorFlow don't list the viable version range, + # just the minimum version of bazel that will work. The latest version of + # bazel doesn't seem to work, so for now we force them to use min version. + # Need to investigate further. + + # See _TF_MIN_BAZEL_VERSION and _TF_MAX_BAZEL_VERSION in configure.py + depends_on('bazel@0.27.1:0.29.1', type='build', when='@2.1:') + depends_on('bazel@0.24.1:0.26.1', type='build', when='@1.15:2.0') + # See call to check_bazel_version in configure.py + depends_on('bazel@0.24.1:0.25.2', type='build', when='@1.14.0') + depends_on('bazel@0.19.0:0.21.0', type='build', when='@1.13.0:1.13.2') + depends_on('bazel@0.24.1:0.25.0', type='build', when='@1.12.1') + depends_on('bazel@0.15.0', type='build', when='@1.10:1.12.0,1.12.2:1.12.3') + depends_on('bazel@0.10.0', type='build', when='@1.7:1.9') + # See call to check_version in tensorflow/workspace.bzl + depends_on('bazel@0.5.4', type='build', when='@1.4:1.6') + # See MIN_BAZEL_VERSION in configure + depends_on('bazel@0.4.5', type='build', when='@1.2:1.3') + # See call to check_version in WORKSPACE + depends_on('bazel@0.4.2', type='build', when='@1.0:1.1') + depends_on('bazel@0.3.2', type='build', when='@0.12.0:0.12.1') + depends_on('bazel@0.3.0', type='build', when='@0.11.0') + depends_on('bazel@0.2.0', type='build', when='@0.9:0.10') + depends_on('bazel@0.1.4', type='build', when='@0.7:0.8') + depends_on('bazel@0.1.1', type='build', when='@0.5:0.6') + + depends_on('swig', type='build') + depends_on('py-setuptools', type='build') + depends_on('py-future', type='build', when='^python@:2') + + # Listed under REQUIRED_PACKAGES in tensorflow/tools/pip_package/setup.py + depends_on('py-absl-py@0.7.0:', type=('build', 'run'), when='@1.12.1,1.14:') + depends_on('py-absl-py@0.1.6:', type=('build', 'run'), when='@1.5:') + depends_on('py-astor@0.6.0:', type=('build', 'run'), when='@1.6:') + depends_on('py-backports-weakref@1.0:', type=('build', 'run'), when='@1.3: ^python@:3.3') + depends_on('py-backports-weakref@1.0rc1', type=('build', 'run'), when='@1.2.0:1.2.1') + depends_on('py-enum34@1.1.6:', type=('build', 'run'), when='@1.5: ^python@:3.3') + depends_on('py-enum34@1.1.6:', type=('build', 'run'), when='@1.4.0:1.4.1') + depends_on('py-gast@0.2.2', type=('build', 'run'), when='@1.15:') + depends_on('py-gast@0.2.0:', type=('build', 'run'), when='@1.6:') + depends_on('py-google-pasta@0.1.6:', type=('build', 'run'), when='@1.14:') + depends_on('py-google-pasta@0.1.2:', type=('build', 'run'), when='@1.12.1') + depends_on('py-keras-applications@1.0.8:', type=('build', 'run'), when='@1.15:') + depends_on('py-keras-applications@1.0.6:', type=('build', 'run'), when='@1.12:') + depends_on('py-keras-applications@1.0.5:', type=('build', 'run'), when='@1.11:') + depends_on('py-keras-preprocessing@1.1.0:', type=('build', 'run'), when='@2.1:') + depends_on('py-keras-preprocessing@1.0.5:', type=('build', 'run'), when='@1.12:') + depends_on('py-keras-preprocessing@1.0.3:', type=('build', 'run'), when='@1.11:') + depends_on('py-numpy@1.16.0:1.999', type=('build', 'run'), when='@1.13.2,1.15:') + depends_on('py-numpy@1.14.5:1.999', type=('build', 'run'), when='@1.12.1,1.14.0') + depends_on('py-numpy@1.13.3:1.14.5', type=('build', 'run'), when='@1.10.0:1.10.1') + depends_on('py-numpy@1.13.3:', type=('build', 'run'), when='@1.6:') + depends_on('py-numpy@1.12.1:', type=('build', 'run'), when='@1.4:') + depends_on('py-numpy@1.11.0:', type=('build', 'run'), when='@0.11:') + depends_on('py-numpy@1.10.1:', type=('build', 'run'), when='@0.7.1: platform=darwin') + depends_on('py-numpy@1.8.2:', type=('build', 'run'), when='@0.6:') + depends_on('py-numpy@1.9.2:', type=('build', 'run'), when='@0.5.0') + depends_on('py-opt-einsum@2.3.2:', type=('build', 'run'), when='@1.15:') + depends_on('py-protobuf@3.8.0:', type=('build', 'run'), when='@2.1:') + depends_on('py-protobuf@3.6.1:', type=('build', 'run'), when='@1.12:') + depends_on('py-protobuf@3.6.0:', type=('build', 'run'), when='@1.10:') + depends_on('py-protobuf@3.4.0:', type=('build', 'run'), when='@1.5:') + depends_on('py-protobuf@3.3.0:', type=('build', 'run'), when='@1.3:') + depends_on('py-protobuf@3.2.0:', type=('build', 'run'), when='@1.1:') + depends_on('py-protobuf@3.1.0:', type=('build', 'run'), when='@0.12.1:') + depends_on('py-protobuf@3.1.0', type=('build', 'run'), when='@0.12.0') + depends_on('py-protobuf@3.0.0', type=('build', 'run'), when='@0.11.0') + depends_on('py-protobuf@3.0.0b2', type=('build', 'run'), when='@0.7.1:0.10') + depends_on('py-protobuf@3.0.0a3', type=('build', 'run'), when='@0.6:0.7.0') + # tensorboard + # tensorflow-estimator + depends_on('py-termcolor@1.1.0:', type=('build', 'run'), when='@1.6:') + depends_on('py-wrapt@1.11.1:', type=('build', 'run'), when='@1.12.1,1.14:') + depends_on('py-wheel', type=('build', 'run'), when='@0.6:') + depends_on('py-wheel@0.26:', type=('build', 'run'), when='@0.6: ^python@3:') + depends_on('py-mock@2.0.0:', type=('build', 'run'), when='@0.10: ^python@:2') + depends_on('py-functools32@3.2.3:', type=('build', 'run'), when='@1.15: ^python@:2') + depends_on('py-six@1.12.0:', type=('build', 'run'), when='@2.1:') + depends_on('py-six@1.10.0:', type=('build', 'run'), when='@:2.0') + depends_on('py-scipy@1.2.2', type=('build', 'run'), when='@2.1: ^python@:2') + depends_on('py-scipy@1.4.1', type=('build', 'run'), when='@2.1: ^python@3:') + depends_on('py-grpcio@1.8.6:', type=('build', 'run'), when='@1.6:1.7') + if sys.byteorder == 'little': + # Only builds correctly on little-endian machines + depends_on('py-grpcio@1.8.6:', type=('build', 'run'), when='@1.8:') + + # Listed under TEST_PACKAGES in tensorflow/tools/pip_package/setup.py + depends_on('py-scipy@0.15.1:', type='test') + + # TODO: add packages for some of these dependencies + depends_on('mkl', when='+mkl') + depends_on('curl', when='+gcp') + # depends_on('computecpp', when='+opencl+computecpp') + # depends_on('trisycl', when='+opencl~computepp') + depends_on('cudnn', when='+cuda') + depends_on('cudnn@6.5', when='@0.5:0.6 +cuda') + # depends_on('tensorrt', when='+tensorrt') + depends_on('nccl', when='+nccl') + depends_on('mpi', when='+mpi') + # depends_on('android-ndk@10:18', when='+android') + # depends_on('android-sdk', when='+android') + + # Check configure and configure.py to see when these variants are supported + conflicts('+mkl', when='@:1.0') + conflicts('+mkl', when='platform=darwin', msg='Darwin is not yet supported') + conflicts('+jemalloc', when='@:0') + conflicts('+jemalloc', when='platform=darwin', msg='Currently jemalloc is only support on Linux platform') + conflicts('+jemalloc', when='platform=cray', msg='Currently jemalloc is only support on Linux platform') + conflicts('+jemalloc', when='platform=bgq', msg='Currently jemalloc is only support on Linux platform') + conflicts('+gcp', when='@:0.8') + conflicts('+hdfs', when='@:0.10') + conflicts('+aws', when='@:1.3') + conflicts('+kafka', when='@:1.5,2.1:') + conflicts('+ignite', when='@:1.11,2.1:') + conflicts('+xla', when='@:0') + conflicts('+gdr', when='@:1.3') + conflicts('+verbs', when='@:1.1') + conflicts('+ngraph', when='@:1.10') + conflicts('+opencl', when='@:0.11') + conflicts('+computecpp', when='@:0.11') + conflicts('+computecpp', when='~opencl') + conflicts('+rocm', when='@:1.11') + conflicts('+cuda', when='platform=darwin', msg='There is no GPU support for macOS') + conflicts('cuda_arch=none', when='+cuda', msg='Must specify CUDA compute capabilities of your GPU, see https://developer.nvidia.com/cuda-gpus') + conflicts('cuda_arch=20', when='@1.12.1,1.14:', msg='TensorFlow only supports compute capabilities >= 3.5') + conflicts('cuda_arch=30', when='@1.12.1,1.14:', msg='TensorFlow only supports compute capabilities >= 3.5') + conflicts('cuda_arch=32', when='@1.12.1,1.14:', msg='TensorFlow only supports compute capabilities >= 3.5') + conflicts('cuda_arch=20', when='@1.4:1.12.0,1.12.2:1.12.3', msg='Only compute capabilities 3.0 or higher are supported') + conflicts('+tensorrt', when='@:1.5') + conflicts('+tensorrt', when='~cuda') + conflicts('+tensorrt', when='platform=darwin', msg='Currently TensorRT is only supported on Linux platform') + conflicts('+tensorrt', when='platform=cray', msg='Currently TensorRT is only supported on Linux platform') + conflicts('+tensorrt', when='platform=bgq', msg='Currently TensorRT is only supported on Linux platform') + conflicts('+nccl', when='@:1.7') + conflicts('+nccl', when='~cuda') + conflicts('+nccl', when='platform=darwin', msg='Currently NCCL is only supported on Linux platform') + conflicts('+nccl', when='platform=cray', msg='Currently NCCL is only supported on Linux platform') + conflicts('+nccl', when='platform=bgq', msg='Currently NCCL is only supported on Linux platform') + conflicts('+mpi', when='@:1.2') + conflicts('+android', when='@:1.4') + conflicts('+ios', when='@:1.12.0,1.12.2:1.13') + conflicts('+ios', when='platform=linux', msg='iOS support only available on macOS') + conflicts('+ios', when='platform=cray', msg='iOS support only available on macOS') + conflicts('+ios', when='platform=bgq', msg='iOS support only available on macOS') + conflicts('+monolithic', when='@:1.3') + conflicts('+numa', when='@:1.12.0,1.12.2:1.13') + conflicts('+dynamic_kernels', when='@:1.12.0,1.12.2:1.12.3') + + # TODO: why is this needed? + patch('url-zlib.patch', when='@0.10.0') + # TODO: why is this needed? + patch('crosstool.patch', when='@0.10.0+cuda') + # Avoid build error: "no such package '@io_bazel_rules_docker..." + patch('io_bazel_rules_docker2.patch', when='@1.15:2.0') + # Avoide build error: "name 'new_http_archive' is not defined" + patch('http_archive.patch', when='@1.12.3') + + phases = ['configure', 'build', 'install'] + + # https://www.tensorflow.org/install/source + def setup_build_environment(self, env): + spec = self.spec + + # Please specify the location of python + env.set('PYTHON_BIN_PATH', spec['python'].command.path) + + # Please input the desired Python library path to use + env.set('PYTHON_LIB_PATH', site_packages_dir) + + # Ensure swig is in PATH or set SWIG_PATH + env.set('SWIG_PATH', spec['swig'].prefix.bin.swig) + + # Do you wish to build TensorFlow with MKL support? + if '+mkl' in spec: + env.set('TF_NEED_MKL', '1') + + # Do you wish to download MKL LIB from the web? + env.set('TF_DOWNLOAD_MKL', '0') + + # Please specify the location where MKL is installed + env.set('MKL_INSTALL_PATH', spec['mkl'].prefix) + else: + env.set('TF_NEED_MKL', '0') + + # Do you wish to build TensorFlow with jemalloc as malloc support? + if '+jemalloc' in spec: + env.set('TF_NEED_JEMALLOC', '1') + else: + env.set('TF_NEED_JEMALLOC', '0') + + # Do you wish to build TensorFlow with Google Cloud Platform support? + if '+gcp' in spec: + env.set('TF_NEED_GCP', '1') + else: + env.set('TF_NEED_GCP', '0') + + # Do you wish to build TensorFlow with Hadoop File System support? + if '+hdfs' in spec: + env.set('TF_NEED_HDFS', '1') + else: + env.set('TF_NEED_HDFS', '0') + + # Do you wish to build TensorFlow with Amazon AWS Platform support? + if '+aws' in spec: + env.set('TF_NEED_AWS', '1') + env.set('TF_NEED_S3', '1') + else: + env.set('TF_NEED_AWS', '0') + env.set('TF_NEED_S3', '0') + + # Do you wish to build TensorFlow with Apache Kafka Platform support? + if '+kafka' in spec: + env.set('TF_NEED_KAFKA', '1') + else: + env.set('TF_NEED_KAFKA', '0') + + # Do you wish to build TensorFlow with Apache Ignite support? + if '+ignite' in spec: + env.set('TF_NEED_IGNITE', '1') + else: + env.set('TF_NEED_IGNITE', '0') + + # Do you wish to build TensorFlow with XLA JIT support? + if '+xla' in spec: + env.set('TF_ENABLE_XLA', '1') + else: + env.set('TF_ENABLE_XLA', '0') + + # Do you wish to build TensorFlow with GDR support? + if '+gdr' in spec: + env.set('TF_NEED_GDR', '1') + else: + env.set('TF_NEED_GDR', '0') + + # Do you wish to build TensorFlow with VERBS support? + if '+verbs' in spec: + env.set('TF_NEED_VERBS', '1') + else: + env.set('TF_NEED_VERBS', '0') + + # Do you wish to build TensorFlow with nGraph support? + if '+ngraph' in spec: + env.set('TF_NEED_NGRAPH', '1') + else: + env.set('TF_NEED_NGRAPH', '0') + + # Do you wish to build TensorFlow with OpenCL SYCL support? + if '+opencl' in spec: + env.set('TF_NEED_OPENCL_SYCL', '1') + env.set('TF_NEED_OPENCL', '1') + + # Please specify which C++ compiler should be used as the host + # C++ compiler + env.set('HOST_CXX_COMPILER', spack_cxx) + + # Please specify which C compiler should be used as the host + # C compiler + env.set('HOST_C_COMPILER', spack_cc) + + # Do you wish to build TensorFlow with ComputeCPP support? + if '+computecpp' in spec: + env.set('TF_NEED_COMPUTECPP', '1') + + # Please specify the location where ComputeCpp is installed + env.set('COMPUTECPP_TOOLKIT_PATH', spec['computecpp'].prefix) + else: + env.set('TF_NEED_COMPUTECPP', '0') + + # Please specify the location of the triSYCL include directory + env.set('TRISYCL_INCLUDE_DIR', spec['trisycl'].prefix.include) + else: + env.set('TF_NEED_OPENCL_SYCL', '0') + env.set('TF_NEED_OPENCL', '0') + + # Do you wish to build TensorFlow with ROCm support? + if '+rocm' in spec: + env.set('TF_NEED_ROCM', '1') + else: + env.set('TF_NEED_ROCM', '0') + + # Do you wish to build TensorFlow with CUDA support? + if '+cuda' in spec: + env.set('TF_NEED_CUDA', '1') + + # Do you want to use clang as CUDA compiler? + env.set('TF_CUDA_CLANG', '0') + + # Please specify which gcc nvcc should use as the host compiler + env.set('GCC_HOST_COMPILER_PATH', spack_cc) + + cuda_paths = [ + spec['cuda'].prefix, + spec['cudnn'].prefix, + ] + + # Do you wish to build TensorFlow with TensorRT support? + if '+tensorrt' in spec: + env.set('TF_NEED_TENSORRT', '1') + + cuda_paths.append(spec['tensorrt'].prefix) + + # Please specify the TensorRT version you want to use + env.set('TF_TENSORRT_VERSION', + spec['tensorrt'].version.up_to(1)) + + # Please specify the location where TensorRT is installed + env.set('TENSORRT_INSTALL_PATH', spec['tensorrt'].prefix) + else: + env.set('TF_NEED_TENSORRT', '0') + env.unset('TF_TENSORRT_VERSION') + + # Please specify the CUDA SDK version you want to use + env.set('TF_CUDA_VERSION', spec['cuda'].version.up_to(2)) + + # Please specify the cuDNN version you want to use + env.set('TF_CUDNN_VERSION', spec['cudnn'].version.up_to(1)) + + if '+nccl' in spec: + cuda_paths.append(spec['nccl'].prefix) + + # Please specify the locally installed NCCL version to use + env.set('TF_NCCL_VERSION', spec['nccl'].version.up_to(1)) + + # Please specify the location where NCCL is installed + env.set('NCCL_INSTALL_PATH', spec['nccl'].prefix) + env.set('NCCL_HDR_PATH', spec['nccl'].prefix.include) + else: + env.unset('TF_NCCL_VERSION') + + # Please specify the comma-separated list of base paths to + # look for CUDA libraries and headers + env.set('TF_CUDA_PATHS', ','.join(cuda_paths)) + + # Please specify the location where CUDA toolkit is installed + env.set('CUDA_TOOLKIT_PATH', spec['cuda'].prefix) + + # Please specify the location where CUDNN library is installed + env.set('CUDNN_INSTALL_PATH', spec['cudnn'].prefix) + + # Please specify a list of comma-separated CUDA compute + # capabilities you want to build with. You can find the compute + # capability of your device at: + # https://developer.nvidia.com/cuda-gpus. + # Please note that each additional compute capability significantly + # increases your build time and binary size, and that TensorFlow + # only supports compute capabilities >= 3.5 + capabilities = ','.join('{0:.1f}'.format( + float(i) / 10.0) for i in spec.variants['cuda_arch'].value) + env.set('TF_CUDA_COMPUTE_CAPABILITIES', capabilities) + else: + env.set('TF_NEED_CUDA', '0') + + # Do you wish to download a fresh release of clang? (Experimental) + env.set('TF_DOWNLOAD_CLANG', '0') + + # Do you wish to build TensorFlow with MPI support? + if '+mpi' in spec: + env.set('TF_NEED_MPI', '1') + + # Please specify the MPI toolkit folder + env.set('MPI_HOME', spec['mpi'].prefix) + else: + env.set('TF_NEED_MPI', '0') + env.unset('MPI_HOME') + + # Please specify optimization flags to use during compilation when + # bazel option '--config=opt' is specified + env.set('CC_OPT_FLAGS', spec.target.optimization_flags( + spec.compiler.name, spec.compiler.version)) + + # Would you like to interactively configure ./WORKSPACE for + # Android builds? + if '+android' in spec: + env.set('TF_SET_ANDROID_WORKSPACE', '1') + + # Please specify the home path of the Android NDK to use + env.set('ANDROID_NDK_HOME', spec['android-ndk'].prefix) + env.set('ANDROID_NDK_API_LEVEL', spec['android-ndk'].version) + + # Please specify the home path of the Android SDK to use + env.set('ANDROID_SDK_HOME', spec['android-sdk'].prefix) + env.set('ANDROID_SDK_API_LEVEL', spec['android-sdk'].version) + + # Please specify the Android SDK API level to use + env.set('ANDROID_API_LEVEL', spec['android-sdk'].version) + + # Please specify an Android build tools version to use + env.set('ANDROID_BUILD_TOOLS_VERSION', spec['android-sdk'].version) + else: + env.set('TF_SET_ANDROID_WORKSPACE', '0') + + # Do you wish to build TensorFlow with iOS support? + if '+ios' in spec: + env.set('TF_CONFIGURE_IOS', '1') + else: + env.set('TF_CONFIGURE_IOS', '0') + + # set tmpdir to a non-NFS filesystem + # (because bazel uses ~/.cache/bazel) + # TODO: This should be checked for non-nfsy filesystem, but the current + # best idea for it is to check + # subprocess.call([ + # 'stat', '--file-system', '--format=%T', tmp_path + # ]) + # to not be nfs. This is only valid for Linux and we'd like to + # stay at least also OSX compatible + tmp_path = '/tmp/spack/tf' + mkdirp(tmp_path) + env.set('TEST_TMPDIR', tmp_path) + + def configure(self, spec, prefix): + # NOTE: configure script is interactive. If you set the appropriate + # environment variables, this interactivity is skipped. If you don't, + # Spack hangs during the configure phase. Use `spack build-env` to + # determine which environment variables must be set for a particular + # version. + configure() + + @run_after('configure') + def post_configure_fixes(self): + spec = self.spec + if spec.satisfies('@1.5.0: ~android'): + # env variable is somehow ignored -> brute force + # TODO: find a better solution + filter_file(r'if workspace_has_any_android_rule\(\)', + r'if True', + 'configure.py') + + # version dependent fixes + if spec.satisfies('@1.3.0:1.5.0'): + # checksum for protobuf that bazel downloads (@github) changed + filter_file(r'sha256 = "6d43b9d223ce09e5d4ce8b0060cb8a7513577a35a64c7e3dad10f0703bf3ad93"', + r'sha256 = "e5fdeee6b28cf6c38d61243adff06628baa434a22b5ebb7432d2a7fbabbdb13d"', + 'tensorflow/workspace.bzl') + # starting with tensorflow 1.3, tensorboard becomes a dependency + # (...but is not really needed? Tensorboard should depend on + # tensorflow, not the other way!) + # -> remove from list of required packages + filter_file(r"'tensorflow-tensorboard", + r"#'tensorflow-tensorboard", + 'tensorflow/tools/pip_package/setup.py') + if spec.satisfies('@1.5.0: ~gcp'): + # google cloud support seems to be installed on default, leading + # to boringssl error manually set the flag to false to avoid + # installing gcp support + # https://github.com/tensorflow/tensorflow/issues/20677#issuecomment-404634519 + filter_file(r'--define with_gcp_support=true', + r'--define with_gcp_support=false', + '.tf_configure.bazelrc') + if spec.satisfies('@1.6.0:'): + # tensorboard name changed + filter_file(r"'tensorboard >=", + r"#'tensorboard >=", + 'tensorflow/tools/pip_package/setup.py') + if spec.satisfies('@1.8.0: ~opencl'): + # 1.8.0 and 1.9.0 aborts with numpy import error during python_api + # generation somehow the wrong PYTHONPATH is used... + # set --distinct_host_configuration=false as a workaround + # https://github.com/tensorflow/tensorflow/issues/22395#issuecomment-431229451 + filter_file('build --action_env TF_NEED_OPENCL_SYCL="0"', + 'build --action_env TF_NEED_OPENCL_SYCL="0"\n' + 'build --distinct_host_configuration=false\n' + 'build --action_env PYTHONPATH="{0}"'.format( + env['PYTHONPATH']), + '.tf_configure.bazelrc') + if spec.satisfies('@1.13.1'): + # tensorflow_estimator is an API for tensorflow + # tensorflow-estimator imports tensorflow during build, so + # tensorflow has to be set up first + filter_file(r"'tensorflow_estimator >=", + r"#'tensorflow_estimator >=", + 'tensorflow/tools/pip_package/setup.py') + if spec.satisfies('@2.0.0:'): + # now it depends on the nightly versions... + filter_file(r"'tf-estimator-nightly >=", + r"#'tf-estimator-nightly >=", + 'tensorflow/tools/pip_package/setup.py') + filter_file(r"REQUIRED_PACKAGES\[i\] = 'tb-nightly >=", + r"pass #REQUIRED_PACKAGES\[i\] = 'tb-nightly >=", + 'tensorflow/tools/pip_package/setup.py') + filter_file(r"'tb-nightly >=", + r"#'tb-nightly >=", + 'tensorflow/tools/pip_package/setup.py') + + if spec.satisfies('@1.13.1 +nccl'): + filter_file( + r'^build --action_env NCCL_INSTALL_PATH=.*', + r'build --action_env NCCL_INSTALL_PATH="' + + spec['nccl'].libs.directories[0] + '"', + '.tf_configure.bazelrc') + filter_file( + r'^build --action_env NCCL_HDR_PATH=.*', + r'build --action_env NCCL_HDR_PATH="' + + spec['nccl'].prefix.include + '"', + '.tf_configure.bazelrc') + + if spec.satisfies('+cuda'): + libs = spec['cuda'].libs.directories + libs.extend(spec['cudnn'].libs.directories) + if '+nccl' in spec: + libs.extend(spec['nccl'].libs.directories) + if '+tensorrt' in spec: + libs.extend(spec['tensorrt'].libs.directories) + slibs = ':'.join(libs) + + filter_file('build --action_env TF_NEED_OPENCL_SYCL="0"', + 'build --action_env TF_NEED_OPENCL_SYCL="0"\n' + 'build --action_env LD_LIBRARY_PATH="' + slibs + '"', + '.tf_configure.bazelrc') + + def build(self, spec, prefix): + tmp_path = env['TEST_TMPDIR'] + + # https://docs.bazel.build/versions/master/command-line-reference.html + args = [ + # Don't allow user or system .bazelrc to override build settings + '--nohome_rc', + '--nosystem_rc', + # Bazel does not work properly on NFS, switch to /tmp + '--output_user_root=' + tmp_path, + 'build', + # Spack logs don't handle colored output well + '--color=no', + '--jobs={0}'.format(make_jobs), + '--config=opt', + # Enable verbose output for failures + '--verbose_failures', + # Show (formatted) subcommands being executed + '--subcommands=pretty_print', + # Ask bazel to explain what it's up to + # Needs a filename as argument + '--explain=explainlogfile.txt', + # Increase verbosity of explanation, + '--verbose_explanations', + ] + + # See .bazelrc for when each config flag is supported + if spec.satisfies('@1.12.1:'): + if '+mkl' in spec: + args.append('--config=mkl') + + if '+monolithic' in spec: + args.append('--config=monolithic') + + if '+gdr' in spec: + args.append('--config=gdr') + + if '+verbs' in spec: + args.append('--config=verbs') + + if '+ngraph' in spec: + args.append('--config=ngraph') + + if '+dynamic_kernels' in spec: + args.append('--config=dynamic_kernels') + + if '+cuda' in spec: + args.append('--config=cuda') + + if '~aws' in spec: + args.append('--config=noaws') + + if '~gcp' in spec: + args.append('--config=nogcp') + + if '~hdfs' in spec: + args.append('--config=nohdfs') + + if '~nccl' in spec: + args.append('--config=nonccl') + + if spec.satisfies('@1.12.1:2.0'): + if '~ignite' in spec: + args.append('--config=noignite') + + if '~kafka' in spec: + args.append('--config=nokafka') + + if spec.satisfies('@1.12.1,1.14:'): + if '+numa' in spec: + args.append('--config=numa') + + if spec.satisfies('@2:'): + args.append('--config=v2') + + if spec.satisfies('%gcc@5:'): + args.append('--cxxopt=-D_GLIBCXX_USE_CXX11_ABI=0') + + args.append('//tensorflow/tools/pip_package:build_pip_package') + + bazel(*args) + + build_pip_package = Executable( + 'bazel-bin/tensorflow/tools/pip_package/build_pip_package') + build_pip_package(tmp_path) + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + for fn in glob.iglob(join_path( + '../bazel-bin/tensorflow/tools/pip_package', + 'build_pip_package.runfiles/org_tensorflow/*')): + dst = os.path.basename(fn) + if not os.path.exists(dst): + os.symlink(fn, dst) + for fn in glob.iglob('../tensorflow/tools/pip_package/*'): + dst = os.path.basename(fn) + if not os.path.exists(dst): + os.symlink(fn, dst) + + # macOS is case-insensitive, and BUILD file in directory + # containing setup.py causes the following error message: + # error: could not create 'build': File exists + # Delete BUILD file to prevent this. + os.remove('BUILD') + + setup_py('install', '--prefix={0}'.format(prefix), + '--single-version-externally-managed', '--root=/') + + @run_after('install') + @on_package_attributes(run_tests=True) + def import_module_test(self): + with working_dir('spack-test', create=True): + for module in self.import_modules: + python('-c', 'import {0}'.format(module)) diff --git a/var/spack/repos/builtin/packages/py-tensorflow/url-zlib.patch b/var/spack/repos/builtin/packages/py-tensorflow/url-zlib.patch new file mode 100644 index 0000000000..9c4fdba09c --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tensorflow/url-zlib.patch @@ -0,0 +1,13 @@ +--- tensorflow-0.10.0/tensorflow/workspace.bzl 2016-09-08 23:49:36.000000000 +0200 ++++ tensorflow-0.10.0/tensorflow/workspace.bzl 2017-01-31 09:11:07.391869277 +0100 +@@ -198,7 +198,7 @@ def tf_workspace(path_prefix = "", tf_re + + native.new_http_archive( + name = "zlib_archive", +- url = "http://zlib.net/zlib-1.2.8.tar.gz", +- sha256 = "36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d", ++ url = "http://zlib.net/zlib-1.2.11.tar.gz", ++ sha256 = "c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1", + build_file = path_prefix + "zlib.BUILD", + ) + diff --git a/var/spack/repos/builtin/packages/py-termcolor/package.py b/var/spack/repos/builtin/packages/py-termcolor/package.py index 4b1cc5a1a1..f6319e6dac 100644 --- a/var/spack/repos/builtin/packages/py-termcolor/package.py +++ b/var/spack/repos/builtin/packages/py-termcolor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-terminado/package.py b/var/spack/repos/builtin/packages/py-terminado/package.py index 6df259b230..9eb91c12aa 100644 --- a/var/spack/repos/builtin/packages/py-terminado/package.py +++ b/var/spack/repos/builtin/packages/py-terminado/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-testinfra/package.py b/var/spack/repos/builtin/packages/py-testinfra/package.py index de91317908..bae58db30d 100644 --- a/var/spack/repos/builtin/packages/py-testinfra/package.py +++ b/var/spack/repos/builtin/packages/py-testinfra/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-testpath/package.py b/var/spack/repos/builtin/packages/py-testpath/package.py new file mode 100644 index 0000000000..717f63dc6b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-testpath/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTestpath(PythonPackage): + """Testpath is a collection of utilities for Python code working with + files and commands.""" + + homepage = "https://github.com/jupyter/testpath" + url = "https://pypi.io/packages/source/t/testpath/testpath-0.4.2.tar.gz" + + version('0.4.2', sha256='b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8') diff --git a/var/spack/repos/builtin/packages/py-testrepository/package.py b/var/spack/repos/builtin/packages/py-testrepository/package.py new file mode 100644 index 0000000000..881191bc3f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-testrepository/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTestrepository(PythonPackage): + """A repository of test results.""" + + homepage = "https://launchpad.net/testrepository" + url = "https://pypi.io/packages/source/t/testrepository/testrepository-0.0.20.tar.gz" + + import_modules = [ + 'testrepository', 'testrepository.arguments', + 'testrepository.commands', 'testrepository.repository', + 'testrepository.tests', 'testrepository.tests.arguments', + 'testrepository.tests.commands', 'testrepository.tests.repository', + 'testrepository.tests.ui', 'testrepository.ui', + ] + + version('0.0.20', sha256='752449bc98c20253ec4611c40564aea93d435a5bf3ff672208e01cc10e5858eb') + + depends_on('py-setuptools', type='build') + depends_on('py-fixtures', type=('build', 'run')) + depends_on('py-python-subunit@0.0.18:', type=('build', 'run')) + depends_on('py-testtools@0.9.30:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-testresources/package.py b/var/spack/repos/builtin/packages/py-testresources/package.py new file mode 100644 index 0000000000..4468655863 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-testresources/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTestresources(PythonPackage): + """Testresources, a pyunit extension for managing expensive test resources. + """ + + homepage = "https://launchpad.net/testresources" + url = "https://pypi.io/packages/source/t/testresources/testresources-2.0.1.tar.gz" + + version('2.0.1', sha256='ee9d1982154a1e212d4e4bac6b610800bfb558e4fb853572a827bc14a96e4417') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-testscenarios/package.py b/var/spack/repos/builtin/packages/py-testscenarios/package.py new file mode 100644 index 0000000000..0dc8a07d46 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-testscenarios/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTestscenarios(PythonPackage): + """Testscenarios, a pyunit extension for dependency injection""" + + homepage = "https://launchpad.net/testscenarios" + url = "https://pypi.io/packages/source/t/testscenarios/testscenarios-0.5.0.tar.gz" + + version('0.5.0', sha256='c257cb6b90ea7e6f8fef3158121d430543412c9a87df30b5dde6ec8b9b57a2b6') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-testtools/package.py b/var/spack/repos/builtin/packages/py-testtools/package.py new file mode 100644 index 0000000000..11a59423ec --- /dev/null +++ b/var/spack/repos/builtin/packages/py-testtools/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTesttools(PythonPackage): + """Extensions to the Python standard library unit testing framework.""" + + homepage = "https://github.com/testing-cabal/testtools" + url = "https://pypi.io/packages/source/t/testtools/testtools-2.3.0.tar.gz" + + version('2.3.0', sha256='5827ec6cf8233e0f29f51025addd713ca010061204fdea77484a2934690a0559') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-tetoolkit/package.py b/var/spack/repos/builtin/packages/py-tetoolkit/package.py index c53b4a0494..de755e15f3 100644 --- a/var/spack/repos/builtin/packages/py-tetoolkit/package.py +++ b/var/spack/repos/builtin/packages/py-tetoolkit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-text-unidecode/package.py b/var/spack/repos/builtin/packages/py-text-unidecode/package.py new file mode 100644 index 0000000000..768b8a3dd8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-text-unidecode/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTextUnidecode(PythonPackage): + """text-unidecode is the most basic port of the Text::Unidecode Perl + library.""" + + homepage = "https://github.com/kmike/text-unidecode/" + url = "https://pypi.io/packages/source/t/text-unidecode/text-unidecode-1.3.tar.gz" + + version('1.3', sha256='bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-texttable/package.py b/var/spack/repos/builtin/packages/py-texttable/package.py index 2dee0f93ed..1aec6a03f6 100644 --- a/var/spack/repos/builtin/packages/py-texttable/package.py +++ b/var/spack/repos/builtin/packages/py-texttable/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-theano/package.py b/var/spack/repos/builtin/packages/py-theano/package.py index 78e77fec03..c7c95fd0e3 100644 --- a/var/spack/repos/builtin/packages/py-theano/package.py +++ b/var/spack/repos/builtin/packages/py-theano/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class PyTheano(PythonPackage): +class PyTheano(PythonPackage, CudaPackage): """Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs.""" @@ -20,22 +20,20 @@ class PyTheano(PythonPackage): version('1.0.1', sha256='88d8aba1fe2b6b75eacf455d01bc7e31e838c5a0fb8c13dde2d9472495ff4662') version('0.8.2', sha256='7463c8f7ed1a787bf881f36d38a38607150186697e7ce7e78bfb94b7c6af8930') - variant('gpu', default=False, - description='Builds with support for GPUs via CUDA and cuDNN') - depends_on('python@2.6:2.8,3.3:') depends_on('py-setuptools', type=('build', 'run')) - depends_on('py-scipy@0.11:', type=('build', 'run')) - depends_on('py-numpy@1.7.1:', type=('build', 'run')) + depends_on('py-numpy@1.9.1:', type=('build', 'run')) + depends_on('py-scipy@0.14:', type=('build', 'run')) depends_on('py-six@1.9.0:', type=('build', 'run')) depends_on('blas') - depends_on('cuda', when='+gpu') - depends_on('cudnn', when='+gpu') - depends_on('py-pygpu', when='+gpu', type=('build', 'run')) - depends_on('libgpuarray', when='+gpu') + depends_on('cuda', when='+cuda') + depends_on('cudnn', when='+cuda') + depends_on('py-pygpu', when='+cuda', type=('build', 'run')) + depends_on('libgpuarray', when='+cuda') depends_on('py-nose@1.3.0:', type='test') - depends_on('py-nose-parameterized@0.5.0:', type='test') + depends_on('py-parameterized', type='test') + depends_on('py-flake8', type='test') diff --git a/var/spack/repos/builtin/packages/py-thirdorder/package.py b/var/spack/repos/builtin/packages/py-thirdorder/package.py new file mode 100644 index 0000000000..66b01f0d88 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-thirdorder/package.py @@ -0,0 +1,37 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyThirdorder(PythonPackage): + """It helps ShengBTE users create FORCE_CONSTANTS_3RD files efficiently""" + + homepage = "http://www.shengbte.org" + url = "http://www.shengbte.org/downloads/thirdorder-v1.1.1-8526f47.tar.bz2" + + version('1.1.1-8526f47', '5e1cc8d6ffa7efdb7325c397ca236863ea8a9c5bed1c558acca68b140f89167e') + + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-scipy', type=('build', 'run')) + depends_on('spglib', type=('build', 'run')) + + def patch(self): + setupfile = FileFilter('setup.py') + setupfile.filter('LIBRARY_DIRS = .*', 'LIBRARY_DIRS = ["%s"]' + % self.spec['spglib'].prefix.lib) + setupfile.filter('INCLUDE_DIRS = .*', 'INCLUDE_DIRS = ["%s"]' + % self.spec['spglib'].prefix.include) + + sourcefile = FileFilter('thirdorder_core.c') + sourcefile.filter('#include "spglib.*"', '#include "spglib.h"') + + @run_after('install') + def post_install(self): + mkdirp(self.prefix.bin) + install('thirdorder_espresso.py', self.prefix.bin) + install('thirdorder_vasp.py', self.prefix.bin) + install('thirdorder_castep.py', self.prefix.bin) + install('thirdorder_common.py', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/py-tifffile/package.py b/var/spack/repos/builtin/packages/py-tifffile/package.py index f90e68530c..b8e3afb165 100644 --- a/var/spack/repos/builtin/packages/py-tifffile/package.py +++ b/var/spack/repos/builtin/packages/py-tifffile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-toml/package.py b/var/spack/repos/builtin/packages/py-toml/package.py index f24e4c8eda..baccd323ef 100644 --- a/var/spack/repos/builtin/packages/py-toml/package.py +++ b/var/spack/repos/builtin/packages/py-toml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-tomopy/package.py b/var/spack/repos/builtin/packages/py-tomopy/package.py index b838561efd..0b7f814775 100644 --- a/var/spack/repos/builtin/packages/py-tomopy/package.py +++ b/var/spack/repos/builtin/packages/py-tomopy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-toolz/package.py b/var/spack/repos/builtin/packages/py-toolz/package.py index e4e591d0a8..058d1a9283 100644 --- a/var/spack/repos/builtin/packages/py-toolz/package.py +++ b/var/spack/repos/builtin/packages/py-toolz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py index 9325b2504c..e40bc840fe 100644 --- a/var/spack/repos/builtin/packages/py-torch/package.py +++ b/var/spack/repos/builtin/packages/py-torch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,8 @@ from spack import * -class PyTorch(PythonPackage): +# TODO: try switching to CMakePackage for more control over build +class PyTorch(PythonPackage, CudaPackage): """Tensors and Dynamic neural networks in Python with strong GPU acceleration.""" @@ -50,26 +51,29 @@ class PyTorch(PythonPackage): ] version('master', branch='master', submodules=True) + version('1.4.0', tag='v1.4.0', submodules=True) + version('1.3.1', tag='v1.3.1', submodules=True) version('1.3.0', tag='v1.3.0', submodules=True) version('1.2.0', tag='v1.2.0', submodules=True) version('1.1.0', tag='v1.1.0', submodules=True) version('1.0.1', tag='v1.0.1', submodules=True) version('1.0.0', tag='v1.0.0', submodules=True) - version('0.4.1', tag='v0.4.1', submodules=True) + version('0.4.1', tag='v0.4.1', submodules=True, + submodules_delete=['third_party/nervanagpu']) version('0.4.0', tag='v0.4.0', submodules=True) version('0.3.1', tag='v0.3.1', submodules=True) - variant('cuda', default=True, description='Enables CUDA build') - variant('cudnn', default=False, description='Enables the cuDNN build') + variant('cuda', default=True, description='Build with CUDA') + variant('cudnn', default=True, description='Enables the cuDNN build') variant('magma', default=False, description='Enables the MAGMA build') variant('fbgemm', default=False, description='Enables the FBGEMM build') variant('test', default=False, description='Enables the test build') variant('miopen', default=False, description='Enables the MIOpen build') - variant('mkldnn', default=False, description='Enables use of MKLDNN') + variant('mkldnn', default=True, description='Enables use of MKLDNN') variant('nnpack', default=False, description='Enables NNPACK build') variant('qnnpack', default=False, description='Enables QNNPACK build (quantized 8-bit operators)') variant('distributed', default=False, description='Enables distributed (c10d, gloo, mpi, etc.) build') - variant('nccl', default=False, description='Use Spack-installed NCCL') + variant('nccl', default=True, description='Use Spack-installed NCCL') variant('caffe2', default=False, description='Enables Caffe2 operators build') variant('gloo', default=False, description='Enables features related to distributed support') variant('opencv', default=False, description='Enables use of OpenCV for additional operators') @@ -98,16 +102,44 @@ class PyTorch(PythonPackage): conflicts('+zstd', when='@:1.0') conflicts('+tbb', when='@:1.1') + cuda_arch_conflict = ('This version of Torch/Caffe2 only supports compute ' + 'capabilities ') + + conflicts('cuda_arch=none', when='+cuda+caffe2', + msg='Must specify CUDA compute capabilities of your GPU, see ' + 'https://developer.nvidia.com/cuda-gpus') + conflicts('cuda_arch=52', when='@1.3.0:+cuda+caffe2', + msg=cuda_arch_conflict + '>=5.3') + conflicts('cuda_arch=50', when='@1.3.0:+cuda+caffe2', + msg=cuda_arch_conflict + '>=5.3') + conflicts('cuda_arch=35', when='@1.3.0:+cuda+caffe2', + msg=cuda_arch_conflict + '>=5.3') + conflicts('cuda_arch=32', when='@1.3.0:+cuda+caffe2', + msg=cuda_arch_conflict + '>=5.3') + conflicts('cuda_arch=30', when='@1.3.0:+cuda+caffe2', + msg=cuda_arch_conflict + '>=5.3') + conflicts('cuda_arch=30', when='@1.2.0:+cuda+caffe2', + msg=cuda_arch_conflict + '>=3.2') + conflicts('cuda_arch=20', when='@1.0.0:+cuda+caffe2', + msg=cuda_arch_conflict + '>=3.0') + # Required dependencies depends_on('cmake@3.5:', type='build') + # Use Ninja generator to speed up build times + # Automatically used if found + depends_on('ninja@1.5:', type='build') depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') - depends_on('py-numpy', type=('run', 'build')) + depends_on('py-numpy', type=('build', 'run')) depends_on('py-future', when='@1.1: ^python@:2', type='build') - depends_on('py-pyyaml', type=('run', 'build')) - depends_on('py-typing', when='@0.4: ^python@:3.4', type=('run', 'build')) + depends_on('py-pyyaml', type=('build', 'run')) + depends_on('py-typing', when='@0.4: ^python@:3.4', type=('build', 'run')) + depends_on('py-pybind11', when='@0.4:', type=('build', 'run')) depends_on('blas') depends_on('lapack') + depends_on('protobuf', when='@0.4:') + depends_on('eigen', when='@0.4:') + # TODO: replace all third_party packages with Spack packages # Optional dependencies depends_on('cuda@7.5:', when='+cuda', type=('build', 'link', 'run')) @@ -116,13 +148,15 @@ class PyTorch(PythonPackage): depends_on('cudnn@7:', when='@1.1:+cudnn') depends_on('magma', when='+magma') # TODO: add dependency: https://github.com/pytorch/FBGEMM - depends_on('fbgemm', when='+fbgemm') + # depends_on('fbgemm', when='+fbgemm') # TODO: add dependency: https://github.com/ROCmSoftwarePlatform/MIOpen - depends_on('miopen', when='+miopen') - depends_on('mkl', when='+mkldnn') + # depends_on('miopen', when='+miopen') + # TODO: See if there is a way to use an external mkldnn installation. + # Currently, only older versions of py-torch use an external mkldnn + # library. + depends_on('intel-mkl-dnn', when='@0.4:0.4.1+mkldnn') # TODO: add dependency: https://github.com/Maratyszcza/NNPACK - depends_on('nnpack', when='+nnpack') - # TODO: add dependency: https://github.com/pytorch/QNNPACK + # depends_on('nnpack', when='+nnpack') depends_on('qnnpack', when='+qnnpack') depends_on('mpi', when='+distributed') depends_on('nccl', when='+nccl') @@ -137,11 +171,14 @@ class PyTorch(PythonPackage): depends_on('tbb', when='+tbb') # Test dependencies - depends_on('ninja', type='test') depends_on('py-hypothesis', type='test') depends_on('py-six', type='test') depends_on('py-psutil', type='test') + # Both build and install run cmake/make/make install + # Only run once to speed up build times + phases = ['install'] + def setup_build_environment(self, env): def enable_or_disable(variant, keyword='USE', var=None, newer=False): """Set environment variable to enable or disable support for a @@ -169,11 +206,27 @@ class PyTorch(PythonPackage): else: env.set('NO_' + var, 'ON') + # Build in parallel to speed up build times env.set('MAX_JOBS', make_jobs) + # Spack logs have trouble handling colored output + env.set('COLORIZE_OUTPUT', 'OFF') + + # Don't use vendored third-party libraries + env.set('BUILD_CUSTOM_PROTOBUF', 'OFF') + env.set('USE_PYTORCH_QNNPACK', 'OFF') + env.set('USE_SYSTEM_EIGEN_INSTALL', 'ON') + env.set('pybind11_DIR', self.spec['py-pybind11'].prefix) + env.set('pybind11_INCLUDE_DIR', + self.spec['py-pybind11'].prefix.include) + enable_or_disable('cuda') if '+cuda' in self.spec: env.set('CUDA_HOME', self.spec['cuda'].prefix) + torch_cuda_arch = ';'.join('{0:.1f}'.format(float(i) / 10.0) for i + in + self.spec.variants['cuda_arch'].value) + env.set('TORCH_CUDA_ARCH_LIST', torch_cuda_arch) enable_or_disable('cudnn') if '+cudnn' in self.spec: @@ -184,15 +237,14 @@ class PyTorch(PythonPackage): enable_or_disable('fbgemm') enable_or_disable('test', keyword='BUILD') - enable_or_disable('miopen') if '+miopen' in self.spec: env.set('MIOPEN_LIB_DIR', self.spec['miopen'].libs.directories[0]) env.set('MIOPEN_INCLUDE_DIR', self.spec['miopen'].prefix.include) env.set('MIOPEN_LIBRARY', self.spec['miopen'].libs[0]) enable_or_disable('mkldnn') - if '+mkldnn' in self.spec: - env.set('MKLDNN_HOME', self.spec['intel-mkl'].prefix) + if '@0.4:0.4.1+mkldnn' in self.spec: + env.set('MKLDNN_HOME', self.spec['intel-mkl-dnn'].prefix) enable_or_disable('nnpack') enable_or_disable('qnnpack') @@ -207,7 +259,6 @@ class PyTorch(PythonPackage): enable_or_disable('caffe2', keyword='BUILD', var='CAFFE2_OPS') enable_or_disable('gloo', newer=True) - enable_or_disable('gloo', var='GLOO_IBVERBS', newer=True) enable_or_disable('opencv', newer=True) enable_or_disable('openmp', newer=True) enable_or_disable('ffmpeg', newer=True) @@ -218,15 +269,19 @@ class PyTorch(PythonPackage): env.set('PYTORCH_BUILD_VERSION', self.version) env.set('PYTORCH_BUILD_NUMBER', 0) - # BLAS to be used by Caffe2. Can be MKL, Eigen, ATLAS, or OpenBLAS. + # BLAS to be used by Caffe2 if '^mkl' in self.spec: env.set('BLAS', 'MKL') - elif '^eigen' in self.spec: - env.set('BLAS', 'Eigen') elif '^atlas' in self.spec: env.set('BLAS', 'ATLAS') elif '^openblas' in self.spec: env.set('BLAS', 'OpenBLAS') + elif '^veclibfort' in self.spec: + env.set('BLAS', 'vecLib') + elif '^libflame' in self.spec: + env.set('BLAS', 'FLAME') + elif '^eigen' in self.spec: + env.set('BLAS', 'Eigen') enable_or_disable('redis', newer=True) enable_or_disable('zstd', newer=True) diff --git a/var/spack/repos/builtin/packages/py-torchvision/package.py b/var/spack/repos/builtin/packages/py-torchvision/package.py index d369cef54b..bfef2202e2 100644 --- a/var/spack/repos/builtin/packages/py-torchvision/package.py +++ b/var/spack/repos/builtin/packages/py-torchvision/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class PyTorchvision(PythonPackage): architectures, and common image transformations for computer vision.""" homepage = "https://github.com/pytorch/vision" - url = "https://github.com/pytorch/vision/archive/v0.4.0.tar.gz" + url = "https://github.com/pytorch/vision/archive/v0.5.0.tar.gz" maintainers = ['adamjstewart'] import_modules = [ @@ -21,6 +21,9 @@ class PyTorchvision(PythonPackage): 'torchvision.models.detection' ] + version('0.5.0', sha256='eb9afc93df3d174d975ee0914057a9522f5272310b4d56c150b955c287a4d74d') + version('0.4.2', sha256='1184a27eab85c9e784bacc6f9d6fec99e168ab4eda6047ef9f709e7fdb22d8f9') + version('0.4.1', sha256='053689351272b3bd2ac3e6ba51efd284de0e4ca4a301f54674b949f1e62b7176') version('0.4.0', sha256='c270d74e568bad4559fed4544f6dd1e22e2eb1c60b088e04a5bd5787c4150589') version('0.3.0', sha256='c205f0618c268c6ed2f8abb869ef6eb83e5339c1336c243ad321a2f2a85195f0') @@ -29,7 +32,9 @@ class PyTorchvision(PythonPackage): depends_on('py-six', type=('build', 'run')) depends_on('py-torch@1.2.0:', when='@0.4.0:', type=('build', 'run')) depends_on('py-torch@1.1.0:', type=('build', 'run')) - depends_on('py-pillow@4.1.1:', type=('build', 'run')) # or py-pillow-simd + # https://github.com/pytorch/vision/issues/1712 + depends_on('py-pillow@4.1.1:6', when='@:0.4', type=('build', 'run')) # or py-pillow-simd + depends_on('py-pillow@4.1.1:', when='@0.5:', type=('build', 'run')) # or py-pillow-simd # Many of the datasets require additional dependencies to use. # These can be installed after the fact. diff --git a/var/spack/repos/builtin/packages/py-tornado/package.py b/var/spack/repos/builtin/packages/py-tornado/package.py index 0a1fa8df0d..064311439e 100644 --- a/var/spack/repos/builtin/packages/py-tornado/package.py +++ b/var/spack/repos/builtin/packages/py-tornado/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-tox/package.py b/var/spack/repos/builtin/packages/py-tox/package.py new file mode 100644 index 0000000000..28fa5a380b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tox/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyTox(PythonPackage): + """tox is a generic virtualenv management and test command line tool.""" + + homepage = "https://tox.readthedocs.org/" + url = "https://pypi.io/packages/source/t/tox/tox-3.14.2.tar.gz" + + version('3.14.2', sha256='7efd010a98339209f3a8292f02909b51c58417bfc6838ab7eca14cf90f96117a') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-importlib-metadata@1.1.0:', when='^python@:3.7', type=('build', 'run')) + depends_on('py-packaging@14:', type=('build', 'run')) + depends_on('py-pluggy@0.12.0:0.999', type=('build', 'run')) + depends_on('py-py@1.4.17:1.999', type=('build', 'run')) + depends_on('py-six@1.0.0:1.999', type=('build', 'run')) + depends_on('py-virtualenv@16.0.0:', type=('build', 'run')) + depends_on('py-toml@0.9.4:', type=('build', 'run')) + depends_on('py-filelock@3.0.0:3.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-tqdm/package.py b/var/spack/repos/builtin/packages/py-tqdm/package.py index fd3ac93510..be2ed3cecb 100644 --- a/var/spack/repos/builtin/packages/py-tqdm/package.py +++ b/var/spack/repos/builtin/packages/py-tqdm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-traceback2/package.py b/var/spack/repos/builtin/packages/py-traceback2/package.py index cdd2212963..766acea59a 100644 --- a/var/spack/repos/builtin/packages/py-traceback2/package.py +++ b/var/spack/repos/builtin/packages/py-traceback2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-traitlets/package.py b/var/spack/repos/builtin/packages/py-traitlets/package.py index 945e469bf2..9c5695209d 100644 --- a/var/spack/repos/builtin/packages/py-traitlets/package.py +++ b/var/spack/repos/builtin/packages/py-traitlets/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-treehash/package.py b/var/spack/repos/builtin/packages/py-treehash/package.py index f8eedcea6f..8925504b74 100644 --- a/var/spack/repos/builtin/packages/py-treehash/package.py +++ b/var/spack/repos/builtin/packages/py-treehash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py index 222d0da566..95090a2694 100644 --- a/var/spack/repos/builtin/packages/py-tuiview/package.py +++ b/var/spack/repos/builtin/packages/py-tuiview/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-twine/package.py b/var/spack/repos/builtin/packages/py-twine/package.py index d7ddcebd16..46ca3ae9b8 100644 --- a/var/spack/repos/builtin/packages/py-twine/package.py +++ b/var/spack/repos/builtin/packages/py-twine/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-twisted/package.py b/var/spack/repos/builtin/packages/py-twisted/package.py index fcfb04fc05..52f3d4039f 100644 --- a/var/spack/repos/builtin/packages/py-twisted/package.py +++ b/var/spack/repos/builtin/packages/py-twisted/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-typed-ast/package.py b/var/spack/repos/builtin/packages/py-typed-ast/package.py index 492d63cbc2..ddbb6ff519 100644 --- a/var/spack/repos/builtin/packages/py-typed-ast/package.py +++ b/var/spack/repos/builtin/packages/py-typed-ast/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-typesentry/package.py b/var/spack/repos/builtin/packages/py-typesentry/package.py index 5e17a26188..0fbd891ae9 100644 --- a/var/spack/repos/builtin/packages/py-typesentry/package.py +++ b/var/spack/repos/builtin/packages/py-typesentry/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-typing-extensions/package.py b/var/spack/repos/builtin/packages/py-typing-extensions/package.py index bb981b8519..7a2b3ab5fb 100644 --- a/var/spack/repos/builtin/packages/py-typing-extensions/package.py +++ b/var/spack/repos/builtin/packages/py-typing-extensions/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-typing/package.py b/var/spack/repos/builtin/packages/py-typing/package.py index bfa9a2d49a..1bc1b0c704 100644 --- a/var/spack/repos/builtin/packages/py-typing/package.py +++ b/var/spack/repos/builtin/packages/py-typing/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-tzlocal/package.py b/var/spack/repos/builtin/packages/py-tzlocal/package.py index 18b1471998..354653f7a5 100644 --- a/var/spack/repos/builtin/packages/py-tzlocal/package.py +++ b/var/spack/repos/builtin/packages/py-tzlocal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,7 @@ class PyTzlocal(PythonPackage): homepage = "https://github.com/regebro/tzlocal" url = "https://pypi.io/packages/source/t/tzlocal/tzlocal-1.3.tar.gz" + version('2.0.0', sha256='949b9dd5ba4be17190a80c0268167d7e6c92c62b30026cf9764caf3e308e5590') version('1.3', sha256='d160c2ce4f8b1831dabfe766bd844cf9012f766539cf84139c2faac5201882ce') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-udunits/package.py b/var/spack/repos/builtin/packages/py-udunits/package.py deleted file mode 100644 index b7fb343439..0000000000 --- a/var/spack/repos/builtin/packages/py-udunits/package.py +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * -import os - - -class PyUdunits(PythonPackage): - """The MetOffice cf_units Python interface to the UDUNITS-2 Library.""" - homepage = "https://github.com/SciTools/cf_units" - url = "https://github.com/SciTools/cf_units/archive/v1.1.3.tar.gz" - - version('1.1.3', sha256='cc27f4f06c99d242c36beb8dc5c517e1b1124a8c65ca3f76f372b9674aa320ba') - - maintainers = ['citibeth'] - - depends_on('py-setuptools', type='build') - depends_on('py-six', type=('build', 'run')) - depends_on('py-netcdf4', type=('build', 'run')) - depends_on('udunits2') - - # See: https://github.com/SciTools/cf_units/blob/master/cf_units/etc/site.cfg.template - # udunits2_path = /path/to/libudunits2.so - # udunits2_xml_path = /path/to/udunits2.xml - site_cfg_template = """[System] -udunits2_path = %s -udunits2_xml_path = %s -""" - - @run_after('install') - def configure_template(self): - spec = self.spec - - cfg_templates = find(spec.prefix, ['site.cfg.template']) - if len(cfg_templates) != 1: - tty.die( - 'Found %d instances of site.cfg.template, wanted 1' % - len(cfg_templates)) - cfg_template = cfg_templates[0] - - cfg = os.path.join(os.path.split(cfg_template)[0], 'site.cfg') - - udunits2_xml_path = os.path.join( - spec['udunits2'].prefix, 'share', 'udunits', 'udunits2.xml') - - with open(cfg, 'w') as fout: - fout.write(self.site_cfg_template % - (spec['udunits2'].libs, udunits2_xml_path)) diff --git a/var/spack/repos/builtin/packages/py-ujson/package.py b/var/spack/repos/builtin/packages/py-ujson/package.py new file mode 100644 index 0000000000..45e9b280e8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-ujson/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyUjson(PythonPackage): + """Ultra fast JSON decoder and encoder written in C with Python + bindings.""" + + homepage = "https://github.com/esnme/ultrajson" + url = "https://pypi.io/packages/source/u/ujson/ujson-1.35.tar.gz" + + version('1.35', sha256='f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-umalqurra/package.py b/var/spack/repos/builtin/packages/py-umalqurra/package.py new file mode 100644 index 0000000000..c96dd625a5 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-umalqurra/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class PyUmalqurra(PythonPackage): + """Date Api that support Hijri Umalqurra calendar.""" + + homepage = "https://github.com/tytkal/python-hijiri-ummalqura" + url = "https://pypi.io/packages/source/u/umalqurra/umalqurra-0.2.tar.gz" + + version('0.2', sha256='719f6a36f908ada1c29dae0d934dd0f1e1f6e3305784edbec23ad719397de678') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-umi-tools/package.py b/var/spack/repos/builtin/packages/py-umi-tools/package.py index a4740c0797..3a89b102a1 100644 --- a/var/spack/repos/builtin/packages/py-umi-tools/package.py +++ b/var/spack/repos/builtin/packages/py-umi-tools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-unicycler/package.py b/var/spack/repos/builtin/packages/py-unicycler/package.py index 6950d87a71..441f66289a 100644 --- a/var/spack/repos/builtin/packages/py-unicycler/package.py +++ b/var/spack/repos/builtin/packages/py-unicycler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-unittest2/package.py b/var/spack/repos/builtin/packages/py-unittest2/package.py index 7961a2e2f7..1838843874 100644 --- a/var/spack/repos/builtin/packages/py-unittest2/package.py +++ b/var/spack/repos/builtin/packages/py-unittest2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py index 53dbfa38ec..bf20186afd 100644 --- a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py +++ b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-uritemplate/package.py b/var/spack/repos/builtin/packages/py-uritemplate/package.py index 219976a22a..9b901e6a2f 100644 --- a/var/spack/repos/builtin/packages/py-uritemplate/package.py +++ b/var/spack/repos/builtin/packages/py-uritemplate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-urllib3/package.py b/var/spack/repos/builtin/packages/py-urllib3/package.py index 2cfadd5c11..891897c1b3 100644 --- a/var/spack/repos/builtin/packages/py-urllib3/package.py +++ b/var/spack/repos/builtin/packages/py-urllib3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-urwid/package.py b/var/spack/repos/builtin/packages/py-urwid/package.py index 2e91029a10..bf606f81b7 100644 --- a/var/spack/repos/builtin/packages/py-urwid/package.py +++ b/var/spack/repos/builtin/packages/py-urwid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-us/package.py b/var/spack/repos/builtin/packages/py-us/package.py new file mode 100644 index 0000000000..81ea11e9d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-us/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyUs(PythonPackage): + """US state meta information and other fun stuff.""" + + homepage = "https://pypi.org/project/us/" + url = "https://pypi.io/packages/source/u/us/us-1.0.0.tar.gz" + + version('1.0.0', sha256='09dc9ba763e2e4399e6a042104f3e415a7de6bfa4df6f557b4f19e3ba9a22fda') + + depends_on('py-setuptools', type='build') + depends_on('py-jellyfish@0.5.6', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-usgs/package.py b/var/spack/repos/builtin/packages/py-usgs/package.py index 6a3dffd5b2..14d20b62cd 100644 --- a/var/spack/repos/builtin/packages/py-usgs/package.py +++ b/var/spack/repos/builtin/packages/py-usgs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-uwsgi/package.py b/var/spack/repos/builtin/packages/py-uwsgi/package.py new file mode 100644 index 0000000000..aed1882b04 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-uwsgi/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyUwsgi(PythonPackage): + """Web Application framework for low overhead web services""" + + homepage = "https://github.com/unbit/uwsgi/" + url = "https://pypi.org/packages/source/u/uwsgi/uwsgi-2.0.18.tar.gz" + + version('2.0.18', sha256='4972ac538800fb2d421027f49b4a1869b66048839507ccf0aa2fda792d99f583') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-vcversioner/package.py b/var/spack/repos/builtin/packages/py-vcversioner/package.py index 4f68c42bd1..7feda4a213 100644 --- a/var/spack/repos/builtin/packages/py-vcversioner/package.py +++ b/var/spack/repos/builtin/packages/py-vcversioner/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-vermin/package.py b/var/spack/repos/builtin/packages/py-vermin/package.py new file mode 100644 index 0000000000..97ac237a72 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-vermin/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyVermin(PythonPackage): + """Concurrently detect the minimum Python versions needed to run code.""" + + homepage = "https://github.com/netromdk/vermin" + url = "https://github.com/netromdk/vermin/archive/v0.10.0.tar.gz" + + import_modules = ['vermin'] + + version('0.10.0', sha256='3458a4d084bba5c95fd7208888aaf0e324a07ee092786ee4e5529f539ab4951f') + + depends_on('python@2.7:', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) + + def test(self): + make('test') diff --git a/var/spack/repos/builtin/packages/py-vine/package.py b/var/spack/repos/builtin/packages/py-vine/package.py new file mode 100644 index 0000000000..3598b0030c --- /dev/null +++ b/var/spack/repos/builtin/packages/py-vine/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyVine(PythonPackage): + """Promises, promises, promises.""" + + homepage = "https://pypi.org/project/vine/" + url = "https://pypi.io/packages/source/v/vine/vine-1.2.0.tar.gz" + + version('1.3.0', sha256='133ee6d7a9016f177ddeaf191c1f58421a1dcc6ee9a42c58b34bed40e1d2cd87') + version('1.2.0', sha256='ee4813e915d0e1a54e5c1963fde0855337f82655678540a6bc5996bca4165f76') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py b/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py index 9e9648dc13..287a4152dc 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py index d8e45ede31..3a1c593023 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py b/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py index f41eee94d8..235761f58a 100644 --- a/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-voluptuous/package.py b/var/spack/repos/builtin/packages/py-voluptuous/package.py new file mode 100644 index 0000000000..1d497d8ea2 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-voluptuous/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyVoluptuous(PythonPackage): + """Voluptous, despite the name, is a Python data validation library.""" + homepage = "https://github.com/alecthomas/voluptuous" + url = "https://pypi.io/packages/source/v/voluptuous/voluptuous-0.11.5.tar.gz" + + version('0.11.7', sha256='2abc341dbc740c5e2302c7f9b8e2e243194fb4772585b991931cb5b22e9bf456') + version('0.11.6', sha256='d2ca99ae1d1ed0313e8965720d1d75a780fc7f312fea4e3dbbb56ccfe5a8306d') + version('0.11.5', sha256='567a56286ef82a9d7ae0628c5842f65f516abcb496e74f3f59f1d7b28df314ef') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-vsc-base/package.py b/var/spack/repos/builtin/packages/py-vsc-base/package.py index 77537a2cb3..159eace26d 100644 --- a/var/spack/repos/builtin/packages/py-vsc-base/package.py +++ b/var/spack/repos/builtin/packages/py-vsc-base/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-vsc-install/package.py b/var/spack/repos/builtin/packages/py-vsc-install/package.py index fb0a4c2a83..fb0e2135d5 100644 --- a/var/spack/repos/builtin/packages/py-vsc-install/package.py +++ b/var/spack/repos/builtin/packages/py-vsc-install/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-wand/package.py b/var/spack/repos/builtin/packages/py-wand/package.py index ac4f82fd5b..17a5af30b3 100644 --- a/var/spack/repos/builtin/packages/py-wand/package.py +++ b/var/spack/repos/builtin/packages/py-wand/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,7 +20,7 @@ class PyWand(PythonPackage): depends_on('py-setuptools', type='build') # provides libmagickwand - depends_on('image-magick') + depends_on('imagemagick') depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) depends_on('py-sphinx@1:', type='build', when='+docs') diff --git a/var/spack/repos/builtin/packages/py-warlock/package.py b/var/spack/repos/builtin/packages/py-warlock/package.py index 31f2c307ba..60e36680e3 100644 --- a/var/spack/repos/builtin/packages/py-warlock/package.py +++ b/var/spack/repos/builtin/packages/py-warlock/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-wcsaxes/package.py b/var/spack/repos/builtin/packages/py-wcsaxes/package.py index b654e18e4e..eff494c3c6 100644 --- a/var/spack/repos/builtin/packages/py-wcsaxes/package.py +++ b/var/spack/repos/builtin/packages/py-wcsaxes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-wcwidth/package.py b/var/spack/repos/builtin/packages/py-wcwidth/package.py index 2b9c5151e7..150ad6793c 100644 --- a/var/spack/repos/builtin/packages/py-wcwidth/package.py +++ b/var/spack/repos/builtin/packages/py-wcwidth/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-weave/package.py b/var/spack/repos/builtin/packages/py-weave/package.py index a973aee3ed..bb45340d84 100644 --- a/var/spack/repos/builtin/packages/py-weave/package.py +++ b/var/spack/repos/builtin/packages/py-weave/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-webencodings/package.py b/var/spack/repos/builtin/packages/py-webencodings/package.py index 199d8e3fca..fd65a0655d 100644 --- a/var/spack/repos/builtin/packages/py-webencodings/package.py +++ b/var/spack/repos/builtin/packages/py-webencodings/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-webkit-server/package.py b/var/spack/repos/builtin/packages/py-webkit-server/package.py index 11703d596d..c3aebca85e 100644 --- a/var/spack/repos/builtin/packages/py-webkit-server/package.py +++ b/var/spack/repos/builtin/packages/py-webkit-server/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-weblogo/package.py b/var/spack/repos/builtin/packages/py-weblogo/package.py index 59de581a4b..d48fb5b381 100644 --- a/var/spack/repos/builtin/packages/py-weblogo/package.py +++ b/var/spack/repos/builtin/packages/py-weblogo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-werkzeug/package.py b/var/spack/repos/builtin/packages/py-werkzeug/package.py index 058d3e74d2..ca02ac51d6 100644 --- a/var/spack/repos/builtin/packages/py-werkzeug/package.py +++ b/var/spack/repos/builtin/packages/py-werkzeug/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-whatshap/package.py b/var/spack/repos/builtin/packages/py-whatshap/package.py index cc9ceb5d32..62ff90ff82 100644 --- a/var/spack/repos/builtin/packages/py-whatshap/package.py +++ b/var/spack/repos/builtin/packages/py-whatshap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py index 0554e214cb..94df34a8f9 100644 --- a/var/spack/repos/builtin/packages/py-wheel/package.py +++ b/var/spack/repos/builtin/packages/py-wheel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py index 589e733c77..fc54ebc5a8 100644 --- a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py +++ b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,4 +16,4 @@ class PyWidgetsnbextension(PythonPackage): depends_on('py-setuptools', type='build') depends_on('python@2.7:2.8,3.3:') - depends_on('py-jupyter-notebook@4.2.0:', type=('build', 'run')) + depends_on('py-notebook@4.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-wradlib/package.py b/var/spack/repos/builtin/packages/py-wradlib/package.py new file mode 100644 index 0000000000..14ae8b347a --- /dev/null +++ b/var/spack/repos/builtin/packages/py-wradlib/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyWradlib(PythonPackage): + """wradlib is designed to assist you in the most important steps of + processing weather radar data. These may include: reading common data + formats, georeferencing, converting reflectivity to rainfall intensity, + identifying and correcting typical error sources (such as clutter or + attenuation) and visualising the data.""" + + homepage = "https://docs.wradlib.org" + url = "https://pypi.io/packages/source/w/wradlib/wradlib-1.5.0.tar.gz" + + version('1.5.0', sha256='9bf0742d7235ea830e83c2269f6b5d1afd83d92696efce0a7bcdb0c4f6604784') + + depends_on('py-setuptools', type='build') + + # recommended versions from https://docs.wradlib.org/en/stable/installation.html#dependencies + depends_on('py-numpy@1.16:', type=('build', 'run')) + depends_on('py-matplotlib@3.0.2:', type=('build', 'run')) + depends_on('py-scipy@1.2.0:', type=('build', 'run')) + depends_on('py-h5py@2.9:', type=('build', 'run')) + depends_on('py-netcdf4@1.4.2:', type=('build', 'run')) + depends_on('py-xarray@0.11.3:', type=('build', 'run')) + depends_on('py-xmltodict@0.11:', type=('build', 'run')) + depends_on('py-semver', type=('build', 'run')) + depends_on('py-deprecation', type=('build', 'run')) + depends_on('py-requests', type=('build', 'run')) + + depends_on('gdal@2.4.0:+python', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-wrapt/package.py b/var/spack/repos/builtin/packages/py-wrapt/package.py index 7e3bb32f98..c31fe666f4 100644 --- a/var/spack/repos/builtin/packages/py-wrapt/package.py +++ b/var/spack/repos/builtin/packages/py-wrapt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,6 +10,7 @@ class PyWrapt(PythonPackage): """Module for decorators, wrappers and monkey patching.""" homepage = "https://github.com/GrahamDumpleton/wrapt" - url = "https://pypi.io/packages/source/w/wrapt/wrapt-1.10.10.tar.gz" + url = "https://pypi.io/packages/source/w/wrapt/wrapt-1.11.2.tar.gz" + version('1.11.2', sha256='565a021fd19419476b9362b05eeaa094178de64f8361e44468f9e9d7843901e1') version('1.10.10', sha256='42160c91b77f1bc64a955890038e02f2f72986c01d462d53cb6cb039b995cdd9') diff --git a/var/spack/repos/builtin/packages/py-wub/package.py b/var/spack/repos/builtin/packages/py-wub/package.py new file mode 100644 index 0000000000..13e6309667 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-wub/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyWub(PythonPackage): + """Bioinformatics tools and a software library developed by the Oxford + Nanopore Technologies Applications group. + """ + + homepage = "https://github.com/nanoporetech/wub" + url = "https://github.com/nanoporetech/wub/archive/v0.4.0.tar.gz" + + version('0.4.0', sha256='1526aa392bccac71b872211c45f5b403ad3d55f5762e0ed34ff9086bc1dab6fd') + + depends_on('py-six', type=('build', 'run')) + depends_on('py-pytest', type=('build', 'run', 'test')) + depends_on('py-pycmd', type=('build', 'run', 'test')) + depends_on('py-biopython', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run', 'test')) + depends_on('py-matplotlib', type=('build', 'run')) + depends_on('py-seaborn', type=('build', 'run')) + depends_on('py-editdistance', type=('build', 'run', 'test')) + depends_on('py-pandas@0.20.2:', type=('build', 'run')) + depends_on('py-pysam', type=('build', 'run')) + depends_on('py-tqdm', type=('build', 'run')) + depends_on('py-statsmodels', type=('build', 'run')) + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-wxmplot/package.py b/var/spack/repos/builtin/packages/py-wxmplot/package.py new file mode 100644 index 0000000000..0d88748979 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-wxmplot/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyWxmplot(PythonPackage): + """wxPython plotting widgets using matplotlib.""" + + homepage = "https://newville.github.io/wxmplot/" + url = "https://pypi.io/packages/source/w/wxmplot/wxmplot-0.9.38.tar.gz" + + import_modules = ['wxmplot'] + + version('0.9.38', sha256='82dc64abb42bdd03ec7067a3aa2a475001f2bc8e4772149bae47facf460c0081') + + depends_on('py-setuptools', type='build') + depends_on('py-numpy@1.12:', type=('build', 'run')) + depends_on('py-six@1.10:', type=('build', 'run')) + depends_on('py-matplotlib@2.0:', type=('build', 'run')) + depends_on('py-wxpython@4.0.3:', type=('build', 'run')) + depends_on('py-pytest', type='test') diff --git a/var/spack/repos/builtin/packages/py-wxpython/package.py b/var/spack/repos/builtin/packages/py-wxpython/package.py index 4acb9de6c5..7bbe5a8a8c 100644 --- a/var/spack/repos/builtin/packages/py-wxpython/package.py +++ b/var/spack/repos/builtin/packages/py-wxpython/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-xarray/package.py b/var/spack/repos/builtin/packages/py-xarray/package.py index 006b282643..6615247e5c 100644 --- a/var/spack/repos/builtin/packages/py-xarray/package.py +++ b/var/spack/repos/builtin/packages/py-xarray/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,8 +12,23 @@ class PyXarray(PythonPackage): homepage = "https://github.com/pydata/xarray" url = "https://pypi.io/packages/source/x/xarray/xarray-0.9.1.tar.gz" + version('0.14.0', sha256='a8b93e1b0af27fa7de199a2d36933f1f5acc9854783646b0f1b37fed9b4da091') + version('0.13.0', sha256='80e5746ffdebb96b997dba0430ff02d98028ef3828e6db6106cbbd6d62e32825') + version('0.12.0', sha256='856fd062c55208a248ac3784cac8d3524b355585387043efc92a4188eede57f3') + version('0.11.0', sha256='636964baccfca0e5d69220ac4ecb948d561addc76f47704064dcbe399e03a818') version('0.9.1', sha256='89772ed0e23f0e71c3fb8323746374999ecbe79c113e3fadc7ae6374e6dc0525') - depends_on('py-setuptools', type='build') - depends_on('py-pandas@0.15.0:', type=('build', 'run')) - depends_on('py-numpy@1.7:', type=('build', 'run')) + depends_on('python@2.7:2.8,3.5:', when='@0.11:', type=('build', 'run')) + depends_on('python@3.5:', when='@0.12', type=('build', 'run')) + depends_on('python@3.5.3:', when='@0.13', type=('build', 'run')) + depends_on('python@3.6:', when='@0.14:', type=('build', 'run')) + + depends_on('py-setuptools', type='build') + + depends_on('py-pandas@0.15.0:', when='@0.9.1', type=('build', 'run')) + depends_on('py-pandas@0.19.2:', when='@0.11:0.13', type=('build', 'run')) + depends_on('py-pandas@0.24:', when='@0.14:', type=('build', 'run')) + + depends_on('py-numpy@1.7:', when='@0.9.1', type=('build', 'run')) + depends_on('py-numpy@1.12:', when='@0.11:0.13', type=('build', 'run')) + depends_on('py-numpy@1.14:', when='@0.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-xattr/package.py b/var/spack/repos/builtin/packages/py-xattr/package.py index 0d29e673e2..8375fa8c09 100644 --- a/var/spack/repos/builtin/packages/py-xattr/package.py +++ b/var/spack/repos/builtin/packages/py-xattr/package.py @@ -1,19 +1,20 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * - class PyXattr(PythonPackage): """A python interface to access extended file attributes, - sans libattr dependency""" + sans libattr dependency. + """ homepage = "http://pyxattr.k1024.org/" - git = "https://github.com/fwang2/pyxattr.git" + url = "https://pypi.io/packages/source/x/xattr/xattr-0.9.6.tar.gz" + git = "https://github.com/iustin/pyxattr.git" - version('develop', branch='dev') + version('master', branch='master') + version('0.9.6', sha256='7cb1b28eeab4fe99cc4350e831434142fce658f7d03f173ff7722144e6a47458') depends_on('python@2.7:') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-xdot/package.py b/var/spack/repos/builtin/packages/py-xdot/package.py index ecdc47e494..684df310d9 100644 --- a/var/spack/repos/builtin/packages/py-xdot/package.py +++ b/var/spack/repos/builtin/packages/py-xdot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,12 +11,12 @@ class PyXdot(PythonPackage): dot language.""" homepage = "https://github.com/jrfonseca/xdot.py" - url = "https://github.com/jrfonseca/xdot.py/archive/0.9.tar.gz" + url = "https://pypi.io/packages/source/x/xdot/xdot-1.0.tar.gz" git = "https://github.com/jrfonseca/xdot.py.git" - version('master', branch="master") - version('1.0', sha256='a8594f94f43f938e01e42ff6015c7e00e3ee1a00c7f06d6287d8c939ffa94f76') - version('0.9', sha256='df7790db573d7a5512e6fa618d9051508c43cf64ca432d97c2207c87b6f20dbd') + version('master', branch='master') + version('1.0', sha256='7e067896d729af82f1fd0758e265f129944d469c30f550e3f15dbdb751cc42a1') + version('0.9', sha256='a33701664ecfefe7c7313a120a587e87334f3a566409bc451538fcde5edd6907') # setuptools is required at runtime to avoid: # No module named 'pkg_resources' @@ -46,17 +46,17 @@ class PyXdot(PythonPackage): python3 = spec['python'].command python3('-m', 'compileall', dst) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): spec = self.spec - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['pango'].prefix.lib, - 'girepository-1.0')) - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['atk'].prefix.lib, - 'girepository-1.0')) - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['gdk-pixbuf'].prefix.lib, - 'girepository-1.0')) - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['gtkplus'].prefix.lib, - 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['pango'].prefix.lib, + 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['atk'].prefix.lib, + 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['gdk-pixbuf'].prefix.lib, + 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['gtkplus'].prefix.lib, + 'girepository-1.0')) diff --git a/var/spack/repos/builtin/packages/py-xenv/package.py b/var/spack/repos/builtin/packages/py-xenv/package.py index cd87ff1e06..c52b71098a 100644 --- a/var/spack/repos/builtin/packages/py-xenv/package.py +++ b/var/spack/repos/builtin/packages/py-xenv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-xlrd/package.py b/var/spack/repos/builtin/packages/py-xlrd/package.py index 1c23bf825b..ae155a964d 100644 --- a/var/spack/repos/builtin/packages/py-xlrd/package.py +++ b/var/spack/repos/builtin/packages/py-xlrd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-xlsxwriter/package.py b/var/spack/repos/builtin/packages/py-xlsxwriter/package.py index 520a50e0a7..6989800313 100644 --- a/var/spack/repos/builtin/packages/py-xlsxwriter/package.py +++ b/var/spack/repos/builtin/packages/py-xlsxwriter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-xlwt/package.py b/var/spack/repos/builtin/packages/py-xlwt/package.py new file mode 100644 index 0000000000..981f3e5df7 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-xlwt/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class PyXlwt(PythonPackage): + """Library to create spreadsheet files compatible with + MS Excel 97/2000/XP/2003 XLS files, on any platform, + with Python 2.6, 2.7, 3.3+.""" + + homepage = "https://pypi.org/project/xlwt/" + url = "https://pypi.io/packages/source/x/xlwt/xlwt-1.3.0.tar.gz" + + version('1.3.0', sha256='c59912717a9b28f1a3c2a98fd60741014b06b043936dcecbc113eaaada156c88') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-xmlrunner/package.py b/var/spack/repos/builtin/packages/py-xmlrunner/package.py index 266a30a95c..c6e7f3a21f 100644 --- a/var/spack/repos/builtin/packages/py-xmlrunner/package.py +++ b/var/spack/repos/builtin/packages/py-xmlrunner/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-xmltodict/package.py b/var/spack/repos/builtin/packages/py-xmltodict/package.py new file mode 100644 index 0000000000..49a3fd4bd8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-xmltodict/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyXmltodict(PythonPackage): + """xmltodict is a Python module that makes working with XML feel like + you are working with JSON.""" + + homepage = "https://github.com/martinblech/xmltodict" + url = "https://pypi.io/packages/source/x/xmltodict/xmltodict-0.12.0.tar.gz" + + version('0.12.0', sha256='50d8c638ed7ecb88d90561beedbf720c9b4e851a9fa6c47ebd64e99d166d8a21') + + depends_on('py-setuptools', type='build') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-xopen/package.py b/var/spack/repos/builtin/packages/py-xopen/package.py index 8a22562784..5fd62e5266 100644 --- a/var/spack/repos/builtin/packages/py-xopen/package.py +++ b/var/spack/repos/builtin/packages/py-xopen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-xpyb/package.py b/var/spack/repos/builtin/packages/py-xpyb/package.py index f5cf29a28e..7960870492 100644 --- a/var/spack/repos/builtin/packages/py-xpyb/package.py +++ b/var/spack/repos/builtin/packages/py-xpyb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py b/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py index 26890b992c..766432857c 100644 --- a/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py +++ b/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-yajl/package.py b/var/spack/repos/builtin/packages/py-yajl/package.py new file mode 100644 index 0000000000..b6e95ff8e8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-yajl/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyYajl(PythonPackage): + """Python bindings for the Yajl JSON encoder/decoder library.""" + + homepage = "https://github.com/rtyler/py-yajl" + url = "https://pypi.io/packages/source/y/yajl/yajl-0.3.5.tar.gz" + + version('0.3.5', sha256='432321ea613692a4782a2368a300f57b59c64a3c8508c7465af3fdc045e7bcc2') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-yamlreader/package.py b/var/spack/repos/builtin/packages/py-yamlreader/package.py index 88a7656968..2a11c38345 100644 --- a/var/spack/repos/builtin/packages/py-yamlreader/package.py +++ b/var/spack/repos/builtin/packages/py-yamlreader/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-yapf/package.py b/var/spack/repos/builtin/packages/py-yapf/package.py index 233404d0ea..15d60af233 100644 --- a/var/spack/repos/builtin/packages/py-yapf/package.py +++ b/var/spack/repos/builtin/packages/py-yapf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-yt/package.py b/var/spack/repos/builtin/packages/py-yt/package.py index 6866482ae5..461e21217b 100644 --- a/var/spack/repos/builtin/packages/py-yt/package.py +++ b/var/spack/repos/builtin/packages/py-yt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-ytopt/package.py b/var/spack/repos/builtin/packages/py-ytopt/package.py index 395cb32f87..18cfcac443 100644 --- a/var/spack/repos/builtin/packages/py-ytopt/package.py +++ b/var/spack/repos/builtin/packages/py-ytopt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-zarr/package.py b/var/spack/repos/builtin/packages/py-zarr/package.py new file mode 100644 index 0000000000..0e1dbbeaae --- /dev/null +++ b/var/spack/repos/builtin/packages/py-zarr/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyZarr(PythonPackage): + """Zarr is a Python package providing an implementation of chunked, + compressed, N-dimensional arrays.""" + + homepage = "https://zarr.readthedocs.io" + url = "https://pypi.io/packages/source/z/zarr/zarr-2.3.2.tar.gz" + + version('2.3.2', sha256='c62d0158fb287151c978904935a177b3d2d318dea3057cfbeac8541915dfa105') + + depends_on('py-asciitree', type=('build', 'run')) + depends_on('py-fasteners', type=('build', 'run')) + depends_on('py-msgpack', type=('build', 'run')) + depends_on('py-setuptools@18.1:', type='build') + depends_on('py-setuptools-scm@1.5.5:', type='build') + depends_on('py-numcodecs@0.6.2:', type=('build', 'run')) + depends_on('py-numpy@1.7:', type=('build', 'run')) + depends_on('py-scandir', type=('build', 'run'), when='^python@:3.4') diff --git a/var/spack/repos/builtin/packages/py-zc-buildout/package.py b/var/spack/repos/builtin/packages/py-zc-buildout/package.py new file mode 100644 index 0000000000..6aa1938369 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-zc-buildout/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyZcBuildout(PythonPackage): + """System for managing development buildouts""" + + homepage = "http://buildout.org/" + url = "https://pypi.io/packages/source/z/zc.buildout/zc.buildout-2.13.1.tar.gz" + + version('2.13.1', sha256='3d14d07226963a517295dfad5879d2799e2e3b65b2c61c71b53cb80f5ab11484') + + depends_on('py-setuptools@8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-zc-lockfile/package.py b/var/spack/repos/builtin/packages/py-zc-lockfile/package.py new file mode 100644 index 0000000000..707448e813 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-zc-lockfile/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyZcLockfile(PythonPackage): + """Basic inter-process locks""" + + homepage = "https://www.python.org/pypi/zc.lockfile" + url = "https://pypi.io/packages/source/z/zc.lockfile/zc.lockfile-1.4.tar.gz" + + version('1.4', sha256='95a8e3846937ab2991b61703d6e0251d5abb9604e18412e2714e1b90db173253') + + depends_on('py-setuptools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-zipp/package.py b/var/spack/repos/builtin/packages/py-zipp/package.py index 668cc76574..31b4d73fdd 100644 --- a/var/spack/repos/builtin/packages/py-zipp/package.py +++ b/var/spack/repos/builtin/packages/py-zipp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-zope-event/package.py b/var/spack/repos/builtin/packages/py-zope-event/package.py index af746d1218..6ad1049a89 100644 --- a/var/spack/repos/builtin/packages/py-zope-event/package.py +++ b/var/spack/repos/builtin/packages/py-zope-event/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-zope-interface/package.py b/var/spack/repos/builtin/packages/py-zope-interface/package.py index 743cb7594d..5f6094ca41 100644 --- a/var/spack/repos/builtin/packages/py-zope-interface/package.py +++ b/var/spack/repos/builtin/packages/py-zope-interface/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/py-zxcvbn/package.py b/var/spack/repos/builtin/packages/py-zxcvbn/package.py new file mode 100644 index 0000000000..d95f9d60ab --- /dev/null +++ b/var/spack/repos/builtin/packages/py-zxcvbn/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyZxcvbn(PythonPackage): + """A realistic password strength estimator. + + This is a Python implementation of the library created by the team at + Dropbox.""" + + homepage = "https://github.com/dwolfhub/zxcvbn-python" + url = "https://github.com/dwolfhub/zxcvbn-python/archive/v4.4.25.tar.gz" + + version('4.4.28', sha256='b7275765acdf8028c21aa502d742e56de2252bac604c04ba5e336c39f88d5576') + version('4.4.27', sha256='9b84927fff7b4cc557b63a49adbd74f7a92026e25edd9e1b2867c1610d15fa5d') + version('4.4.26', sha256='ee498e9257742972950f33540f0e36112db14c636417ce5b53d99a492dad8aba') + version('4.4.25', sha256='dfb4d5aee8b59361572e2c12e7982bb22dbf9a1e8ac1c10c8ffea2c72712aabf') + + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/pythia6/package.py b/var/spack/repos/builtin/packages/pythia6/package.py index a1a8632c2a..4da5ec24d6 100644 --- a/var/spack/repos/builtin/packages/pythia6/package.py +++ b/var/spack/repos/builtin/packages/pythia6/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/pythia8/package.py b/var/spack/repos/builtin/packages/pythia8/package.py new file mode 100644 index 0000000000..8f2ec41b54 --- /dev/null +++ b/var/spack/repos/builtin/packages/pythia8/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Pythia8(AutotoolsPackage): + """The Pythia program is a standard tool for the generation of events in + high-energy collisions, comprising a coherent set of physics models for + the evolution from a few-body hard process to a complex multiparticle + final state.""" + + homepage = "http://home.thep.lu.se/Pythia/" + url = "http://home.thep.lu.se/~torbjorn/pythia8/pythia8244.tgz" + + version('8301', sha256='51382768eb9aafb97870dca1909516422297b64ef6a6b94659259b3e4afa7f06') + version('8244', sha256='e34880f999daf19cdd893a187123927ba77d1bf851e30f6ea9ec89591f4c92ca', preferred=True) + version('8240', sha256='d27495d8ca7707d846f8c026ab695123c7c78c7860f04e2c002e483080418d8d') + version('8235', sha256='e82f0d6165a8250a92e6aa62fb53201044d8d853add2fdad6d3719b28f7e8e9d') + version('8230', sha256='332fad0ed4f12e6e0cb5755df0ae175329bc16bfaa2ae472d00994ecc99cd78d') + version('8212', sha256='f8fb4341c7e8a8be3347eb26b00329a388ccf925313cfbdba655a08d7fd5a70e') + + variant('shared', default=True, description='Build shared library') + + depends_on('rsync', type='build') + + def configure_args(self): + args = [] + + if '+shared' in self.spec: + args.append('--enable-shared') + + return args diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index a92d1c6c79..37d65c54c0 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,8 +31,11 @@ class Python(AutotoolsPackage): maintainers = ['adamjstewart'] + version('3.8.1', sha256='c7cfa39a43b994621b245e029769e9126caa2a93571cee2e743b213cceac35fb') version('3.8.0', sha256='f1069ad3cae8e7ec467aa98a6565a62a48ef196cb8f1455a245a08db5e1792df') - version('3.7.4', sha256='d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3', preferred=True) + version('3.7.6', sha256='aeee681c235ad336af116f08ab6563361a0c81c537072c1b309d6e4050aa2114', preferred=True) + version('3.7.5', sha256='8ecc681ea0600bbfb366f2b173f727b205bb825d93d2f0b286bc4e58d37693da') + version('3.7.4', sha256='d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3') version('3.7.3', sha256='d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff') version('3.7.2', sha256='f09d83c773b9cc72421abba2c317e4e6e05d919f9bcf34468e192b6a6c8e328d') version('3.7.1', sha256='36c1b81ac29d0f8341f727ef40864d99d8206897be96be73dc34d4739c9c9f06') @@ -67,6 +70,15 @@ class Python(AutotoolsPackage): extendable = True + # Variants to avoid cyclical dependencies for concretizer + variant('libxml2', default=True, + description='Use a gettext library build with libxml2') + + variant( + 'debug', default=False, + description="debug build with extra checks (this is high overhead)" + ) + # --enable-shared is known to cause problems for some users on macOS # See http://bugs.python.org/issue29846 variant('shared', default=sys.platform != 'darwin', @@ -108,7 +120,8 @@ class Python(AutotoolsPackage): variant('tix', default=False, description='Build Tix module') depends_on('pkgconfig@0.9.0:', type='build') - depends_on('gettext') + depends_on('gettext +libxml2', when='+libxml2') + depends_on('gettext ~libxml2', when='~libxml2') # Optional dependencies # See detect_modules() in setup.py for details @@ -147,7 +160,7 @@ class Python(AutotoolsPackage): # Fixes build with the Intel compilers # https://github.com/python/cpython/pull/16717 - patch('intel-3.6.7.patch', when='@3.6.7:3.6.8,3.7.1: %intel') + patch('intel-3.6.7.patch', when='@3.6.7:3.6.8,3.7.1:3.7.5 %intel') # For more information refer to this bug report: # https://bugs.python.org/issue29712 @@ -239,6 +252,11 @@ class Python(AutotoolsPackage): spec.satisfies('@2.7.12:2.8,3.5.2:', strict=True): config_args.append('--with-icc') + if '+debug' in spec: + config_args.append('--with-pydebug') + else: + config_args.append('--without-pydebug') + if '+shared' in spec: config_args.append('--enable-shared') else: @@ -289,6 +307,10 @@ class Python(AutotoolsPackage): spec['tcl'].libs.ld_flags, spec['tk'].libs.ld_flags) ]) + # https://docs.python.org/3.8/library/sqlite3.html#f1 + if spec.satisfies('@3.2: +sqlite3'): + config_args.append('--enable-loadable-sqlite-extensions') + return config_args @run_after('install') @@ -391,7 +413,8 @@ class Python(AutotoolsPackage): ] filter_file(spack_cc, self.compiler.cc, *filenames, **kwargs) - filter_file(spack_cxx, self.compiler.cxx, *filenames, **kwargs) + if spack_cxx and self.compiler.cxx: + filter_file(spack_cxx, self.compiler.cxx, *filenames, **kwargs) @run_after('install') def symlink(self): @@ -623,11 +646,15 @@ class Python(AutotoolsPackage): and symlinks it to ``/usr/local``. Users may not know the actual installation directory and add ``/usr/local`` to their ``packages.yaml`` unknowingly. Query the python executable to - determine exactly where it is installed.""" + determine exactly where it is installed. Fall back on + ``spec['python'].prefix`` if that doesn't work.""" dag_hash = self.spec.dag_hash() if dag_hash not in self._homes: - prefix = self.get_config_var('prefix') + try: + prefix = self.get_config_var('prefix') + except ProcessError: + prefix = self.prefix self._homes[dag_hash] = Prefix(prefix) return self._homes[dag_hash] @@ -666,14 +693,20 @@ class Python(AutotoolsPackage): @property def headers(self): - config_h = self.get_config_h_filename() + try: + config_h = self.get_config_h_filename() - if not os.path.exists(config_h): - includepy = self.get_config_var('INCLUDEPY') - msg = 'Unable to locate {0} headers in {1}' - raise RuntimeError(msg.format(self.name, includepy)) + if not os.path.exists(config_h): + includepy = self.get_config_var('INCLUDEPY') + msg = 'Unable to locate {0} headers in {1}' + raise RuntimeError(msg.format(self.name, includepy)) + + headers = HeaderList(config_h) + except ProcessError: + headers = find_headers( + 'pyconfig', self.prefix.include, recursive=True) + config_h = headers[0] - headers = HeaderList(config_h) headers.directories = [os.path.dirname(config_h)] return headers @@ -693,6 +726,9 @@ class Python(AutotoolsPackage): def easy_install_file(self): return join_path(self.site_packages_dir, "easy-install.pth") + def setup_run_environment(self, env): + env.prepend_path('CPATH', os.pathsep.join(self.headers.directories)) + def setup_dependent_build_environment(self, env, dependent_spec): """Set PYTHONPATH to include the site-packages directory for the extension and any other python extensions it depends on.""" diff --git a/var/spack/repos/builtin/packages/qbank/package.py b/var/spack/repos/builtin/packages/qbank/package.py index fa362d6b5a..95a3782778 100644 --- a/var/spack/repos/builtin/packages/qbank/package.py +++ b/var/spack/repos/builtin/packages/qbank/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -36,11 +36,9 @@ class Qbank(Package): phases = ['configure', 'build', 'install'] def configure_args(self): - prefix = self.prefix - config_args = [ - '--prefix', prefix, - '--logdir', join_path(prefix, 'var', 'log', 'qbank') + '--prefix', self.prefix, + '--logdir', self.prefix.var.log.qbank ] return config_args @@ -59,11 +57,8 @@ class Qbank(Package): make('install') if '+doc' in spec: - install_tree('doc', join_path(prefix, 'doc')) - - def setup_environment(self, spack_env, run_env): - spec = self.spec - prefix = self.prefix + install_tree('doc', prefix.doc) - if '+doc' in spec: - run_env.prepend_path('MANPATH', join_path(prefix, 'doc')) + def setup_run_environment(self, env): + if '+doc' in self.spec: + env.prepend_path('MANPATH', self.prefix.doc) diff --git a/var/spack/repos/builtin/packages/qbox/package.py b/var/spack/repos/builtin/packages/qbox/package.py index 52def22bbd..c857991bde 100644 --- a/var/spack/repos/builtin/packages/qbox/package.py +++ b/var/spack/repos/builtin/packages/qbox/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/qca/package.py b/var/spack/repos/builtin/packages/qca/package.py index 7b2b02cac6..cbf1da8932 100644 --- a/var/spack/repos/builtin/packages/qca/package.py +++ b/var/spack/repos/builtin/packages/qca/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/qemu/package.py b/var/spack/repos/builtin/packages/qemu/package.py new file mode 100644 index 0000000000..d595989e01 --- /dev/null +++ b/var/spack/repos/builtin/packages/qemu/package.py @@ -0,0 +1,105 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Qemu(AutotoolsPackage): + """QEMU is a generic and open source machine emulator and virtualizer.""" + + homepage = "https://www.qemu.org" + url = "https://download.qemu.org/qemu-4.1.1.tar.xz" + + maintainers = ['anderbubble'] + + version('4.1.1', sha256='ed6fdbbdd272611446ff8036991e9b9f04a2ab2e3ffa9e79f3bab0eb9a95a1d2') + version('4.1.0', sha256='656e60218689bdeec69903087fd7582d5d3e72238d02f4481d8dc6d79fd909c6') + version('4.0.1', sha256='f2674dd6053ef1d48593aa1f0a50c5ac9039f7a059ecb6f9b8307f3fb2fcedad') + version('4.0.0', sha256='13a93dfe75b86734326f8d5b475fde82ec692d5b5a338b4262aeeb6b0fa4e469') + version('3.1.1.1', sha256='b148fc3c7382c5addd915db433383160ca7b840bc6ea90bb0d35c6b253526d56') + version('3.1.1', sha256='d7c69fef3fb4bfbac99e3f2ac9fb8d6409db4faadf2e37337d544e3fdb4fde3a') + version('3.1.0', sha256='6a0508df079a0a33c2487ca936a56c12122f105b8a96a44374704bef6c69abfc') + version('3.0.1', sha256='cf5747aa3bf0e7ec6cb166f48be4680097c333ce320e8e58140980b0d99512f3') + version('3.0.0', sha256='8d7af64fe8bd5ea5c3bdf17131a8b858491bcce1ee3839425a6d91fb821b5713') + version('2.12.1', sha256='33583800e0006cd00b78226b85be5a27c8e3b156bed2e60e83ecbeb7b9b8364f') + version('2.12.0', sha256='e69301f361ff65bf5dabd8a19196aeaa5613c1b5ae1678f0823bdf50e7d5c6fc') + version('2.11.2', sha256='02d2b2cf5526b642b174596d9b3a8716184f9e79710bc68bf6d9fec175b3821b') + version('2.11.1', sha256='8a5145d1f8bd2eadc6776f3e13c68cd28d01349e30639bdbcb26ac588d668686') + version('2.11.0', sha256='c9d34a79024eae080ce3853aa9afe503824520eefb440190383003081ce7f437') + version('2.10.2', sha256='fcfdaa1ecdaac8aead616fe811bfb8fe4a8f2cd59796aa446c5175b5af0e829f') + version('2.10.1', sha256='1dd51a908fc68c7d935b0b31fb184c5669bc23b5a1b081816e824714f2a11caa') + version('2.10.0', sha256='55d81ac987a4821d2744359c026d766459319ba9c013746570369068d93ff335') + version('2.9.1', sha256='4350b3d1d75f1e6a562d975687e181f61ceaf3ac94e6b629f87e24cbe680d03d') + version('2.9.0', sha256='f01cc33e3c5fd5fd2534ce14e369b6b111d7e54e4a4977f8c37eae668176b022') + version('2.8.1.1', sha256='7b50634d729dcabe4a96d74062832274fa2f4c883e82904f5e6955f801edab54') + version('2.8.1', sha256='4d4d2f62c0f7977fb1d49ba4894b2d5e43b8bf8a442be77d42701262c9166440') + version('2.8.0', sha256='656c3d408e367de7eca85ea488228d5bb7c68f4a6dc0b1966b529524bd6b938c') + version('2.7.1', sha256='7fd448219b43bb61f8b5eb37e465298d503abc84156c9dd6e73c9dc6902a2831') + version('2.7.0', sha256='ea5186cffe3ea5e7e903a3f96905aa5596bde2cda445b1ce4fa00024da6c1371') + version('2.6.2', sha256='bd4b00c47d47ac45518bce2e9bc1a7d24f2df102dcdeedecca699cdbdde2ff2b') + version('2.6.1', sha256='b7e17b0c8a92c99317b984ed5aad85603c475e58f8fe70d75aef1936d22822f0') + version('2.6.0', sha256='d0ddb3e80686003feb7e37dae9531237544ee94f91f36b3c49e87ae11e84393c') + version('2.5.1.1', sha256='29b00bfa8933831122eb43521ff02b462ae4e5bcef77de6309015cbb19d3743f') + version('2.5.1', sha256='bd630bb8dffb3d8579bc9c88534debc941215f346801d78fcae9a71becec84b0') + version('2.5.0', sha256='0b2de3ec698135c20d73c4e67f854590e5eadebcc8bfa8484fe59643370ce002') + version('2.4.1', sha256='b5049109656c98558584cfe0125d7994d8eba987f6f92dca289f44efcd0bb231') + version('2.4.0.1', sha256='7ffebc51f7ff61324524eef7a7ec47596c4e53b3d45ba76141b32884dd7f8cbc') + version('2.4.0', sha256='38be58b62b52115e902439c98c61f3bd4773c0113b62f5b153533fc0fae3f485') + version('2.3.1', sha256='da78995a818146e4ded948cd7590a75b9e5b042f8be28a79bfae1f669819075c') + version('2.3.0', sha256='8cea969890681a4069b1beaa82b89728991f1ca701a0184af50210305078bf5f') + version('2.2.1', sha256='1d8f976255db2d3d280ab0d31a11ea5c39da5ddfdec157475b6c335d017ed978') + version('2.2.0', sha256='ffd9a4bf2df9cd8607924690caae1c6ed79681412449e3679b1308dbc1d64b9a') + version('2.1.3', sha256='26231047738ba53e3eef6caafa97dae6194307b9b34040436292446f12853c10') + version('2.1.2', sha256='4d710187d189f42130c3b0a83d091ed6f97fa6ad152d0e87d48fbb5cc73f661a') + version('2.1.1', sha256='ed40d0616f6c10d0f70d67c5672383aa2b426e22565e48a85aa135ab95b97e98') + version('2.1.0', sha256='ece4d8e9b99ba1671ab3a6ed67ab1f65f85912a8b6318a1350b36088408887f5') + version('2.0.2', sha256='1a7a4479796474ebfc2991ea3eeb62a3dd7375cc427089bb474d6c13dd732307') + version('2.0.0', sha256='8b4a6243e0cec451438f1d5283b3097700298728c046e3fb80814c0b45cb649d') + version('1.7.2', sha256='8897908a564a8be8adaaca5f963285b602de3bec57b187e8575a3808ead350fe') + version('1.7.0', sha256='d9338f59ca570d55e4611f133a1c474620b629067afcd3fba0914e0a2c098dae') + version('1.6.2', sha256='e7bf52efb9842386c3c4e47a48f39327ba3ece12e203c169f2faf4bd2a0c0961') + version('1.6.1', sha256='9d7805e9486116704b546411641a77ed25d306c586036fc3933a7740e190d3b1') + version('1.6.0', sha256='491678c5a94c85c287e3525f1496168fcba6d30752d17ccad91f648bb72f06cf') + version('1.5.3', sha256='bab87866283a49cd7b5f8bf9c136e24715c741f4ec0605742736a958f178cec0') + version('1.5.2', sha256='a0322e5f3004d4c383b075c9c583be39098df35dcf33caa9ba2f2847dd8b99c6') + version('1.5.1', sha256='1286c204c7f50559e61e7ee22842925da30fbbf9ec28d3109d1b195442ebc17d') + version('1.5.0', sha256='04177f655efde974c24b3c2fee22f3138768905b94aa1597fa70868a727396af') + version('1.4.2', sha256='1ac21bd817495599e6db700086c7b1422746a3d30bf531e5e4dcf555ed7e44ad') + version('1.4.1', sha256='62c8240f1c6d72c6c134d8fd466821391c33729cdb82569f3a55e0aa05d18f98') + version('1.4.0', sha256='82d31db238216a53348293ebf06ef00673301a73e0b5d25a4be3c7f8b9ba6f6d') + version('1.3.1', sha256='eb098fcd46676071ac1eec49d558a8cf15a73f344e880f6f033620e94ec46af3') + version('1.3.0', sha256='425d220e6ddcf043486343bf4ae0953b53e5c715bd9ed4d1705becc409661b59') + version('1.2.2', sha256='d81f1d52c08a6fd842c519c0f50ab9b1d0d0f469922402f4552b5515644f9e00') + version('1.2.1', sha256='7ccee3c0d67cf506d85ab1bb80b8bc6734fff7f610c34745798e3945d68a53fc') + version('1.2.0', sha256='ba1fc4cc582d3e6f267a72d864c4c8d2f7ee53b160ef338ae4e64e041e6b6c11') + version('1.1.2', sha256='715aba5e05d48a3af69f704840e8a478a0474d0fb75d846e197dac8942c29ad4') + version('1.1.1', sha256='e28722fd676fed34cfdc07581fd2547a766a1785c71f391ed1f2f4f4e923df64') + version('1.1.0-1', sha256='3a58fbaef1715ac3fa40e534d499873b66039b6adb409a22df11d45a5332e21c') + version('1.1.0', sha256='d9899cf9842f2fe4b0dc3c659dabc8ae32e192151f5be3709a1cd7be5a2c0a9a') + version('1.0.1', sha256='a0548ac6221fce09a5a6877c8db19e8755e175f97b934e69a449170a604825dd') + version('1.0', sha256='6b75305f49cdff890df52a3a341060e8909592d8a9a9b330bb6808153b0a2078') + version('0.15.1', sha256='e25d068d753d1a7d498ae6fdf916da08c3a1aa9ddfb4c5078750009359bb3a75') + version('0.15.0', sha256='6a319f56b9f68c9de3f0b4bf5a6a47e065f4bde50e64f715e12819b2e6f92e4d') + version('0.14.1', sha256='274de48593d153d4cb4c487c902eafcdbd3224f1b846ff832aba03396d8453c7') + version('0.14.0', sha256='fbe4e1d04bf57faeb53c6ae2a2a280504a3c8c9cd1f47db6180c1f8d7e48364d') + version('0.13.0', sha256='69ff5503313fbfcb7b911f2129f16f61a61c7d1a7f13e73f8d6537eaac31e924') + version('0.12.4', sha256='935b243bcf461bb0c6e6c938cd21498edbe204861c4db0869a42cca2f33ff95c') + version('0.12.3', sha256='813cbbe26d521f1081774a4e041b3f068f41481071ba01a4154b4876eaafea90') + version('0.12.2', sha256='26a67f6a9e288117833e498cc02ed61e1e9439e6275ddfe2478da62cdf20e9ba') + version('0.12.1', sha256='2865bde4ab2c53e257755cb8f281ee6fba5a9bf54bc3c503edfa36dc03b484fd') + version('0.12.0', sha256='e885a7bdd8923f828aba3a924ad992c81c0c67f80265279017dd71b5acafd84e') + version('0.11.0', sha256='cc1d141a91e180c9a151369592bcd6b864c9bf581f2db837ab365aec1533bb3e') + version('0.10.6', sha256='5727770bb8cea75e6bd76e0911008217a0fd07ed84ae82d967c7bdd98f9c7749') + version('0.10.5', sha256='59ac82c32b6493bf0a6042ef39549368ad8f0d3ec2151ab040f4ce28c93d751e') + version('0.10.4', sha256='db46889bc8908318e15f26f4bde8eb31824cb117d9234afb77a348ad4b6f5050') + version('0.10.3', sha256='4a5393ff47493a80d28a53ce307bffa52a066fd82045a5598b8da074a2f7dfe7') + version('0.10.2', sha256='2d62bcad5ef7609813381e77a6422fec3d4cbd6347f4297b687510ab4d32e813') + version('0.10.1', sha256='632b8942d8c85b36997ce3ed893bc34c868b432fbaadd4ea86994ca881d6665b') + version('0.10.0', sha256='cd554729fa9d0ec17164afbc1cea62d02bde3db8e16db3fd1b8e71d8e1b3dd41') + version('0.9.1', sha256='a9655a471d0649f5540b890447b35849c162d9b986bf2bbddcb68461748e0f42') + + depends_on('glib@2.40:') + depends_on('pixman@0.21.8:') diff --git a/var/spack/repos/builtin/packages/qhull/package.py b/var/spack/repos/builtin/packages/qhull/package.py index 9e156aaf44..d5ec542ce6 100644 --- a/var/spack/repos/builtin/packages/qhull/package.py +++ b/var/spack/repos/builtin/packages/qhull/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/qjson/package.py b/var/spack/repos/builtin/packages/qjson/package.py index 28aa3acd7e..389cda9835 100644 --- a/var/spack/repos/builtin/packages/qjson/package.py +++ b/var/spack/repos/builtin/packages/qjson/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/qmcpack/package.py b/var/spack/repos/builtin/packages/qmcpack/package.py index 67041e455a..6676e7a0f2 100644 --- a/var/spack/repos/builtin/packages/qmcpack/package.py +++ b/var/spack/repos/builtin/packages/qmcpack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -54,22 +54,29 @@ class Qmcpack(CMakePackage, CudaPackage): variant('gui', default=False, description='Install with Matplotlib (long installation time)') variant('qe', default=True, - description='Install with patched Quantum Espresso 6.4.0') + description='Install with patched Quantum Espresso 6.4.1') # cuda variant implies mixed precision variant by default, but there is # no way to express this in variant syntax, need something like # variant('+mixed', default=True, when='+cuda', description="...") - # conflicts + # high-level variant conflicts conflicts( '+phdf5', when='~mpi', msg='Parallel collective I/O requires MPI-enabled QMCPACK. ' 'Please add "~phdf5" to the Spack install line for serial QMCPACK.') - conflicts('+soa', - when='+cuda', - msg='QMCPACK SOA variant does not exist for CUDA') + conflicts( + '+soa', + when='+cuda@:3.4.0', + msg='QMCPACK CUDA+SOA variant does not exist prior to v. 3.5.0.') + + conflicts( + '+qe', + when='~mpi', + msg='Serial QMCPACK with serial QE converter not supported. ' + 'Configure in serial QE + serial HDF5 will not run correctly.') conflicts('^openblas+ilp64', msg='QMCPACK does not support OpenBLAS 64-bit integer variant') @@ -110,12 +117,11 @@ class Qmcpack(CMakePackage, CudaPackage): depends_on('mpi', when='+mpi') # HDF5 - depends_on('hdf5+hl+fortran', when='+qe') - depends_on('hdf5+hl+fortran+mpi', when='+qe+mpi') - depends_on('hdf5+hl+fortran~mpi', when='+qe~mpi') - depends_on('hdf5~hl~fortran', when='~qe') - depends_on('hdf5~hl~fortran+mpi', when='~qe+mpi') - depends_on('hdf5~hl~fortran~mpi', when='~qe~mpi') + depends_on('hdf5~mpi', when='~phdf5') + depends_on('hdf5+mpi', when='+phdf5') + depends_on('hdf5+hl+fortran~mpi', when='+qe~phdf5') + depends_on('hdf5+hl+fortran+mpi', when='+qe+phdf5') + # Math libraries depends_on('blas') depends_on('lapack') @@ -138,11 +144,11 @@ class Qmcpack(CMakePackage, CudaPackage): patch_checksum = '57cb1b06ee2653a87c3acc0dd4f09032fcf6ce6b8cbb9677ae9ceeb6a78f85e2' depends_on('quantum-espresso@6.4.1+mpi hdf5=parallel', patches=patch(patch_url, sha256=patch_checksum), - when='+qe+mpi', type='run') + when='+qe+phdf5', type='run') - depends_on('quantum-espresso@6.4.1~scalapack~mpi hdf5=serial', + depends_on('quantum-espresso@6.4.1+mpi hdf5=serial', patches=patch(patch_url, sha256=patch_checksum), - when='+qe~mpi', type='run') + when='+qe~phdf5', type='run') # Backport several patches from recent versions of QMCPACK # The test_numerics unit test is broken prior to QMCPACK 3.3.0 @@ -347,40 +353,37 @@ class Qmcpack(CMakePackage, CudaPackage): install_tree('bin', prefix.bin) # QMCPACK 3.6.0 install directory structure changed, thus there - # thus are two version of the setup_environment method + # thus are two version of the setup_run_environment method @when('@:3.5.0') - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set-up runtime environment for QMCPACK. Set PYTHONPATH for basic analysis scripts and for Nexus.""" - run_env.prepend_path('PYTHONPATH', self.prefix.nexus) + env.prepend_path('PYTHONPATH', self.prefix.nexus) @when('@3.6.0:') - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): """Set-up runtime environment for QMCPACK. Set PYTHONPATH for basic analysis scripts and for Nexus. Binaries are in the 'prefix' directory instead of 'prefix.bin' which is not set by the default module environment""" - run_env.prepend_path('PATH', self.prefix) - run_env.prepend_path('PYTHONPATH', self.prefix) + env.prepend_path('PATH', self.prefix) + env.prepend_path('PYTHONPATH', self.prefix) @run_after('build') @on_package_attributes(run_tests=True) - def check(self): + def check_install(self): """Run ctest after building binary. It can take over 24 hours to run all the regression tests, here we - only run the unit tests and short tests. If the unit tests fail, - the QMCPACK installation aborts. On the other hand, the short tests - are too strict and often fail, but are still useful to run. In the - future, the short tests will be more reasonable in terms of quality - assurance (i.e. they will not be so strict), but will be sufficient to - validate QMCPACK in production.""" + only run the unit tests and deterministic tests. If the unit tests + fail, the QMCPACK installation aborts. If the deterministic tests + fails, QMCPACK will still install and emit a warning message.""" with working_dir(self.build_directory): - ctest('-L', 'unit') + ctest('-R', 'unit') try: - ctest('-R', 'short') + ctest('-R', 'deterministic', '-LE', 'unstable') except ProcessError: - warn = 'Unit tests passed, but short tests have failed.\n' - warn += 'Please review failed tests before proceeding\n' - warn += 'with production calculations.\n' + warn = 'Unit tests passed, but deterministic tests failed.\n' + warn += 'Please report this failure to:\n' + warn += 'https://github.com/QMCPACK/qmcpack/issues' tty.msg(warn) diff --git a/var/spack/repos/builtin/packages/qmd-progress/package.py b/var/spack/repos/builtin/packages/qmd-progress/package.py index 4731980029..7d7a6cfda6 100644 --- a/var/spack/repos/builtin/packages/qmd-progress/package.py +++ b/var/spack/repos/builtin/packages/qmd-progress/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/qnnpack/package.py b/var/spack/repos/builtin/packages/qnnpack/package.py new file mode 100644 index 0000000000..a5c1f73e71 --- /dev/null +++ b/var/spack/repos/builtin/packages/qnnpack/package.py @@ -0,0 +1,83 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Qnnpack(CMakePackage): + """QNNPACK (Quantized Neural Networks PACKage) is a mobile-optimized + library for low-precision high-performance neural network inference. + QNNPACK provides implementation of common neural network operators on + quantized 8-bit tensors.""" + + homepage = "https://github.com/pytorch/QNNPACK" + git = "https://github.com/pytorch/QNNPACK.git" + + version('master', branch='master') + + depends_on('cmake@3.5:', type='build') + + resource( + name='cpuinfo', + git='https://github.com/Maratyszcza/cpuinfo.git', + destination='deps', + placement='cpuinfo' + ) + resource( + name='fp16', + git='https://github.com/Maratyszcza/FP16.git', + destination='deps', + placement='fp16' + ) + resource( + name='fxdiv', + git='https://github.com/Maratyszcza/FXdiv.git', + destination='deps', + placement='fxdiv' + ) + resource( + name='googlebenchmark', + url='https://github.com/google/benchmark/archive/v1.4.1.zip', + sha256='61ae07eb5d4a0b02753419eb17a82b7d322786bb36ab62bd3df331a4d47c00a7', + destination='deps', + placement='googlebenchmark', + ) + resource( + name='googletest', + url='https://github.com/google/googletest/archive/release-1.8.0.zip', + sha256='f3ed3b58511efd272eb074a3a6d6fb79d7c2e6a0e374323d1e6bcbcc1ef141bf', + destination='deps', + placement='googletest', + ) + resource( + name='psimd', + git='https://github.com/Maratyszcza/psimd.git', + destination='deps', + placement='psimd' + ) + resource( + name='pthreadpool', + git='https://github.com/Maratyszcza/pthreadpool.git', + destination='deps', + placement='pthreadpool' + ) + + def cmake_args(self): + return [ + '-DCPUINFO_SOURCE_DIR={0}'.format( + join_path(self.stage.source_path, 'deps/cpuinfo')), + '-DFP16_SOURCE_DIR={0}'.format( + join_path(self.stage.source_path, 'deps/fp16')), + '-DFXDIV_SOURCE_DIR={0}'.format( + join_path(self.stage.source_path, 'deps/fxdiv')), + '-DPSIMD_SOURCE_DIR={0}'.format( + join_path(self.stage.source_path, 'deps/psimd')), + '-DPTHREADPOOL_SOURCE_DIR={0}'.format( + join_path(self.stage.source_path, 'deps/pthreadpool')), + '-DGOOGLEBENCHMARK_SOURCE_DIR={0}'.format( + join_path(self.stage.source_path, 'deps/googlebenchmark')), + '-DGOOGLETEST_SOURCE_DIR={0}'.format( + join_path(self.stage.source_path, 'deps/googletest')), + ] diff --git a/var/spack/repos/builtin/packages/qorts/package.py b/var/spack/repos/builtin/packages/qorts/package.py index c40aa26a2b..89a4ea2508 100644 --- a/var/spack/repos/builtin/packages/qorts/package.py +++ b/var/spack/repos/builtin/packages/qorts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/qperf/package.py b/var/spack/repos/builtin/packages/qperf/package.py new file mode 100644 index 0000000000..1de0100db0 --- /dev/null +++ b/var/spack/repos/builtin/packages/qperf/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Qperf(AutotoolsPackage): + """ + The qperf measures bandwidth and latency between two nodes. It can work + over TCP/IP as well as the RDMA transports. + """ + + homepage = "https://github.com/linux-rdma/qperf" + url = "https://github.com/linux-rdma/qperf/archive/v0.4.10.tar.gz" + + version('0.4.11', sha256='b0ef2ffe050607566d06102b4ef6268aad08fdc52898620d429096e7b0767e75') + version('0.4.10', sha256='94e26725b4f962eacca36d8ef48cd1fb5043721ac82c3f44018319e47a96cf6b') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + + def autoreconf(self, spec, prefix): + sh = which('sh') + sh('autogen.sh') diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py index f26de74c69..185bd1f421 100644 --- a/var/spack/repos/builtin/packages/qrupdate/package.py +++ b/var/spack/repos/builtin/packages/qrupdate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/qscintilla/package.py b/var/spack/repos/builtin/packages/qscintilla/package.py new file mode 100644 index 0000000000..9bee719c13 --- /dev/null +++ b/var/spack/repos/builtin/packages/qscintilla/package.py @@ -0,0 +1,68 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +class Qscintilla(QMakePackage): + """ + QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control. + """ + + homepage = "https://www.riverbankcomputing.com/software/qscintilla/intro" + url = "https://www.riverbankcomputing.com/static/Downloads/QScintilla/2.11.2/QScintilla_gpl-2.11.2.tar.gz" + + version('2.11.2', sha256='029bdc476a069fda2cea3cd937ba19cc7fa614fb90578caef98ed703b658f4a1') + # Newer versions of Qscintilla won't build, so prefer the following version + version('2.10.2', sha256='14b31d20717eed95ea9bea4cd16e5e1b72cee7ebac647cba878e0f6db6a65ed0', preferred=True) + + variant('designer', default=False, description="Enable pluging for Qt-Designer") + # No 'python' variant, since Python bindings will be + # built by PyQt5+qsci instead + + depends_on('qt') + + @run_before('qmake') + def chdir(self): + os.chdir(str(self.stage.source_path) + '/Qt4Qt5') + + def qmake_args(self): + # below, DEFINES ... gets rid of ...regex...errors during build + # although, there shouldn't be such errors since we use '-std=c++11' + args = ['CONFIG+=-std=c++11', 'DEFINES+=NO_CXX11_REGEX=1'] + return args + + # When INSTALL_ROOT is unset, qscintilla is installed under qt_prefix + # giving 'Nothing Installed Error' + def setup_build_environment(self, env): + env.set('INSTALL_ROOT', self.prefix) + + def setup_run_environment(self, env): + env.prepend_path('QT_PLUGIN_PATH', self.prefix.plugins) + + # Fix install prefix + @run_after('qmake') + def fix_install_path(self): + makefile = FileFilter('Makefile') + makefile.filter(r'\$\(INSTALL_ROOT\)' + + self.spec['qt'].prefix, '$(INSTALL_ROOT)') + + @run_after('install') + def postinstall(self): + # Make designer plugin + if '+designer' in self.spec: + with working_dir(os.path.join(self.stage.source_path, + 'designer-Qt4Qt5')): + qscipro = FileFilter('designer.pro') + qscipro.filter('TEMPLATE = lib', + 'TEMPLATE = lib\nINCLUDEPATH += ../Qt4Qt5\n') + + qmake() + make() + makefile = FileFilter('Makefile') + makefile.filter(r'\$\(INSTALL_ROOT\)' + + self.spec['qt'].prefix, '$(INSTALL_ROOT)') + make('install') diff --git a/var/spack/repos/builtin/packages/qt-creator/package.py b/var/spack/repos/builtin/packages/qt-creator/package.py index 9b23300a65..6b37a1a6c7 100644 --- a/var/spack/repos/builtin/packages/qt-creator/package.py +++ b/var/spack/repos/builtin/packages/qt-creator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,7 +9,7 @@ from spack import * class QtCreator(QMakePackage): """The Qt Creator IDE.""" homepage = 'https://www.qt.io/ide/' - url = 'http://download.qt.io/official_releases/qtcreator/4.3/4.3.1/qt-creator-opensource-src-4.3.1.tar.gz' + url = 'http://download.qt.io/official_releases/qtcreator/4.8/4.8.0/qt-creator-opensource-src-4.8.0.tar.gz' list_url = 'http://download.qt.io/official_releases/qtcreator/' list_depth = 2 @@ -32,8 +32,8 @@ class QtCreator(QMakePackage): url = 'http://download.qt.io/official_releases/qtcreator/{0}/{1}/qt-creator-opensource-src-{1}.tar.gz' return url.format(version.up_to(2), version) - def setup_environment(self, spack_env, run_env): - spack_env.set('INSTALL_ROOT', self.prefix) + def setup_build_environment(self, env): + env.set('INSTALL_ROOT', self.prefix) def qmake_args(self): return ['-r'] diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 55e59cb788..1bc0f1df93 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,6 +21,8 @@ class Qt(Package): phases = ['configure', 'build', 'install'] + version('5.14.1', sha256='6f17f488f512b39c2feb57d83a5e0a13dcef32999bea2e2a8f832f54a29badb8') + version('5.14.0', sha256='be9a77cd4e1f9d70b58621d0753be19ea498e6b0da0398753e5038426f76a8ba') version('5.13.1', sha256='adf00266dc38352a166a9739f1a24a1e36f1be9c04bf72e16e142a256436974e') version('5.12.5', sha256='a2299e21db7767caf98242767bffb18a2a88a42fee2d6a393bedd234f8c91298') version('5.12.2', sha256='59b8cb4e728450b21224dcaaa40eb25bafc5196b6988f2225c394c6b7f881ff5') @@ -117,6 +119,10 @@ class Qt(Package): patch('qt4-gcc8.3-asm-volatile-fix.patch', when='@4') patch('qt5-gcc8.3-asm-volatile-fix.patch', when='@5.0.0:5.12.1') + # patch overflow builtins + patch('qt5_11-intel-overflow.patch', when='@5.11') + patch('qt5_12-intel-overflow.patch', when='@5.12:') + # Build-only dependencies depends_on("pkgconfig", type='build') depends_on("flex", when='+webkit', type='build') @@ -135,11 +141,12 @@ class Qt(Package): depends_on("gtkplus", when='+gtk') depends_on("openssl", when='+ssl') depends_on("sqlite", when='+sql', type=('build', 'run')) + depends_on("sqlite+column_metadata", when='+sql%intel', type=('build', 'run')) depends_on("libpng@1.2.57", when='@3') depends_on("pcre+multibyte", when='@5.0:5.8') depends_on("inputproto", when='@:5.8') - depends_on("openssl@:1.0.999", when='@:5.9+ssl') + depends_on("openssl@:1.0.999", when='@:5.9+ssl~krellpatch') depends_on("glib", when='@4:') depends_on("libpng", when='@4:') @@ -160,7 +167,8 @@ class Qt(Package): depends_on("xcb-util-keysyms") depends_on("xcb-util-renderutil") depends_on("xcb-util-wm") - depends_on("libxext", when='@3:4.99') + depends_on("libxext") + depends_on("libxrender") conflicts('+framework', msg="QT cannot be built as a framework except on macOS.") else: @@ -169,6 +177,10 @@ class Qt(Package): use_xcode = True + # Mapping for compilers/systems in the QT 'mkspecs' + compiler_mapping = {'intel': 'icc', 'clang': 'clang-libc++', 'gcc': 'g++'} + platform_mapping = {'darwin': 'macx'} + def url_for_version(self, version): # URL keeps getting more complicated with every release url = self.list_url @@ -218,6 +230,25 @@ class Qt(Package): def setup_dependent_package(self, module, dependent_spec): module.qmake = Executable(join_path(self.spec.prefix.bin, 'qmake')) + def get_mkspec(self): + """Determine the mkspecs root directory and QT platform. + """ + spec = self.spec + cname = spec.compiler.name + cname = self.compiler_mapping.get(cname, cname) + pname = spec.architecture.platform + pname = self.platform_mapping.get(pname, pname) + + qtplat = None + mkspec_dir = 'qtbase/mkspecs' if spec.satisfies('@5:') else 'mkspecs' + for subdir in ('', 'unsupported'): + platdirname = "".join([subdir, pname, "-", cname]) + if os.path.exists(os.path.join(mkspec_dir, platdirname)): + qtplat = platdirname + break + + return (mkspec_dir, qtplat) + @when('@4 platform=darwin') def patch(self): ogl = self.spec['opengl'] if '+opengl' in self.spec else None @@ -275,32 +306,40 @@ class Qt(Package): ] filter_file(r'(\+=.*)debug_and_release', r'\1', *files_to_filter) - @when('@4') # *NOT* darwin/mac + @when('@4: %gcc') # *NOT* darwin/mac gcc def patch(self): - # Fix qmake compilers in the default mkspec - filter_file('^QMAKE_CC .*', 'QMAKE_CC = cc', - 'mkspecs/common/g++-base.conf') - filter_file('^QMAKE_CXX .*', 'QMAKE_CXX = c++', - 'mkspecs/common/g++-base.conf') + (mkspec_dir, platform) = self.get_mkspec() + + def conf(name): + return os.path.join(mkspec_dir, 'common', name + '.conf') - # Necessary to build with GCC 6 and other modern compilers - # http://stackoverflow.com/questions/10354371/ - filter_file('(^QMAKE_CXXFLAGS .*)', r'\1 -std=gnu++98', - 'mkspecs/common/gcc-base.conf') + # Fix qmake compilers in the default mkspec + filter_file('^QMAKE_CC .*', 'QMAKE_CC = cc', conf('g++-base')) + filter_file('^QMAKE_CXX .*', 'QMAKE_CXX = c++', conf('g++-base')) + # Don't error out on undefined symbols filter_file('^QMAKE_LFLAGS_NOUNDEF .*', 'QMAKE_LFLAGS_NOUNDEF = ', - 'mkspecs/common/g++-unix.conf') + conf('g++-unix')) - @when('@5') + if self.spec.satisfies('@4'): + # Necessary to build with GCC 6 and other modern compilers + # http://stackoverflow.com/questions/10354371/ + with open(conf('gcc-base'), 'a') as f: + f.write("QMAKE_CXXFLAGS += -std=gnu++98\n") + + @when('@4: %intel') def patch(self): - # Fix qmake compilers in the default mkspec - filter_file('^QMAKE_CC .*', 'QMAKE_CC = cc', - 'qtbase/mkspecs/common/g++-base.conf') - filter_file('^QMAKE_CXX .*', 'QMAKE_CXX = c++', - 'qtbase/mkspecs/common/g++-base.conf') + (mkspec_dir, platform) = self.get_mkspec() + conf_file = os.path.join(mkspec_dir, platform, "qmake.conf") - filter_file('^QMAKE_LFLAGS_NOUNDEF .*', 'QMAKE_LFLAGS_NOUNDEF = ', - 'qtbase/mkspecs/common/g++-unix.conf') + # Intel's `ar` equivalent might not be in the path: replace it with + # explicit + xiar = os.path.join(os.path.dirname(self.compiler.cc), 'xiar') + filter_file(r'\bxiar\b', xiar, conf_file) + + if self.spec.satisfies('@4'): + with open(conf_file, 'a') as f: + f.write("QMAKE_CXXFLAGS += -std=gnu++98\n") @property def common_config_args(self): @@ -314,8 +353,8 @@ class Qt(Package): '-release', '-confirm-license', '-openssl-linked', - '{0}'.format(openssl.libs.search_flags), - '{0}'.format(openssl.headers.include_flags), + openssl.libs.search_flags, + openssl.headers.include_flags, '-optimized-qmake', '-no-pch', ] @@ -339,7 +378,11 @@ class Qt(Package): config_args.append('-no-openssl') if '+sql' in self.spec: - config_args.append('-system-sqlite') + sqlite = self.spec['sqlite'] + config_args.extend([ + '-system-sqlite', + '-R', sqlite.prefix.lib, + ]) else: comps = ['db2', 'ibase', 'oci', 'tds', 'mysql', 'odbc', 'psql', 'sqlite', 'sqlite2'] @@ -356,19 +399,19 @@ class Qt(Package): harfbuzz = self.spec['harfbuzz'] config_args.extend([ '-system-harfbuzz', - '{0}'.format(harfbuzz.libs.search_flags), - '{0}'.format(harfbuzz.headers.include_flags), + harfbuzz.libs.search_flags, + harfbuzz.headers.include_flags, '-system-pcre', - '{0}'.format(pcre.libs.search_flags), - '{0}'.format(pcre.headers.include_flags) + pcre.libs.search_flags, + pcre.headers.include_flags ]) if self.spec.satisfies('@5.7:'): dc = self.spec['double-conversion'] config_args.extend([ '-system-doubleconversion', - '{0}'.format(dc.libs.search_flags), - '{0}'.format(dc.headers.include_flags) + dc.libs.search_flags, + dc.headers.include_flags ]) if '@:5.7.1' in self.spec: @@ -376,19 +419,27 @@ class Qt(Package): else: # FIXME: those could work for other versions png = self.spec['libpng'] + config_args.append('-system-libpng') + if not png.external: + config_args.extend([ + png.libs.search_flags, + png.headers.include_flags + ]) + jpeg = self.spec['jpeg'] + config_args.append('-system-libjpeg') + if not jpeg.external: + config_args.extend([ + jpeg.libs.search_flags, + jpeg.headers.include_flags, + ]) zlib = self.spec['zlib'] - config_args.extend([ - '-system-libpng', - '{0}'.format(png.libs.search_flags), - '{0}'.format(png.headers.include_flags), - '-system-libjpeg', - '{0}'.format(jpeg.libs.search_flags), - '{0}'.format(jpeg.headers.include_flags), - '-system-zlib', - '{0}'.format(zlib.libs.search_flags), - '{0}'.format(zlib.headers.include_flags) - ]) + config_args.append('-system-zlib') + if not zlib.external: + config_args.extend([ + zlib.libs.search_flags, + zlib.headers.include_flags + ]) if '@:5.7.0' in self.spec: config_args.extend([ @@ -415,22 +466,13 @@ class Qt(Package): if MACOS_VERSION: config_args.append('-{0}framework'.format( '' if '+framework' in self.spec else 'no-')) - if '@5:' in self.spec and MACOS_VERSION: - config_args.extend([ - '-no-xcb-xlib', - '-no-pulseaudio', - '-no-alsa', - ]) - if self.spec.satisfies('@:5.11'): - config_args.append('-no-xinput2') - # FIXME: else: -system-xcb ? + (_, qtplat) = self.get_mkspec() + if qtplat is not None: + config_args.extend(['-platform', qtplat]) return config_args - # Don't disable all the database drivers, but should - # really get them into spack at some point. - @when('@3') def configure(self, spec, prefix): # A user reported that this was necessary to link Qt3 on ubuntu. @@ -472,51 +514,56 @@ class Qt(Package): sdkpath = which('xcrun')('--show-sdk-path', output=str).strip() config_args.extend([ '-cocoa', - '-platform', 'unsupported/macx-clang-libc++', '-sdk', sdkpath]) configure(*config_args) - @when('@5.0:5.6') - def configure(self, spec, prefix): - webkit_args = [] if '+webkit' in spec else ['-skip', 'qtwebkit'] - configure('-no-eglfs', - '-no-directfb', - '-{0}gtkstyle'.format('' if '+gtk' in spec else 'no-'), - *(webkit_args + self.common_config_args)) - - @when('@5.7:') + @when('@5') def configure(self, spec, prefix): config_args = self.common_config_args + version = self.version + + config_args.extend([ + '-no-eglfs', + '-no-directfb', + '-{0}gtk{1}'.format( + '' if '+gtk' in spec else 'no-', + '' if version >= Version('5.7') else 'style') + ]) - if not MACOS_VERSION: + if MACOS_VERSION: config_args.extend([ - '-system-xcb', + '-no-xcb-xlib', + '-no-pulseaudio', + '-no-alsa', ]) + if version < Version('5.12'): + config_args.append('-no-xinput2') + else: + # Linux-only QT5 dependencies + config_args.append('-system-xcb') if '~webkit' in spec: config_args.extend([ - '-skip', 'webengine', + '-skip', + 'webengine' if version >= Version('5.7') else 'qtwebkit', ]) - if '~opengl' in spec and spec.satisfies('@5.10:'): - config_args.extend([ - '-skip', 'webglplugin', - ]) + if spec.satisfies('@5.7'): + config_args.extend(['-skip', 'virtualkeyboard']) - if self.version > Version('5.8'): + if version >= Version('5.8'): # relies on a system installed wayland, i.e. no spack package yet # https://wayland.freedesktop.org/ubuntu16.04.html # https://wiki.qt.io/QtWayland config_args.extend(['-skip', 'wayland']) - if spec.satisfies('@5.7'): - config_args.extend(['-skip', 'virtualkeyboard']) + if version >= Version('5.10') and '~opengl' in spec: + config_args.extend([ + '-skip', 'webglplugin', + ]) - configure('-no-eglfs', - '-no-directfb', - '-{0}gtk'.format('' if '+gtk' in spec else 'no-'), - *config_args) + configure(*config_args) def build(self, spec, prefix): make() diff --git a/var/spack/repos/builtin/packages/qt/qt5_11-intel-overflow.patch b/var/spack/repos/builtin/packages/qt/qt5_11-intel-overflow.patch new file mode 100644 index 0000000000..5bb0b1e03e --- /dev/null +++ b/var/spack/repos/builtin/packages/qt/qt5_11-intel-overflow.patch @@ -0,0 +1,11 @@ +--- a/qtbase/src/corelib/global/qnumeric_p.h 2018-11-25 06:51:11.000000000 -0600 ++++ b/qtbase/src/corelib/global/qnumeric_p.h 2020-01-07 14:13:12.103818264 -0600 +@@ -168,7 +168,7 @@ + // size_t. Implementations for 8- and 16-bit types will work but may not be as + // efficient. Implementations for 64-bit may be missing on 32-bit platforms. + +-#if (defined(Q_CC_GNU) && (Q_CC_GNU >= 500) || (defined(Q_CC_INTEL) && !defined(Q_OS_WIN))) || QT_HAS_BUILTIN(__builtin_add_overflowx) ++#if (defined(Q_CC_GNU) && (Q_CC_GNU >= 500) && !defined(Q_CC_INTEL) || (defined(Q_CC_INTEL) && (Q_CC_INTEL >= 1800) && (Q_CC_GNU >= 500) && !defined(Q_OS_WIN))) || QT_HAS_BUILTIN(__builtin_add_overflowx) + // GCC 5, ICC 18, and Clang 3.8 have builtins to detect overflows + + template <typename T> inline diff --git a/var/spack/repos/builtin/packages/qt/qt5_12-intel-overflow.patch b/var/spack/repos/builtin/packages/qt/qt5_12-intel-overflow.patch new file mode 100644 index 0000000000..bfe5c8e4f3 --- /dev/null +++ b/var/spack/repos/builtin/packages/qt/qt5_12-intel-overflow.patch @@ -0,0 +1,11 @@ +--- a/qtbase/src/corelib/global/qnumeric_p.h 2019-08-31 03:29:31.000000000 -0500 ++++ b/qtbase/src/corelib/global/qnumeric_p.h 2020-01-06 14:23:40.719851927 -0600 +@@ -231,7 +231,7 @@ + // size_t. Implementations for 8- and 16-bit types will work but may not be as + // efficient. Implementations for 64-bit may be missing on 32-bit platforms. + +-#if (defined(Q_CC_GNU) && (Q_CC_GNU >= 500) || (defined(Q_CC_INTEL) && !defined(Q_OS_WIN))) || QT_HAS_BUILTIN(__builtin_add_overflow) ++#if (defined(Q_CC_GNU) && (Q_CC_GNU >= 500) && !defined(Q_CC_INTEL) || (defined(Q_CC_INTEL) && (Q_CC_INTEL >= 1800) && (Q_CC_GNU >= 500) && !defined(Q_OS_WIN))) || QT_HAS_BUILTIN(__builtin_add_overflow) + // GCC 5, ICC 18, and Clang 3.8 have builtins to detect overflows + + template <typename T> inline diff --git a/var/spack/repos/builtin/packages/qtgraph/package.py b/var/spack/repos/builtin/packages/qtgraph/package.py index 3d4a7307eb..01096dbc17 100644 --- a/var/spack/repos/builtin/packages/qtgraph/package.py +++ b/var/spack/repos/builtin/packages/qtgraph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,11 +25,11 @@ class Qtgraph(QMakePackage): depends_on("graphviz@2.40.1:", when='@develop') depends_on("graphviz@2.40.1", when='@1.0.0.0:') - def setup_environment(self, spack_env, run_env): - """Set up the compile and runtime environments for a package.""" - spack_env.set('GRAPHVIZ_ROOT', self.spec['graphviz'].prefix) - spack_env.set('INSTALL_ROOT', self.prefix) + def setup_build_environment(self, env): + env.set('GRAPHVIZ_ROOT', self.spec['graphviz'].prefix) + env.set('INSTALL_ROOT', self.prefix) + def setup_run_environment(self, env): # What library suffix should be used based on library existence if os.path.isdir(self.prefix.lib64): lib_dir = self.prefix.lib64 @@ -38,9 +38,7 @@ class Qtgraph(QMakePackage): # The implementor has set up the library and include paths in # a non-conventional way. We reflect that here. - run_env.prepend_path( - 'LD_LIBRARY_PATH', join_path( - lib_dir, - '{0}'.format(self.spec['qt'].version.up_to(3)))) + env.prepend_path('LD_LIBRARY_PATH', join_path( + lib_dir, '{0}'.format(self.spec['qt'].version.up_to(3)))) - run_env.prepend_path('CPATH', self.prefix.include.QtGraph) + env.prepend_path('CPATH', self.prefix.include.QtGraph) diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py index 923d9a329f..dbf2bee790 100644 --- a/var/spack/repos/builtin/packages/qthreads/package.py +++ b/var/spack/repos/builtin/packages/qthreads/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/qtkeychain/package.py b/var/spack/repos/builtin/packages/qtkeychain/package.py index f44f9633a8..c7ebfa822e 100644 --- a/var/spack/repos/builtin/packages/qtkeychain/package.py +++ b/var/spack/repos/builtin/packages/qtkeychain/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/quantum-espresso/package.py b/var/spack/repos/builtin/packages/quantum-espresso/package.py index 2c68a6fbf5..5e41de8a5c 100644 --- a/var/spack/repos/builtin/packages/quantum-espresso/package.py +++ b/var/spack/repos/builtin/packages/quantum-espresso/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,10 +17,13 @@ class QuantumEspresso(Package): """ homepage = 'http://quantum-espresso.org' - url = 'https://gitlab.com/QEF/q-e/-/archive/qe-6.4.1/q-e-qe-6.4.1.tar.gz' + url = 'https://gitlab.com/QEF/q-e/-/archive/qe-6.5/q-e-qe-6.5.tar.gz' git = 'https://gitlab.com/QEF/q-e.git' + maintainers = ['naromero77'] + version('develop', branch='develop') + version('6.5', sha256='258b2a8a6280e86dad779e5c56356d8b35dc96d12ff33dabeee914bc03d6d602') version('6.4.1', sha256='b0d7e9f617b848753ad923d8c6ca5490d5d82495f82b032b71a0ff2f2e9cfa08') version('6.4', sha256='781366d03da75516fdcf9100a1caadb26ccdd1dedd942a6f8595ff0edca74bfe') version('6.3', sha256='4067c8fffa957aabbd5cf2439e2fcb6cf3752325393c67a17d99fd09edf8689c') @@ -86,21 +89,28 @@ class QuantumEspresso(Package): msg='elpa is a parallel library and needs MPI support' ) - # HDF5 support introduced in 6.1 - hdf5_warning = 'HDF5 support only in QE 6.1 and later' - conflicts('hdf5=parallel', when='@:6.0', msg=hdf5_warning) - conflicts('hdf5=serial', when='@:6.0', msg=hdf5_warning) - + # HDF5 support introduced in 6.1.0, but the configure had some limitations. + # In recent tests (Oct 2019), GCC and Intel work with the HDF5 Spack + # package for the default variant. This is only for hdf5=parallel variant. + # Support, for hdf5=serial was introduced in 6.4.1 but required a patch + # for the serial (no MPI) case. This patch was to work around an issue + # that only manifested itself inside the Spack environment. conflicts( 'hdf5=parallel', - when='~mpi', - msg='parallel HDF5 requires MPI support' + when='@:6.0', + msg='parallel HDF5 support only in QE 6.1.0 and later' ) conflicts( 'hdf5=serial', - when='~mpi @6.1:6.3', - msg='serial HDF5 in serial QE only works in develop version' + when='@:6.4.0', + msg='serial HDF5 support only in QE 6.4.1 and later' + ) + + conflicts( + 'hdf5=parallel', + when='~mpi', + msg='parallel HDF5 requires MPI support' ) # Elpa is formally supported by @:5.4.0, but QE configure searches @@ -146,6 +156,13 @@ class QuantumEspresso(Package): sha256='b776890d008e16cca28c31299c62f47de0ba606b900b17cbc27c041f45e564ca', when='@6.3:6.3.0') + # QE 6.4.1 patch to work around configure issues that only appear in the + # Spack environment. We now are able to support: + # `spack install qe~mpi~scalapack hdf5=serial` + patch('https://gitlab.com/QEF/q-e/commit/5fb1195b0844e1052b7601f18ab5c700f9cbe648.diff', + sha256='b1aa3179ee1c069964fb9c21f3b832aebeae54947ce8d3cc1a74e7b154c3c10f', + when='@6.4.1:6.5.0') + def install(self, spec, prefix): prefix_path = prefix.bin if '@:5.4.0' in spec else prefix @@ -233,34 +250,18 @@ class QuantumEspresso(Package): if spec.variants['hdf5'].value != 'none': options.append('--with-hdf5={0}'.format(spec['hdf5'].prefix)) + if '@6.4.1' or '@6.5' in spec: + options.extend([ + '--with-hdf5-include={0}'.format( + spec['hdf5'].headers.directories[0] + ), + '--with-hdf5-libs={0}'.format( + spec['hdf5:hl,fortran'].libs.ld_flags + ) + ]) configure(*options) - # Apparently the build system of QE is so broken that - # make_inc needs to be modified manually: - # - # 1. The variable reported on stdout as HDF5_LIBS is actually - # called HDF5_LIB (singular) - # 2. The link flags omit a few `-L` from the line, and this - # causes the linker to break - # 3. Serial HDF5 case is supported both with and without MPI. - # - # Below we try to match the entire HDF5_LIB line and substitute - # with the list of libraries that needs to be linked. - if spec.variants['hdf5'].value != 'none': - make_inc = join_path(self.stage.source_path, 'make.inc') - hdf5_libs = ' '.join(spec['hdf5:hl,fortran'].libs) - filter_file(r'HDF5_LIB([\s]*)=([\s\w\-\/.,]*)', - 'HDF5_LIB = {0}'.format(hdf5_libs), - make_inc) - if spec.variants['hdf5'].value == 'serial': - # Note that there is a benign side effect with this filter - # file statement. It replaces an instance of MANUAL_DFLAGS - # that is a comment in make.inc. - filter_file(r'MANUAL_DFLAGS([\s]*)=([\s]*)', - 'MANUAL_DFLAGS = -D__HDF5_SERIAL', - make_inc) - if '+epw' in spec: make('all', 'epw') else: diff --git a/var/spack/repos/builtin/packages/quinoa/package.py b/var/spack/repos/builtin/packages/quinoa/package.py index 7b0d95d910..e29c953f3e 100644 --- a/var/spack/repos/builtin/packages/quinoa/package.py +++ b/var/spack/repos/builtin/packages/quinoa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/qwt/package.py b/var/spack/repos/builtin/packages/qwt/package.py index 43de3816fb..be7aba6372 100644 --- a/var/spack/repos/builtin/packages/qwt/package.py +++ b/var/spack/repos/builtin/packages/qwt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,6 +16,7 @@ class Qwt(QMakePackage): homepage = "http://qwt.sourceforge.net/" url = "https://sourceforge.net/projects/qwt/files/qwt/6.1.3/qwt-6.1.3.tar.bz2" + version('6.1.4', sha256='1529215329e51fc562e0009505a838f427919a18b362afff441f035b2d9b5bd9') version('6.1.3', sha256='f3ecd34e72a9a2b08422fb6c8e909ca76f4ce5fa77acad7a2883b701f4309733') version('5.2.2', sha256='36bf2ee51ca9c74fde1322510ffd39baac0db60d5d410bb157968a78d9c1464b') diff --git a/var/spack/repos/builtin/packages/qwtpolar/package.py b/var/spack/repos/builtin/packages/qwtpolar/package.py index 852d014cef..9c70dc162a 100644 --- a/var/spack/repos/builtin/packages/qwtpolar/package.py +++ b/var/spack/repos/builtin/packages/qwtpolar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py index 556049e22c..07591bc8dd 100644 --- a/var/spack/repos/builtin/packages/r-a4/package.py +++ b/var/spack/repos/builtin/packages/r-a4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,12 +9,15 @@ from spack import * class RA4(RPackage): """Automated Affymetrix Array Analysis Umbrella Package.""" - homepage = "https://www.bioconductor.org/packages/a4/" + homepage = "https://bioconductor.org/packages/a4" git = "https://git.bioconductor.org/packages/a4.git" + version('1.32.0', commit='03770d4e53be4eed1bd0ab8f8cddba66854b4712') + version('1.30.0', commit='771e01ae3aaac1c4db12f781c41d90fa7191b64d') + version('1.28.0', commit='e81a8c15e1062ed9433e2d4d333f0484bc0e8bfb') + version('1.26.0', commit='e6af2cba5b684f81cc6e44dbc432916f75a2f774') version('1.24.0', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-a4base', type=('build', 'run')) depends_on('r-a4preproc', type=('build', 'run')) depends_on('r-a4classif', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py index 53d80c567c..306d42a273 100644 --- a/var/spack/repos/builtin/packages/r-a4base/package.py +++ b/var/spack/repos/builtin/packages/r-a4base/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,14 +7,17 @@ from spack import * class RA4base(RPackage): - """Automated Affymetrix Array Analysis.""" + """Automated Affymetrix Array Analysis Base Package.""" - homepage = "https://www.bioconductor.org/packages/a4Base/" + homepage = "https://bioconductor.org/packages/a4Base" git = "https://git.bioconductor.org/packages/a4Base.git" + version('1.32.0', commit='8a1e15d25494c54db8c1de5dbbd69e628569e3d7') + version('1.30.0', commit='fc370b2bd8286acc1e42a10344d91974f5b94229') + version('1.28.0', commit='3918a9ebafa065027c29620ee4d83789cb02f932') + version('1.26.0', commit='9b8ee4a8be90f5035a4b105ecebb8bb5b50cd0d9') version('1.24.0', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-biobase', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-annaffy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4classif/package.py b/var/spack/repos/builtin/packages/r-a4classif/package.py index 6117d3bb7c..38cc611b41 100644 --- a/var/spack/repos/builtin/packages/r-a4classif/package.py +++ b/var/spack/repos/builtin/packages/r-a4classif/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,12 +9,15 @@ from spack import * class RA4classif(RPackage): """Automated Affymetrix Array Analysis Classification Package.""" - homepage = "https://www.bioconductor.org/packages/a4Classif/" + homepage = "https://bioconductor.org/packages/a4Classif" git = "https://git.bioconductor.org/packages/a4Classif.git" + version('1.32.0', commit='aa4f22df2da54b71e1a238d2b9cbcb3afa6f7f88') + version('1.30.0', commit='b62841bff2f8894a3011a4e74afc37076d1322a3') + version('1.28.0', commit='3464011f6c3ddb41b78acc47e775539034287be7') + version('1.26.0', commit='bc4018c3c441e1840bb3e2959c07611489439a50') version('1.24.0', commit='ca06bf274c87a73fc12c29a6eea4b90289fe30b1') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-a4core', type=('build', 'run')) depends_on('r-a4preproc', type=('build', 'run')) depends_on('r-mlinterfaces', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4core/package.py b/var/spack/repos/builtin/packages/r-a4core/package.py index e5a78fec2f..d89db83f1d 100644 --- a/var/spack/repos/builtin/packages/r-a4core/package.py +++ b/var/spack/repos/builtin/packages/r-a4core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,11 +9,14 @@ from spack import * class RA4core(RPackage): """Automated Affymetrix Array Analysis Core Package.""" - homepage = "https://www.bioconductor.org/packages/a4Core/" + homepage = "https://bioconductor.org/packages/a4Core" git = "https://git.bioconductor.org/packages/a4Core.git" + version('1.32.0', commit='2916a29723bdd514d5d987f89725d141d1d2dfce') + version('1.30.0', commit='e392b1b4339a34f93d5d9bc520a1a9385ea63141') + version('1.28.0', commit='39b6ee29bc2f2fdc5733438c14dc02f8abc6460b') + version('1.26.0', commit='e7be935f20b486165a2b27dbbf9e99ba07151bcd') version('1.24.0', commit='c871faa3e1ab6be38a9ea3018816cf31b58b0ed3') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-biobase', type=('build', 'run')) depends_on('r-glmnet', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py index 78db0cc963..934b6b6129 100644 --- a/var/spack/repos/builtin/packages/r-a4preproc/package.py +++ b/var/spack/repos/builtin/packages/r-a4preproc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,10 +9,13 @@ from spack import * class RA4preproc(RPackage): """Automated Affymetrix Array Analysis Preprocessing Package.""" - homepage = "https://www.bioconductor.org/packages/a4Preproc/" + homepage = "https://bioconductor.org/packages/a4Preproc" git = "https://git.bioconductor.org/packages/a4Preproc.git" + version('1.32.0', commit='0da742e500892b682feeb39256906282ad20c558') + version('1.30.0', commit='e6fb9fa2e7c703974e6ca10c0e9681b097b05978') + version('1.28.0', commit='435d66727f1187020d034a1beaf4cd8bd4f76981') + version('1.26.0', commit='be7403acc06670c05ead1adaf60533b0fe3a65ea') version('1.24.0', commit='651014b8102807aea4f1274e34e083e70b5e7ee7') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-annotationdbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4reporting/package.py b/var/spack/repos/builtin/packages/r-a4reporting/package.py index bf6c5264b7..a99ce79bda 100644 --- a/var/spack/repos/builtin/packages/r-a4reporting/package.py +++ b/var/spack/repos/builtin/packages/r-a4reporting/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,11 +9,14 @@ from spack import * class RA4reporting(RPackage): """Automated Affymetrix Array Analysis Reporting Package.""" - homepage = "https://www.bioconductor.org/packages/a4Reporting" + homepage = "https://bioconductor.org/packages/a4Reporting" git = "https://git.bioconductor.org/packages/a4Reporting.git" + version('1.32.0', commit='8d781899c625892080eb50f322694dd640d5f792') + version('1.30.0', commit='ae9b9ade45cfac2636d0445a7e0a029dfe3b9390') + version('1.28.0', commit='0fe72f48374353c39479a45e5516d0709f8c9ef7') + version('1.26.0', commit='cce201502e2d3b28fd2823b66d9f81b034dc7eaa') version('1.24.0', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-annaffy', type=('build', 'run')) depends_on('r-xtable', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-abadata/package.py b/var/spack/repos/builtin/packages/r-abadata/package.py index 2f4f6f1ebc..3fdc18a8c0 100644 --- a/var/spack/repos/builtin/packages/r-abadata/package.py +++ b/var/spack/repos/builtin/packages/r-abadata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,24 @@ from spack import * class RAbadata(RPackage): - """Provides the data for the gene expression enrichment analysis - conducted in the package 'ABAEnrichment'. The package includes three - datasets which are derived from the Allen Brain Atlas: (1) Gene - expression data from Human Brain (adults) averaged across donors, - (2) Gene expression data from the Developing Human Brain pooled into - five age categories and averaged across donors and (3) a developmental - effect score based on the Developing Human Brain expression data. - All datasets are restricted to protein coding genes.""" + """Averaged gene expression in human brain regions from Allen Brain Atlas. - homepage = "https://bioconductor.org/packages/ABAData/" - url = "https://bioconductor.org/packages/release/data/experiment/src/contrib/ABAData_1.14.0.tar.gz" + Provides the data for the gene expression enrichment analysis conducted + in the package 'ABAEnrichment'. The package includes three datasets + which are derived from the Allen Brain Atlas: (1) Gene expression data + from Human Brain (adults) averaged across donors, (2) Gene expression + data from the Developing Human Brain pooled into five age categories and + averaged across donors and (3) a developmental effect score based on the + Developing Human Brain expression data. All datasets are restricted to + protein coding genes.""" - version('1.14.0', sha256='d203d968044c292cdfab57a4d6bf52dfb60470bd78b4c9bd88892577ac42b2b7') + homepage = "https://bioconductor.org/packages/ABAData" + git = "https://git.bioconductor.org/packages/ABAData.git" + + version('1.14.0', commit='ed7460e7d2948684db69dd4b4f8e135af50198bd') + version('1.12.0', commit='9c2f0fbda75b06a0807bd714528915920899282d') + version('1.10.0', commit='197edb2c3fc733c9e44dde2b9b86ecedcd2c5e1a') + version('1.8.0', commit='181a4af1af349064eb432255970e925ae2564e1a') + version('1.6.0', commit='517c18a3d1809dde0291eeb47dd2545c7cfcdabe') + + depends_on('r@3.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/package.py index 8c0708ed81..13ff668a73 100644 --- a/var/spack/repos/builtin/packages/r-abaenrichment/package.py +++ b/var/spack/repos/builtin/packages/r-abaenrichment/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,28 +7,37 @@ from spack import * class RAbaenrichment(RPackage): - """The package ABAEnrichment is designed to test for enrichment - of user defined candidate genes in the set of expressed genes in - different human brain regions. The core function 'aba_enrich' - integrates the expression of the candidate gene set (averaged - across donors) and the structural information of the brain using - an ontology, both provided by the Allen Brain Atlas project. - 'aba_enrich' interfaces the ontology enrichment software FUNC to - perform the statistical analyses. Additional functions provided - in this package like 'get_expression' and 'plot_expression' - facilitate exploring the expression data. From version 1.3.5 - onwards genomic regions can be provided as input, too; and from - version 1.5.9 onwards the function 'get_annotated_genes' offers - an easy way to obtain annotations of genes to enriched or - user-defined brain regions.""" - - homepage = "https://bioconductor.org/packages/ABAEnrichment/" + """Gene expression enrichment in human brain regions. + + The package ABAEnrichment is designed to test for enrichment of user + defined candidate genes in the set of expressed genes in different human + brain regions. The core function 'aba_enrich' integrates the expression + of the candidate gene set (averaged across donors) and the structural + information of the brain using an ontology, both provided by the Allen + Brain Atlas project. 'aba_enrich' interfaces the ontology enrichment + software FUNC to perform the statistical analyses. Additional functions + provided in this package like 'get_expression' and 'plot_expression' + facilitate exploring the expression data, and besides the standard + candidate vs. background gene set enrichment, also three additional + tests are implemented, e.g. for cases when genes are ranked instead of + divided into candidate and background.""" + + homepage = "https://bioconductor.org/packages/ABAEnrichment" git = "https://git.bioconductor.org/packages/ABAEnrichment.git" + version('1.14.1', commit='e1ebfb5de816b924af16675a5ba9ed1a6b527b23') + version('1.12.0', commit='1320e932deafd71d67c7a6f758d15b00d6d7f7d7') + version('1.10.0', commit='15f33ccb694a91d2d2067c937682c4bc952def6c') + version('1.8.0', commit='cb8155ee9a04fb55b2a2e8c23df7c0be15bb2624') version('1.6.0', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1') - depends_on('r@3.4.0:3.4.9', when='@1.6.0') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-gplots', type=('build', 'run')) - depends_on('r-gtools', type=('build', 'run')) - depends_on('r-abadata', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-rcpp@0.11.5:', type=('build', 'run')) + depends_on('r-gplots@2.14.2:', type=('build', 'run')) + depends_on('r-gtools@3.5.0:', type=('build', 'run')) + depends_on('r-abadata@0.99.2:', type=('build', 'run')) + + depends_on('r@3.4:', when='@1.8.0:', type=('build', 'run')) + depends_on('r-data-table@1.10.4:', when='@1.8.0:', type=('build', 'run')) + + depends_on('r-gofuncr@1.1.2:', when='@1.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py index e7ebcfa000..72e8013b64 100644 --- a/var/spack/repos/builtin/packages/r-abind/package.py +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-absseq/package.py b/var/spack/repos/builtin/packages/r-absseq/package.py index 7e418ddf3d..13b9c1b7f7 100644 --- a/var/spack/repos/builtin/packages/r-absseq/package.py +++ b/var/spack/repos/builtin/packages/r-absseq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,23 @@ from spack import * class RAbsseq(RPackage): - """Inferring differential expression genes by absolute counts - difference between two groups, utilizing Negative binomial - distribution and moderating fold-change according to heterogeneity - of dispersion across expression level.""" + """ABSSeq: a new RNA-Seq analysis method based on modelling absolute + expression differences. - homepage = "https://www.bioconductor.org/packages/ABSSeq/" + Inferring differential expression genes by absolute counts difference + between two groups, utilizing Negative binomial distribution and + moderating fold-change according to heterogeneity of dispersion across + expression level.""" + + homepage = "https://bioconductor.org/packages/ABSSeq" git = "https://git.bioconductor.org/packages/ABSSeq.git" + version('1.38.0', commit='b686d92f0f0efdb835982efe761d059bc24b34ce') + version('1.36.0', commit='bd419072432cba4ef58b4b37b3c69c85d78b1c4a') + version('1.34.1', commit='0c3a2514ef644c6e0de3714bc91959a302c9e006') + version('1.32.3', commit='189d81c3d70f957bf50780f76a6ddcee499b4784') version('1.22.8', commit='a67ba49bc156a4522092519644f3ec83d58ebd6a') - depends_on('r@3.4.0:3.4.9', when='@1.22.8') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-locfit', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py index 4b49104897..83af5e4cc0 100644 --- a/var/spack/repos/builtin/packages/r-acde/package.py +++ b/var/spack/repos/builtin/packages/r-acde/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,21 +7,27 @@ from spack import * class RAcde(RPackage): - """This package provides a multivariate inferential analysis method - for detecting differentially expressed genes in gene expression data. - It uses artificial components, close to the data's principal - components but with an exact interpretation in terms of differential - genetic expression, to identify differentially expressed genes while - controlling the false discovery rate (FDR). The methods on this - package are described in the vignette or in the article - 'Multivariate Method for Inferential Identification of - Differentially Expressed Genes in Gene Expression Experiments' by - J. P. Acosta, L. Lopez-Kleine and S. Restrepo - (2015, pending publication).""" + """Artificial Components Detection of Differentially Expressed Genes. - homepage = "https://www.bioconductor.org/packages/acde/" - url = "https://bioconductor.org/packages/release/bioc/src/contrib/acde_1.14.0.tar.gz" + This package provides a multivariate inferential analysis method for + detecting differentially expressed genes in gene expression data. It + uses artificial components, close to the data's principal components but + with an exact interpretation in terms of differential genetic + expression, to identify differentially expressed genes while controlling + the false discovery rate (FDR). The methods on this package are + described in the vignette or in the article 'Multivariate Method for + Inferential Identification of Differentially Expressed Genes in Gene + Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo + (2015, pending publication).""" - version('1.14.0', sha256='e8d9ad688610d4b72cab729141dc46fce580c97128d929885336bb138345b788') + homepage = "https://bioconductor.org/packages/acde" + git = "https://git.bioconductor.org/packages/acde.git" - depends_on('r-boot', type=('build', 'run')) + version('1.14.0', commit='6017c7436a46f186b2a3cea9d2b93274f6dd3417') + version('1.12.0', commit='f6ce5926ac915c2d73436f47daf7f9791645dad4') + version('1.10.0', commit='2c303dec45f3c70bf333a6eacae568a08d5ca010') + version('1.8.0', commit='f7fc3e1dce958445f920d3b28b56abde70bfb9de') + version('1.6.0', commit='244c81f435a077bf7895ea565fa6695e8b079f67') + + depends_on('r@3.3:', type=('build', 'run')) + depends_on('r-boot@1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acepack/package.py b/var/spack/repos/builtin/packages/r-acepack/package.py index f0690b027a..e116916827 100644 --- a/var/spack/repos/builtin/packages/r-acepack/package.py +++ b/var/spack/repos/builtin/packages/r-acepack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py index 88b6fa3742..7e83884223 100644 --- a/var/spack/repos/builtin/packages/r-acgh/package.py +++ b/var/spack/repos/builtin/packages/r-acgh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,23 @@ from spack import * class RAcgh(RPackage): - """Functions for reading aCGH data from image analysis output files - and clone information files, creation of aCGH S3 objects for storing - these data. Basic methods for accessing/replacing, subsetting, - printing and plotting aCGH objects.""" + """Classes and functions for Array Comparative Genomic Hybridization data.. - homepage = "https://www.bioconductor.org/packages/aCGH/" + Functions for reading aCGH data from image analysis output files and + clone information files, creation of aCGH S3 objects for storing these + data. Basic methods for accessing/replacing, subsetting, printing and + plotting aCGH objects.""" + + homepage = "https://bioconductor.org/packages/aCGH" git = "https://git.bioconductor.org/packages/aCGH.git" + version('1.62.0', commit='3b68b69c3380fa3b66dfb060457628a4a9c22d4f') + version('1.60.0', commit='ae581758aaa1755448f0cfef5adfb30d1e820b21') + version('1.58.0', commit='2decc79a21bff5a14d708cdc654e351515b20d3e') + version('1.56.0', commit='f3531ec99fc181044bdcb6a01c9976029efb6235') version('1.54.0', commit='be2ed339449f55c8d218e10c435e4ad356683693') - depends_on('r@3.4.0:3.4.9', when='@1.54.0') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-multtest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py index 19ecf0fc99..c3d2e0a7fc 100644 --- a/var/spack/repos/builtin/packages/r-acme/package.py +++ b/var/spack/repos/builtin/packages/r-acme/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,21 +7,27 @@ from spack import * class RAcme(RPackage): - """ACME (Algorithms for Calculating Microarray Enrichment) is a set - of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, - or other experiments that result in regions of the genome showing - "enrichment". It does not rely on a specific array technology - (although the array should be a "tiling" array), is very general - (can be applied in experiments resulting in regions of enrichment), - and is very insensitive to array noise or normalization methods. - It is also very fast and can be applied on whole-genome tiling array - experiments quite easily with enough memory.""" + """Algorithms for Calculating Microarray Enrichment (ACME). - homepage = "https://www.bioconductor.org/packages/ACME/" + ACME (Algorithms for Calculating Microarray Enrichment) is a set of + tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or + other experiments that result in regions of the genome showing + "enrichment". It does not rely on a specific array technology (although + the array should be a "tiling" array), is very general (can be applied + in experiments resulting in regions of enrichment), and is very + insensitive to array noise or normalization methods. It is also very + fast and can be applied on whole-genome tiling array experiments quite + easily with enough memory.""" + + homepage = "https://bioconductor.org/packages/ACME" git = "https://git.bioconductor.org/packages/ACME.git" + version('2.40.0', commit='38499e512998d54d874a0bfdc173f4ba5de5f01a') + version('2.38.0', commit='cd03196428e8adf62e84f25c4d4545429e2c908b') + version('2.36.0', commit='39e056435b9775d35e7f7fc5446c2c3cafe15670') + version('2.34.0', commit='1f53d43e420e245423fdf2711d0dcb345f829469') version('2.32.0', commit='76372255d7714a0c8128a11c028bf70214dac407') - depends_on('r@3.4.0:3.4.9', when='@2.32.0') - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-biobase@2.5.5:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ada/package.py b/var/spack/repos/builtin/packages/r-ada/package.py index 03e2a0305e..e7c860cd65 100644 --- a/var/spack/repos/builtin/packages/r-ada/package.py +++ b/var/spack/repos/builtin/packages/r-ada/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-adabag/package.py b/var/spack/repos/builtin/packages/r-adabag/package.py index 640e339e15..9d4986fca6 100644 --- a/var/spack/repos/builtin/packages/r-adabag/package.py +++ b/var/spack/repos/builtin/packages/r-adabag/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ade4/package.py b/var/spack/repos/builtin/packages/r-ade4/package.py index 9097af588f..d81b2815a0 100644 --- a/var/spack/repos/builtin/packages/r-ade4/package.py +++ b/var/spack/repos/builtin/packages/r-ade4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-adegenet/package.py b/var/spack/repos/builtin/packages/r-adegenet/package.py index 00ea41d638..3eac280830 100644 --- a/var/spack/repos/builtin/packages/r-adegenet/package.py +++ b/var/spack/repos/builtin/packages/r-adegenet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py index f70aa7996c..29dd6a088f 100644 --- a/var/spack/repos/builtin/packages/r-adsplit/package.py +++ b/var/spack/repos/builtin/packages/r-adsplit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,20 +7,26 @@ from spack import * class RAdsplit(RPackage): - """This package implements clustering of microarray gene expression - profiles according to functional annotations. For each term genes - are annotated to, splits into two subclasses are computed and a - significance of the supporting gene set is determined.""" + """Annotation-Driven Clustering. - homepage = "https://www.bioconductor.org/packages/adSplit/" + This package implements clustering of microarray gene expression + profiles according to functional annotations. For each term genes are + annotated to, splits into two subclasses are computed and a significance + of the supporting gene set is determined.""" + + homepage = "https://bioconductor.org/packages/adSplit" git = "https://git.bioconductor.org/packages/adSplit.git" + version('1.54.0', commit='ce8fb61f4a3d0942294da2baa28be1472acb0652') + version('1.52.0', commit='3bd105dbd76c52798b7d52f60c17de62ef13da19') + version('1.50.0', commit='a02e2c994e78ececd5a248575109c5ed36c969db') + version('1.48.0', commit='57dfcd93b9232cf53f05c34179ecb759bb7aff46') version('1.46.0', commit='7e81a83f34d371447f491b3a146bf6851e260c7c') - depends_on('r@3.4.0:3.4.9', when='@1.46.0') + depends_on('r@2.1.0:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-cluster', type=('build', 'run')) - depends_on('r-go-db', type=('build', 'run')) - depends_on('r-kegg-db', type=('build', 'run')) - depends_on('r-multtest', type=('build', 'run')) + depends_on('r-biobase@1.5.12:', type=('build', 'run')) + depends_on('r-cluster@1.9.1:', type=('build', 'run')) + depends_on('r-go-db@1.8.1:', type=('build', 'run')) + depends_on('r-kegg-db@1.8.1:', type=('build', 'run')) + depends_on('r-multtest@1.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aer/package.py b/var/spack/repos/builtin/packages/r-aer/package.py index 59e03886d4..0b9cb5aaf1 100644 --- a/var/spack/repos/builtin/packages/r-aer/package.py +++ b/var/spack/repos/builtin/packages/r-aer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py index c998207b74..c2814bbca0 100644 --- a/var/spack/repos/builtin/packages/r-affxparser/package.py +++ b/var/spack/repos/builtin/packages/r-affxparser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,24 @@ from spack import * class RAffxparser(RPackage): - """Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). - It provides methods for fast and memory efficient parsing of - Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- - and binary-based files are supported. Currently, there are methods - for reading chip definition file (CDF) and a cell intensity file (CEL). - These files can be read either in full or in part. For example, - probe signals from a few probesets can be extracted very quickly - from a set of CEL files into a convenient list structure.""" + """Affymetrix File Parsing SDK. - homepage = "https://www.bioconductor.org/packages/affxparser/" + Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It + provides methods for fast and memory efficient parsing of Affymetrix + files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based + files are supported. Currently, there are methods for reading chip + definition file (CDF) and a cell intensity file (CEL). These files can + be read either in full or in part. For example, probe signals from a few + probesets can be extracted very quickly from a set of CEL files into a + convenient list structure.""" + + homepage = "https://bioconductor.org/packages/affxparser" git = "https://git.bioconductor.org/packages/affxparser.git" + version('1.56.0', commit='20d27701ad2bdfacf34d857bb8ecb4f505b4d056') + version('1.54.0', commit='dce83d23599a964086a84ced4afd13fc43e7cd4f') + version('1.52.0', commit='8e0c4b89ee1cb4ff95f58a5dd947249dc718bc58') + version('1.50.0', commit='01ef641727eadc2cc17b5dbb0b1432364436e3d5') version('1.48.0', commit='2461ea88f310b59c4a9a997a4b3dadedbd65a4aa') - depends_on('r@3.4.0:3.4.9', when='@1.48.0') + depends_on('r@2.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py index af454aefd7..06d65f113a 100644 --- a/var/spack/repos/builtin/packages/r-affy/package.py +++ b/var/spack/repos/builtin/packages/r-affy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,19 +7,27 @@ from spack import * class RAffy(RPackage): - """The package contains functions for exploratory oligonucleotide array + """Methods for Affymetrix Oligonucleotide Arrays. + + The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.""" - homepage = "https://bioconductor.org/packages/affy/" + homepage = "https://bioconductor.org/packages/affy" git = "https://git.bioconductor.org/packages/affy.git" + version('1.62.0', commit='097ab4aa98a1700c5fae65d07bed44a477714605') + version('1.60.0', commit='fcae363e58b322ad53584d9e15e80fa2f9d17206') + version('1.58.0', commit='4698231f45f225228f56c0708cd477ad450b4ee6') + version('1.56.0', commit='d36a7b8f05b1ef60162d94e75037d45c48f88871') version('1.54.0', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-affyio', type=('build', 'run')) - depends_on('r-biocinstaller', type=('build', 'run')) + depends_on('r@2.8.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.12:', type=('build', 'run')) + depends_on('r-biobase@2.5.5:', type=('build', 'run')) + depends_on('r-affyio@1.13.3:', type=('build', 'run')) + depends_on('r-biocinstaller', when='@1.54.0:1.58.0', type=('build', 'run')) depends_on('r-preprocesscore', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.54.0') + + depends_on('r-biocmanager', when='@1.60.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affycomp/package.py b/var/spack/repos/builtin/packages/r-affycomp/package.py index 58d14736a6..aa434c3de9 100644 --- a/var/spack/repos/builtin/packages/r-affycomp/package.py +++ b/var/spack/repos/builtin/packages/r-affycomp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,19 @@ from spack import * class RAffycomp(RPackage): - """The package contains functions that can be used to compare - expression measures for Affymetrix Oligonucleotide Arrays.""" + """Graphics Toolbox for Assessment of Affymetrix Expression Measures. - homepage = "https://www.bioconductor.org/packages/affycomp/" + The package contains functions that can be used to compare expression + measures for Affymetrix Oligonucleotide Arrays.""" + + homepage = "https://bioconductor.org/packages/affycomp" git = "https://git.bioconductor.org/packages/affycomp.git" + version('1.60.0', commit='5dbe61fa04941529a0fc70b728021c8e00c4ba0c') + version('1.58.0', commit='99607b2c4aad37e3e63eccbd12d0d533762f28ef') + version('1.56.0', commit='b0994da338be19396e647c680059fd35341b50a2') + version('1.54.0', commit='65281c1ca37147c2a54ad3722a8d5ff0ffa5acc5') version('1.52.0', commit='1b97a1cb21ec93bf1e5c88d5d55b988059612790') - depends_on('r@3.4.0:3.4.9', when='@1.52.0') - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('r-biobase@2.3.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affycompatible/package.py b/var/spack/repos/builtin/packages/r-affycompatible/package.py index 163c3a5468..0baa5f8bd0 100644 --- a/var/spack/repos/builtin/packages/r-affycompatible/package.py +++ b/var/spack/repos/builtin/packages/r-affycompatible/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,19 +7,25 @@ from spack import * class RAffycompatible(RPackage): - """This package provides an interface to Affymetrix chip annotation - and sample attribute files. The package allows an easy way for users - to download and manage local data bases of Affynmetrix NetAffx - annotation files. The package also provides access to GeneChip - Operating System (GCOS) and GeneChip Command Console - (AGCC)-compatible sample annotation files.""" + """Affymetrix GeneChip software compatibility. - homepage = "https://www.bioconductor.org/packages/AffyCompatible/" + This package provides an interface to Affymetrix chip annotation and + sample attribute files. The package allows an easy way for users to + download and manage local data bases of Affynmetrix NetAffx annotation + files. The package also provides access to GeneChip Operating System + (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation + files.""" + + homepage = "https://bioconductor.org/packages/AffyCompatible" git = "https://git.bioconductor.org/packages/AffyCompatible.git" + version('1.44.0', commit='98a27fbe880551fd32a5febb6c7bde0807eac476') + version('1.42.0', commit='699303cc20f292591e2faa12e211c588efb9eaa8') + version('1.40.0', commit='44838bdb5e8c26afbd898c49ed327ddd1a1d0301') + version('1.38.0', commit='d47ee3a3a3d3bce11121e80fe02ee216b9199b12') version('1.36.0', commit='dbbfd43a54ae1de6173336683a9461084ebf38c3') - depends_on('r@3.4.0:3.4.9', when=('@1.36.0')) - depends_on('r-xml', type=('build', 'run')) - depends_on('r-rcurl', type=('build', 'run')) + depends_on('r@2.7.0:', type=('build', 'run')) + depends_on('r-xml@2.8-1:', type=('build', 'run')) + depends_on('r-rcurl@0.8-1:', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py index 10e35b6cd7..4df3ea750e 100644 --- a/var/spack/repos/builtin/packages/r-affycontam/package.py +++ b/var/spack/repos/builtin/packages/r-affycontam/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,15 +7,21 @@ from spack import * class RAffycontam(RPackage): - """structured corruption of cel file data to demonstrate QA - effectiveness.""" + """structured corruption of affymetrix cel file data. - homepage = "https://www.bioconductor.org/packages/affyContam/" + structured corruption of cel file data to demonstrate QA + effectiveness""" + + homepage = "https://bioconductor.org/packages/affyContam" git = "https://git.bioconductor.org/packages/affyContam.git" + version('1.42.0', commit='8a5e94a5ae8c2ecfafa6177b84a6e8ab07e14fbe') + version('1.40.0', commit='dfd5fd6ae04941dddbda03f656540b71b2fbc614') + version('1.38.0', commit='84651e8eade61619afefc83bb290047da101a5bc') + version('1.36.0', commit='aeb684a7d3f6fa9243f3946d214de53649fa4fd6') version('1.34.0', commit='03529f26d059c19e069cdda358dbf7789b6d4c40') - depends_on('r@3.4.0:3.4.9', when=('@1.34.0')) + depends_on('r@2.7.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-affydata', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py index b7aad34a95..bdb1467a9c 100644 --- a/var/spack/repos/builtin/packages/r-affycoretools/package.py +++ b/var/spack/repos/builtin/packages/r-affycoretools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,15 +7,21 @@ from spack import * class RAffycoretools(RPackage): - """Various wrapper functions that have been written to streamline - the more common analyses that a core Biostatistician might see.""" + """Functions useful for those doing repetitive analyses with Affymetrix + GeneChips. - homepage = "https://www.bioconductor.org/packages/affycoretools/" + Various wrapper functions that have been written to streamline the more + common analyses that a core Biostatistician might see.""" + + homepage = "https://bioconductor.org/packages/affycoretools" git = "https://git.bioconductor.org/packages/affycoretools.git" + version('1.56.0', commit='71eab04056a8d696470420a600b14900186be898') + version('1.54.0', commit='1e1f9680bc3e1fa443f4a81ce5ab81349959b845') + version('1.52.2', commit='2f98c74fad238b94c1e453b972524ab7b573b0de') + version('1.50.6', commit='4be92bcb55d7bace2a110865b7530dcfac14e76e') version('1.48.0', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99') - depends_on('r@3.4.0:3.4.9', when='@1.48.0') depends_on('r-biobase', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) @@ -33,3 +39,5 @@ class RAffycoretools(RPackage): depends_on('r-edger', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) + + depends_on('r-dbi', when='@1.50.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affydata/package.py b/var/spack/repos/builtin/packages/r-affydata/package.py index c5bcc2c329..720477642f 100644 --- a/var/spack/repos/builtin/packages/r-affydata/package.py +++ b/var/spack/repos/builtin/packages/r-affydata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,14 +7,20 @@ from spack import * class RAffydata(RPackage): - """Example datasets of a slightly large size. They represent 'real - world examples', unlike the artificial examples included in the - package affy.""" + """Affymetrix Data for Demonstration Purpose. - homepage = "https://www.bioconductor.org/packages/affydata/" - url = "https://www.bioconductor.org/packages/release/data/experiment/src/contrib/affydata_1.32.0.tar.gz" + Example datasets of a slightly large size. They represent 'real world + examples', unlike the artificial examples included in the package + affy.""" - version('1.32.0', sha256='059e05a2b8908720801d684d5617d5d5e45db7a5999c5659a22daf87658538d1') + homepage = "https://bioconductor.org/packages/affydata" + git = "https://git.bioconductor.org/packages/affydata.git" - depends_on('r@3.4.0:3.4.9', when=('@1.24.0')) - depends_on('r-affy', type=('build', 'run')) + version('1.32.0', commit='c7cef93f6edd23024f4b1985b90e89058874c2bd') + version('1.30.0', commit='d5408d84b37ebae73b40a448dd52baf7b4a13bea') + version('1.28.0', commit='a106a5514c352bf0bbc624ded58a93886d4ce96f') + version('1.26.0', commit='eb0a44a39990b361f9fb1094837ffafb320f39a9') + version('1.24.0', commit='663991606507572f083232e2b393d901270291d4') + + depends_on('r@2.4.0:', type=('build', 'run')) + depends_on('r-affy@1.23.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyexpress/package.py b/var/spack/repos/builtin/packages/r-affyexpress/package.py index f281ebecb9..c01d921fa2 100644 --- a/var/spack/repos/builtin/packages/r-affyexpress/package.py +++ b/var/spack/repos/builtin/packages/r-affyexpress/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,15 +7,21 @@ from spack import * class RAffyexpress(RPackage): - """The purpose of this package is to provide a comprehensive and - easy-to-use tool for quality assessment and to identify differentially - expressed genes in the Affymetrix gene expression data.""" + """Affymetrix Quality Assessment and Analysis Tool. - homepage = "https://www.bioconductor.org/packages/AffyExpress/" + The purpose of this package is to provide a comprehensive and easy-to- + use tool for quality assessment and to identify differentially expressed + genes in the Affymetrix gene expression data.""" + + homepage = "https://bioconductor.org/packages/AffyExpress" git = "https://git.bioconductor.org/packages/AffyExpress.git" + version('1.50.0', commit='8b98703b63396df9692afb0e15b594658125cc96') + version('1.48.0', commit='dbaed516b7529ef4f7588aafaf3c5f1d53a9bb92') + version('1.46.0', commit='2add4a4436e21aa20f1ededbfd5f1365a3d28c85') + version('1.44.0', commit='7517bc8b363ceb107d5dca66dd74f94edefde52a') version('1.42.0', commit='f5c5cf6173f4419e25f4aeff5e6b705a40abc371') - depends_on('r@3.4.0:3.4.9', when='@1.42.0') - depends_on('r-affy', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-affy@1.23.4:', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyilm/package.py b/var/spack/repos/builtin/packages/r-affyilm/package.py index a32532a55f..45ea59fb14 100644 --- a/var/spack/repos/builtin/packages/r-affyilm/package.py +++ b/var/spack/repos/builtin/packages/r-affyilm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,19 +7,24 @@ from spack import * class RAffyilm(RPackage): - """affyILM is a preprocessing tool which estimates gene - expression levels for Affymetrix Gene Chips. Input from - physical chemistry is employed to first background subtract - intensities before calculating concentrations on behalf - of the Langmuir model.""" + """Linear Model of background subtraction and the Langmuir isotherm. - homepage = "https://www.bioconductor.org/packages/affyILM/" + affyILM is a preprocessing tool which estimates gene expression levels + for Affymetrix Gene Chips. Input from physical chemistry is employed to + first background subtract intensities before calculating concentrations + on behalf of the Langmuir model.""" + + homepage = "https://bioconductor.org/packages/affyILM" git = "https://git.bioconductor.org/packages/affyILM.git" + version('1.36.0', commit='619ced931ba72860ce4cb41c841bbca1636a1132') + version('1.34.0', commit='2c02ed2d8fa9a9585d41cf4db0b75d0a07ad8564') + version('1.32.0', commit='860f2ddada80435d309ba334eff3fab503817755') + version('1.30.0', commit='c07d91ae52a2a48f0a5f212c3ecf3243741bee13') version('1.28.0', commit='307bee3ebc599e0ea4a1d6fa8d5511ccf8bef7de') - depends_on('r@3.4.0:3.4.9', when='@1.28.0') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-gcrma', type=('build', 'run')) - depends_on('r-affxparser', type=('build', 'run')) + depends_on('r-affxparser@1.16.0:', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py index 4ef1265271..5379253475 100644 --- a/var/spack/repos/builtin/packages/r-affyio/package.py +++ b/var/spack/repos/builtin/packages/r-affyio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,14 +7,20 @@ from spack import * class RAffyio(RPackage): - """Routines for parsing Affymetrix data files based upon file format + """Tools for parsing Affymetrix data files. + + Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.""" - homepage = "https://bioconductor.org/packages/affyio/" + homepage = "https://bioconductor.org/packages/affyio" git = "https://git.bioconductor.org/packages/affyio.git" + version('1.54.0', commit='c0e306e1805a556a1074d1af1acdd18e0a04477f') + version('1.52.0', commit='9da725ac1098a22a370fa96eb03e51e4f6d5d963') + version('1.50.0', commit='911ea4f8e4cdf7b649b87ef7ed1a5f5b111ef38a') + version('1.48.0', commit='01727a4492c3a0d50453fc91892e04bf5f7fcadb') version('1.46.0', commit='977597f2772e08273d86579486f452170566c880') + depends_on('r@2.6.0:', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.46.0') diff --git a/var/spack/repos/builtin/packages/r-affypdnn/package.py b/var/spack/repos/builtin/packages/r-affypdnn/package.py index 703859244f..b78e98745e 100644 --- a/var/spack/repos/builtin/packages/r-affypdnn/package.py +++ b/var/spack/repos/builtin/packages/r-affypdnn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,19 @@ from spack import * class RAffypdnn(RPackage): - """The package contains functions to perform the PDNN method - described by Li Zhang et al.""" + """Probe Dependent Nearest Neighbours (PDNN) for the affy package. - homepage = "https://www.bioconductor.org/packages/affypdnn/" + The package contains functions to perform the PDNN method described by + Li Zhang et al.""" + + homepage = "https://bioconductor.org/packages/affypdnn" git = "https://git.bioconductor.org/packages/affypdnn.git" + version('1.58.0', commit='83d8b6b0d9606845bd77dbf7164dd5b160f32ccf') + version('1.56.0', commit='5fd9c5265fb895a1f646cf72e8d5169669d979f2') + version('1.54.0', commit='ea971b1b9cc443695a6614bef92e8e116ee87d55') + version('1.52.0', commit='17d74c593ce4f0dfd43f13a5016e482c1399d21e') version('1.50.0', commit='97ff68e9f51f31333c0330435ea23b212b3ed18a') - depends_on('r@3.4.0:3.4.9', when='@1.50.0') - depends_on('r-affy', type=('build', 'run')) + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('r-affy@1.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyplm/package.py b/var/spack/repos/builtin/packages/r-affyplm/package.py index 036aa6dcf3..29ca0119bd 100644 --- a/var/spack/repos/builtin/packages/r-affyplm/package.py +++ b/var/spack/repos/builtin/packages/r-affyplm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,21 +7,27 @@ from spack import * class RAffyplm(RPackage): - """A package that extends and improves the functionality of - the base affy package. Routines that make heavy use of compiled - code for speed. Central focus is on implementation of methods - for fitting probe-level models and tools using these models. - PLM based quality assessment tools.""" + """Methods for fitting probe-level models. - homepage = "https://www.bioconductor.org/packages/affyPLM/" + A package that extends and improves the functionality of the base affy + package. Routines that make heavy use of compiled code for speed. + Central focus is on implementation of methods for fitting probe-level + models and tools using these models. PLM based quality assessment + tools.""" + + homepage = "https://bioconductor.org/packages/affyPLM" git = "https://git.bioconductor.org/packages/affyPLM.git" + version('1.60.0', commit='b11e377d6af3fd0f28aba8195ebf171003da1a9d') + version('1.58.0', commit='32764c7691d9a72a301d50042a8844112887a1c8') + version('1.56.0', commit='13dfc558281af9a177d4d592c34cf7ace629af0e') + version('1.54.0', commit='09cf5f6e01dd2d0aae3e9ddab27301f04bfd645c') version('1.52.1', commit='e8613a6018c4ee58045df6bf19128844f50a1f43') - depends_on('r@3.4.0:3.4.9', when='@1.52.1') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-affy', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.6.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.3.2:', type=('build', 'run')) + depends_on('r-affy@1.11.0:', type=('build', 'run')) + depends_on('r-biobase@2.17.8:', type=('build', 'run')) depends_on('r-gcrma', type=('build', 'run')) - depends_on('r-preprocesscore', type=('build', 'run')) + depends_on('r-preprocesscore@1.5.1:', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyqcreport/package.py b/var/spack/repos/builtin/packages/r-affyqcreport/package.py index 1092c436f4..17c7fa1661 100644 --- a/var/spack/repos/builtin/packages/r-affyqcreport/package.py +++ b/var/spack/repos/builtin/packages/r-affyqcreport/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,22 @@ from spack import * class RAffyqcreport(RPackage): - """This package creates a QC report for an AffyBatch object. - The report is intended to allow the user to quickly assess the - quality of a set of arrays in an AffyBatch object.""" + """QC Report Generation for affyBatch objects. - homepage = "https://www.bioconductor.org/packages/affyQCReport/" + This package creates a QC report for an AffyBatch object. The report is + intended to allow the user to quickly assess the quality of a set of + arrays in an AffyBatch object.""" + + homepage = "https://bioconductor.org/packages/affyQCReport" git = "https://git.bioconductor.org/packages/affyQCReport.git" + version('1.62.0', commit='92d4124b688b90a6a9b8a21ab9d13d92b368cee4') + version('1.60.0', commit='d0c15b1c56fc1caf6f114877ea6c1b8483a0dcfa') + version('1.58.0', commit='14be93a1e7a6d1a64c38ed2f53e0c52a389b2a1b') + version('1.56.0', commit='5c824045c7364155eafc2dd5bb342374aa1ca072') version('1.54.0', commit='5572e9981dc874b78b4adebf58080cac3fbb69e1') - depends_on('r@3.4.0:3.4.9', when='@1.54.0') - depends_on('r-biobase', type=('build', 'run')) + depends_on('r-biobase@1.13.16:', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-affyplm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py index bfbbdad428..f03e50594f 100644 --- a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py +++ b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,23 @@ from spack import * class RAffyrnadegradation(RPackage): - """The package helps with the assessment and correction of - RNA degradation effects in Affymetrix 3' expression arrays. - The parameter d gives a robust and accurate measure of RNA - integrity. The correction removes the probe positional bias, - and thus improves comparability of samples that are affected - by RNA degradation.""" + """Analyze and correct probe positional bias in microarray data due to RNA + degradation. - homepage = "https://www.bioconductor.org/packages/AffyRNADegradation/" + The package helps with the assessment and correction of RNA degradation + effects in Affymetrix 3' expression arrays. The parameter d gives a + robust and accurate measure of RNA integrity. The correction removes the + probe positional bias, and thus improves comparability of samples that + are affected by RNA degradation.""" + + homepage = "https://bioconductor.org/packages/AffyRNADegradation" git = "https://git.bioconductor.org/packages/AffyRNADegradation.git" + version('1.30.0', commit='620c464fb09248e1c7a122828eab59a4fb778cc1') + version('1.28.0', commit='aff91d78fa9e76edaa3ef6a9a43b98b86cc44c24') + version('1.26.0', commit='6ab03ad624701464280bf7dfe345d200e846298a') + version('1.24.0', commit='1f85f3da4720cef94623828713eb84d8accbcf8a') version('1.22.0', commit='0fa78f8286494711a239ded0ba587b0de47c15d3') - depends_on('r@3.4.0:3.4.9', when='@1.22.0') + depends_on('r@2.9.0:', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-agdex/package.py b/var/spack/repos/builtin/packages/r-agdex/package.py index c9bf147975..03aea88d09 100644 --- a/var/spack/repos/builtin/packages/r-agdex/package.py +++ b/var/spack/repos/builtin/packages/r-agdex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,14 +7,20 @@ from spack import * class RAgdex(RPackage): - """A tool to evaluate agreement of differential expression - for cross-species genomics.""" + """Agreement of Differential Expression Analysis. - homepage = "http://bioconductor.org/packages/AGDEX/" + A tool to evaluate agreement of differential expression for cross- + species genomics""" + + homepage = "https://bioconductor.org/packages/AGDEX" git = "https://git.bioconductor.org/packages/AGDEX.git" + version('1.32.0', commit='254ad2c876ab9ac48c3c3b395160dccabc084acf') + version('1.30.0', commit='d6cc21ed7e11e6644399495fa5f8b36368625d4b') + version('1.28.0', commit='7d78ee424485018b73cd019ceaed7a2ed53adf3f') + version('1.26.0', commit='260bc641111770176707d4d43e67b5877bf5eb82') version('1.24.0', commit='29c6bcfa6919a5c6d8bcb36b44e75145a60ce7b5') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-gseabase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-agilp/package.py b/var/spack/repos/builtin/packages/r-agilp/package.py index 971c2c4b84..fdc829b212 100644 --- a/var/spack/repos/builtin/packages/r-agilp/package.py +++ b/var/spack/repos/builtin/packages/r-agilp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,11 +7,17 @@ from spack import * class RAgilp(RPackage): - """Agilent expression array processing package.""" + """Agilent expression array processing package. - homepage = "http://bioconductor.org/packages/agilp/" + More about what it does (maybe more than one line)""" + + homepage = "https://bioconductor.org/packages/agilp" git = "https://git.bioconductor.org/packages/agilp.git" + version('3.16.0', commit='2900d6066317f21d076b3a043b16f32eca168c47') + version('3.14.0', commit='8feb047d70216013462ea7806e9227d192b60c61') + version('3.12.0', commit='a86dea1b03b2b56c2c8317d4b10903fb8948ffcb') + version('3.10.0', commit='cffec1004704a0c5119a50e3ad474897978981be') version('3.8.0', commit='c772a802af1b4c0741f2edd78053a0425160ea53') - depends_on('r@3.4.0:3.4.9', when='@3.8.0') + depends_on('r@2.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-agimicrorna/package.py b/var/spack/repos/builtin/packages/r-agimicrorna/package.py index 8c905a69dc..77444f68a3 100644 --- a/var/spack/repos/builtin/packages/r-agimicrorna/package.py +++ b/var/spack/repos/builtin/packages/r-agimicrorna/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,21 @@ from spack import * class RAgimicrorna(RPackage): - """Processing and Analysis of Agilent microRNA data.""" + """Processing and Differential Expression Analysis of Agilent microRNA + chips.""" - homepage = "https://www.bioconductor.org/packages/AgiMicroRna/" + homepage = "https://bioconductor.org/packages/AgiMicroRna" git = "https://git.bioconductor.org/packages/AgiMicroRna.git" + version('2.34.0', commit='aaa8cdd70ed2696c313f6240ffbfa044f0d97a7a') + version('2.32.0', commit='681ae17d07e8e533f798a607b761b71a31f407d8') + version('2.30.0', commit='99b5a8284cfe3e93c3ae85a2436e87101b9599dd') + version('2.28.0', commit='62c4a12f1168c7aa1ab46d2c97090ef71478328e') version('2.26.0', commit='6dd74bae47986f2a23d03e3f1f9f78f701dd8053') - depends_on('r@3.4.0:3.4.9', when='@2.26.0') - depends_on('r-affycoretools', type=('build', 'run')) - depends_on('r-preprocesscore', type=('build', 'run')) - depends_on('r-affy', type=('build', 'run')) - depends_on('r-limma', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) + depends_on('r-limma', type=('build', 'run')) + depends_on('r-affy@1.22:', type=('build', 'run')) + depends_on('r-preprocesscore', type=('build', 'run')) + depends_on('r-affycoretools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aims/package.py b/var/spack/repos/builtin/packages/r-aims/package.py index baf7f878b6..72bb4bc0b4 100644 --- a/var/spack/repos/builtin/packages/r-aims/package.py +++ b/var/spack/repos/builtin/packages/r-aims/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,23 @@ from spack import * class RAims(RPackage): - """This package contains the AIMS implementation. It contains - necessary functions to assign the five intrinsic molecular - subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, - Normal-like). Assignments could be done on individual samples - as well as on dataset of gene expression data.""" + """AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype. - homepage = "http://bioconductor.org/packages/AIMS/" + This package contains the AIMS implementation. It contains necessary + functions to assign the five intrinsic molecular subtypes (Luminal A, + Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be + done on individual samples as well as on dataset of gene expression + data.""" + + homepage = "https://bioconductor.org/packages/AIMS" git = "https://git.bioconductor.org/packages/AIMS.git" + version('1.16.0', commit='86cb8c998ade3003cd34a5405b218ae07d97bf84') + version('1.14.1', commit='4125c4217a7e4f00169b5ba65dcc3778fdd33c6f') + version('1.12.0', commit='d7eaa723d19a6aca37df244fd0b3d5426ed0a626') + version('1.10.0', commit='972945980b39168502a02ac3aa396f9b99fb3d71') version('1.8.0', commit='86b866c20e191047492c51b43e3f73082c3f8357') - depends_on('r@3.4.0:3.4.9', when='@1.8.0') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-e1071', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/package.py index 856f7b50ae..8b8d5635da 100644 --- a/var/spack/repos/builtin/packages/r-aldex2/package.py +++ b/var/spack/repos/builtin/packages/r-aldex2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,26 +7,33 @@ from spack import * class RAldex2(RPackage): - """A differential abundance analysis for the comparison of - two or more conditions. For example, single-organism and - meta-RNA-seq high-throughput sequencing assays, or of - selected and unselected values from in-vitro sequence selections. - Uses a Dirichlet-multinomial model to infer abundance from counts, - that has been optimized for three or more experimental replicates. - Infers sampling variation and calculates the expected false - discovery rate given the biological and sampling variation - using the Wilcox rank test or Welches t-test (aldex.ttest) or - the glm and Kruskal Wallis tests (aldex.glm). Reports both P - and fdr values calculated by the Benjamini Hochberg correction.""" - - homepage = "http://bioconductor.org/packages/ALDEx2/" + """Analysis Of Differential Abundance Taking Sample Variation Into Account. + + A differential abundance analysis for the comparison of two or more + conditions. Useful for analyzing data from standard RNA-seq or meta-RNA- + seq assays as well as selected and unselected values from in-vitro + sequence selections. Uses a Dirichlet-multinomial model to infer + abundance from counts, optimized for three or more experimental + replicates. The method infers biological and sampling variation to + calculate the expected false discovery rate, given the variation, based + on a Wilcoxon Rank Sum test and Welch's t-test (via aldex.ttest), a + Kruskal-Wallis test (via aldex.kw), a generalized linear model (via + aldex.glm), or a correlation test (via aldex.corr). All tests report + p-values and Benjamini-Hochberg corrected p-values.""" + + homepage = "https://bioconductor.org/packages/ALDEx2" git = "https://git.bioconductor.org/packages/ALDEx2.git" + version('1.16.0', commit='bd698a896a5bea91187e3060e56a147bad1d586f') + version('1.14.1', commit='a8b970c594a00a37c064227bf312d5f89dccabe8') + version('1.12.0', commit='9efde428d22a0be1fe7b6655d45ddce8fcded180') + version('1.10.0', commit='e43f99e4009ad4d5ed200cc8a19faf7091c0c98a') version('1.8.0', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1') - depends_on('r@3.4.0:3.4.9', when='@1.8.0') depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-summarizedexperiment', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) + + depends_on('r-multtest', when='@1.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py index cb55456cb9..d90389605e 100644 --- a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py +++ b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,24 +7,30 @@ from spack import * class RAllelicimbalance(RPackage): - """Provides a framework for allelic specific expression - investigation using RNA-seq data.""" + """Investigates Allele Specific Expression. - homepage = "http://bioconductor.org/packages/AllelicImbalance/" + Provides a framework for allelic specific expression investigation using + RNA-seq data.""" + + homepage = "https://bioconductor.org/packages/AllelicImbalance" git = "https://git.bioconductor.org/packages/AllelicImbalance.git" + version('1.22.0', commit='04692e367e8c6aac475d06adfd7cfa629baab05a') + version('1.20.0', commit='4cd3a789d872151b0d906ec419677271fecdf7c3') + version('1.18.0', commit='6d6eed7487e9207dba556bc76283bcc7745808ea') + version('1.16.0', commit='85f652ae8a0dd15535819b6e934065182df5544a') version('1.14.0', commit='35958534945819baafde0e13d1eb4d05a514142c') - depends_on('r@3.4.0:3.4.9', when='@1.14.0') + depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-summarizedexperiment', type=('build', 'run')) + depends_on('r-summarizedexperiment@0.2.0:', type=('build', 'run')) depends_on('r-genomicalignments', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-bsgenome', type=('build', 'run')) depends_on('r-variantannotation', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-rsamtools', type=('build', 'run')) depends_on('r-genomicfeatures', type=('build', 'run')) @@ -35,3 +41,15 @@ class RAllelicimbalance(RPackage): depends_on('r-seqinr', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.8:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-genomicalignments@1.15.6:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-bsgenome@1.47.3:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-variantannotation@1.25.11:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.31.3:', when='@1.18.0:', type=('build', 'run')) + + depends_on('r-rsamtools@1.99.3:', when='@1.22.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-alpine/package.py b/var/spack/repos/builtin/packages/r-alpine/package.py index c169833a45..cf8a203975 100644 --- a/var/spack/repos/builtin/packages/r-alpine/package.py +++ b/var/spack/repos/builtin/packages/r-alpine/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,15 +7,21 @@ from spack import * class RAlpine(RPackage): - """Fragment sequence bias modeling and correction for RNA-seq - transcript abundance estimation.""" + """alpine. - homepage = "http://bioconductor.org/packages/alpine/" + Fragment sequence bias modeling and correction for RNA-seq transcript + abundance estimation.""" + + homepage = "https://bioconductor.org/packages/alpine" git = "https://git.bioconductor.org/packages/alpine.git" + version('1.10.0', commit='bf22597eb2c6c6aaa26900ed4ece96ce7256e77c') + version('1.8.0', commit='ddaa0b4517f0909460aa1bd33c8e43dc6c8d23d4') + version('1.6.0', commit='ea55fcb3cedb5caa20d8264bb29a4975041f5274') + version('1.4.0', commit='c85beb208fd6bfc0a61a483a98498b589640f946') version('1.2.0', commit='896872e6071769e1ac2cf786974edb8b875c45eb') - depends_on('r@3.4.0:3.4.9', when='@1.2.0') + depends_on('r@3.3:', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-als/package.py b/var/spack/repos/builtin/packages/r-als/package.py index f686341854..bf696f7123 100644 --- a/var/spack/repos/builtin/packages/r-als/package.py +++ b/var/spack/repos/builtin/packages/r-als/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-alsace/package.py b/var/spack/repos/builtin/packages/r-alsace/package.py index 00a21e60ca..d039edd0f6 100644 --- a/var/spack/repos/builtin/packages/r-alsace/package.py +++ b/var/spack/repos/builtin/packages/r-alsace/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,24 @@ from spack import * class RAlsace(RPackage): - """Alternating Least Squares (or Multivariate Curve Resolution) - for analytical chemical data, in particular hyphenated data where - the first direction is a retention time axis, and the second a - spectral axis. Package builds on the basic als function from the - ALS package and adds functionality for high-throughput analysis, - including definition of time windows, clustering of profiles, - retention time correction, etcetera.""" + """ALS for the Automatic Chemical Exploration of mixtures. - homepage = "https://www.bioconductor.org/packages/alsace/" + Alternating Least Squares (or Multivariate Curve Resolution) for + analytical chemical data, in particular hyphenated data where the first + direction is a retention time axis, and the second a spectral axis. + Package builds on the basic als function from the ALS package and adds + functionality for high-throughput analysis, including definition of time + windows, clustering of profiles, retention time correction, etcetera.""" + + homepage = "https://bioconductor.org/packages/alsace" git = "https://git.bioconductor.org/packages/alsace.git" + version('1.20.0', commit='47f1cf8daafc864e5e3418009f349ce85d6b0389') + version('1.18.0', commit='c9fc43c7b441de43b14ef1be69926c4c4a566191') + version('1.16.0', commit='5a51a19aeccbba0123222201cb7a228559f29653') + version('1.14.0', commit='aebb13b00eb850f9569391c4c92183b55b70ae89') version('1.12.0', commit='1364c65bbff05786d05c02799fd44fd57748fae3') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-als', type=('build', 'run')) - depends_on('r-ptw', type=('build', 'run')) + depends_on('r-ptw@1.0.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py index b774502a26..d49a46bff3 100644 --- a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py +++ b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,23 @@ from spack import * class RAltcdfenvs(RPackage): - """Convenience data structures and functions to handle cdfenvs.""" + """alternative CDF environments (aka probeset mappings). - homepage = "https://www.bioconductor.org/packages/altcdfenvs/" + Convenience data structures and functions to handle cdfenvs""" + + homepage = "https://bioconductor.org/packages/altcdfenvs" git = "https://git.bioconductor.org/packages/altcdfenvs.git" + version('2.46.0', commit='90a11e748a5af98cabfd6670a5b7b256420d172b') + version('2.44.0', commit='d804f6432422bd532abab415710f890b36cc8133') + version('2.42.0', commit='00ec6461877a063d938494b8ed0cd273a3b20b85') + version('2.40.0', commit='517a208f49f168bdd3cde40ed216282c417237d7') version('2.38.0', commit='2e92b9da76dbe50af4bf33c525134e29e9809291') - depends_on('r@3.4.0:3.4.9', when='@2.38.0') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.7:', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-biobase@2.15.1:', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-makecdfenv', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-amap/package.py b/var/spack/repos/builtin/packages/r-amap/package.py index 36cdc693f3..cfc312a9e9 100644 --- a/var/spack/repos/builtin/packages/r-amap/package.py +++ b/var/spack/repos/builtin/packages/r-amap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ampliqueso/package.py b/var/spack/repos/builtin/packages/r-ampliqueso/package.py index 64009d8bd5..94292707b9 100644 --- a/var/spack/repos/builtin/packages/r-ampliqueso/package.py +++ b/var/spack/repos/builtin/packages/r-ampliqueso/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,26 +7,32 @@ from spack import * class RAmpliqueso(RPackage): - """The package provides tools and reports for the analysis of - amplicon sequencing panels, such as AmpliSeq.""" + """Analysis of amplicon enrichment panels. - homepage = "https://www.bioconductor.org/packages/ampliQueso/" + The package provides tools and reports for the analysis of amplicon + sequencing panels, such as AmpliSeq""" + + homepage = "https://bioconductor.org/packages/3.8/bioc/html/ampliQueso.html" git = "https://git.bioconductor.org/packages/ampliQueso.git" + version('1.21.0', commit='ed99c5194a452ee299a93e981da2224e4dab5bdd') + version('1.20.0', commit='ed064ffe9c5f2b47136e5f0f2e2c4214af4deae8') + version('1.18.0', commit='c27fa51094135ef8da52cd2b34a27ec6454abd8e') + version('1.16.0', commit='25d2543ff9dedef4f966f999c95cdf87185d3bb3') version('1.14.0', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b') - depends_on('r@3.4.0:3.4.9', when='@1.14.0') - depends_on('r-samr', type=('build', 'run')) - depends_on('r-deseq', type=('build', 'run')) - depends_on('r-edger', type=('build', 'run')) - depends_on('r-xtable', type=('build', 'run')) - depends_on('r-statmod', type=('build', 'run')) - depends_on('r-genefilter', type=('build', 'run')) - depends_on('r-variantannotation', type=('build', 'run')) - depends_on('r-foreach', type=('build', 'run')) - depends_on('r-doparallel', type=('build', 'run')) - depends_on('r-gplots', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-rgl', type=('build', 'run')) + depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r-rnaseqmap@2.17.1:', type=('build', 'run')) depends_on('r-knitr', type=('build', 'run')) - depends_on('r-rnaseqmap', type=('build', 'run')) + depends_on('r-rgl', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-gplots', type=('build', 'run')) + depends_on('r-doparallel', type=('build', 'run')) + depends_on('r-foreach', type=('build', 'run')) + depends_on('r-variantannotation', type=('build', 'run')) + depends_on('r-genefilter', type=('build', 'run')) + depends_on('r-statmod', type=('build', 'run')) + depends_on('r-xtable', type=('build', 'run')) + depends_on('r-edger', type=('build', 'run')) + depends_on('r-deseq', type=('build', 'run')) + depends_on('r-samr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-analysispageserver/package.py b/var/spack/repos/builtin/packages/r-analysispageserver/package.py index 8e71cc5a8e..d72e3c5a50 100644 --- a/var/spack/repos/builtin/packages/r-analysispageserver/package.py +++ b/var/spack/repos/builtin/packages/r-analysispageserver/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,15 +7,21 @@ from spack import * class RAnalysispageserver(RPackage): - """AnalysisPageServer is a modular system that enables sharing - of customizable R analyses via the web.""" + """A framework for sharing interactive data and plots from R through the + web. - homepage = "https://www.bioconductor.org/packages/AnalysisPageServer/" + AnalysisPageServer is a modular system that enables sharing of + customizable R analyses via the web.""" + + homepage = "https://bioconductor.org/packages/AnalysisPageServer" git = "https://git.bioconductor.org/packages/AnalysisPageServer.git" + version('1.18.1', commit='08bd85e872d3f2b0c1fa148cf30bcd2d1a29b630') + version('1.16.0', commit='67b063523f80e2af1d26262367ff50f34e195174') + version('1.14.0', commit='620c0ea1e129ddd1a0866e2c9d7c3fcf06a8baf4') + version('1.12.0', commit='146501974ef1938ee1ec4eb293ea7eeca331a0dc') version('1.10.0', commit='876c87073be116fa15a1afdd407e21152eb80d50') - depends_on('r@3.4.0:3.4.9', when='@1.10.0') depends_on('r-log4r', type=('build', 'run')) depends_on('r-rjson', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-anaquin/package.py b/var/spack/repos/builtin/packages/r-anaquin/package.py index a8b13ab853..10a8e15160 100644 --- a/var/spack/repos/builtin/packages/r-anaquin/package.py +++ b/var/spack/repos/builtin/packages/r-anaquin/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,22 +7,28 @@ from spack import * class RAnaquin(RPackage): - """The project is intended to support the use of sequins - (synthetic sequencing spike-in controls) owned and made available - by the Garvan Institute of Medical Research. The goal is to - provide a standard open source library for quantitative analysis, - modelling and visualization of spike-in controls.""" + """Statistical analysis of sequins. - homepage = "https://www.bioconductor.org/packages/Anaquin/" + The project is intended to support the use of sequins (synthetic + sequencing spike-in controls) owned and made available by the Garvan + Institute of Medical Research. The goal is to provide a standard open + source library for quantitative analysis, modelling and visualization of + spike-in controls.""" + + homepage = "https://bioconductor.org/packages/Anaquin" git = "https://git.bioconductor.org/packages/Anaquin.git" + version('2.8.0', commit='f591d420740b77881ae0a4c16b208c63d460c601') + version('2.6.1', commit='22b6c71697fe1e2db8f6d18f77728d0fd96fa6d6') + version('2.4.0', commit='0d6ae80ff622151a782e4774ca274f06024a71d2') + version('2.2.0', commit='739f4ed2b73c43f934fd65a993ecb48242a5d5da') version('1.2.0', commit='584d1970cc9dc1d354f9a6d7c1306bd7e8567119') - depends_on('r@3.4.0:3.4.9', when='@1.2.0') - depends_on('r-deseq2', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-locfit', type=('build', 'run')) - depends_on('r-qvalue', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) + depends_on('r@3.3:', type=('build', 'run')) + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) depends_on('r-rocr', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-knitr', type=('build', 'run')) + depends_on('r-qvalue', type=('build', 'run')) + depends_on('r-locfit', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-deseq2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aneufinder/package.py b/var/spack/repos/builtin/packages/r-aneufinder/package.py index 9dc0384bf9..ece9dc0c9a 100644 --- a/var/spack/repos/builtin/packages/r-aneufinder/package.py +++ b/var/spack/repos/builtin/packages/r-aneufinder/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,21 +7,28 @@ from spack import * class RAneufinder(RPackage): - """This package implements functions for CNV calling, plotting, - export and analysis from whole-genome single cell sequencing data.""" + """Analysis of Copy Number Variation in Single-Cell-Sequencing Data. - homepage = "https://www.bioconductor.org/packages/AneuFinder/" + AneuFinder implements functions for copy-number detection, breakpoint + detection, and karyotype and heterogeneity analysis in single-cell whole + genome sequencing and strand-seq data.""" + + homepage = "https://bioconductor.org/packages/AneuFinder" git = "https://git.bioconductor.org/packages/AneuFinder.git" + version('1.12.1', commit='e788fd0c864f0bf0abd93df44c6d42f82eb37e0e') + version('1.10.2', commit='56578ae69abac93dfea6bcac1fc205b14b6ba9dd') + version('1.8.0', commit='36a729d244add5aafbe21c37a1baaea6a50354d3') + version('1.6.0', commit='0cfbdd1951fb4df5622e002260cfa86294d65d1d') version('1.4.0', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e') - depends_on('r@3.4.0:3.4.9', when='@1.4.0') + depends_on('r@3.3:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-cowplot', type=('build', 'run')) depends_on('r-aneufinderdata', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) depends_on('r-doparallel', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biocgenerics', when='@1.4.0:1.6.0', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) @@ -33,6 +40,10 @@ class RAneufinder(RPackage): depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) depends_on('r-ggdendro', type=('build', 'run')) + depends_on('r-ggrepel', type=('build', 'run')) depends_on('r-reordercluster', type=('build', 'run')) depends_on('r-mclust', type=('build', 'run')) - depends_on('r-ggrepel', type=('build', 'run')) + + depends_on('r-ecp', when='@1.8.0:', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.10.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py index 4cee62c83c..18d1ec2534 100644 --- a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py +++ b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,12 +7,18 @@ from spack import * class RAneufinderdata(RPackage): - """Whole-genome single cell sequencing data for demonstration - purposes in the AneuFinder package.""" + """WGSCS Data for Demonstration Purposes. - homepage = "https://www.bioconductor.org/packages/AneuFinderData/" + Whole-genome single cell sequencing data for demonstration purposes in + the AneuFinder package.""" + + homepage = "https://bioconductor.org/packages/AneuFinderData" git = "https://git.bioconductor.org/packages/AneuFinderData.git" + version('1.12.0', commit='7350f38856b6278e07eca141f7f3cb24bc60c3a1') + version('1.10.0', commit='ef7fc27f9af4f178fa45a21aba30709e1ebde035') + version('1.8.0', commit='4f00f8d5f2e968fea667a7feafc0a4607d6e0c6e') + version('1.6.0', commit='8fe5b221619aab75fe84c9094708d240dd1e6730') version('1.4.0', commit='55c8807ee4a37a2eb6d0defafaf843f980b22c40') - depends_on('r@3.4.0:3.4.9', when='@1.4.0') + depends_on('r@3.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-animation/package.py b/var/spack/repos/builtin/packages/r-animation/package.py index 69426a1cd7..a60ad02998 100644 --- a/var/spack/repos/builtin/packages/r-animation/package.py +++ b/var/spack/repos/builtin/packages/r-animation/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,7 +22,7 @@ class RAnimation(RPackage): depends_on('r@2.14:', type=('build', 'run')) depends_on('r-magick', when='@2.6:', type=('build', 'run')) - depends_on('image-magick') + depends_on('imagemagick') depends_on('ffmpeg') depends_on('swftools') depends_on('texlive') diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py index ba0481bda2..596be2a18f 100644 --- a/var/spack/repos/builtin/packages/r-annaffy/package.py +++ b/var/spack/repos/builtin/packages/r-annaffy/package.py @@ -1,26 +1,31 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -# -# from spack import * class RAnnaffy(RPackage): - """Functions for handling data from Bioconductor Affymetrix - annotation data packages. Produces compact HTML and text - reports including experimental data and URL links to many - online databases. Allows searching biological metadata - using various criteria.""" + """Annotation tools for Affymetrix biological metadata. + + Functions for handling data from Bioconductor Affymetrix annotation data + packages. Produces compact HTML and text reports including experimental + data and URL links to many online databases. Allows searching biological + metadata using various criteria.""" - homepage = "https://www.bioconductor.org/packages/annaffy/" + homepage = "https://bioconductor.org/packages/annaffy" git = "https://git.bioconductor.org/packages/annaffy.git" + version('1.56.0', commit='8c8e16aa0f3073880c39684fd8e554a052ec6233') + version('1.54.0', commit='e1b3bf10515255eb994cd8bdf85697ea728c3484') + version('1.52.0', commit='ef84030163045f702941c8d5a59fbd4a09f30e2c') + version('1.50.0', commit='a822e20f3e961a8afa5eb23536343115a33fb259') version('1.48.0', commit='89a03c64ac9df5d963ed60b87893a3fffa6798a0') - depends_on('r@3.4.0:3.4.9', when='@1.48.0') + depends_on('r@2.5.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-go-db', type=('build', 'run')) depends_on('r-kegg-db', type=('build', 'run')) + depends_on('r-annotationdbi@0.1.15:', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py index 5fc2ba5c2d..da58ce0c2a 100644 --- a/var/spack/repos/builtin/packages/r-annotate/package.py +++ b/var/spack/repos/builtin/packages/r-annotate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,24 @@ from spack import * class RAnnotate(RPackage): - """Using R enviroments for annotation.""" + """Annotation for microarrays. - homepage = "https://www.bioconductor.org/packages/annotate/" + Using R enviroments for annotation.""" + + homepage = "https://bioconductor.org/packages/annotate" git = "https://git.bioconductor.org/packages/annotate.git" + version('1.62.0', commit='19af0b39747ea83fe8fe9b8bbb6036363bc815cd') + version('1.60.1', commit='9d8f87db02bf0c1593e79da754335a24d3a8ed16') version('1.58.0', commit='d1b5dd5feb8793f4f816d9a4aecbebb5ec7df7bc') + version('1.56.2', commit='95ec3b004f5356bd78b2a60cbf7f93e0d48cf346') version('1.54.0', commit='860cc5b696795a31b18beaf4869f9c418d74549e') - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-annotationdbi@1.27.5:', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) - depends_on('r-rcurl', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) depends_on('r-xtable', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.54.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.58.0', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) + depends_on('r-rcurl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py index 8c917104ef..8ffc832848 100644 --- a/var/spack/repos/builtin/packages/r-annotationdbi/package.py +++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,19 +7,28 @@ from spack import * class RAnnotationdbi(RPackage): - """Provides user interface and database connection code for - annotation data packages using SQLite data storage.""" + """Manipulation of SQLite-based annotations in Bioconductor. - homepage = "https://www.bioconductor.org/packages/AnnotationDbi/" + Implements a user-friendly interface for querying SQLite-based + annotation data packages.""" + + homepage = "https://bioconductor.org/packages/AnnotationDbi" git = "https://git.bioconductor.org/packages/AnnotationDbi.git" + version('1.46.1', commit='ff260913741d0fcf9487eeb1f44a6c6968ced5b9') + version('1.44.0', commit='ce191b08cfd612d014431325c26c91b11c5f13ac') version('1.42.1', commit='71085b47ea2e1ef929bebe8b17eb8e8a573f98e3') + version('1.40.0', commit='e34dff07e10402eecbf95604a512bc1fc4edb127') version('1.38.2', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36') - depends_on('r@3.4.0:3.4.9', when='@1.38.2', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.42.1', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.7.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) + depends_on('r-biobase@1.17.0:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.23.1:', when='@1.40.0:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.29.2:', when='@1.46.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annotationfilter/package.py b/var/spack/repos/builtin/packages/r-annotationfilter/package.py index 5e76c4f6a5..2705074a7a 100644 --- a/var/spack/repos/builtin/packages/r-annotationfilter/package.py +++ b/var/spack/repos/builtin/packages/r-annotationfilter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,21 @@ from spack import * class RAnnotationfilter(RPackage): - """This package provides class and other infrastructure to implement - filters for manipulating Bioconductor annotation resources. The - filters will be used by ensembldb, Organism.dplyr, and other - packages.""" + """Facilities for Filtering Bioconductor Annotation Resources. - homepage = "https://bioconductor.org/packages/AnnotationFilter/" + This package provides class and other infrastructure to implement + filters for manipulating Bioconductor annotation resources. The filters + will be used by ensembldb, Organism.dplyr, and other packages.""" + + homepage = "https://bioconductor.org/packages/AnnotationFilter" git = "https://git.bioconductor.org/packages/AnnotationFilter.git" + version('1.8.0', commit='9bf70ead899e32e84e2908f2b29cd38250d2d1ed') + version('1.6.0', commit='fa40a7e17e93fac9e85091ff93f256adf145dec3') + version('1.4.0', commit='acbd3309f478843a7899bd9773af5f19f986b829') + version('1.2.0', commit='744b82915d7b85031de462d9d0a2bf9fdfd0e29d') version('1.0.0', commit='a9f79b26defe3021eea60abe16ce1fa379813ec9') + depends_on('r@3.4.0:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-lazyeval', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.0.0') diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py index fbf7d266ff..cffa1d1dbd 100644 --- a/var/spack/repos/builtin/packages/r-annotationforge/package.py +++ b/var/spack/repos/builtin/packages/r-annotationforge/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,19 +7,24 @@ from spack import * class RAnnotationforge(RPackage): - """Provides code for generating Annotation packages and - their databases. Packages produced are intended to be used - with AnnotationDbi.""" + """Tools for building SQLite-based annotation data packages. - homepage = "https://www.bioconductor.org/packages/AnnotationForge/" + Provides code for generating Annotation packages and their databases. + Packages produced are intended to be used with AnnotationDbi.""" + + homepage = "https://bioconductor.org/packages/AnnotationForge" git = "https://git.bioconductor.org/packages/AnnotationForge.git" + version('1.26.0', commit='5d181f32df1fff6446af64a2538a7d25c23fe46e') + version('1.24.0', commit='3e1fe863573e5b0f69f35a9ad6aebce11ef83d0d') + version('1.22.2', commit='8eafb1690c1c02f6291ccbb38ac633d54b8217f8') + version('1.20.0', commit='7b440f1570cb90acce8fe2fa8d3b5ac34f638882') version('1.18.2', commit='44ca3d4ef9e9825c14725ffdbbaa57ea059532e1') - depends_on('r@3.4.0:3.4.9', when='@1.18.2') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.7.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) + depends_on('r-biobase@1.17.0:', type=('build', 'run')) + depends_on('r-annotationdbi@1.33.14:', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py index 0465d3c126..4437ec2c14 100644 --- a/var/spack/repos/builtin/packages/r-annotationhub/package.py +++ b/var/spack/repos/builtin/packages/r-annotationhub/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,25 +7,39 @@ from spack import * class RAnnotationhub(RPackage): - """This package provides a client for the Bioconductor AnnotationHub web + """Client to access AnnotationHub resources. + + This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from - standard locations (e.g., UCSC, Ensembl) can be discovered. The - resource includes metadata about each resource, e.g., a textual - description, tags, and date of modification. The client creates and - manages a local cache of files retrieved by the user, helping with - quick and reproducible access.""" + standard locations (e.g., UCSC, Ensembl) can be discovered. The resource + includes metadata about each resource, e.g., a textual description, + tags, and date of modification. The client creates and manages a local + cache of files retrieved by the user, helping with quick and + reproducible access.""" - homepage = "https://bioconductor.org/packages/AnnotationHub/" + homepage = "https://bioconductor.org/packages/AnnotationHub" git = "https://git.bioconductor.org/packages/AnnotationHub.git" + version('2.16.1', commit='f8cefaae603b782e1c1ad277a3fb89d44e3aa1ed') + version('2.14.5', commit='993a98ce3de04a0bbddcbde5b1ab2a9550275a12') + version('2.12.1', commit='471407bd9cdc612e01deb071c91bd9e5f1ea5e55') + version('2.10.1', commit='b7cb668de9b9625ac2beb3dcde1fa39e289eec29') version('2.8.3', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c') + depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) depends_on('r-biocinstaller', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-annotationdbi@1.31.19:', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-interactivedisplaybase', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-yaml', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.8.3') + + depends_on('r-curl', when='@2.10.1:', type=('build', 'run')) + + depends_on('r-biocmanager', when='@2.14.5:', type=('build', 'run')) + + depends_on('r-biocfilecache@1.5.1:', when='@2.16.1:', type=('build', 'run')) + depends_on('r-rappdirs', when='@2.16.1:', type=('build', 'run')) + depends_on('r-dplyr', when='@2.16.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ape/package.py b/var/spack/repos/builtin/packages/r-ape/package.py index c028e56842..b67a872986 100644 --- a/var/spack/repos/builtin/packages/r-ape/package.py +++ b/var/spack/repos/builtin/packages/r-ape/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-argparse/package.py b/var/spack/repos/builtin/packages/r-argparse/package.py index 25c05ebcf8..bfd15a6c08 100644 --- a/var/spack/repos/builtin/packages/r-argparse/package.py +++ b/var/spack/repos/builtin/packages/r-argparse/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-askpass/package.py b/var/spack/repos/builtin/packages/r-askpass/package.py index ea3bcd0572..c87c23cc68 100644 --- a/var/spack/repos/builtin/packages/r-askpass/package.py +++ b/var/spack/repos/builtin/packages/r-askpass/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py index f1b7b88ccf..d0c0f6a829 100644 --- a/var/spack/repos/builtin/packages/r-assertthat/package.py +++ b/var/spack/repos/builtin/packages/r-assertthat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-backports/package.py b/var/spack/repos/builtin/packages/r-backports/package.py index c15cb48fee..c715bafc1e 100644 --- a/var/spack/repos/builtin/packages/r-backports/package.py +++ b/var/spack/repos/builtin/packages/r-backports/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bamsignals/package.py b/var/spack/repos/builtin/packages/r-bamsignals/package.py index c296426285..59d8dceae2 100644 --- a/var/spack/repos/builtin/packages/r-bamsignals/package.py +++ b/var/spack/repos/builtin/packages/r-bamsignals/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,20 +7,30 @@ from spack import * class RBamsignals(RPackage): - """This package allows to efficiently obtain count vectors - from indexed bam files. It counts the number of reads in given - genomic ranges and it computes reads profiles and coverage - profiles. It also handles paired-end data.""" + """Extract read count signals from bam files. - homepage = "https://www.bioconductor.org/packages/bamsignals/" + This package allows to efficiently obtain count vectors from indexed bam + files. It counts the number of reads in given genomic ranges and it + computes reads profiles and coverage profiles. It also handles paired- + end data.""" + + homepage = "https://bioconductor.org/packages/bamsignals" git = "https://git.bioconductor.org/packages/bamsignals.git" + version('1.16.0', commit='dba9a4ae1613d2700f122ade1e9b90ca8fce5657') + version('1.14.0', commit='3107d3a35830e879eeddf127a81016ea1ca9b53d') + version('1.12.1', commit='06b6282df377cf9db58e8016be4ac8ddcc960939') + version('1.10.0', commit='7499312ce71e8680680eda10b49d7dff682fc776') version('1.8.0', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23') - depends_on('r@3.4.0:3.4.9', when='@1.8.0') + depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.10.6:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) depends_on('r-rhtslib', type=('build', 'run')) + + depends_on('r-rhtslib@1.12.1:', when='@1.12.1:', type=('build', 'run')) + + depends_on('r-rhtslib@1.13.1:', when='@1.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-base64/package.py b/var/spack/repos/builtin/packages/r-base64/package.py index 67c69434bb..eb72a27388 100644 --- a/var/spack/repos/builtin/packages/r-base64/package.py +++ b/var/spack/repos/builtin/packages/r-base64/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py index 6d7e0b0a8c..3e49d856d8 100644 --- a/var/spack/repos/builtin/packages/r-base64enc/package.py +++ b/var/spack/repos/builtin/packages/r-base64enc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bayesm/package.py b/var/spack/repos/builtin/packages/r-bayesm/package.py index 6481b69fb1..dd2d009f4a 100644 --- a/var/spack/repos/builtin/packages/r-bayesm/package.py +++ b/var/spack/repos/builtin/packages/r-bayesm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bbmisc/package.py b/var/spack/repos/builtin/packages/r-bbmisc/package.py index aa29c826b7..6bc0688330 100644 --- a/var/spack/repos/builtin/packages/r-bbmisc/package.py +++ b/var/spack/repos/builtin/packages/r-bbmisc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-beachmat/package.py b/var/spack/repos/builtin/packages/r-beachmat/package.py new file mode 100644 index 0000000000..9ba18d7592 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-beachmat/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBeachmat(RPackage): + """Compiling Bioconductor to Handle Each Matrix Type. + + Provides a consistent C++ class interface for reading from and writing + data to a variety of commonly used matrix types. Ordinary matrices and + several sparse/dense Matrix classes are directly supported, third-party + S4 classes may be supported by external linkage, while all other + matrices are handled by DelayedArray block processing.""" + + homepage = "https://bioconductor.org/packages/beachmat" + git = "https://git.bioconductor.org/packages/beachmat.git" + + version('2.0.0', commit='2bdac6ce7b636fd16f78641a0bcc2181670107ab') + version('1.4.0', commit='e3b7a21cae0080d077a0d40e35d1d148f088720a') + version('1.2.1', commit='ebae81772045a314e568c2f7d73ea3b27e7bf7d8') + version('1.0.2', commit='6bd57b91d6428ac916f46572d685d3cb01a757f7') + + depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-rhdf5lib', when='@1.0.2:1.4.0', type=('build', 'run')) + depends_on('r-hdf5array', when='@1.0.2:1.4.0', type=('build', 'run')) + depends_on('r-delayedarray', type=('build', 'run')) + depends_on('r-rcpp@0.12.14:', when='@1.0.2:1.4.0', type=('build', 'run')) + depends_on('r-rhdf5', when='@1.0.2:1.4.0', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.2.1:1.4.0', type=('build', 'run')) + depends_on('r-rhdf5lib@1.1.4:', when='@1.2.1', type=('build', 'run')) + depends_on('r-hdf5array@1.7.3:', when='@1.2.1', type=('build', 'run')) + depends_on('r-delayedarray@0.5.30:', when='@1.2.1', type=('build', 'run')) + + depends_on('r-hdf5array@1.9.5:', when='@1.4.0', type=('build', 'run')) + depends_on('r-delayedarray@0.7.38:', when='@1.4.0', type=('build', 'run')) + depends_on('r-biocgenerics', when='@1.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-beanplot/package.py b/var/spack/repos/builtin/packages/r-beanplot/package.py index a2b93950ff..1edacea4a0 100644 --- a/var/spack/repos/builtin/packages/r-beanplot/package.py +++ b/var/spack/repos/builtin/packages/r-beanplot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-beeswarm/package.py b/var/spack/repos/builtin/packages/r-beeswarm/package.py new file mode 100644 index 0000000000..4b4821e0fa --- /dev/null +++ b/var/spack/repos/builtin/packages/r-beeswarm/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBeeswarm(RPackage): + """beeswarm: The Bee Swarm Plot, an Alternative to Stripchart""" + + homepage = "http://www.cbs.dtu.dk/~eklund/beeswarm/" + url = "https://cloud.r-project.org/src/contrib/beeswarm_0.2.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/beeswarm" + + version('0.2.3', sha256='0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843') diff --git a/var/spack/repos/builtin/packages/r-bfast/package.py b/var/spack/repos/builtin/packages/r-bfast/package.py index 54b07e9e61..f2250effb7 100644 --- a/var/spack/repos/builtin/packages/r-bfast/package.py +++ b/var/spack/repos/builtin/packages/r-bfast/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bfastspatial/package.py b/var/spack/repos/builtin/packages/r-bfastspatial/package.py index 57c201ebba..82b751da7a 100644 --- a/var/spack/repos/builtin/packages/r-bfastspatial/package.py +++ b/var/spack/repos/builtin/packages/r-bfastspatial/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bglr/package.py b/var/spack/repos/builtin/packages/r-bglr/package.py index 68f87952ed..267e18d959 100644 --- a/var/spack/repos/builtin/packages/r-bglr/package.py +++ b/var/spack/repos/builtin/packages/r-bglr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py index 603bad10f8..6065f5609f 100644 --- a/var/spack/repos/builtin/packages/r-bh/package.py +++ b/var/spack/repos/builtin/packages/r-bh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-biasedurn/package.py b/var/spack/repos/builtin/packages/r-biasedurn/package.py index 429ed842a9..8defc86345 100644 --- a/var/spack/repos/builtin/packages/r-biasedurn/package.py +++ b/var/spack/repos/builtin/packages/r-biasedurn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bibtex/package.py b/var/spack/repos/builtin/packages/r-bibtex/package.py index 8fd9a0154e..840aa5b06c 100644 --- a/var/spack/repos/builtin/packages/r-bibtex/package.py +++ b/var/spack/repos/builtin/packages/r-bibtex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bindr/package.py b/var/spack/repos/builtin/packages/r-bindr/package.py index 92b38f8bc8..bdb58185b7 100644 --- a/var/spack/repos/builtin/packages/r-bindr/package.py +++ b/var/spack/repos/builtin/packages/r-bindr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bindrcpp/package.py b/var/spack/repos/builtin/packages/r-bindrcpp/package.py index 32261fc3c6..68347869ad 100644 --- a/var/spack/repos/builtin/packages/r-bindrcpp/package.py +++ b/var/spack/repos/builtin/packages/r-bindrcpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bio3d/package.py b/var/spack/repos/builtin/packages/r-bio3d/package.py new file mode 100644 index 0000000000..b65ab46afe --- /dev/null +++ b/var/spack/repos/builtin/packages/r-bio3d/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBio3d(RPackage): + """bio3d: Biological Structure Analysis""" + + homepage = "http://thegrantlab.org/bio3d/" + url = "https://cloud.r-project.org/src/contrib/bio3d_2.3-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bio3d" + + version('2.3-4', sha256='f9b39ab242cbedafcd98c1732cb1f5c0dd9ef66e28be39695e3420dd93e2bafe') + + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py index 1ff0d25de5..5481b80cdf 100644 --- a/var/spack/repos/builtin/packages/r-biobase/package.py +++ b/var/spack/repos/builtin/packages/r-biobase/package.py @@ -1,23 +1,27 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -# from spack import * class RBiobase(RPackage): - """Functions that are needed by many other packages - or which replace R functions.""" + """Biobase: Base functions for Bioconductor. + + Functions that are needed by many other packages or which replace R + functions.""" - homepage = "https://www.bioconductor.org/packages/Biobase/" + homepage = "https://bioconductor.org/packages/Biobase" git = "https://git.bioconductor.org/packages/Biobase.git" + version('2.44.0', commit='bde2077f66047986297ec35a688751cdce150dd3') + version('2.42.0', commit='3e5bd466b99e3cc4af1b0c3b32687fa56d6f8e4d') version('2.40.0', commit='6555edbbcb8a04185ef402bfdea7ed8ac72513a5') version('2.38.0', commit='83f89829e0278ac014b0bc6664e621ac147ba424') version('2.36.2', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075') - depends_on('r-biocgenerics@0.16.1:', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.36.2', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@2.40.0', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-biocgenerics@0.3.2:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.27.1:', when='@2.42.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocfilecache/package.py b/var/spack/repos/builtin/packages/r-biocfilecache/package.py new file mode 100644 index 0000000000..378532e558 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocfilecache/package.py @@ -0,0 +1,34 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBiocfilecache(RPackage): + """Manage Files Across Sessions. + + This package creates a persistent on-disk cache of files that the user + can add, update, and retrieve. It is useful for managing resources (such + as custom Txdb objects) that are costly or difficult to create, web + resources, and data files used across sessions.""" + + homepage = "https://bioconductor.org/packages/BiocFileCache" + git = "https://git.bioconductor.org/packages/BiocFileCache.git" + + version('1.8.0', commit='0e3542b6aae849b01240d8055a48da1b267bd5a0') + version('1.6.0', commit='c2de6c1cdef6294e5d0adea31e4ebf25865742ba') + version('1.4.0', commit='a2c473d17f78899c7899b9638faea8c30735eb80') + version('1.2.3', commit='d78bf5b46c8a329f5ddef879fe51230444bc42f8') + version('1.0.1', commit='dbf4e8dd4d8d9f475066cd033481efe95c56df75') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-dbplyr@1.0.0:', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-rsqlite', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) + depends_on('r-rappdirs', type=('build', 'run')) + depends_on('r-httr', type=('build', 'run')) + + depends_on('r-curl', when='@1.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py index 347bcc22bc..dc403c878e 100644 --- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,17 @@ from spack import * class RBiocgenerics(RPackage): - """S4 generic functions needed by many Bioconductor packages.""" + """S4 generic functions used in Bioconductor. - homepage = "https://www.bioconductor.org/packages/BiocGenerics/" + The package defines S4 generic functions used in Bioconductor.""" + + homepage = "https://bioconductor.org/packages/BiocGenerics" git = "https://git.bioconductor.org/packages/BiocGenerics.git" version('0.30.0', commit='fc7c3af4a5635a30988a062ed09332c13ca1d1a8') + version('0.28.0', commit='041fc496504f2ab1d4d863fffb23372db214394b') version('0.26.0', commit='5b2a6df639e48c3cd53789e0b174aec9dda6b67d') version('0.24.0', commit='3db111e8c1f876267da89f4f0c5406a9d5c31cd1') version('0.22.1', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad') - depends_on('r@3.4.0:3.4.9', when='@0.22.1', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@0.26.0', type=('build', 'run')) - depends_on('r@3.6.0:', when='@0.30.0', type=('build', 'run')) + depends_on('r@3.6.0:', when='@0.30.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocinstaller/package.py b/var/spack/repos/builtin/packages/r-biocinstaller/package.py index fe1e132691..09d942279f 100644 --- a/var/spack/repos/builtin/packages/r-biocinstaller/package.py +++ b/var/spack/repos/builtin/packages/r-biocinstaller/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,12 +7,20 @@ from spack import * class RBiocinstaller(RPackage): - """This package is used to install and update Bioconductor, CRAN, - and (some) github packages.""" + """Install/Update Bioconductor, CRAN, and github Packages. - homepage = "https://bioconductor.org/packages/BiocInstaller/" + This package is used to install and update Bioconductor, CRAN, and + (some) github packages.""" + + homepage = "https://bioconductor.org/packages/3.8/bioc/html/BiocInstaller.html" git = "https://git.bioconductor.org/packages/BiocInstaller.git" + version('1.33.1', commit='6193f31c18e7e64d91e0e15ed0ba6924eda1416f') + version('1.32.1', commit='4c2a39e1cae470af3a5cf1491715f272b70f4bb4') + version('1.30.0', commit='27bcb7a378cb5d8b5d23b7b840340463f7e090bc') + version('1.28.0', commit='7261763529a0a1f730cde8a1bbdbf454c3e25603') version('1.26.1', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98') - depends_on('r@3.4.0:3.4.9', when='@1.26.1') + depends_on('r@3.4.0:', type=('build', 'run')) + + depends_on('r@3.5.0:', when='@1.30.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocmanager/package.py b/var/spack/repos/builtin/packages/r-biocmanager/package.py new file mode 100644 index 0000000000..d31929e914 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocmanager/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBiocmanager(RPackage): + """BiocManager: Access the Bioconductor Project Package Repository""" + + homepage = "https://cloud.r-project.org/package=BiocManager" + url = "https://cloud.r-project.org/src/contrib/BiocManager_1.30.10.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/BiocManager" + + version('1.30.10', sha256='f3b7a412b42be0ab8df5fcd9bf981876ba9e5c55bc5faaca7af7ede3b6d0c90e') diff --git a/var/spack/repos/builtin/packages/r-biocneighbors/package.py b/var/spack/repos/builtin/packages/r-biocneighbors/package.py new file mode 100644 index 0000000000..dd2d8619fe --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocneighbors/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBiocneighbors(RPackage): + """Nearest Neighbor Detection for Bioconductor Packages. + + Implements exact and approximate methods for nearest neighbor detection, + in a framework that allows them to be easily switched within + Bioconductor packages or workflows. Exact searches can be performed + using the k-means for k-nearest neighbors algorithm or with vantage + point trees. Approximate searches can be performed using the Annoy or + HNSW libraries. Searching on either Euclidean or Manhattan distances is + supported. Parallelization is achieved for all methods by using + BiocParallel. Functions are also provided to search for all neighbors + within a given distance.""" + + homepage = "https://bioconductor.org/packages/BiocNeighbors" + git = "https://git.bioconductor.org/packages/BiocNeighbors.git" + + version('1.2.0', commit='f754c6300f835142536a4594ddf750481e0fe273') + version('1.0.0', commit='e252fc04b6d22097f2c5f74406e77d85e7060770') + + depends_on('r@3.5:', when='@1.0.0', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-rcppannoy', type=('build', 'run')) + + depends_on('r-biocgenerics', when='@1.2.0:', type=('build', 'run')) + depends_on('r-rcpphnsw', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py index cee7cffd53..14fd27a8b5 100644 --- a/var/spack/repos/builtin/packages/r-biocparallel/package.py +++ b/var/spack/repos/builtin/packages/r-biocparallel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,22 @@ from spack import * class RBiocparallel(RPackage): - """This package provides modified versions and novel implementation of + """Bioconductor facilities for parallel evaluation. + + This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.""" - homepage = "https://bioconductor.org/packages/BiocParallel/" + homepage = "https://bioconductor.org/packages/BiocParallel" git = "https://git.bioconductor.org/packages/BiocParallel.git" + version('1.18.1', commit='348264af782d7dcd41a1879400f348f836767f6e') + version('1.16.6', commit='7f7a54c47f4949b600b9fd568289a519496bc4d4') version('1.14.2', commit='1d5a44960b19e9dbbca04c7290c8c58b0a7fc299') + version('1.12.0', commit='2143a9addceed0151a27b95c70aadd2add5cbace') version('1.10.1', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d') depends_on('r-futile-logger', type=('build', 'run')) depends_on('r-snow', type=('build', 'run')) - depends_on('r-bh', type=('build', 'link', 'run'), when='@1.14.2:') - depends_on('r@3.4.0:3.4.9', when='@1.10.1', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.14.2', type=('build', 'run')) + + depends_on('r-bh', when='@1.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocsingular/package.py b/var/spack/repos/builtin/packages/r-biocsingular/package.py new file mode 100644 index 0000000000..5531981958 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocsingular/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBiocsingular(RPackage): + """Singular Value Decomposition for Bioconductor Packages. + + Implements exact and approximate methods for singular value + decomposition and principal components analysis, in a framework that + allows them to be easily switched within Bioconductor packages or + workflows. Where possible, parallelization is achieved using the + BiocParallel framework.""" + + homepage = "https://bioconductor.org/packages/BiocSingular" + git = "https://git.bioconductor.org/packages/BiocSingular.git" + + version('1.0.0', commit='d2b091c072d0312698c9bb6611eb1bdf8aebf833') + + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-delayedarray', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r-irlba', type=('build', 'run')) + depends_on('r-rsvd', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-beachmat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocstyle/package.py b/var/spack/repos/builtin/packages/r-biocstyle/package.py index d3d0435c6b..b9ec8c5fe0 100644 --- a/var/spack/repos/builtin/packages/r-biocstyle/package.py +++ b/var/spack/repos/builtin/packages/r-biocstyle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,23 @@ from spack import * class RBiocstyle(RPackage): - """Provides standard formatting styles for Bioconductor PDF and HTML - documents. Package vignettes illustrate use and functionality.""" + """Standard styles for vignettes and other Bioconductor documents. - homepage = "https://www.bioconductor.org/packages/BiocStyle/" + Provides standard formatting styles for Bioconductor PDF and HTML + documents. Package vignettes illustrate use and functionality.""" + + homepage = "https://bioconductor.org/packages/BiocStyle" git = "https://git.bioconductor.org/packages/BiocStyle.git" + version('2.12.0', commit='0fba3fe6e6a38504f9aadcd3dc95bb83d7e92498') + version('2.10.0', commit='8fc946044c6b6a8a3104ddbc546baed49ee3aa70') + version('2.8.2', commit='3210c19ec1e5e0ed8d5a2d31da990aa47b42dbd8') + version('2.6.1', commit='5ff52cbb439a45575d0f58c4f7a83195a8b7337b') version('2.4.1', commit='ef10764b68ac23a3a7a8ec3b6a6436187309c138') depends_on('r-bookdown', type=('build', 'run')) depends_on('r-knitr@1.12:', type=('build', 'run')) depends_on('r-rmarkdown@1.2:', type=('build', 'run')) depends_on('r-yaml', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.4.1') + + depends_on('r-biocmanager', when='@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biom-utils/package.py b/var/spack/repos/builtin/packages/r-biom-utils/package.py index 7377db73a1..bd57636a67 100644 --- a/var/spack/repos/builtin/packages/r-biom-utils/package.py +++ b/var/spack/repos/builtin/packages/r-biom-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-biomart/package.py b/var/spack/repos/builtin/packages/r-biomart/package.py index 6e82f30218..6e24a66a41 100644 --- a/var/spack/repos/builtin/packages/r-biomart/package.py +++ b/var/spack/repos/builtin/packages/r-biomart/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,22 +7,26 @@ from spack import * class RBiomart(RPackage): - """In recent years a wealth of biological data has become available in + """Interface to BioMart databases (i.e. Ensembl). + + In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite - (http://www.biomart.org). The package enables retrieval of large amounts - of data in a uniform way without the need to know the underlying - database schemas or write complex SQL queries. Examples of BioMart - databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and - dbSNP mapped to Ensembl. These major databases give biomaRt users direct - access to a diverse set of data and enable a wide range of powerful - online queries from gene annotation to database mining.""" - - homepage = "https://bioconductor.org/packages/biomaRt/" + (<http://www.biomart.org>). The package enables retrieval of large + amounts of data in a uniform way without the need to know the underlying + database schemas or write complex SQL queries. The most prominent + examples of BioMart databases are maintain by Ensembl, which provides + biomaRt users direct access to a diverse set of data and enables a wide + range of powerful online queries from gene annotation to database + mining.""" + + homepage = "https://bioconductor.org/packages/biomaRt" git = "https://git.bioconductor.org/packages/biomaRt.git" + version('2.40.5', commit='ed9ddafb0d620168ea8e3ab4884f3457b8525c68') + version('2.38.0', commit='16b997aba19a90a1c5fa64c442b1e7fcff99a658') version('2.36.1', commit='5634e57e20199f9dc1f8b927eb3893143fc02f4f') version('2.34.2', commit='a7030915fbc6120cc6812aefdedba423a207459b') version('2.32.1', commit='f84d74424fa599f6d08f8db4612ca09914a9087f') @@ -30,8 +34,7 @@ class RBiomart(RPackage): depends_on('r-xml', type=('build', 'run')) depends_on('r-rcurl', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-progress', type=('build', 'run'), when='@2.34.2:') - depends_on('r-stringr', type=('build', 'run'), when='@2.34.2:') - depends_on('r-httr', type=('build', 'run'), when='@2.34.2:') - depends_on('r@3.4.0:3.4.9', when='@2.32.1:2.35.9', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@2.36.1', type=('build', 'run')) + + depends_on('r-progress', when='@2.34.2:', type=('build', 'run')) + depends_on('r-stringr', when='@2.34.2:', type=('build', 'run')) + depends_on('r-httr', when='@2.34.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biomformat/package.py b/var/spack/repos/builtin/packages/r-biomformat/package.py index 4a5382beae..8c3d9a7d63 100644 --- a/var/spack/repos/builtin/packages/r-biomformat/package.py +++ b/var/spack/repos/builtin/packages/r-biomformat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,23 +7,29 @@ from spack import * class RBiomformat(RPackage): - """This is an R package for interfacing with the BIOM format. This - package includes basic tools for reading biom-format files, accessing - and subsetting data tables from a biom object (which is more complex - than a single table), as well as limited support for writing a - biom-object back to a biom-format file. The design of this API is - intended to match the python API and other tools included with the - biom-format project, but with a decidedly "R flavor" that should be - familiar to R users. This includes S4 classes and methods, as well - as extensions of common core functions/methods.""" + """An interface package for the BIOM file format. - homepage = "https://www.bioconductor.org/packages/biomformat/" + This is an R package for interfacing with the BIOM format. This package + includes basic tools for reading biom-format files, accessing and + subsetting data tables from a biom object (which is more complex than a + single table), as well as limited support for writing a biom-object back + to a biom-format file. The design of this API is intended to match the + python API and other tools included with the biom-format project, but + with a decidedly "R flavor" that should be familiar to R users. This + includes S4 classes and methods, as well as extensions of common core + functions/methods.""" + + homepage = "https://bioconductor.org/packages/biomformat" git = "https://git.bioconductor.org/packages/biomformat.git" + version('1.12.0', commit='6e946123bb59da262cbb0c17dc5ab49328a89d4a') + version('1.10.1', commit='e67c6f4b70201f748fa49a4938e1af0cd0613f09') + version('1.8.0', commit='acd207377b24e4d8310eaff06c16dcfe6c04509a') + version('1.6.0', commit='61fb8c7b34ad561c3c46cacc0dd1957be56da85e') version('1.4.0', commit='83b4b1883bc56ea93a0a6ca90fc1b18712ef0f1a') - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-plyr@1.8:', type=('build', 'run')) + depends_on('r-jsonlite@0.9.16:', type=('build', 'run')) + depends_on('r-matrix@1.2:', type=('build', 'run')) depends_on('r-rhdf5', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.4.0') diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py index d57e9d8a44..a0bd89cfe0 100644 --- a/var/spack/repos/builtin/packages/r-biostrings/package.py +++ b/var/spack/repos/builtin/packages/r-biostrings/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,23 +7,34 @@ from spack import * class RBiostrings(RPackage): - """Memory efficient string containers, string matching algorithms, and - other utilities, for fast manipulation of large biological sequences - or sets of sequences.""" + """Efficient manipulation of biological strings. - homepage = "https://bioconductor.org/packages/Biostrings/" + Memory efficient string containers, string matching algorithms, and + other utilities, for fast manipulation of large biological sequences or + sets of sequences.""" + + homepage = "https://bioconductor.org/packages/Biostrings" git = "https://git.bioconductor.org/packages/Biostrings.git" + version('2.52.0', commit='b78fe7c1f3cdbbb7affb1ca7164fe5a1f8b868f5') + version('2.50.2', commit='025e734641a93f6c5d44243297cb4264ea0e34a2') version('2.48.0', commit='aa3599a7d259d658014d087b86d71ab1deb5f12b') + version('2.46.0', commit='3bf6978c155498b50607d1bb471d1687d185a0fa') version('2.44.2', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.15.6:', when='@2.48.0', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.25:', when='@2.48.0', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) + depends_on('r@2.8.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.6:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-iranges@2.9.18:', when='@2.44.2:2.46.0', type=('build', 'run')) + depends_on('r-xvector@0.11.6:', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.25:', when='@2.48.0:', type=('build', 'run')) depends_on('r-iranges@2.13.24:', when='@2.48.0', type=('build', 'run')) - depends_on('r-xvector', type=('build', 'run')) - depends_on('r-xvector@0.19.8:', when='@2.48.0', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.44.2', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@2.48.0', type=('build', 'run')) + depends_on('r-xvector@0.19.8:', when='@2.48.0:', type=('build', 'run')) + + depends_on('r@3.5.0:', when='@2.50.2:', type=('build', 'run')) + depends_on('r-xvector@0.21.4:', when='@2.50.2:', type=('build', 'run')) + depends_on('r-iranges', when='@2.50.2:', type=('build', 'run')) + + depends_on('r-s4vectors@0.21.13:', when='@2.52.0:', type=('build', 'run')) + depends_on('r-xvector@0.23.2:', when='@2.52.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biovizbase/package.py b/var/spack/repos/builtin/packages/r-biovizbase/package.py index f26e3325a8..61ba92c203 100644 --- a/var/spack/repos/builtin/packages/r-biovizbase/package.py +++ b/var/spack/repos/builtin/packages/r-biovizbase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,33 +7,40 @@ from spack import * class RBiovizbase(RPackage): - """The biovizBase package is designed to provide a set of - utilities, color schemes and conventions for genomic data. - It serves as the base for various high-level packages for - biological data visualization. This saves development effort - and encourages consistency.""" + """Basic graphic utilities for visualization of genomic data.. - homepage = "http://bioconductor.org/packages/biovizBase/" + The biovizBase package is designed to provide a set of utilities, color + schemes and conventions for genomic data. It serves as the base for + various high-level packages for biological data visualization. This + saves development effort and encourages consistency.""" + + homepage = "https://bioconductor.org/packages/biovizBase" git = "https://git.bioconductor.org/packages/biovizBase.git" + version('1.32.0', commit='de044bf236cdcd71214ae7b77689a8f0ab4f5cc8') + version('1.30.1', commit='b6776d0470e2920f71127652f185f68ca1fd2c82') + version('1.28.2', commit='43d09060028665a237b04bfeb9e2575782b08063') + version('1.26.0', commit='640742f48384f01d117b70dc5c64737e97ae9b4b') version('1.24.0', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) depends_on('r-hmisc', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-dichromat', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-iranges@1.99.28:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.5.14:', type=('build', 'run')) + depends_on('r-genomicranges@1.23.21:', type=('build', 'run')) depends_on('r-summarizedexperiment', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) - depends_on('r-genomicalignments', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) + depends_on('r-biostrings@2.33.11:', type=('build', 'run')) + depends_on('r-rsamtools@1.17.28:', type=('build', 'run')) + depends_on('r-genomicalignments@1.1.16:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.21.19:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-variantannotation', type=('build', 'run')) - depends_on('r-ensembldb', type=('build', 'run')) - depends_on('r-annotationfilter', type=('build', 'run')) + depends_on('r-variantannotation@1.11.4:', type=('build', 'run')) + depends_on('r-ensembldb@1.99.13:', type=('build', 'run')) + depends_on('r-annotationfilter@0.99.8:', type=('build', 'run')) + + depends_on('r-rlang', when='@1.28.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bit/package.py b/var/spack/repos/builtin/packages/r-bit/package.py index 49d2c0bd1d..f792e9e6f9 100644 --- a/var/spack/repos/builtin/packages/r-bit/package.py +++ b/var/spack/repos/builtin/packages/r-bit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bit64/package.py b/var/spack/repos/builtin/packages/r-bit64/package.py index 64b5dbc8a5..3f3d71fc74 100644 --- a/var/spack/repos/builtin/packages/r-bit64/package.py +++ b/var/spack/repos/builtin/packages/r-bit64/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bitops/package.py b/var/spack/repos/builtin/packages/r-bitops/package.py index 58bfcd76ea..0c78b1e1b5 100644 --- a/var/spack/repos/builtin/packages/r-bitops/package.py +++ b/var/spack/repos/builtin/packages/r-bitops/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-blob/package.py b/var/spack/repos/builtin/packages/r-blob/package.py index f2d1fdfed6..af2c39362d 100644 --- a/var/spack/repos/builtin/packages/r-blob/package.py +++ b/var/spack/repos/builtin/packages/r-blob/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-blockmodeling/package.py b/var/spack/repos/builtin/packages/r-blockmodeling/package.py index f1333ba7c0..08257860f6 100644 --- a/var/spack/repos/builtin/packages/r-blockmodeling/package.py +++ b/var/spack/repos/builtin/packages/r-blockmodeling/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bookdown/package.py b/var/spack/repos/builtin/packages/r-bookdown/package.py index e56af27d9e..a1df872699 100644 --- a/var/spack/repos/builtin/packages/r-bookdown/package.py +++ b/var/spack/repos/builtin/packages/r-bookdown/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py index 9e79231c0e..5e9eb012f0 100644 --- a/var/spack/repos/builtin/packages/r-boot/package.py +++ b/var/spack/repos/builtin/packages/r-boot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py index 5dacd7ed82..80d075c547 100644 --- a/var/spack/repos/builtin/packages/r-brew/package.py +++ b/var/spack/repos/builtin/packages/r-brew/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-broom/package.py b/var/spack/repos/builtin/packages/r-broom/package.py index 3f863da071..bd0f70b070 100644 --- a/var/spack/repos/builtin/packages/r-broom/package.py +++ b/var/spack/repos/builtin/packages/r-broom/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-bsgenome/package.py b/var/spack/repos/builtin/packages/r-bsgenome/package.py index 1578380eb7..afbc8225dd 100644 --- a/var/spack/repos/builtin/packages/r-bsgenome/package.py +++ b/var/spack/repos/builtin/packages/r-bsgenome/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,25 +7,36 @@ from spack import * class RBsgenome(RPackage): - """Infrastructure shared by all the Biostrings-based genome data - packages.""" + """Software infrastructure for efficient representation of full genomes and + their SNPs.""" - homepage = "https://www.bioconductor.org/packages/BSgenome/" + homepage = "https://bioconductor.org/packages/BSgenome" git = "https://git.bioconductor.org/packages/BSgenome.git" + version('1.52.0', commit='5398eba1cb56a873b29c04a7ce6858d5d60ff75b') + version('1.50.0', commit='43910755f7477e4fe9bb968f186fddbb2f7355f9') + version('1.48.0', commit='092a1b90482ace329cbd8ca2a338e91449acb93e') version('1.46.0', commit='bdfbd6d09820993585b8231ddea5e11c99008dc5') version('1.44.2', commit='105b00588a758d5ec7c347a7dff2756aea4516a0') + depends_on('r@2.8.0:', type=('build', 'run')) depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) depends_on('r-s4vectors@0.9.36:', type=('build', 'run')) - depends_on('r-iranges@2.1.33:', type=('build', 'run'), when='@1.44.2') - depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.46.0') - depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'), when='@1.44.2') - depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.46.0') - depends_on('r-genomicranges@1.27.6:', type=('build', 'run'), when='@1.44.2') - depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.46.0') + depends_on('r-iranges@2.1.33:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.6:', type=('build', 'run')) depends_on('r-biostrings@2.35.3:', type=('build', 'run')) depends_on('r-rtracklayer@1.25.8:', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) depends_on('r-xvector', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.44.2:') + depends_on('r-rsamtools', type=('build', 'run')) + + depends_on('r-iranges@2.11.16:', when='@1.46.0:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.46.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.29.14:', when='@1.46.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.28:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.16:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.10:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-rtracklayer@1.39.7:', when='@1.48.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bumphunter/package.py b/var/spack/repos/builtin/packages/r-bumphunter/package.py index 797bf43f25..e40d70fc88 100644 --- a/var/spack/repos/builtin/packages/r-bumphunter/package.py +++ b/var/spack/repos/builtin/packages/r-bumphunter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,15 +7,22 @@ from spack import * class RBumphunter(RPackage): - """Tools for finding bumps in genomic data""" + """Bump Hunter. - homepage = "http://bioconductor.org/packages/bumphunter/" + Tools for finding bumps in genomic data""" + + homepage = "https://bioconductor.org/packages/bumphunter" git = "https://git.bioconductor.org/packages/bumphunter.git" + version('1.26.0', commit='606bee8708a0911ced3efb197970b4c9fa52f2fa') + version('1.24.5', commit='29b874033a38e86103b58ef2d4a55f285758147b') + version('1.22.0', commit='fb71b193f4ef7fa12d100441e6eb498765f7afde') + version('1.20.0', commit='c9d8e7ab0c19299988e5d7fa74970312e9a1eac0') version('1.16.0', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a') - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-iranges@2.3.23:', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) @@ -27,4 +34,7 @@ class RBumphunter(RPackage): depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-genomicfeatures', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.16.0') + + depends_on('r@3.4:', when='@1.20.0:', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.24.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-c50/package.py b/var/spack/repos/builtin/packages/r-c50/package.py index 68705e3a21..f92f57de8d 100644 --- a/var/spack/repos/builtin/packages/r-c50/package.py +++ b/var/spack/repos/builtin/packages/r-c50/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-cairo/package.py b/var/spack/repos/builtin/packages/r-cairo/package.py index 58f892369a..d6cb5c93a2 100644 --- a/var/spack/repos/builtin/packages/r-cairo/package.py +++ b/var/spack/repos/builtin/packages/r-cairo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-callr/package.py b/var/spack/repos/builtin/packages/r-callr/package.py index 5ed4f0a698..3c964e0400 100644 --- a/var/spack/repos/builtin/packages/r-callr/package.py +++ b/var/spack/repos/builtin/packages/r-callr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py index 6f98b07ff1..eab030ef3c 100644 --- a/var/spack/repos/builtin/packages/r-car/package.py +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-cardata/package.py b/var/spack/repos/builtin/packages/r-cardata/package.py index 6e9c430d7f..c2b3d3b7c2 100644 --- a/var/spack/repos/builtin/packages/r-cardata/package.py +++ b/var/spack/repos/builtin/packages/r-cardata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py index e203e3d2ed..7d7631c66d 100644 --- a/var/spack/repos/builtin/packages/r-caret/package.py +++ b/var/spack/repos/builtin/packages/r-caret/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-caroline/package.py b/var/spack/repos/builtin/packages/r-caroline/package.py index a72a4977db..13d6771f3e 100644 --- a/var/spack/repos/builtin/packages/r-caroline/package.py +++ b/var/spack/repos/builtin/packages/r-caroline/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-category/package.py b/var/spack/repos/builtin/packages/r-category/package.py index 85f4455a6b..3e933e3ecb 100644 --- a/var/spack/repos/builtin/packages/r-category/package.py +++ b/var/spack/repos/builtin/packages/r-category/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,14 +7,20 @@ from spack import * class RCategory(RPackage): - """A collection of tools for performing category analysis.""" + """Category Analysis. - homepage = "https://www.bioconductor.org/packages/Category/" + A collection of tools for performing category (gene set enrichment) + analysis.""" + + homepage = "https://bioconductor.org/packages/Category" git = "https://git.bioconductor.org/packages/Category.git" + version('2.50.0', commit='d96f0b29cb778f6697b44d7ba7b0abd7086074a9') + version('2.48.1', commit='941819a3d9dd129f47b4ea00fa74032e405be3a5') + version('2.46.0', commit='c8aeee4dee3fb120f25e0647dd06e895a3ffbc2a') + version('2.44.0', commit='eaba50c1a801ba7983e6ffdf41ab0fc9cfe5a626') version('2.42.1', commit='382c817a2371671a72f8f949dfb4050361ebabcd') - depends_on('r@3.4.0:3.4.9', when='@2.42.1') depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-catools/package.py b/var/spack/repos/builtin/packages/r-catools/package.py index 087847f99b..c8a2b9a5f0 100644 --- a/var/spack/repos/builtin/packages/r-catools/package.py +++ b/var/spack/repos/builtin/packages/r-catools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-cdcfluview/package.py b/var/spack/repos/builtin/packages/r-cdcfluview/package.py index e4421546e9..d00215eb28 100644 --- a/var/spack/repos/builtin/packages/r-cdcfluview/package.py +++ b/var/spack/repos/builtin/packages/r-cdcfluview/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-cellranger/package.py b/var/spack/repos/builtin/packages/r-cellranger/package.py index 7da69c1395..d2a6aeeb4d 100644 --- a/var/spack/repos/builtin/packages/r-cellranger/package.py +++ b/var/spack/repos/builtin/packages/r-cellranger/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-checkmate/package.py b/var/spack/repos/builtin/packages/r-checkmate/package.py index 2ec531fcf4..7904ee365b 100644 --- a/var/spack/repos/builtin/packages/r-checkmate/package.py +++ b/var/spack/repos/builtin/packages/r-checkmate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py index c212794956..4bed14e6e1 100644 --- a/var/spack/repos/builtin/packages/r-checkpoint/package.py +++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,7 @@ class RCheckpoint(RPackage): date as if you had a CRAN time machine.""" homepage = "https://cloud.r-project.org/package=checkpoint" - url = "https://cloud.r-project.org/src/contrib/checkpoint_0.3.18.tar.gz" + url = "https://cloud.r-project.org/src/contrib/checkpoint_0.4.6.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/checkpoint" version('0.4.6', sha256='fd1a5edb5cb1a40d7ed26bb196de566110fe2ef62e70b4e947c003576a03ebb2') diff --git a/var/spack/repos/builtin/packages/r-chemometrics/package.py b/var/spack/repos/builtin/packages/r-chemometrics/package.py index 6ce8e29ecf..b4b8f01804 100644 --- a/var/spack/repos/builtin/packages/r-chemometrics/package.py +++ b/var/spack/repos/builtin/packages/r-chemometrics/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,8 +7,9 @@ from spack import * class RChemometrics(RPackage): - """R companion to the book "Introduction to Multivariate Statistical Analysis - in Chemometrics" written by K. Varmuza and P. Filzmoser (2009).""" + """R companion to the book "Introduction to Multivariate Statistical + Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser + (2009).""" homepage = "https://cloud.r-project.org/package=chemometrics" url = "https://cloud.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz" diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py index 43bd8f20e2..f47ab66c6f 100644 --- a/var/spack/repos/builtin/packages/r-chron/package.py +++ b/var/spack/repos/builtin/packages/r-chron/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-circlize/package.py b/var/spack/repos/builtin/packages/r-circlize/package.py index d8d8ac2e7f..ea9dc2e012 100644 --- a/var/spack/repos/builtin/packages/r-circlize/package.py +++ b/var/spack/repos/builtin/packages/r-circlize/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py index ff585126c8..d15932eae2 100644 --- a/var/spack/repos/builtin/packages/r-class/package.py +++ b/var/spack/repos/builtin/packages/r-class/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-classint/package.py b/var/spack/repos/builtin/packages/r-classint/package.py index a3d5050b8a..66f2e095a9 100644 --- a/var/spack/repos/builtin/packages/r-classint/package.py +++ b/var/spack/repos/builtin/packages/r-classint/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-cli/package.py b/var/spack/repos/builtin/packages/r-cli/package.py index 268f062b97..7f5cc52a0c 100644 --- a/var/spack/repos/builtin/packages/r-cli/package.py +++ b/var/spack/repos/builtin/packages/r-cli/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-clipr/package.py b/var/spack/repos/builtin/packages/r-clipr/package.py index 10198a42e2..7ea728fe97 100644 --- a/var/spack/repos/builtin/packages/r-clipr/package.py +++ b/var/spack/repos/builtin/packages/r-clipr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-clisymbols/package.py b/var/spack/repos/builtin/packages/r-clisymbols/package.py index 057fa67b9b..c5ed8c3e9f 100644 --- a/var/spack/repos/builtin/packages/r-clisymbols/package.py +++ b/var/spack/repos/builtin/packages/r-clisymbols/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-clue/package.py b/var/spack/repos/builtin/packages/r-clue/package.py new file mode 100644 index 0000000000..30893dccaf --- /dev/null +++ b/var/spack/repos/builtin/packages/r-clue/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RClue(RPackage): + """clue: Cluster Ensembles""" + + homepage = "https://cloud.r-project.org/package=clue" + url = "https://cloud.r-project.org/src/contrib/clue_0.3-57.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/clue" + + version('0.3-57', sha256='6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py index 8b657d5c44..34a504e751 100644 --- a/var/spack/repos/builtin/packages/r-cluster/package.py +++ b/var/spack/repos/builtin/packages/r-cluster/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-clustergeneration/package.py b/var/spack/repos/builtin/packages/r-clustergeneration/package.py index ccae368dde..c7cd14d97c 100644 --- a/var/spack/repos/builtin/packages/r-clustergeneration/package.py +++ b/var/spack/repos/builtin/packages/r-clustergeneration/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py index 88a3b3107b..2f71d6df7a 100644 --- a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py +++ b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,22 +7,36 @@ from spack import * class RClusterprofiler(RPackage): - """This package implements methods to analyze and visualize functional - profiles (GO and KEGG) of gene and gene clusters.""" + """statistical analysis and visualization of functional profiles for genes + and gene clusters. - homepage = "https://www.bioconductor.org/packages/clusterProfiler/" + This package implements methods to analyze and visualize functional + profiles (GO and KEGG) of gene and gene clusters.""" + + homepage = "https://bioconductor.org/packages/clusterProfiler" git = "https://git.bioconductor.org/packages/clusterProfiler.git" + version('3.12.0', commit='6ec88d10832bdfd938e9c065b377015eedb7eee2') + version('3.10.1', commit='39927ef7ff6f97e27557bcf4147e2133b364fd3c') + version('3.8.1', commit='81e1a7ac49e4713703c55f87f945b20de5e7ab36') + version('3.6.0', commit='ff15e3dba69b93bc872d5f5d07821cd9ae20d829') version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7') - depends_on('r@3.4.0:3.4.9', when='@3.4.4') - depends_on('r-tidyr', type=('build', 'run')) - depends_on('r-rvcheck', type=('build', 'run')) - depends_on('r-qvalue', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-gosemsim', type=('build', 'run')) - depends_on('r-go-db', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r@3.3.1:', type=('build', 'run')) + depends_on('r-dose@3.1.3:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-dose', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-go-db', type=('build', 'run')) + depends_on('r-gosemsim@2.0.0:', when='@3.4.4:3.6.0', type=('build', 'run')) + depends_on('r-gosemsim', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-qvalue', type=('build', 'run')) + depends_on('r-rvcheck', type=('build', 'run')) + depends_on('r-tidyr', type=('build', 'run')) + + depends_on('r-dose@3.3.2:', when='@3.6.0:', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@3.8.1:', type=('build', 'run')) + depends_on('r-dose@3.5.1:', when='@3.8.1:', type=('build', 'run')) + depends_on('r-enrichplot@0.99.7:', when='@3.8.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py index bc06676d85..1eadf7f279 100644 --- a/var/spack/repos/builtin/packages/r-cner/package.py +++ b/var/spack/repos/builtin/packages/r-cner/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,22 +7,29 @@ from spack import * class RCner(RPackage): - """"Large-scale identification and advanced visualization of sets of - conserved noncoding elements.""" + """CNE Detection and Visualization. - homepage = "https://bioconductor.org/packages/CNEr/" + Large-scale identification and advanced visualization of sets of + conserved noncoding elements.""" + + homepage = "https://bioconductor.org/packages/CNEr" git = "https://git.bioconductor.org/packages/CNEr.git" + version('1.20.0', commit='9c25d8e8f6f5fd8a5311f554c86e7ca1140a4ca5') + version('1.18.1', commit='66aa88af04364c81832f3b09bad898f3c117f606') + version('1.16.1', commit='a2bec4b98d5938709f959a69c151f553ef357941') version('1.14.0', commit='b8634d65c51728c815127e22b45eba7c9b9db897') + version('1.12.1', commit='90d611f9cd19a73d0fe92ab03ef428519d64c017') + depends_on('r@3.2.2:', type=('build', 'run')) depends_on('r-biostrings@2.33.4:', type=('build', 'run')) - depends_on('r-dbi@0.7:', type=('build', 'run')) depends_on('r-rsqlite@0.11.4:', type=('build', 'run')) depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run')) depends_on('r-genomicranges@1.23.16:', type=('build', 'run')) depends_on('r-rtracklayer@1.25.5:', type=('build', 'run')) depends_on('r-xvector@0.5.4:', type=('build', 'run')) depends_on('r-genomicalignments@1.1.9:', type=('build', 'run')) + depends_on('r-dbi@0.6:', type=('build', 'run')) depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) depends_on('r-iranges@2.5.27:', type=('build', 'run')) depends_on('r-readr@0.2.2:', type=('build', 'run')) @@ -32,6 +39,8 @@ class RCner(RPackage): depends_on('r-powerlaw@0.60.3:', type=('build', 'run')) depends_on('r-annotate@1.50.0:', type=('build', 'run')) depends_on('r-go-db@3.3.0:', type=('build', 'run')) - depends_on('r-keggrest@1.14.0:', type=('build', 'run')) depends_on('r-r-utils@2.3.0:', type=('build', 'run')) - depends_on('r@3.4.3:3.4.9', when='@1.14.0') + depends_on('r-keggrest@1.14.0:', type=('build', 'run')) + + depends_on('r@3.4:', when='@1.14.0:', type=('build', 'run')) + depends_on('r-dbi@0.7:', when='@1.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-coda/package.py b/var/spack/repos/builtin/packages/r-coda/package.py index fd884ea86c..98397e80af 100644 --- a/var/spack/repos/builtin/packages/r-coda/package.py +++ b/var/spack/repos/builtin/packages/r-coda/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py index 60ea74198a..a1e189a942 100644 --- a/var/spack/repos/builtin/packages/r-codetools/package.py +++ b/var/spack/repos/builtin/packages/r-codetools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-coin/package.py b/var/spack/repos/builtin/packages/r-coin/package.py index 5b83e7d6a1..5e65ba4922 100644 --- a/var/spack/repos/builtin/packages/r-coin/package.py +++ b/var/spack/repos/builtin/packages/r-coin/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py index 8e68f4a366..8e1d6a700b 100644 --- a/var/spack/repos/builtin/packages/r-colorspace/package.py +++ b/var/spack/repos/builtin/packages/r-colorspace/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-combinat/package.py b/var/spack/repos/builtin/packages/r-combinat/package.py index 7adf666972..25323c66c5 100644 --- a/var/spack/repos/builtin/packages/r-combinat/package.py +++ b/var/spack/repos/builtin/packages/r-combinat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-commonmark/package.py b/var/spack/repos/builtin/packages/r-commonmark/package.py index 27afc8cfea..79d831d895 100644 --- a/var/spack/repos/builtin/packages/r-commonmark/package.py +++ b/var/spack/repos/builtin/packages/r-commonmark/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-complexheatmap/package.py b/var/spack/repos/builtin/packages/r-complexheatmap/package.py index 7cf86dfd66..6d4469ed09 100644 --- a/var/spack/repos/builtin/packages/r-complexheatmap/package.py +++ b/var/spack/repos/builtin/packages/r-complexheatmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,20 +7,34 @@ from spack import * class RComplexheatmap(RPackage): - """Complex heatmaps are efficient to visualize associations between - different sources of data sets and reveal potential structures. Here - the ComplexHeatmap package provides a highly flexible way to arrange - multiple heatmaps and supports self-defined annotation graphics.""" + """Make Complex Heatmaps. - homepage = "https://bioconductor.org/packages/ComplexHeatmap/" + Complex heatmaps are efficient to visualize associations between + different sources of data sets and reveal potential patterns. Here the + ComplexHeatmap package provides a highly flexible way to arrange + multiple heatmaps and supports various annotation graphics.""" + + homepage = "https://bioconductor.org/packages/ComplexHeatmap" git = "https://git.bioconductor.org/packages/ComplexHeatmap.git" + version('2.0.0', commit='97863d8ddfe36a52df0149b0b040dc386a03d2e4') + version('1.20.0', commit='1501ecc92fda07efa3652e41626b21741951ce0f') + version('1.18.1', commit='be0dd9d666a219c61335efe0dac50b2eed2a8825') + version('1.17.1', commit='f647c97e556d9e918a17be15883a0b72a91d688f') version('1.14.0', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34') - depends_on('r-circlize', type=('build', 'run')) + depends_on('r@3.1.2:', type=('build', 'run')) + depends_on('r-circlize@0.3.4:', type=('build', 'run')) depends_on('r-getoptlong', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r-dendextend', type=('build', 'run')) - depends_on('r-globaloptions', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.14.0') + depends_on('r-dendextend@1.0.1:', when='@1.14.0:1.17.1', type=('build', 'run')) + depends_on('r-globaloptions@0.0.10:', type=('build', 'run')) + + depends_on('r-circlize@0.4.1:', when='@1.17.1:', type=('build', 'run')) + + depends_on('r-globaloptions@0.1.0:', when='@1.20.0:', type=('build', 'run')) + + depends_on('r-circlize@0.4.5:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-clue', when='@2.0.0:', type=('build', 'run')) + depends_on('r-png', when='@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-compositions/package.py b/var/spack/repos/builtin/packages/r-compositions/package.py index 5077a7e651..49c8c48e9c 100644 --- a/var/spack/repos/builtin/packages/r-compositions/package.py +++ b/var/spack/repos/builtin/packages/r-compositions/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-condop/package.py b/var/spack/repos/builtin/packages/r-condop/package.py new file mode 100644 index 0000000000..2a51e5f3db --- /dev/null +++ b/var/spack/repos/builtin/packages/r-condop/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RCondop(RPackage): + """CONDOP: Condition-Dependent Operon Predictions. + + An implementation of the computational strategy for the comprehensive + analysis of condition-dependent operon maps in prokaryotes proposed by + Fortino et al. (2014) <doi:10.1186/1471-2105-15-145>. It uses RNA-seq + transcriptome profiles to improve prokaryotic operon map inference.""" + + homepage = "https://cloud.r-project.org/package=CONDOP" + url = "https://cloud.r-project.org/src/contrib/CONDOP_1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/CONDOP" + + version('1.0', sha256='3a855880f5c6b33f949c7e6de53c8e014b4d72b7024a93878b344d3e52b5296a') + + depends_on('r-mclust', type=('build', 'run')) + depends_on('r-earth', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-seqinr', type=('build', 'run')) + depends_on('r-randomforest', type=('build', 'run')) + depends_on('r-rminer', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-genomeinfodb', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-construct/package.py b/var/spack/repos/builtin/packages/r-construct/package.py index 1ec973752f..04ca748153 100644 --- a/var/spack/repos/builtin/packages/r-construct/package.py +++ b/var/spack/repos/builtin/packages/r-construct/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-convevol/package.py b/var/spack/repos/builtin/packages/r-convevol/package.py index 398e905016..e3771856a3 100644 --- a/var/spack/repos/builtin/packages/r-convevol/package.py +++ b/var/spack/repos/builtin/packages/r-convevol/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-corhmm/package.py b/var/spack/repos/builtin/packages/r-corhmm/package.py index 41043b8a1c..d4c8d6d5e0 100644 --- a/var/spack/repos/builtin/packages/r-corhmm/package.py +++ b/var/spack/repos/builtin/packages/r-corhmm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-corpcor/package.py b/var/spack/repos/builtin/packages/r-corpcor/package.py index ad4f8fc61c..2ecc478894 100644 --- a/var/spack/repos/builtin/packages/r-corpcor/package.py +++ b/var/spack/repos/builtin/packages/r-corpcor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-corrplot/package.py b/var/spack/repos/builtin/packages/r-corrplot/package.py index 490d0966b8..0cf25830ed 100644 --- a/var/spack/repos/builtin/packages/r-corrplot/package.py +++ b/var/spack/repos/builtin/packages/r-corrplot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-covr/package.py b/var/spack/repos/builtin/packages/r-covr/package.py index 22becf9e7e..b3daeac584 100644 --- a/var/spack/repos/builtin/packages/r-covr/package.py +++ b/var/spack/repos/builtin/packages/r-covr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-cowplot/package.py b/var/spack/repos/builtin/packages/r-cowplot/package.py index 3d3bd5549b..8b5ba4e174 100644 --- a/var/spack/repos/builtin/packages/r-cowplot/package.py +++ b/var/spack/repos/builtin/packages/r-cowplot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py index 123da7c0d3..ebb0aa75be 100644 --- a/var/spack/repos/builtin/packages/r-crayon/package.py +++ b/var/spack/repos/builtin/packages/r-crayon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-crosstalk/package.py b/var/spack/repos/builtin/packages/r-crosstalk/package.py index b505bd68e2..63d29bda13 100644 --- a/var/spack/repos/builtin/packages/r-crosstalk/package.py +++ b/var/spack/repos/builtin/packages/r-crosstalk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-crul/package.py b/var/spack/repos/builtin/packages/r-crul/package.py index e2d4410ebc..1f68e69287 100644 --- a/var/spack/repos/builtin/packages/r-crul/package.py +++ b/var/spack/repos/builtin/packages/r-crul/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ctc/package.py b/var/spack/repos/builtin/packages/r-ctc/package.py index 8c8c170072..7fbe647f6c 100644 --- a/var/spack/repos/builtin/packages/r-ctc/package.py +++ b/var/spack/repos/builtin/packages/r-ctc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,18 @@ from spack import * class RCtc(RPackage): - """Tools for export and import classification trees and clusters - to other programs""" + """Cluster and Tree Conversion.. - homepage = "https://www.bioconductor.org/packages/release/bioc/html/ctc.html" + Tools for export and import classification trees and clusters to other + programs""" + + homepage = "https://bioconductor.org/packages/ctc" git = "https://git.bioconductor.org/packages/ctc.git" + version('1.58.0', commit='c41df03ac149db20c5e337142142d61cfb9b43fb') + version('1.56.0', commit='cbd5befdda4630799f8fe0d868d83b094e3d352f') version('1.54.0', commit='0c3df81dfc8fabe12e11884bed44b64e11fd6d4e') + version('1.52.0', commit='ffff8693cab5ebad610d139367f089418f1830a1') + version('1.50.0', commit='4ee7519c3e5172e140c2658b4cf5271d229acc7e') depends_on('r-amap', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.54.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py index 8651d1fb42..e137d8bc59 100644 --- a/var/spack/repos/builtin/packages/r-cubature/package.py +++ b/var/spack/repos/builtin/packages/r-cubature/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-cubist/package.py b/var/spack/repos/builtin/packages/r-cubist/package.py index 36c0eeb35e..9738b682ad 100644 --- a/var/spack/repos/builtin/packages/r-cubist/package.py +++ b/var/spack/repos/builtin/packages/r-cubist/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py index 01a385f2f3..25081b86f7 100644 --- a/var/spack/repos/builtin/packages/r-curl/package.py +++ b/var/spack/repos/builtin/packages/r-curl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dada2/package.py b/var/spack/repos/builtin/packages/r-dada2/package.py new file mode 100644 index 0000000000..da4be89f98 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dada2/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RDada2(RPackage): + """Accurate sample inference from amplicon data with single nucleotide + resolution""" + + homepage = "http://benjjneb.github.io/dada2/" + url = "https://github.com/benjjneb/dada2/archive/v1.14.tar.gz" + + version('1.14', sha256='19980b9d7b0a0e80e86010357cae11d1fc07c2d02067c4445169143cf1f99906') + + depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-rcpp@0.12.0:', type=('build', 'run')) + depends_on('r-biostrings@2.42.1:', type=('build', 'run')) + depends_on('r-ggplot2@2.1.0:', type=('build', 'run')) + depends_on('r-reshape2@1.4.1:', type=('build', 'run')) + depends_on('r-shortread@1.32.0:', type=('build', 'run')) + depends_on('r-rcppparallel@4.3.0:', type=('build', 'run')) + depends_on('r-iranges@2.6.0:', type=('build', 'run')) + depends_on('r-xvector@0.16.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.22.0:', type=('build', 'run')) + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-data-table/package.py b/var/spack/repos/builtin/packages/r-data-table/package.py index e9e2bc0440..b9a008eff0 100644 --- a/var/spack/repos/builtin/packages/r-data-table/package.py +++ b/var/spack/repos/builtin/packages/r-data-table/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dbi/package.py b/var/spack/repos/builtin/packages/r-dbi/package.py index b927abd2a3..49cfa2a22e 100644 --- a/var/spack/repos/builtin/packages/r-dbi/package.py +++ b/var/spack/repos/builtin/packages/r-dbi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dbplyr/package.py b/var/spack/repos/builtin/packages/r-dbplyr/package.py index 2f88bb3fc8..b73d44a34f 100644 --- a/var/spack/repos/builtin/packages/r-dbplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dbplyr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-debugme/package.py b/var/spack/repos/builtin/packages/r-debugme/package.py index 590fe5f23a..9d8146d31b 100644 --- a/var/spack/repos/builtin/packages/r-debugme/package.py +++ b/var/spack/repos/builtin/packages/r-debugme/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py index 10652164c8..b4f79d524c 100644 --- a/var/spack/repos/builtin/packages/r-delayedarray/package.py +++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,37 +7,42 @@ from spack import * class RDelayedarray(RPackage): - """Wrapping an array-like object (typically an on-disk object) in a - DelayedArray object allows one to perform common array operations on it - without loading the object in memory. In order to reduce memory usage - and optimize performance, operations on the object are either delayed - or executed using a block processing mechanism. Note that this also - works on in-memory array-like objects like DataFrame objects (typically - with Rle columns), Matrix objects, and ordinary arrays and data frames. + """A unified framework for working transparently with on-disk and in-memory + array-like datasets. + Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage - and optimize performance, operations on the object are either delayed - or executed using a block processing mechanism. Note that this also - works on in-memory array-like objects like DataFrame objects (typically - with Rle columns), Matrix objects, and ordinary arrays and data - frames.""" + and optimize performance, operations on the object are either delayed or + executed using a block processing mechanism. Note that this also works + on in-memory array-like objects like DataFrame objects (typically with + Rle columns), Matrix objects, and ordinary arrays and data frames.""" - homepage = "https://bioconductor.org/packages/DelayedArray/" + homepage = "https://bioconductor.org/packages/DelayedArray" git = "https://git.bioconductor.org/packages/DelayedArray.git" - version('0.6.5', commit='7d1cb6477cb024c38bf1ee0c9155e010249ed94e') + version('0.10.0', commit='4781d073110a3fd1e20c4083b6b2b0f260d0cb0a') + version('0.8.0', commit='7c23cf46558de9dbe7a42fba516a9bb660a0f19f') + version('0.6.6', commit='bdb0ac0eee71edd40ccca4808f618fa77f595a64') version('0.4.1', commit='ffe932ef8c255614340e4856fc6e0b44128a27a1') version('0.2.7', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4') - depends_on('r-biocparallel', when='@0.6.5:', type=('build', 'run')) + depends_on('r@3.4:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.25.1:', when='@0.6.5', type=('build', 'run')) - depends_on('r-s4vectors@0.14.3:', when='@0.2.7', type=('build', 'run')) - depends_on('r-s4vectors@0.15.3:', when='@0.4.1', type=('build', 'run')) - depends_on('r-s4vectors@0.17.43:', when='@0.6.5', type=('build', 'run')) + depends_on('r-s4vectors@0.14.3:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.11.17:', when='@0.4.1:', type=('build', 'run')) depends_on('r-matrixstats', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@0.2.7', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@0.6.5', type=('build', 'run')) + + depends_on('r-s4vectors@0.15.3:', when='@0.4.1:', type=('build', 'run')) + depends_on('r-iranges@2.11.17:', when='@0.4.1:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.25.1:', when='@0.6.6:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.43:', when='@0.6.6:', type=('build', 'run')) + depends_on('r-biocparallel', when='@0.6.6:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.27.1:', when='@0.8.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.19.15:', when='@0.8.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.21.7:', when='@0.10.0:', type=('build', 'run')) + depends_on('r-iranges@2.17.3:', when='@0.10.0:', type=('build', 'run')) + depends_on('r-matrix', when='@0.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py new file mode 100644 index 0000000000..3898c8d15f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py @@ -0,0 +1,41 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RDelayedmatrixstats(RPackage): + """Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects. + + A port of the 'matrixStats' API for use with DelayedMatrix objects from + the 'DelayedArray' package. High-performing functions operating on rows + and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / + rowRanks(), and col / rowSds(). Functions optimized per data type and + for subsetted calculations such that both memory usage and processing + time is minimized.""" + + homepage = "https://bioconductor.org/packages/DelayedMatrixStats" + git = "https://git.bioconductor.org/packages/DelayedMatrixStats.git" + + version('1.6.1', commit='4378d1898a403305a94b122c4f36d1215fa7708d') + version('1.4.0', commit='eb5b390ef99651fe87a346848f807de95afe8971') + version('1.2.0', commit='de868e730be6280dfad41a280ab09f4d3083c9ac') + version('1.0.3', commit='e29a3444980ff727c5b12286884b06dfaebf5b5b') + + depends_on('r-delayedarray', type=('build', 'run')) + depends_on('r-matrixstats@0.53.1:', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + + depends_on('r-delayedarray@0.5.27:', when='@1.2.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.5:', when='@1.2.0:', type=('build', 'run')) + + depends_on('r-delayedarray@0.7.37:', when='@1.4.0:', type=('build', 'run')) + depends_on('r-hdf5array@1.7.10:', when='@1.4.0:', type=('build', 'run')) + depends_on('r-biocparallel', when='@1.4.0:', type=('build', 'run')) + + depends_on('r-delayedarray@0.9.8:', when='@1.6.1:', type=('build', 'run')) + depends_on('r-matrixstats@0.55.0:', when='@1.6.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-deldir/package.py b/var/spack/repos/builtin/packages/r-deldir/package.py index b2fdd549ad..5654a5c403 100644 --- a/var/spack/repos/builtin/packages/r-deldir/package.py +++ b/var/spack/repos/builtin/packages/r-deldir/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dendextend/package.py b/var/spack/repos/builtin/packages/r-dendextend/package.py index 746867f19d..d5bd7f4af0 100644 --- a/var/spack/repos/builtin/packages/r-dendextend/package.py +++ b/var/spack/repos/builtin/packages/r-dendextend/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-deoptim/package.py b/var/spack/repos/builtin/packages/r-deoptim/package.py index 3105f98e61..e4dc1f87a6 100644 --- a/var/spack/repos/builtin/packages/r-deoptim/package.py +++ b/var/spack/repos/builtin/packages/r-deoptim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-deoptimr/package.py b/var/spack/repos/builtin/packages/r-deoptimr/package.py index 9102c744b9..5531bc894b 100644 --- a/var/spack/repos/builtin/packages/r-deoptimr/package.py +++ b/var/spack/repos/builtin/packages/r-deoptimr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-desc/package.py b/var/spack/repos/builtin/packages/r-desc/package.py index 9504ed5052..b3b61283ed 100644 --- a/var/spack/repos/builtin/packages/r-desc/package.py +++ b/var/spack/repos/builtin/packages/r-desc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-deseq/package.py b/var/spack/repos/builtin/packages/r-deseq/package.py index dc60c09f45..107d581494 100644 --- a/var/spack/repos/builtin/packages/r-deseq/package.py +++ b/var/spack/repos/builtin/packages/r-deseq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,24 @@ from spack import * class RDeseq(RPackage): - """Estimate variance-mean dependence in count data from - high-throughput sequencing assays and test for differential - expression based on a model using the negative binomial - distribution.""" + """Differential gene expression analysis based on the negative binomial + distribution. - homepage = "https://www.bioconductor.org/packages/DESeq/" + Estimate variance-mean dependence in count data from high-throughput + sequencing assays and test for differential expression based on a model + using the negative binomial distribution""" + + homepage = "https://bioconductor.org/packages/DESeq" git = "https://git.bioconductor.org/packages/DESeq.git" + version('1.36.0', commit='db4af67b49d3bd8c321d19efbe9415cd2e4ddb7e') + version('1.34.1', commit='e86f1b03a30bc02de4bfd4a0759af2f65cb48c62') + version('1.32.0', commit='e3d623b815b53d79eae7cdd09d097cc6098d28c9') + version('1.30.0', commit='90c93d991dd980d538c13b0361d3345f9546794e') version('1.28.0', commit='738371466e6ccf00179fd35b617c8ba0e1e91630') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) + depends_on('r-biocgenerics@0.7.5:', type=('build', 'run')) + depends_on('r-biobase@2.21.7:', type=('build', 'run')) depends_on('r-locfit', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py index ac9f7257de..8d0fbc2900 100644 --- a/var/spack/repos/builtin/packages/r-deseq2/package.py +++ b/var/spack/repos/builtin/packages/r-deseq2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,24 +7,27 @@ from spack import * class RDeseq2(RPackage): - """Estimate variance-mean dependence in count data from - high-throughput sequencing assays and test for differential - expression based on a model using the negative binomial - distribution.""" + """Differential gene expression analysis based on the negative binomial + distribution. - homepage = "https://www.bioconductor.org/packages/DESeq2/" + Estimate variance-mean dependence in count data from high-throughput + sequencing assays and test for differential expression based on a model + using the negative binomial distribution.""" + + homepage = "https://bioconductor.org/packages/DESeq2" git = "https://git.bioconductor.org/packages/DESeq2.git" + version('1.24.0', commit='3ce7fbbebac526b726a6f85178063d02eb0314bf') + version('1.22.2', commit='3c6a89b61add635d6d468c7fa00192314f8ca4ce') version('1.20.0', commit='7e88ea5c5e68473824ce0af6e10f19e22374cb7c') version('1.18.1', commit='ef65091d46436af68915124b752f5e1cc55e93a7') - version('1.16.1', commit='0a815574382704a08ef8b906eceb0296f81cded5') + version('1.16.1', commit='f41d9df2de25fb57054480e50bc208447a6d82fb') - depends_on("r-rcpparmadillo", type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-summarizedexperiment', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.1.6:', type=('build', 'run')) + depends_on('r-biocgenerics@0.7.5:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) @@ -32,6 +35,5 @@ class RDeseq2(RPackage): depends_on('r-geneplotter', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-hmisc', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.16.1:1.19', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.20.0', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) + depends_on('r-rcpparmadillo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-desolve/package.py b/var/spack/repos/builtin/packages/r-desolve/package.py index a0e705394d..88918d33f5 100644 --- a/var/spack/repos/builtin/packages/r-desolve/package.py +++ b/var/spack/repos/builtin/packages/r-desolve/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py index b132f9dcbf..9b4c4a2332 100644 --- a/var/spack/repos/builtin/packages/r-devtools/package.py +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py index dc86a07bd1..08bcb255c5 100644 --- a/var/spack/repos/builtin/packages/r-diagrammer/package.py +++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dicekriging/package.py b/var/spack/repos/builtin/packages/r-dicekriging/package.py index 7ce3fedd96..ace01e38a4 100644 --- a/var/spack/repos/builtin/packages/r-dicekriging/package.py +++ b/var/spack/repos/builtin/packages/r-dicekriging/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py index 90434ae515..5fbadf1af3 100644 --- a/var/spack/repos/builtin/packages/r-dichromat/package.py +++ b/var/spack/repos/builtin/packages/r-dichromat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-diffusionmap/package.py b/var/spack/repos/builtin/packages/r-diffusionmap/package.py index b6508e937a..3002ec28cb 100644 --- a/var/spack/repos/builtin/packages/r-diffusionmap/package.py +++ b/var/spack/repos/builtin/packages/r-diffusionmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py index 875d2e4b76..bb32198c85 100644 --- a/var/spack/repos/builtin/packages/r-digest/package.py +++ b/var/spack/repos/builtin/packages/r-digest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-diptest/package.py b/var/spack/repos/builtin/packages/r-diptest/package.py index e2cedec894..6a13308a66 100644 --- a/var/spack/repos/builtin/packages/r-diptest/package.py +++ b/var/spack/repos/builtin/packages/r-diptest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py index 02e911d5d6..8b692dc475 100644 --- a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py +++ b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,19 +7,25 @@ from spack import * class RDirichletmultinomial(RPackage): - """Dirichlet-multinomial mixture models can be used to describe - variability in microbial metagenomic data. + """Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome + Data. - This package is an interface to code originally made available by - Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed - further in the man page for this package, ?DirichletMultinomial.""" + Dirichlet-multinomial mixture models can be used to describe variability + in microbial metagenomic data. This package is an interface to code + originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE + 7(2): 1-15, as discussed further in the man page for this package, + ?DirichletMultinomial.""" - homepage = "https://bioconductor.org/packages/DirichletMultinomial/" + homepage = "https://bioconductor.org/packages/DirichletMultinomial" git = "https://git.bioconductor.org/packages/DirichletMultinomial.git" + version('1.26.0', commit='7daa84948020811bb8a27d2e633fccfdcdd1018f') + version('1.24.1', commit='50195d9b1986852da29100e77f6f09df5d6e2a35') + version('1.22.0', commit='5864f4298105d12f345f27df77ad13bae4061ca5') version('1.20.0', commit='251529f301da1482551142240aeb6baf8dab2272') + version('1.18.0', commit='81ccc8d83b8ef84f5d3e877bc0a04233a0f63c51') depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) depends_on('gsl') - depends_on('r@3.4.0:') diff --git a/var/spack/repos/builtin/packages/r-dismo/package.py b/var/spack/repos/builtin/packages/r-dismo/package.py index 4fb5e5e321..9564211ed1 100644 --- a/var/spack/repos/builtin/packages/r-dismo/package.py +++ b/var/spack/repos/builtin/packages/r-dismo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-diversitree/package.py b/var/spack/repos/builtin/packages/r-diversitree/package.py index bb2c27dac6..d661a11453 100644 --- a/var/spack/repos/builtin/packages/r-diversitree/package.py +++ b/var/spack/repos/builtin/packages/r-diversitree/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dnacopy/package.py b/var/spack/repos/builtin/packages/r-dnacopy/package.py index 85bbd55e3c..4ddea98cdc 100644 --- a/var/spack/repos/builtin/packages/r-dnacopy/package.py +++ b/var/spack/repos/builtin/packages/r-dnacopy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,11 +7,17 @@ from spack import * class RDnacopy(RPackage): - """Implements the circular binary segmentation (CBS) algorithm - to segment DNA copy number data and identify genomic regions - with abnormal copy number.""" + """DNA copy number data analysis. - homepage = "https://www.bioconductor.org/packages/DNAcopy/" + Implements the circular binary segmentation (CBS) algorithm to segment + DNA copy number data and identify genomic regions with abnormal copy + number.""" + + homepage = "https://bioconductor.org/packages/DNAcopy" git = "https://git.bioconductor.org/packages/DNAcopy.git" + version('1.58.0', commit='1954745eafca990d6ddeefe84059c54a8c37df23') + version('1.56.0', commit='e521826f2515b309921272f65db421cbe2ff961a') + version('1.54.0', commit='fe2657936afbce8ee03221461dff4265e3ded4c4') + version('1.52.0', commit='2632fbecec4cef3705b85676942a59188ae9bba4') version('1.50.1', commit='a20153029e28c009df813dbaf13d9f519fafa4e8') diff --git a/var/spack/repos/builtin/packages/r-do-db/package.py b/var/spack/repos/builtin/packages/r-do-db/package.py index 3be01b4dc5..be152d3049 100644 --- a/var/spack/repos/builtin/packages/r-do-db/package.py +++ b/var/spack/repos/builtin/packages/r-do-db/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-domc/package.py b/var/spack/repos/builtin/packages/r-domc/package.py index 3a50cb689e..8df8cbf523 100644 --- a/var/spack/repos/builtin/packages/r-domc/package.py +++ b/var/spack/repos/builtin/packages/r-domc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py index c6e9013fbc..fc06d2f142 100644 --- a/var/spack/repos/builtin/packages/r-doparallel/package.py +++ b/var/spack/repos/builtin/packages/r-doparallel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dorng/package.py b/var/spack/repos/builtin/packages/r-dorng/package.py index 41c5ecac3d..a20cd96356 100644 --- a/var/spack/repos/builtin/packages/r-dorng/package.py +++ b/var/spack/repos/builtin/packages/r-dorng/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py index 8313f4997e..70e5f103d9 100644 --- a/var/spack/repos/builtin/packages/r-dose/package.py +++ b/var/spack/repos/builtin/packages/r-dose/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,27 +7,37 @@ from spack import * class RDose(RPackage): - """This package implements five methods proposed by Resnik, Schlicker, - Jiang, Lin and Wang respectively for measuring semantic similarities - among DO terms and gene products. Enrichment analyses including - hypergeometric model and gene set enrichment analysis are also - implemented for discovering disease associations of high-throughput - biological data.""" - - homepage = "https://www.bioconductor.org/packages/DOSE/" + """Disease Ontology Semantic and Enrichment analysis. + + This package implements five methods proposed by Resnik, Schlicker, + Jiang, Lin and Wang respectively for measuring semantic similarities + among DO terms and gene products. Enrichment analyses including + hypergeometric model and gene set enrichment analysis are also + implemented for discovering disease associations of high-throughput + biological data.""" + + homepage = "https://bioconductor.org/packages/DOSE" git = "https://git.bioconductor.org/packages/DOSE.git" + version('3.10.2', commit='5ea51a2e2a04b4f3cc974cecb4537e14efd6a7e3') + version('3.8.2', commit='4d3d1ca710aa7e4288a412c8d52b054b86a57639') + version('3.6.1', commit='f2967f0482cea39222bfd15767d0f4a5994f241b') + version('3.4.0', commit='dabb70de1a0f91d1767601e871f2f1c16d29a612') version('3.2.0', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b') - depends_on('r@3.4.0:3.4.9', when='@3.2.0') - depends_on('r-scales', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-reshape2', type=('build', 'run')) - depends_on('r-qvalue', type=('build', 'run')) - depends_on('r-igraph', type=('build', 'run')) - depends_on('r-gosemsim', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-fgsea', type=('build', 'run')) - depends_on('r-do-db', type=('build', 'run')) - depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r@3.3.1:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r-do-db', type=('build', 'run')) + depends_on('r-fgsea', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-gosemsim@2.0.0:', type=('build', 'run')) + depends_on('r-igraph', when='@3.2.0:3.4.0', type=('build', 'run')) + depends_on('r-qvalue', type=('build', 'run')) + depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-scales', when='@3.2.0:3.4.0', type=('build', 'run')) + + depends_on('r-rvcheck', when='@3.4.0', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@3.6.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dosnow/package.py b/var/spack/repos/builtin/packages/r-dosnow/package.py index 7ad841b431..18de14a737 100644 --- a/var/spack/repos/builtin/packages/r-dosnow/package.py +++ b/var/spack/repos/builtin/packages/r-dosnow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dotcall64/package.py b/var/spack/repos/builtin/packages/r-dotcall64/package.py new file mode 100644 index 0000000000..b9214c5a95 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dotcall64/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RDotcall64(RPackage): + """dotCall64: Enhanced Foreign Function Interface Supporting Long + Vectors.""" + + homepage = "https://git.math.uzh.ch/reinhard.furrer/dotCall64" + url = "https://cloud.r-project.org/src/contrib/dotCall64_1.0-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dotCall64" + + version('1.0-0', sha256='69318dc6b8aecc54d4f789c8105e672198363b395f1a764ebaeb54c0473d17ad') + + depends_on('r@3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-downloader/package.py b/var/spack/repos/builtin/packages/r-downloader/package.py index 0faeb14227..ecf053e698 100644 --- a/var/spack/repos/builtin/packages/r-downloader/package.py +++ b/var/spack/repos/builtin/packages/r-downloader/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py index a7ed7868d7..d6936c182c 100644 --- a/var/spack/repos/builtin/packages/r-dplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dplyr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dqrng/package.py b/var/spack/repos/builtin/packages/r-dqrng/package.py index ebb82b942c..07109336c3 100644 --- a/var/spack/repos/builtin/packages/r-dqrng/package.py +++ b/var/spack/repos/builtin/packages/r-dqrng/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py index 141b40006b..a4d810b238 100644 --- a/var/spack/repos/builtin/packages/r-dt/package.py +++ b/var/spack/repos/builtin/packages/r-dt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dtw/package.py b/var/spack/repos/builtin/packages/r-dtw/package.py index 8847298c3c..ea6af863ee 100644 --- a/var/spack/repos/builtin/packages/r-dtw/package.py +++ b/var/spack/repos/builtin/packages/r-dtw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py index 0f2448edd2..f4b659eeed 100644 --- a/var/spack/repos/builtin/packages/r-dygraphs/package.py +++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-dynamictreecut/package.py b/var/spack/repos/builtin/packages/r-dynamictreecut/package.py index 856e6efb89..d3da482416 100644 --- a/var/spack/repos/builtin/packages/r-dynamictreecut/package.py +++ b/var/spack/repos/builtin/packages/r-dynamictreecut/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py index f38f6621b3..b853a44f65 100644 --- a/var/spack/repos/builtin/packages/r-e1071/package.py +++ b/var/spack/repos/builtin/packages/r-e1071/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-earth/package.py b/var/spack/repos/builtin/packages/r-earth/package.py new file mode 100644 index 0000000000..e1dc5b293d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-earth/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class REarth(RPackage): + """earth: Multivariate Adaptive Regression Splines. + + Build regression models using the techniques in Friedman's papers + "Fast MARS" and "Multivariate Adaptive Regression Splines" + <doi:10.1214/aos/1176347963>.""" + + homepage = "http://www.milbo.users.sonic.net/earth" + url = "https://cloud.r-project.org/src/contrib/earth_5.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/earth" + + version('5.1.2', sha256='326f98e8c29365ca3cd5584cf2bd6529358f5ef81664cbd494162f92b6c3488d') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-formula@1.2-3:', type=('build', 'run')) + depends_on('r-plotmo@3.5.4:', type=('build', 'run')) + depends_on('r-teachingdemos@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ecp/package.py b/var/spack/repos/builtin/packages/r-ecp/package.py new file mode 100644 index 0000000000..700c1780e0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ecp/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class REcp(RPackage): + """ecp: Non-Parametric Multiple Change-Point Analysis of + MultivariateData""" + + homepage = "https://cloud.r-project.org/package=ecp" + url = "https://cloud.r-project.org/src/contrib/ecp_3.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ecp" + + version('3.1.1', sha256='d2ab194e22e6ab0168222fbccfcf2e25c6cd51a73edc959086b0c6e0a7410268') + + depends_on('r@3.00:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py index b8c2036b56..5d7f481a70 100644 --- a/var/spack/repos/builtin/packages/r-edger/package.py +++ b/var/spack/repos/builtin/packages/r-edger/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,22 +7,30 @@ from spack import * class REdger(RPackage): - """Differential expression analysis of RNA-seq expression profiles with + """Empirical Analysis of Digital Gene Expression Data in R. + + Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, - SAGE and CAGE.""" + Bisulfite-seq, SAGE and CAGE.""" - homepage = "https://bioconductor.org/packages/edgeR/" + homepage = "https://bioconductor.org/packages/edgeR" git = "https://git.bioconductor.org/packages/edgeR.git" - version('3.22.3', commit='e82e54afc9398ac54dc4caba0f7ae5c43e572203') + version('3.26.8', commit='836809e043535f2264e5db8b5c0eabcffe85613f') + version('3.24.3', commit='d1260a2aeba67b9ab7a9b8b197b746814ad0716d') + version('3.22.5', commit='44461aa0412ef4a0d955730f365e44fc64fe1902') + version('3.20.9', commit='acbcbbee939f399673678653678cd9cb4917c4dc') version('3.18.1', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495') + depends_on('r@2.15.0:', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) depends_on('r-locfit', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'link', 'run')) - depends_on('r@3.5.0:3.5.9', when='@3.22.3') - depends_on('r@3.4.0:3.4.9', when='@3.18.1') + + depends_on('r-limma@3.34.5:', when='@3.20.9:', type=('build', 'run')) + depends_on('r-rcpp', when='@3.20.9:', type=('build', 'run')) + + depends_on('r@3.6.0:', when='@3.26.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ellipse/package.py b/var/spack/repos/builtin/packages/r-ellipse/package.py index 43ec1ffd14..bbeec79275 100644 --- a/var/spack/repos/builtin/packages/r-ellipse/package.py +++ b/var/spack/repos/builtin/packages/r-ellipse/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ellipsis/package.py b/var/spack/repos/builtin/packages/r-ellipsis/package.py index 8945722068..4f5349f3e5 100644 --- a/var/spack/repos/builtin/packages/r-ellipsis/package.py +++ b/var/spack/repos/builtin/packages/r-ellipsis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-emmli/package.py b/var/spack/repos/builtin/packages/r-emmli/package.py index 974bb81c8b..1144e2d105 100644 --- a/var/spack/repos/builtin/packages/r-emmli/package.py +++ b/var/spack/repos/builtin/packages/r-emmli/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-energy/package.py b/var/spack/repos/builtin/packages/r-energy/package.py index 161e7efae9..db396a6bf5 100644 --- a/var/spack/repos/builtin/packages/r-energy/package.py +++ b/var/spack/repos/builtin/packages/r-energy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-enrichplot/package.py b/var/spack/repos/builtin/packages/r-enrichplot/package.py new file mode 100644 index 0000000000..8a30292b50 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-enrichplot/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class REnrichplot(RPackage): + """Visualization of Functional Enrichment Result. + + The 'enrichplot' package implements several visualization methods for + interpreting functional enrichment results obtained from ORA or GSEA + analysis. All the visualization methods are developed based on 'ggplot2' + graphics.""" + + homepage = "https://bioconductor.org/packages/enrichplot" + git = "https://git.bioconductor.org/packages/enrichplot.git" + + version('1.4.0', commit='6ffe5d9c5dbe5cbea29f2e0941595475bbbcea0e') + version('1.2.0', commit='2eeaafb571d35a106eba8ae7df014f3201066e8b') + version('1.0.2', commit='ba7726fa0d4b581b7514dcbb04889cdbdd75ff29') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-cowplot', type=('build', 'run')) + depends_on('r-dose@3.5.1:', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggraph', type=('build', 'run')) + depends_on('r-ggridges', type=('build', 'run')) + depends_on('r-gosemsim', type=('build', 'run')) + depends_on('r-igraph', type=('build', 'run')) + depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-upsetr', type=('build', 'run')) + + depends_on('r-europepmc', when='@1.2.0:', type=('build', 'run')) + depends_on('r-ggplotify', when='@1.2.0:', type=('build', 'run')) + depends_on('r-gridextra', when='@1.2.0:', type=('build', 'run')) + depends_on('r-purrr', when='@1.2.0:', type=('build', 'run')) + depends_on('r-rcolorbrewer', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py index ec31c4a9e2..71aaf50c22 100644 --- a/var/spack/repos/builtin/packages/r-ensembldb/package.py +++ b/var/spack/repos/builtin/packages/r-ensembldb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,36 +7,54 @@ from spack import * class REnsembldb(RPackage): - """The package provides functions to create and use transcript centric + """Utilities to create and use Ensembl-based annotation databases. + + The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all - gene/transcript models and annotations from the database, the ensembldb - package provides also a filter framework allowing to retrieve - annotations for specific entries like genes encoded on a chromosome - region or transcript models of lincRNA genes.""" + gene/transcript models and annotations from the database, ensembldb + provides a filter framework allowing to retrieve annotations for + specific entries like genes encoded on a chromosome region or transcript + models of lincRNA genes. EnsDb databases built with ensembldb contain + also protein annotations and mappings between proteins and their + encoding transcripts. Finally, ensembldb provides functions to map + between genomic, transcript and protein coordinates.""" - homepage = "https://bioconductor.org/packages/ensembldb/" + homepage = "https://bioconductor.org/packages/ensembldb" git = "https://git.bioconductor.org/packages/ensembldb.git" + version('2.8.1', commit='a4d8d89c143dca86b364d59dff8e46cc81c41ac0') + version('2.6.8', commit='c2c4f41b4ecc81d5328ce1d380065dfcb5e0c54c') + version('2.4.1', commit='b5b6b94826a2f46a4faecb9dde750ecd3bfaf327') + version('2.2.2', commit='d71610e58aed88dbbe6a74e7a8ddfb7451398060') version('2.0.4', commit='514623d71e3cca7a4e547adb579b5a958702ef86') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) - depends_on('r-annotationfilter', type=('build', 'run')) - depends_on('r-rsqlite', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) + depends_on('r-genomicranges@1.23.21:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.23.18:', type=('build', 'run')) + depends_on('r-annotationfilter@0.99.7:', type=('build', 'run')) + depends_on('r-rsqlite@1.1:', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-annotationdbi@1.31.19:', type=('build', 'run')) depends_on('r-rtracklayer', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-annotationhub', type=('build', 'run')) + depends_on('r-annotationhub', when='@2.0.4:2.2.2', type=('build', 'run')) depends_on('r-rsamtools', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-protgenerics', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) depends_on('r-curl', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', type=('build', 'run')) + + depends_on('r-genomicfeatures@1.29.10:', when='@2.2.2:', type=('build', 'run')) + depends_on('r-annotationfilter@1.1.9:', when='@2.2.2:', type=('build', 'run')) + depends_on('r-iranges@2.11.16:', when='@2.2.2:', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.18:', when='@2.4.1:', type=('build', 'run')) + depends_on('r-iranges@2.13.24:', when='@2.4.1:', type=('build', 'run')) + depends_on('r-biostrings@2.47.9:', when='@2.4.1:', type=('build', 'run')) + + depends_on('r-annotationfilter@1.5.2:', when='@2.6.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ergm/package.py b/var/spack/repos/builtin/packages/r-ergm/package.py index 0a252cfe0f..0b853f1fbd 100644 --- a/var/spack/repos/builtin/packages/r-ergm/package.py +++ b/var/spack/repos/builtin/packages/r-ergm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-europepmc/package.py b/var/spack/repos/builtin/packages/r-europepmc/package.py new file mode 100644 index 0000000000..27480f7787 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-europepmc/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class REuropepmc(RPackage): + """europepmc: R Interface to the Europe PubMed Central RESTful Web + Service""" + + homepage = "http://github.com/ropensci/europepmc/" + url = "https://cloud.r-project.org/src/contrib/europepmc_0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/europepmc" + + version('0.3', sha256='5044a253d223e2bb8502063cd03c0fe4db856467e497d650da7ccd8f75d0f8d9') + + depends_on('r@3.00:', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-httr', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-progress', type=('build', 'run')) + depends_on('r-purrr', type=('build', 'run')) + depends_on('r-urltools', type=('build', 'run')) + depends_on('r-xml2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py index e0f52918a0..d946976bf1 100644 --- a/var/spack/repos/builtin/packages/r-evaluate/package.py +++ b/var/spack/repos/builtin/packages/r-evaluate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-evd/package.py b/var/spack/repos/builtin/packages/r-evd/package.py new file mode 100644 index 0000000000..c30bac399c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-evd/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class REvd(RPackage): + """evd: Functions for Extreme Value Distributions""" + + homepage = "https://cloud.r-project.org/package=evd" + url = "https://cloud.r-project.org/src/contrib/evd_2.3-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/evd" + + version('2.3-3', sha256='2fc5ef2e0c3a2a9392425ddd45914445497433d90fb80b8c363877baee4559b4') diff --git a/var/spack/repos/builtin/packages/r-expint/package.py b/var/spack/repos/builtin/packages/r-expint/package.py index 4bce63d28a..7fc6486a17 100644 --- a/var/spack/repos/builtin/packages/r-expint/package.py +++ b/var/spack/repos/builtin/packages/r-expint/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-expm/package.py b/var/spack/repos/builtin/packages/r-expm/package.py index 6c51216793..af64603e2c 100644 --- a/var/spack/repos/builtin/packages/r-expm/package.py +++ b/var/spack/repos/builtin/packages/r-expm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-factoextra/package.py b/var/spack/repos/builtin/packages/r-factoextra/package.py index a252d0ebde..b5b4caf941 100644 --- a/var/spack/repos/builtin/packages/r-factoextra/package.py +++ b/var/spack/repos/builtin/packages/r-factoextra/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-factominer/package.py b/var/spack/repos/builtin/packages/r-factominer/package.py index a5723eff14..dbae32d420 100644 --- a/var/spack/repos/builtin/packages/r-factominer/package.py +++ b/var/spack/repos/builtin/packages/r-factominer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-fansi/package.py b/var/spack/repos/builtin/packages/r-fansi/package.py index ff24e351bf..7e25449302 100644 --- a/var/spack/repos/builtin/packages/r-fansi/package.py +++ b/var/spack/repos/builtin/packages/r-fansi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-farver/package.py b/var/spack/repos/builtin/packages/r-farver/package.py new file mode 100644 index 0000000000..db4d14228a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-farver/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RFarver(RPackage): + """farver: High Performance Colour Space Manipulation""" + + homepage = "https://github.com/thomasp85/farver" + url = "https://cloud.r-project.org/src/contrib/farver_2.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/farver" + + version('2.0.1', sha256='1642ca1519ef80616ab044ae7f6eaf464118356f2a7875e9d0e3df60ca84012b') diff --git a/var/spack/repos/builtin/packages/r-fastcluster/package.py b/var/spack/repos/builtin/packages/r-fastcluster/package.py index d08a5ddb66..2848a10923 100644 --- a/var/spack/repos/builtin/packages/r-fastcluster/package.py +++ b/var/spack/repos/builtin/packages/r-fastcluster/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-fastmatch/package.py b/var/spack/repos/builtin/packages/r-fastmatch/package.py index c1fa6b2857..5c4c5a4895 100644 --- a/var/spack/repos/builtin/packages/r-fastmatch/package.py +++ b/var/spack/repos/builtin/packages/r-fastmatch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ff/package.py b/var/spack/repos/builtin/packages/r-ff/package.py index 87e0e48ec4..7ff486acaf 100644 --- a/var/spack/repos/builtin/packages/r-ff/package.py +++ b/var/spack/repos/builtin/packages/r-ff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-fftwtools/package.py b/var/spack/repos/builtin/packages/r-fftwtools/package.py index c2708d2b72..4f3074e7c4 100644 --- a/var/spack/repos/builtin/packages/r-fftwtools/package.py +++ b/var/spack/repos/builtin/packages/r-fftwtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py index 81bff39da6..6787e4d33f 100644 --- a/var/spack/repos/builtin/packages/r-fgsea/package.py +++ b/var/spack/repos/builtin/packages/r-fgsea/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,20 +7,30 @@ from spack import * class RFgsea(RPackage): - """The package implements an algorithm for fast gene set enrichment - analysis. Using the fast algorithm allows to make more permutations - and get more fine grained p-values, which allows to use accurate - stantard approaches to multiple hypothesis correction.""" + """Fast Gene Set Enrichment Analysis. - homepage = "https://www.bioconductor.org/packages/fgsea/" + The package implements an algorithm for fast gene set enrichment + analysis. Using the fast algorithm allows to make more permutations and + get more fine grained p-values, which allows to use accurate stantard + approaches to multiple hypothesis correction.""" + + homepage = "https://bioconductor.org/packages/fgsea" git = "https://git.bioconductor.org/packages/fgsea.git" + version('1.10.1', commit='fb06a6ebfb4a195e77e37226d100a2148b90c5f3') + version('1.8.0', commit='bb2898aca9fb23e90770671a83fe23f79bb1841b') + version('1.6.0', commit='52b801b7c2dfd8238fa8f2b402fddb4fda60271d') + version('1.4.1', commit='73de5ff364e520ac99507a9ee5a61a0d23d3c44e') version('1.2.1', commit='99b04eef664204d0dca4b9f8027cd7eefb006b72') - depends_on('r@3.4.0:3.4.9', when='@1.2.1') - depends_on('r-fastmatch', type=('build', 'run')) - depends_on('r-gridextra', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-biocparallel', type=('build', 'run')) - depends_on('r-data-table', type=('build', 'run')) + depends_on('r@3.3:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-data-table', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) + depends_on('r-gridextra', type=('build', 'run')) + depends_on('r-fastmatch', type=('build', 'run')) + + depends_on('r-matrix', when='@1.6.0:', type=('build', 'run')) + + depends_on('r-bh', when='@1.10.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fields/package.py b/var/spack/repos/builtin/packages/r-fields/package.py new file mode 100644 index 0000000000..9d1aae306a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fields/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RFields(RPackage): + """fields: Tools for Spatial Data""" + + homepage = "https://github.com/NCAR/Fields" + url = "https://cloud.r-project.org/src/contrib/fields_9.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fields" + + version('9.9', sha256='262f03c630773b580c7162ab2a031c894ca489fd83989fd8a2f67573306e78e1') + + depends_on('r@3.0:', type=('build', 'run')) + depends_on('r-maps', type=('build', 'run')) + depends_on('r-spam', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py index f2684c872e..5a5c60a782 100644 --- a/var/spack/repos/builtin/packages/r-filehash/package.py +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-findpython/package.py b/var/spack/repos/builtin/packages/r-findpython/package.py index acfc903c33..c6e0754c3c 100644 --- a/var/spack/repos/builtin/packages/r-findpython/package.py +++ b/var/spack/repos/builtin/packages/r-findpython/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-fit-models/package.py b/var/spack/repos/builtin/packages/r-fit-models/package.py index 0cda9e2efc..c7809293a6 100644 --- a/var/spack/repos/builtin/packages/r-fit-models/package.py +++ b/var/spack/repos/builtin/packages/r-fit-models/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-fitdistrplus/package.py b/var/spack/repos/builtin/packages/r-fitdistrplus/package.py index 7a0cdfb107..bef9620500 100644 --- a/var/spack/repos/builtin/packages/r-fitdistrplus/package.py +++ b/var/spack/repos/builtin/packages/r-fitdistrplus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-flashclust/package.py b/var/spack/repos/builtin/packages/r-flashclust/package.py index bf4ef4ffb0..091175742e 100644 --- a/var/spack/repos/builtin/packages/r-flashclust/package.py +++ b/var/spack/repos/builtin/packages/r-flashclust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-flexclust/package.py b/var/spack/repos/builtin/packages/r-flexclust/package.py index 6253dc2701..df2e3bc286 100644 --- a/var/spack/repos/builtin/packages/r-flexclust/package.py +++ b/var/spack/repos/builtin/packages/r-flexclust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-flexmix/package.py b/var/spack/repos/builtin/packages/r-flexmix/package.py index 989ee3ccd1..8cced441c5 100644 --- a/var/spack/repos/builtin/packages/r-flexmix/package.py +++ b/var/spack/repos/builtin/packages/r-flexmix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-fnn/package.py b/var/spack/repos/builtin/packages/r-fnn/package.py index 8da9b999d3..b41b878476 100644 --- a/var/spack/repos/builtin/packages/r-fnn/package.py +++ b/var/spack/repos/builtin/packages/r-fnn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-forcats/package.py b/var/spack/repos/builtin/packages/r-forcats/package.py index 176288c679..f9d2b3858c 100644 --- a/var/spack/repos/builtin/packages/r-forcats/package.py +++ b/var/spack/repos/builtin/packages/r-forcats/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py index f9322f2ea7..d87d126173 100644 --- a/var/spack/repos/builtin/packages/r-foreach/package.py +++ b/var/spack/repos/builtin/packages/r-foreach/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-forecast/package.py b/var/spack/repos/builtin/packages/r-forecast/package.py index 9fac86177a..7b51195eb2 100644 --- a/var/spack/repos/builtin/packages/r-forecast/package.py +++ b/var/spack/repos/builtin/packages/r-forecast/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-foreign/package.py b/var/spack/repos/builtin/packages/r-foreign/package.py index 3ee2e55fbc..a7f322cfc0 100644 --- a/var/spack/repos/builtin/packages/r-foreign/package.py +++ b/var/spack/repos/builtin/packages/r-foreign/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py index 024d5d1ad4..2286379cfb 100644 --- a/var/spack/repos/builtin/packages/r-formatr/package.py +++ b/var/spack/repos/builtin/packages/r-formatr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-formula/package.py b/var/spack/repos/builtin/packages/r-formula/package.py index 7e963e82e2..575a11f0ab 100644 --- a/var/spack/repos/builtin/packages/r-formula/package.py +++ b/var/spack/repos/builtin/packages/r-formula/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-fpc/package.py b/var/spack/repos/builtin/packages/r-fpc/package.py index 9729437db9..adec9cd72b 100644 --- a/var/spack/repos/builtin/packages/r-fpc/package.py +++ b/var/spack/repos/builtin/packages/r-fpc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-fracdiff/package.py b/var/spack/repos/builtin/packages/r-fracdiff/package.py index 0eec16d4e3..8353598e0e 100644 --- a/var/spack/repos/builtin/packages/r-fracdiff/package.py +++ b/var/spack/repos/builtin/packages/r-fracdiff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-fs/package.py b/var/spack/repos/builtin/packages/r-fs/package.py index 59d581838e..9f48c24270 100644 --- a/var/spack/repos/builtin/packages/r-fs/package.py +++ b/var/spack/repos/builtin/packages/r-fs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-futile-logger/package.py b/var/spack/repos/builtin/packages/r-futile-logger/package.py index 39030a14b1..0925af275f 100644 --- a/var/spack/repos/builtin/packages/r-futile-logger/package.py +++ b/var/spack/repos/builtin/packages/r-futile-logger/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-futile-options/package.py b/var/spack/repos/builtin/packages/r-futile-options/package.py index 1c9554f5a4..feca56c4ae 100644 --- a/var/spack/repos/builtin/packages/r-futile-options/package.py +++ b/var/spack/repos/builtin/packages/r-futile-options/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-future-apply/package.py b/var/spack/repos/builtin/packages/r-future-apply/package.py index a0fd59e473..025d406ff5 100644 --- a/var/spack/repos/builtin/packages/r-future-apply/package.py +++ b/var/spack/repos/builtin/packages/r-future-apply/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-future/package.py b/var/spack/repos/builtin/packages/r-future/package.py index d3778bb2c2..a8214cd9ea 100644 --- a/var/spack/repos/builtin/packages/r-future/package.py +++ b/var/spack/repos/builtin/packages/r-future/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gamlss-data/package.py b/var/spack/repos/builtin/packages/r-gamlss-data/package.py index 25b9fde1a5..2cfe4008f5 100644 --- a/var/spack/repos/builtin/packages/r-gamlss-data/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss-data/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gamlss-dist/package.py b/var/spack/repos/builtin/packages/r-gamlss-dist/package.py index 107dacdea6..49a2e5fc56 100644 --- a/var/spack/repos/builtin/packages/r-gamlss-dist/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss-dist/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gamlss/package.py b/var/spack/repos/builtin/packages/r-gamlss/package.py index 0215a7fc19..fbec727878 100644 --- a/var/spack/repos/builtin/packages/r-gamlss/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gbm/package.py b/var/spack/repos/builtin/packages/r-gbm/package.py index 61887664dc..079e4aed67 100644 --- a/var/spack/repos/builtin/packages/r-gbm/package.py +++ b/var/spack/repos/builtin/packages/r-gbm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gbrd/package.py b/var/spack/repos/builtin/packages/r-gbrd/package.py index 0dfe6081db..5f6b9c55c1 100644 --- a/var/spack/repos/builtin/packages/r-gbrd/package.py +++ b/var/spack/repos/builtin/packages/r-gbrd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gcrma/package.py b/var/spack/repos/builtin/packages/r-gcrma/package.py index 2a78008960..f37c63dc68 100644 --- a/var/spack/repos/builtin/packages/r-gcrma/package.py +++ b/var/spack/repos/builtin/packages/r-gcrma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,23 @@ from spack import * class RGcrma(RPackage): - """Background adjustment using sequence information""" + """Background Adjustment Using Sequence Information.""" - homepage = "https://bioconductor.org/packages/gcrma/" + homepage = "https://bioconductor.org/packages/gcrma" git = "https://git.bioconductor.org/packages/gcrma.git" + version('2.56.0', commit='1f37bbfb4d3ed542b1e90704ab0fa8914d5e0224') + version('2.54.0', commit='9515fdbbc766a2a3b2ec61cf530c57bbded77ccc') + version('2.52.0', commit='d6e90b05432d2a8b0583d3fed001811ecdf49d7d') + version('2.50.0', commit='cbba460d131e1073059500b8d7b168a78f963992') version('2.48.0', commit='3ea0eb0b5c15ffb24df76620667ae7996ed715b4') - depends_on('r-affy', type=('build', 'run')) + depends_on('r@2.6.0:', type=('build', 'run')) + depends_on('r-affy@1.23.2:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-affyio', type=('build', 'run')) + depends_on('r-affyio@1.13.3:', type=('build', 'run')) depends_on('r-xvector', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-biostrings@2.11.32:', type=('build', 'run')) depends_on('r-biocinstaller', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.48.0') + + depends_on('r-biocmanager', when='@2.54.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gdalutils/package.py b/var/spack/repos/builtin/packages/r-gdalutils/package.py index 96f5e2f59b..7488b2813d 100644 --- a/var/spack/repos/builtin/packages/r-gdalutils/package.py +++ b/var/spack/repos/builtin/packages/r-gdalutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py index bc4d2441f1..5750daf212 100644 --- a/var/spack/repos/builtin/packages/r-gdata/package.py +++ b/var/spack/repos/builtin/packages/r-gdata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py index 960f98f1f4..3bf613dda2 100644 --- a/var/spack/repos/builtin/packages/r-gdsfmt/package.py +++ b/var/spack/repos/builtin/packages/r-gdsfmt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,22 +7,28 @@ from spack import * class RGdsfmt(RPackage): - """This package provides a high-level R interface to CoreArray Genomic - Data Structure (GDS) data files, which are portable across platforms - with hierarchical structure to store multiple scalable array-oriented - data sets with metadata information. It is suited for large-scale - datasets, especially for data which are much larger than the available - random-access memory. The gdsfmt package offers the efficient - operations specifically designed for integers of less than 8 bits, - since a diploid genotype, like single-nucleotide polymorphism (SNP), - usually occupies fewer bits than a byte. Data compression and - decompression are available with relatively efficient random access. - It is also allowed to read a GDS file in parallel with multiple R - processes supported by the package parallel.""" + """R Interface to CoreArray Genomic Data Structure (GDS) Files. - homepage = "http://bioconductor.org/packages/gdsfmt/" + This package provides a high-level R interface to CoreArray Genomic Data + Structure (GDS) data files, which are portable across platforms with + hierarchical structure to store multiple scalable array-oriented data + sets with metadata information. It is suited for large-scale datasets, + especially for data which are much larger than the available random- + access memory. The gdsfmt package offers the efficient operations + specifically designed for integers of less than 8 bits, since a diploid + genotype, like single-nucleotide polymorphism (SNP), usually occupies + fewer bits than a byte. Data compression and decompression are available + with relatively efficient random access. It is also allowed to read a + GDS file in parallel with multiple R processes supported by the package + parallel.""" + + homepage = "https://bioconductor.org/packages/gdsfmt" git = "https://git.bioconductor.org/packages/gdsfmt.git" + version('1.20.0', commit='b1fbaba0a5ace3dc45daecc85168651cd85dce00') + version('1.18.1', commit='b911b953e9db7988e93ec2010b0ab1e384d073c9') + version('1.16.0', commit='49b011452585e432b983b68466a230c9b71d8a95') version('1.14.1', commit='15743647b7eea5b82d3284858b4591fb6e59959d') + version('1.12.0', commit='d705a95b0bea7be2a2b37e939f45017337ba0fb6') - depends_on('r@3.4.0:3.4.9', when='@1.14.1') + depends_on('r@2.15.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geiger/package.py b/var/spack/repos/builtin/packages/r-geiger/package.py index 92ef12322b..fb5aa1b76c 100644 --- a/var/spack/repos/builtin/packages/r-geiger/package.py +++ b/var/spack/repos/builtin/packages/r-geiger/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py index 73eebbd357..3be80d3bae 100644 --- a/var/spack/repos/builtin/packages/r-genefilter/package.py +++ b/var/spack/repos/builtin/packages/r-genefilter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,20 @@ from spack import * class RGenefilter(RPackage): - """Some basic functions for filtering genes""" + """genefilter: methods for filtering genes from high-throughput + experiments.""" - homepage = "https://bioconductor.org/packages/genefilter/" + homepage = "https://bioconductor.org/packages/genefilter" git = "https://git.bioconductor.org/packages/genefilter.git" + version('1.66.0', commit='1c4c471ccca873bf92dcf0b50f611eaa64c4f0cf') + version('1.64.0', commit='82e91b7751bae997b9c898c219ea201fd02a8512') version('1.62.0', commit='eb119894f015c759f93f458af7733bdb770a22ad') + version('1.60.0', commit='c98f695253c330a9380b2b4ffa27f3b7d66773e4') version('1.58.1', commit='ace2556049677f60882adfe91f8cc96791556fc2') - depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-s4vectors@0.9.42:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-annotate', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.58.1', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.62.0', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genelendatabase/package.py b/var/spack/repos/builtin/packages/r-genelendatabase/package.py index e569d285c2..44559a0ff6 100644 --- a/var/spack/repos/builtin/packages/r-genelendatabase/package.py +++ b/var/spack/repos/builtin/packages/r-genelendatabase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,14 +7,20 @@ from spack import * class RGenelendatabase(RPackage): - """Length of mRNA transcripts for a number of genomes and gene ID - formats, largely based on UCSC table browser""" + """Lengths of mRNA transcripts for a number of genomes. - homepage = "https://bioconductor.org/packages/release/data/experiment/html/geneLenDataBase.html" + Length of mRNA transcripts for a number of genomes and gene ID formats, + largely based on UCSC table browser""" + + homepage = "https://bioconductor.org/packages/geneLenDataBase" git = "https://git.bioconductor.org/packages/geneLenDataBase.git" + version('1.20.0', commit='70a1abed00ee68f7bfa07c42c011f9edae9915e4') + version('1.18.0', commit='77db87e5a4819bf94761fabef0d2ff741a1c5d07') version('1.16.0', commit='c2a8b2359c6c59388853d6f6d15d71dffb17a198') + version('1.14.0', commit='b456b3ffb04eaf335893fdec2bb10f6795dd7e08') + version('1.12.0', commit='85d6536763c12850e6c01da9e2f9e0b9c07601fe') - depends_on('r@3.5.0:3.5.9', when='@1.16.0:', type=('build', 'run')) + depends_on('r@2.11.0:', type=('build', 'run')) depends_on('r-rtracklayer', type=('build', 'run')) depends_on('r-genomicfeatures@1.3.15:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genemeta/package.py b/var/spack/repos/builtin/packages/r-genemeta/package.py new file mode 100644 index 0000000000..b8eb41c46b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-genemeta/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGenemeta(RPackage): + """MetaAnalysis for High Throughput Experiments. + + A collection of meta-analysis tools for analysing high throughput + experimental data""" + + homepage = "https://bioconductor.org/packages/GeneMeta" + git = "https://git.bioconductor.org/packages/GeneMeta.git" + + version('1.56.0', commit='cb2c9e353d34ea9f3db06cb236c7a89674f2682d') + version('1.54.0', commit='932553cd8df82b7df804fccda9bfd4b0f36d79d7') + version('1.52.0', commit='1f21759984a5852c42a19e89ee53ffd72053d49c') + version('1.50.0', commit='0f8603653285698ed451fcbf536a4b3f90015f92') + version('1.48.0', commit='68c65304d37f5a4722cf4c25afb23214c3a2f4c8') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-biobase@2.5.5:', type=('build', 'run')) + depends_on('r-genefilter', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geneplotter/package.py b/var/spack/repos/builtin/packages/r-geneplotter/package.py index d1794933df..460dc46b0d 100644 --- a/var/spack/repos/builtin/packages/r-geneplotter/package.py +++ b/var/spack/repos/builtin/packages/r-geneplotter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,19 +7,21 @@ from spack import * class RGeneplotter(RPackage): - """Functions for plotting genomic data.""" + """Graphics related functions for Bioconductor.""" - homepage = "https://www.bioconductor.org/packages/geneplotter/" + homepage = "https://bioconductor.org/packages/geneplotter" git = "https://git.bioconductor.org/packages/geneplotter.git" + version('1.62.0', commit='1fbaddde11014b453b131860409f89cd784e8e48') + version('1.60.0', commit='6723a9fc0730e146187e79c2ddab6a68186dc5ad') version('1.58.0', commit='2b3f44804d61a40cfe7eaedf74ac9f5a054f7fde') + version('1.56.0', commit='881d25aece3dc00cc4280457ffecdc25e93bb1f1') version('1.54.0', commit='efdd946e092e44e35fde1eb4bcc5ec1d52090940') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-annotate', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.54.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.58.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-generics/package.py b/var/spack/repos/builtin/packages/r-generics/package.py index 0b9e1f681e..6886d22757 100644 --- a/var/spack/repos/builtin/packages/r-generics/package.py +++ b/var/spack/repos/builtin/packages/r-generics/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-genetics/package.py b/var/spack/repos/builtin/packages/r-genetics/package.py new file mode 100644 index 0000000000..1ef79e4ea0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-genetics/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGenetics(RPackage): + """genetics: Population Genetics""" + + homepage = "https://cloud.r-project.org/package=genetics" + url = "https://cloud.r-project.org/src/contrib/genetics_1.3.8.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/genetics" + + version('1.3.8.1.2', sha256='30cb67de2e901578fd802deb7fbfea6c93024c9fb6ea66cad88430a3a2a51eec') + + depends_on('r-combinat', type=('build', 'run')) + depends_on('r-gdata', type=('build', 'run')) + depends_on('r-gtools', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-mvtnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genie3/package.py b/var/spack/repos/builtin/packages/r-genie3/package.py index b86edd6c00..14e7abf982 100644 --- a/var/spack/repos/builtin/packages/r-genie3/package.py +++ b/var/spack/repos/builtin/packages/r-genie3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,17 @@ from spack import * class RGenie3(RPackage): - """This package implements the GENIE3 algorithm for inferring gene - regulatory networks from expression data.""" + """GEne Network Inference with Ensemble of trees. - homepage = "https://bioconductor.org/packages/GENIE3/" + This package implements the GENIE3 algorithm for inferring gene + regulatory networks from expression data.""" + + homepage = "https://bioconductor.org/packages/GENIE3" git = "https://git.bioconductor.org/packages/GENIE3.git" - version('1.2.0', commit='cafe6a1a85095cda6cc3c812eb6f53501fcbaf93') + version('1.6.0', commit='d6a49182e098342afe77f01c322dfc7b72450502') + version('1.4.3', commit='ae719c759f23f09d28fcf1acc45b860cd7761f08') + version('1.2.1', commit='1b56fe8184d521d1bb247f000efe9e2b540604c9') + version('1.0.0', commit='eb7c95ed12ea50d61e8fa20bc2b25ae9d74c302f') depends_on('r-reshape2', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.2.0') diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py index bbf6bf0609..dc4b314142 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,25 +7,29 @@ from spack import * class RGenomeinfodb(RPackage): - """Contains data and functions that define and allow translation between - different chromosome sequence naming conventions (e.g., "chr1" - versus "1"), including a function that attempts to place sequence - names in their natural, rather than lexicographic, order.""" + """Utilities for manipulating chromosome names, including modifying them to + follow a particular naming style. - homepage = "https://bioconductor.org/packages/GenomeInfoDb/" + Contains data and functions that define and allow translation between + different chromosome sequence naming conventions (e.g., "chr1" versus + "1"), including a function that attempts to place sequence names in + their natural, rather than lexicographic, order.""" + + homepage = "https://bioconductor.org/packages/GenomeInfoDb" git = "https://git.bioconductor.org/packages/GenomeInfoDb.git" + version('1.20.0', commit='ea771e3b429ef17fb912fb37333556c6f77f2265') + version('1.18.2', commit='557b75ea7734749a2650d30f5c5d52c57a6bcc6f') version('1.16.0', commit='6543dad89bbc2c275010b329eb114b237fd712fa') version('1.14.0', commit='4978308a57d887b764cc4ce83724ca1758f580f6') version('1.12.3', commit='2deef3f0571b7f622483257bc22d2509ab5a0369') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.13.8:', when='@1.16.0', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.25:', when='@1.16.0', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.12:', when='@1.16.0', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-iranges@1.99.26:', type=('build', 'run')) depends_on('r-rcurl', type=('build', 'run')) depends_on('r-genomeinfodbdata', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.12.3', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.16.0', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.25:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.16.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py index ea436ffaef..93d621e2dc 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,8 +13,11 @@ class RGenomeinfodbdata(RPackage): homepage = "https://bioconductor.org/packages/GenomeInfoDbData/" url = "https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz" + version('1.2.1', sha256='75e6d683a29b8baeec66ba5194aa59a6aa69b04fae5a9c718a105c155fb41711', + url='https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz') version('1.1.0', sha256='6efdca22839c90d455843bdab7c0ecb5d48e3b6c2f7b4882d3210a6bbad4304c', url='https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz') version('0.99.0', sha256='457049804bbd70f218c1c84067a23e83bdecb7304a3e4d8b697fee0b16dc1888') - depends_on('r@3.4.0:3.4.9', when='@0.99.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.1.0', type=('build', 'run')) + + depends_on('r@3.3:', when='@0.99.0:1.1.0', type=('build', 'run')) + depends_on('r@3.5:', when='@1.2.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py index 3ffe5c5cf7..99292cd505 100644 --- a/var/spack/repos/builtin/packages/r-genomicalignments/package.py +++ b/var/spack/repos/builtin/packages/r-genomicalignments/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,35 +7,44 @@ from spack import * class RGenomicalignments(RPackage): - """Provides efficient containers for storing and manipulating short genomic - alignments (typically obtained by aligning short reads to a reference - genome). This includes read counting, computing the coverage, junction - detection, and working with the nucleotide content of the alignments.""" + """Representation and manipulation of short genomic alignments. - homepage = "https://bioconductor.org/packages/GenomicAlignments/" + Provides efficient containers for storing and manipulating short genomic + alignments (typically obtained by aligning short reads to a reference + genome). This includes read counting, computing the coverage, junction + detection, and working with the nucleotide content of the alignments.""" + + homepage = "https://bioconductor.org/packages/GenomicAlignments" git = "https://git.bioconductor.org/packages/GenomicAlignments.git" + version('1.20.1', commit='9dce402071e4cd945de7ff82ea574c79993625fd') + version('1.18.1', commit='8ac41e5981cf343076044f451a984afb651688ab') version('1.16.0', commit='db032a459e5cf05a2a5c2059662a541827112974') version('1.14.2', commit='57b0b35d8b36069d4d94af86af051f0129b28eef') version('1.12.2', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biocgenerics@0.15.3:', type=('build', 'run')) depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) - depends_on('r-s4vectors@0.17.28:', when='@1.16.0', type=('build', 'run')) - depends_on('r-iranges@2.5.36:', when='@1.12.2', type=('build', 'run')) - depends_on('r-iranges@2.11.16:', when='@1.14.2', type=('build', 'run')) - depends_on('r-iranges@2.13.25:', when='@1.16.0', type=('build', 'run')) - depends_on('r-genomeinfodb@1.11.5:', when='@1.12.2', type=('build', 'run')) - depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run')) - depends_on('r-genomicranges@1.27.19:', when='@1.12.2', type=('build', 'run')) - depends_on('r-genomicranges@1.29.14:', when='@1.14.2', type=('build', 'run')) - depends_on('r-genomicranges@1.31.19:', when='@1.16.0', type=('build', 'run')) + depends_on('r-iranges@2.5.36:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.19:', type=('build', 'run')) depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run')) - depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0', type=('build', 'run')) depends_on('r-biostrings@2.37.1:', type=('build', 'run')) - depends_on('r-biostrings@2.47.6:', when='@1.16.0', type=('build', 'run')) depends_on('r-rsamtools@1.21.4:', type=('build', 'run')) - depends_on('r-rsamtools@1.31.2:', when='@1.16.0', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.12.2:1.15.9', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.16.0', type=('build', 'run')) + + depends_on('r-iranges@2.11.16:', when='@1.14.2:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run')) + depends_on('r-genomicranges@1.29.14:', when='@1.14.2:', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.28:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.25:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.19:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.16.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.19.11:', when='@1.18.1:', type=('build', 'run')) + depends_on('r-iranges@2.15.12:', when='@1.18.1:', type=('build', 'run')) + depends_on('r-genomicranges@1.33.4:', when='@1.18.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py index 48015bbebd..b232e467f9 100644 --- a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py +++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,7 +7,9 @@ from spack import * class RGenomicfeatures(RPackage): - """A set of tools and methods for making and manipulating transcript + """Conveniently import and query gene models. + + A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources @@ -16,35 +18,40 @@ class RGenomicfeatures(RPackage): exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.""" - homepage = "http://bioconductor.org/packages/GenomicFeatures/" + homepage = "https://bioconductor.org/packages/GenomicFeatures" git = "https://git.bioconductor.org/packages/GenomicFeatures.git" - version('1.32.2', commit='8487aedc8be85a99f0c3fc90cd62430b3fec3a03') + version('1.36.4', commit='28082ec465c91ccaec6881ff348b380edac1b555') + version('1.34.8', commit='c798b3bb111f4de30632303540074ec1875c1387') + version('1.32.3', commit='80807d88048858846de3750cecb9431a0e5e69e1') + version('1.30.3', commit='496bbf81beebd7c934b8d3dcea001e3e4a7d7dee') version('1.28.5', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.29:', when='@1.32.2', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.23:', when='@1.32.2', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomeinfodb@1.15.4:', when='@1.32.2', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-genomicranges@1.31.17:', when='@1.32.2', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-annotationdbi@1.41.4:', when='@1.32.2', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.9.47:', type=('build', 'run')) + depends_on('r-iranges@2.9.19:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.6:', type=('build', 'run')) + depends_on('r-annotationdbi@1.33.15:', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) - depends_on('r-rsqlite@2.0:', when='@1.28.5:', type=('build', 'run')) + depends_on('r-rsqlite@2.0:', type=('build', 'run')) depends_on('r-rcurl', type=('build', 'run')) depends_on('r-xvector', type=('build', 'run')) - depends_on('r-xvector@0.19.7:', when='@1.32.2', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-biostrings@2.47.6:', when='@1.32.2', type=('build', 'run')) - depends_on('r-rtracklayer', type=('build', 'run')) - depends_on('r-rtracklayer@1.39.7:', when='@1.32.2', type=('build', 'run')) - depends_on('r-biomart', type=('build', 'run')) - depends_on('r-biomart@2.17.1:', when='@1.32.2', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-biobase@2.15.1:', when='@1.32.2', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.28.5', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.32.2', type=('build', 'run')) + depends_on('r-biostrings@2.23.3:', type=('build', 'run')) + depends_on('r-rtracklayer@1.29.24:', type=('build', 'run')) + depends_on('r-biomart@2.17.1:', type=('build', 'run')) + depends_on('r-biobase@2.15.1:', type=('build', 'run')) + + depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.29.14:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-rmysql', when='@1.30.3', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.29:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-iranges@2.13.23:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.4:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.17:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-annotationdbi@1.41.4:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-rtracklayer@1.39.7:', when='@1.32.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py index 887d32f988..9ca2058064 100644 --- a/var/spack/repos/builtin/packages/r-genomicranges/package.py +++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,35 +7,45 @@ from spack import * class RGenomicranges(RPackage): - """The ability to efficiently represent and manipulate genomic annotations + """Representation and manipulation of genomic intervals. + + The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are - defined in the GenomicAlignments and SummarizedExperiment packages + defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.""" - homepage = "https://bioconductor.org/packages/GenomicRanges/" + homepage = "https://bioconductor.org/packages/GenomicRanges" git = "https://git.bioconductor.org/packages/GenomicRanges.git" - version('1.32.6', commit='31426be0fd6b76f7858971dc45aaf6e6d1dbac4e') + version('1.36.1', commit='418e7e5647dd54d81b804455ddfcbc027fd0164a') + version('1.34.0', commit='ebaad5ca61abb67c2c30c132e07531ba4257bccd') + version('1.32.7', commit='4c56dc836dbfd0d228dc810e8d401811cdbc267c') version('1.30.3', commit='e99979054bc50ed8c0109bc54563036c1b368997') version('1.28.6', commit='197472d618f3ed04c795dc6ed435500c29619563') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biocgenerics@0.21.2:', type=('build', 'run')) - depends_on('r-biocgenerics@0.25.3:', when='@1.32.6', type=('build', 'run')) depends_on('r-s4vectors@0.9.47:', type=('build', 'run')) - depends_on('r-s4vectors@0.17.32:', when='@1.32.6', type=('build', 'run')) - depends_on('r-iranges@2.9.11:', when='@1.28.6', type=('build', 'run')) - depends_on('r-iranges@2.11.16:', when='@1.30.3', type=('build', 'run')) - depends_on('r-iranges@2.14.4:', when='@1.32.6', type=('build', 'run')) - depends_on('r-genomeinfodb@1.11.5:', when='@1.28.6', type=('build', 'run')) - depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3', type=('build', 'run')) - depends_on('r-genomeinfodb@1.15.2:', when='@1.32.6', type=('build', 'run')) + depends_on('r-iranges@2.9.11:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run')) depends_on('r-xvector', type=('build', 'run')) - depends_on('r-xvector@0.19.8:', when='@1.32.6', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.28.6', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.32.6', type=('build', 'run')) + + depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.25.3:', when='@1.32.7:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.32:', when='@1.32.7:', type=('build', 'run')) + depends_on('r-iranges@2.14.4:', when='@1.32.7:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.32.7:', type=('build', 'run')) + depends_on('r-xvector@0.19.8:', when='@1.32.7:', type=('build', 'run')) + + depends_on('r-s4vectors@0.19.11:', when='@1.34.0:', type=('build', 'run')) + depends_on('r-iranges@2.15.12:', when='@1.34.0:', type=('build', 'run')) + + depends_on('r-iranges@2.17.1:', when='@1.36.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gensa/package.py b/var/spack/repos/builtin/packages/r-gensa/package.py index e93e9ce9cb..aa055f07df 100644 --- a/var/spack/repos/builtin/packages/r-gensa/package.py +++ b/var/spack/repos/builtin/packages/r-gensa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-geomorph/package.py b/var/spack/repos/builtin/packages/r-geomorph/package.py index 8d03f2d168..d0be730b65 100644 --- a/var/spack/repos/builtin/packages/r-geomorph/package.py +++ b/var/spack/repos/builtin/packages/r-geomorph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-geonames/package.py b/var/spack/repos/builtin/packages/r-geonames/package.py index c8de77d062..23b82a6b44 100644 --- a/var/spack/repos/builtin/packages/r-geonames/package.py +++ b/var/spack/repos/builtin/packages/r-geonames/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-geoquery/package.py b/var/spack/repos/builtin/packages/r-geoquery/package.py index e2451534a4..1a89aba6bb 100644 --- a/var/spack/repos/builtin/packages/r-geoquery/package.py +++ b/var/spack/repos/builtin/packages/r-geoquery/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,32 @@ from spack import * class RGeoquery(RPackage): - """The NCBI Gene Expression Omnibus (GEO) is a public repository of - microarray data. Given the rich and varied nature of this resource, - it is only natural to want to apply BioConductor tools to these data. + """Get data from NCBI Gene Expression Omnibus (GEO). + + The NCBI Gene Expression Omnibus (GEO) is a public repository of + microarray data. Given the rich and varied nature of this resource, it + is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.""" - homepage = "https://bioconductor.org/packages/GEOquery/" + homepage = "https://bioconductor.org/packages/GEOquery" git = "https://git.bioconductor.org/packages/GEOquery.git" + version('2.52.0', commit='3059331eb82ad4947c2d1bef86ff9526e70af643') + version('2.50.5', commit='135c17f8fe535acda14f95a37d1be1ff2bd80f97') + version('2.48.0', commit='6a8d1ca195b5c26fb717ae93beb1a8d9b7031c5e') + version('2.46.15', commit='a52b195ac640caae9679610d5b486b7cb828c0fd') version('2.42.0', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb') depends_on('r-biobase', type=('build', 'run')) - depends_on('r-xml', type=('build', 'run')) - depends_on('r-rcurl', type=('build', 'run')) + depends_on('r-xml', when='@2.42.0', type=('build', 'run')) + depends_on('r-rcurl', when='@2.42.0', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.42.0') + + depends_on('r-readr', when='@2.46.15:', type=('build', 'run')) + depends_on('r-xml2', when='@2.46.15:', type=('build', 'run')) + depends_on('r-dplyr', when='@2.46.15:', type=('build', 'run')) + depends_on('r-tidyr', when='@2.46.15:', type=('build', 'run')) + depends_on('r-magrittr', when='@2.46.15:', type=('build', 'run')) + depends_on('r-limma', when='@2.46.15:', type=('build', 'run')) + + depends_on('r-readr@1.3.1:', when='@2.50.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geor/package.py b/var/spack/repos/builtin/packages/r-geor/package.py index 91c6773e1d..5f1cface6d 100644 --- a/var/spack/repos/builtin/packages/r-geor/package.py +++ b/var/spack/repos/builtin/packages/r-geor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py index ceb3c891f0..afea256fd6 100644 --- a/var/spack/repos/builtin/packages/r-geosphere/package.py +++ b/var/spack/repos/builtin/packages/r-geosphere/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-getopt/package.py b/var/spack/repos/builtin/packages/r-getopt/package.py index 65e1c577ef..b8d7a9bf46 100644 --- a/var/spack/repos/builtin/packages/r-getopt/package.py +++ b/var/spack/repos/builtin/packages/r-getopt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-getoptlong/package.py b/var/spack/repos/builtin/packages/r-getoptlong/package.py index f16e100229..d732f50d08 100644 --- a/var/spack/repos/builtin/packages/r-getoptlong/package.py +++ b/var/spack/repos/builtin/packages/r-getoptlong/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggally/package.py b/var/spack/repos/builtin/packages/r-ggally/package.py index 8ebe105b75..1bcc024793 100644 --- a/var/spack/repos/builtin/packages/r-ggally/package.py +++ b/var/spack/repos/builtin/packages/r-ggally/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggbeeswarm/package.py b/var/spack/repos/builtin/packages/r-ggbeeswarm/package.py new file mode 100644 index 0000000000..22d8e8bd5e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggbeeswarm/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGgbeeswarm(RPackage): + """ggbeeswarm: Categorical Scatter (Violin Point) Plots""" + + homepage = "https://github.com/eclarke/ggbeeswarm" + url = "https://cloud.r-project.org/src/contrib/ggbeeswarm_0.6.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggbeeswarm" + + version('0.6.0', sha256='bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333') + + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-beeswarm', type=('build', 'run')) + depends_on('r-ggplot2@2.0:', type=('build', 'run')) + depends_on('r-vipor', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py index b4918a8a1f..2e52e4edf4 100644 --- a/var/spack/repos/builtin/packages/r-ggbio/package.py +++ b/var/spack/repos/builtin/packages/r-ggbio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,43 +7,59 @@ from spack import * class RGgbio(RPackage): - """The ggbio package extends and specializes the grammar of graphics for + """Visualization tools for genomic data. + + The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence - fragment length, edge-linked interval to data view, mismatch pileup, - and several splicing summaries.""" + fragment length, edge-linked interval to data view, mismatch pileup, and + several splicing summaries.""" - homepage = "http://bioconductor.org/packages/ggbio/" + homepage = "https://bioconductor.org/packages/ggbio" git = "https://git.bioconductor.org/packages/ggbio.git" + version('1.32.0', commit='04bd12fbe0b1c5c6b721a5f927e1352765f9bf88') + version('1.30.0', commit='8b05258b089b06a743352e92058edda06c24cfb7') + version('1.28.5', commit='594521ca556ef7d97cf4882ecfa54d22c2a2faba') + version('1.26.1', commit='b4f4c898c92aa1082aa7574f1e5c2a0dae943fbc') version('1.24.1', commit='ef04c1bca1330f37152bcc21080cbde94849a094') + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-ggplot2@1.0.0:', type=('build', 'run')) depends_on('r-gridextra', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) depends_on('r-gtable', type=('build', 'run')) depends_on('r-hmisc', type=('build', 'run')) - depends_on('r-biovizbase', type=('build', 'run')) + depends_on('r-biovizbase@1.23.3:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.21.10:', type=('build', 'run')) depends_on('r-summarizedexperiment', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) - depends_on('r-genomicalignments', type=('build', 'run')) + depends_on('r-rsamtools@1.17.28:', type=('build', 'run')) + depends_on('r-genomicalignments@1.1.16:', type=('build', 'run')) depends_on('r-bsgenome', type=('build', 'run')) - depends_on('r-variantannotation', type=('build', 'run')) - depends_on('r-rtracklayer', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) + depends_on('r-variantannotation@1.11.4:', type=('build', 'run')) + depends_on('r-rtracklayer@1.25.16:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.17.13:', type=('build', 'run')) depends_on('r-organismdbi', type=('build', 'run')) depends_on('r-ggally', type=('build', 'run')) - depends_on('r-ensembldb', type=('build', 'run')) + depends_on('r-ensembldb@1.99.13:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-annotationfilter', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.24.1') + + depends_on('r-iranges@2.11.16:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-genomicranges@1.29.14:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.29.11:', when='@1.26.1:', type=('build', 'run')) + + depends_on('r-biovizbase@1.28.2:', when='@1.28.5:', type=('build', 'run')) + depends_on('r-rlang', when='@1.28.5:', type=('build', 'run')) + + depends_on('r-biovizbase@1.29.2:', when='@1.30.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggdendro/package.py b/var/spack/repos/builtin/packages/r-ggdendro/package.py index 545fedcf2f..90b9b787e0 100644 --- a/var/spack/repos/builtin/packages/r-ggdendro/package.py +++ b/var/spack/repos/builtin/packages/r-ggdendro/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggforce/package.py b/var/spack/repos/builtin/packages/r-ggforce/package.py new file mode 100644 index 0000000000..d36d2dbead --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggforce/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGgforce(RPackage): + """ggforce: Accelerating 'ggplot2'""" + + homepage = "https://ggforce.data-imaginist.com" + url = "https://cloud.r-project.org/src/contrib/ggforce_0.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggforce" + + version('0.3.1', sha256='a05271da9b226c12ae5fe6bc6eddb9ad7bfe19e1737e2bfcd6d7a89631332211') + + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-ggplot2@3.0.0:', type=('build', 'run')) + depends_on('r-gtable', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-polyclip', type=('build', 'run')) + depends_on('r-rcpp@0.12.2:', type=('build', 'run')) + depends_on('r-rcppeigen', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run')) + depends_on('r-tidyselect', type=('build', 'run')) + depends_on('r-tweenr@0.1.5:', type=('build', 'run')) + depends_on('r-withr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggjoy/package.py b/var/spack/repos/builtin/packages/r-ggjoy/package.py index 6cab9a9cb6..1d5390f0aa 100644 --- a/var/spack/repos/builtin/packages/r-ggjoy/package.py +++ b/var/spack/repos/builtin/packages/r-ggjoy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py index 284d716fe2..fa44828b08 100644 --- a/var/spack/repos/builtin/packages/r-ggmap/package.py +++ b/var/spack/repos/builtin/packages/r-ggmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py index 7b2367abb6..4c44ac0468 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggplotify/package.py b/var/spack/repos/builtin/packages/r-ggplotify/package.py new file mode 100644 index 0000000000..f1ef249a66 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggplotify/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGgplotify(RPackage): + """ggplotify: Convert Plot to 'grob' or 'ggplot' Object""" + + homepage = "https://github.com/GuangchuangYu/ggplotify" + url = "https://cloud.r-project.org/src/contrib/ggplotify_0.0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggplotify" + + version('0.0.3', sha256='7e7953a2933aa7127a0bac54375e3e0219a0744cfc3249c3d7b76065f7a51892') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-gridgraphics', type=('build', 'run')) + depends_on('r-rvcheck', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggpubr/package.py b/var/spack/repos/builtin/packages/r-ggpubr/package.py index 16c4be4ffe..a746f292b3 100644 --- a/var/spack/repos/builtin/packages/r-ggpubr/package.py +++ b/var/spack/repos/builtin/packages/r-ggpubr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggraph/package.py b/var/spack/repos/builtin/packages/r-ggraph/package.py new file mode 100644 index 0000000000..c4cbed3c91 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggraph/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGgraph(RPackage): + """ggraph: An Implementation of Grammar of Graphics for Graphs and + Networks""" + + homepage = "https://github.com/thomasp85/ggraph" + url = "https://cloud.r-project.org/src/contrib/ggraph_2.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggraph" + + version('2.0.0', sha256='4307efe85bfc6a0496797f6b86d6b174ba196538c51b1a6b6af55de0d4e04762') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-ggplot2@3.0.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.2', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-ggforce@0.3.1:', type=('build', 'run')) + depends_on('r-igraph@1.0.0:', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run')) + depends_on('r-gtable', type=('build', 'run')) + depends_on('r-ggrepel', type=('build', 'run')) + depends_on('r-viridis', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-tidygraph', type=('build', 'run')) + depends_on('r-graphlayouts@0.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggrepel/package.py b/var/spack/repos/builtin/packages/r-ggrepel/package.py index e694e6bb5d..affb69a321 100644 --- a/var/spack/repos/builtin/packages/r-ggrepel/package.py +++ b/var/spack/repos/builtin/packages/r-ggrepel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggridges/package.py b/var/spack/repos/builtin/packages/r-ggridges/package.py index 2451b2348e..22fc773bbe 100644 --- a/var/spack/repos/builtin/packages/r-ggridges/package.py +++ b/var/spack/repos/builtin/packages/r-ggridges/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggsci/package.py b/var/spack/repos/builtin/packages/r-ggsci/package.py index 3ce84eae8b..f8dc21d11e 100644 --- a/var/spack/repos/builtin/packages/r-ggsci/package.py +++ b/var/spack/repos/builtin/packages/r-ggsci/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggsignif/package.py b/var/spack/repos/builtin/packages/r-ggsignif/package.py index 4a2e8cb544..142dd9e1ef 100644 --- a/var/spack/repos/builtin/packages/r-ggsignif/package.py +++ b/var/spack/repos/builtin/packages/r-ggsignif/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py index 54bdea87b3..53f26ba5ed 100644 --- a/var/spack/repos/builtin/packages/r-ggvis/package.py +++ b/var/spack/repos/builtin/packages/r-ggvis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gh/package.py b/var/spack/repos/builtin/packages/r-gh/package.py index 779e3e649e..5f63852ce6 100644 --- a/var/spack/repos/builtin/packages/r-gh/package.py +++ b/var/spack/repos/builtin/packages/r-gh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gistr/package.py b/var/spack/repos/builtin/packages/r-gistr/package.py index ce698fa368..b171fe1399 100644 --- a/var/spack/repos/builtin/packages/r-gistr/package.py +++ b/var/spack/repos/builtin/packages/r-gistr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py index 073cc54d3e..4f7613a21a 100644 --- a/var/spack/repos/builtin/packages/r-git2r/package.py +++ b/var/spack/repos/builtin/packages/r-git2r/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py index 3e943d719c..302afa62ae 100644 --- a/var/spack/repos/builtin/packages/r-glimma/package.py +++ b/var/spack/repos/builtin/packages/r-glimma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,28 @@ from spack import * class RGlimma(RPackage): - """This package generates interactive visualisations for analysis of - RNA-sequencing data using output from limma, edgeR or DESeq2 packages - in an HTML page. The interactions are built on top of the popular - static representations of analysis results in order to provide - additional information.""" + """Interactive HTML graphics. - homepage = "https://bioconductor.org/packages/release/bioc/html/Glimma.html" + This package generates interactive visualisations for analysis of RNA- + sequencing data using output from limma, edgeR or DESeq2 packages in an + HTML page. The interactions are built on top of the popular static + representations of analysis results in order to provide additional + information.""" + + homepage = "https://bioconductor.org/packages/Glimma" git = "https://git.bioconductor.org/packages/Glimma.git" - version('1.8.2', commit='f4aa1f05c2890d04b01ad4c0ab27f2f729f2c969') + version('1.12.0', commit='d02174239fe0b47983d6947ed42a1a53b24caecb') + version('1.10.1', commit='ffc7abc36190396598fadec5e9c653441e47be72') + version('1.8.2', commit='7696aca2c023f74d244b6c908a6e7ba52bfcb34b') + version('1.6.0', commit='57572996982806aa7ac155eedb97b03249979610') + version('1.4.0', commit='c613c5334ed7868f36d5716b97fdb6234fb291f8') - depends_on('r@3.5.0:3.5.9', when='@1.8.2:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-biobase', when='@1.4.0:1.6.0', type=('build', 'run')) depends_on('r-edger', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-scater', when='@1.4.0', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@1.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py index a198ca9bee..0df0d76583 100644 --- a/var/spack/repos/builtin/packages/r-glmnet/package.py +++ b/var/spack/repos/builtin/packages/r-glmnet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-globaloptions/package.py b/var/spack/repos/builtin/packages/r-globaloptions/package.py index e1ef617273..3f5b8d20e0 100644 --- a/var/spack/repos/builtin/packages/r-globaloptions/package.py +++ b/var/spack/repos/builtin/packages/r-globaloptions/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-globals/package.py b/var/spack/repos/builtin/packages/r-globals/package.py index cb3eaad818..12b2f974cb 100644 --- a/var/spack/repos/builtin/packages/r-globals/package.py +++ b/var/spack/repos/builtin/packages/r-globals/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-glue/package.py b/var/spack/repos/builtin/packages/r-glue/package.py index 3e547feeb2..b6489eedd7 100644 --- a/var/spack/repos/builtin/packages/r-glue/package.py +++ b/var/spack/repos/builtin/packages/r-glue/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gmodels/package.py b/var/spack/repos/builtin/packages/r-gmodels/package.py index 2655261ef2..c11d4b2e18 100644 --- a/var/spack/repos/builtin/packages/r-gmodels/package.py +++ b/var/spack/repos/builtin/packages/r-gmodels/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gmp/package.py b/var/spack/repos/builtin/packages/r-gmp/package.py index 9df781f8b5..871dea5847 100644 --- a/var/spack/repos/builtin/packages/r-gmp/package.py +++ b/var/spack/repos/builtin/packages/r-gmp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py index 4f0fc1057e..1a91053392 100644 --- a/var/spack/repos/builtin/packages/r-go-db/package.py +++ b/var/spack/repos/builtin/packages/r-go-db/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gofuncr/package.py b/var/spack/repos/builtin/packages/r-gofuncr/package.py new file mode 100644 index 0000000000..22fdb5745f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gofuncr/package.py @@ -0,0 +1,44 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGofuncr(RPackage): + """Gene ontology enrichment using FUNC. + + GOfuncR performs a gene ontology enrichment analysis based on the + ontology enrichment software FUNC. GO-annotations are obtained from + OrganismDb or OrgDb packages ('Homo.sapiens' by default); the GO-graph + is included in the package and updated regularly (27-Mar-2019). GOfuncR + provides the standard candidate vs. background enrichment analysis using + the hypergeometric test, as well as three additional tests: (i) the + Wilcoxon rank-sum test that is used when genes are ranked, (ii) a + binomial test that is used when genes are associated with two counts and + (iii) a Chi-square or Fisher's exact test that is used in cases when + genes are associated with four counts. To correct for multiple testing + and interdependency of the tests, family-wise error rates are computed + based on random permutations of the gene-associated variables. GOfuncR + also provides tools for exploring the ontology graph and the + annotations, and options to take gene-length or spatial clustering of + genes into account. It is also possible to provide custom gene + coordinates, annotations and ontologies.""" + + homepage = "https://bioconductor.org/packages/GOfuncR" + git = "https://git.bioconductor.org/packages/GOfuncR.git" + + version('1.4.0', commit='2f633dc28e3faeddc5346fcdcadf1c29e3fcf709') + version('1.2.0', commit='140a3cea4fe34d32fef9be756f85e337ce3deded') + version('1.0.0', commit='becd4ddde085c5477042adb856e7a4f40dbd648e') + + depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-vioplot@0.2:', type=('build', 'run')) + depends_on('r-rcpp@0.11.5:', type=('build', 'run')) + depends_on('r-mapplots@1.5:', type=('build', 'run')) + depends_on('r-gtools@3.5.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.28.4:', type=('build', 'run')) + depends_on('r-annotationdbi', type=('build', 'run')) + + depends_on('r-iranges', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py index 5f96163567..dc8f3659f6 100644 --- a/var/spack/repos/builtin/packages/r-googlevis/package.py +++ b/var/spack/repos/builtin/packages/r-googlevis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-goplot/package.py b/var/spack/repos/builtin/packages/r-goplot/package.py index fb94c72f3e..d748b99af6 100644 --- a/var/spack/repos/builtin/packages/r-goplot/package.py +++ b/var/spack/repos/builtin/packages/r-goplot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gosemsim/package.py b/var/spack/repos/builtin/packages/r-gosemsim/package.py index 0077bb011e..b7468c9c84 100644 --- a/var/spack/repos/builtin/packages/r-gosemsim/package.py +++ b/var/spack/repos/builtin/packages/r-gosemsim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,20 +7,28 @@ from spack import * class RGosemsim(RPackage): - """The semantic comparisons of Gene Ontology (GO) annotations provide - quantitative ways to compute similarities between genes and gene - groups, and have became important basis for many bioinformatics - analysis approaches. GOSemSim is an R package for semantic similarity - computation among GO terms, sets of GO terms, gene products and gene - clusters. GOSemSim implemented five methods proposed by Resnik, - Schlicker, Jiang, Lin and Wang respectively.""" - - homepage = "https://www.bioconductor.org/packages/GOSemSim/" + """GO-terms Semantic Similarity Measures. + + The semantic comparisons of Gene Ontology (GO) annotations provide + quantitative ways to compute similarities between genes and gene groups, + and have became important basis for many bioinformatics analysis + approaches. GOSemSim is an R package for semantic similarity computation + among GO terms, sets of GO terms, gene products and gene clusters. + GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, + Lin and Wang respectively.""" + + homepage = "https://bioconductor.org/packages/GOSemSim" git = "https://git.bioconductor.org/packages/GOSemSim.git" + version('2.10.0', commit='5db1ecbf2f8d870430d6e587609327d05ba3ad7b') + version('2.8.0', commit='c8c985b2a814cc2365c7f05b2509205e1b6b7f58') + version('2.6.2', commit='2ffe78e89276e804306554965fc0799318ec56ed') + version('2.4.1', commit='0656e845860d14e054670ffc246a1c53f699299c') version('2.2.0', commit='247434790e6c8cf99e5643f569390362b8c87c52') - depends_on('r@3.4.0:3.4.9', when='@2.2.0') + depends_on('r@3.3.2:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-go-db', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@2.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-goseq/package.py b/var/spack/repos/builtin/packages/r-goseq/package.py index 0a4aabeaf4..58f1c71711 100644 --- a/var/spack/repos/builtin/packages/r-goseq/package.py +++ b/var/spack/repos/builtin/packages/r-goseq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,15 +7,21 @@ from spack import * class RGoseq(RPackage): - """Detects Gene Ontology and/or other user defined categories which are + """Gene Ontology analyser for RNA-seq and other length biased data. + + Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data""" - homepage = "https://bioconductor.org/packages/release/bioc/html/goseq.html" + homepage = "https://bioconductor.org/packages/goseq" git = "https://git.bioconductor.org/packages/goseq.git" + version('1.36.0', commit='26c9f7de18889afeee1b571ca1c4ab4d2877ab80') + version('1.34.1', commit='bad217b42cc34423698fbcf701d4e3591aac4474') version('1.32.0', commit='32fcbe647eea17d7d0d7a262610811502c421d36') + version('1.30.0', commit='fa8cafe0766ed0b6a97a4ed3374a709ed9d1daf1') + version('1.28.0', commit='ed0ce332a8972618d740d8a93711dff994657738') - depends_on('r@3.5.0:3.5.9', when='@1.32.0:', type=('build', 'run')) + depends_on('r@2.11.0:', type=('build', 'run')) depends_on('r-biasedurn', type=('build', 'run')) depends_on('r-genelendatabase@1.9.2:', type=('build', 'run')) depends_on('r-mgcv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gostats/package.py b/var/spack/repos/builtin/packages/r-gostats/package.py index 1b61115882..46185bcc36 100644 --- a/var/spack/repos/builtin/packages/r-gostats/package.py +++ b/var/spack/repos/builtin/packages/r-gostats/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,21 +7,31 @@ from spack import * class RGostats(RPackage): - """A set of tools for interacting with GO and microarray data. - A variety of basic manipulation tools for graphs, hypothesis - testing and other simple calculations.""" + """Tools for manipulating GO and microarrays. - homepage = "https://www.bioconductor.org/packages/GOstats/" + A set of tools for interacting with GO and microarray data. A variety of + basic manipulation tools for graphs, hypothesis testing and other simple + calculations.""" + + homepage = "https://bioconductor.org/packages/GOstats" git = "https://git.bioconductor.org/packages/GOstats.git" + version('2.50.0', commit='ee13f84341988d537a5485dcdcfb71f69e6e4930') + version('2.48.0', commit='5db7020f4bab725cd729b32bd1d5e819b31f2485') + version('2.46.0', commit='489d7a437488f77c3010f6212f3b81f4e240cd17') + version('2.44.0', commit='fc64ca2aa37c52656d396d6e46611f39d6efd48a') version('2.42.0', commit='8b29709064a3b66cf1d963b2be0c996fb48c873e') - depends_on('r@3.4.1:3.4.9', when='@2.42.0') - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-category', type=('build', 'run')) - depends_on('r-go-db', type=('build', 'run')) - depends_on('r-graph', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-biobase@1.15.29:', type=('build', 'run')) + depends_on('r-category@2.3.26:', type=('build', 'run')) + depends_on('r-graph@1.15.15:', when='@2.42.0', type=('build', 'run')) + depends_on('r-annotationdbi@0.0.89:', type=('build', 'run')) + depends_on('r-go-db@1.13.0:', type=('build', 'run')) depends_on('r-rbgl', type=('build', 'run')) - depends_on('r-annotate', type=('build', 'run')) + depends_on('r-annotate@1.13.2:', type=('build', 'run')) depends_on('r-annotationforge', type=('build', 'run')) + + depends_on('r-category@2.43.2:', when='@2.44.0:', type=('build', 'run')) + depends_on('r-rgraphviz', when='@2.44.0:', type=('build', 'run')) + depends_on('r-graph', when='@2.44.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gower/package.py b/var/spack/repos/builtin/packages/r-gower/package.py index 72393b714b..bee0ec5ba3 100644 --- a/var/spack/repos/builtin/packages/r-gower/package.py +++ b/var/spack/repos/builtin/packages/r-gower/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gplots/package.py b/var/spack/repos/builtin/packages/r-gplots/package.py index 02b9b74b92..dd74ebd46b 100644 --- a/var/spack/repos/builtin/packages/r-gplots/package.py +++ b/var/spack/repos/builtin/packages/r-gplots/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-graph/package.py b/var/spack/repos/builtin/packages/r-graph/package.py index b962eb198e..057e27a4b2 100644 --- a/var/spack/repos/builtin/packages/r-graph/package.py +++ b/var/spack/repos/builtin/packages/r-graph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,12 +7,18 @@ from spack import * class RGraph(RPackage): - """A package that implements some simple graph handling capabilities.""" + """graph: A package to handle graph data structures. - homepage = "https://www.bioconductor.org/packages/graph/" + A package that implements some simple graph handling capabilities.""" + + homepage = "https://bioconductor.org/packages/graph" git = "https://git.bioconductor.org/packages/graph.git" + version('1.62.0', commit='95223bd63ceb66cfe8d881f992a441de8b8c89a3') + version('1.60.0', commit='e2aecb0a862f32091b16e0036f53367d3edf4c1d') + version('1.58.2', commit='6455d8e7a5a45dc733915942cb71005c1016b6a0') + version('1.56.0', commit='c4abe227dac525757679743e6fb4f49baa34acad') version('1.54.0', commit='2a8b08520096241620421078fc1098f4569c7301') - depends_on('r@2.10:', type=('build', 'run'), when='@1.54.0') - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.11:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-graphlayouts/package.py b/var/spack/repos/builtin/packages/r-graphlayouts/package.py new file mode 100644 index 0000000000..382ccc8077 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-graphlayouts/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGraphlayouts(RPackage): + """graphlayouts: Additional Layout Algorithms for Network Visualizations. + + Several new layout algorithms to visualize networks are provided which are + not part of 'igraph'. Most are based on the concept of stress majorization + by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>. Some more + specific algorithms allow to emphasize hidden group structures in networks + or focus on specific nodes.""" + + homepage = "https://github.com/schochastics/graphlayouts" + url = "https://cloud.r-project.org/src/contrib/graphlayouts_0.5.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/graphlayouts" + + version('0.5.0', sha256='83f61ce07580c5a64c7044c12b20d98ccf138c7e78ff12855cdfc206e1fab10d') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-igraph', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpparmadillo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-grbase/package.py b/var/spack/repos/builtin/packages/r-grbase/package.py index cb057aef3c..5d56958f23 100644 --- a/var/spack/repos/builtin/packages/r-grbase/package.py +++ b/var/spack/repos/builtin/packages/r-grbase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py index 972b2e782a..d32c6dd479 100644 --- a/var/spack/repos/builtin/packages/r-gridbase/package.py +++ b/var/spack/repos/builtin/packages/r-gridbase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py index c37978e0b1..36ce99c75c 100644 --- a/var/spack/repos/builtin/packages/r-gridextra/package.py +++ b/var/spack/repos/builtin/packages/r-gridextra/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gridgraphics/package.py b/var/spack/repos/builtin/packages/r-gridgraphics/package.py new file mode 100644 index 0000000000..7a0485d22d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gridgraphics/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGridgraphics(RPackage): + """gridGraphics: Redraw Base Graphics Using 'grid' Graphics""" + + homepage = "https://github.com/pmur002/gridgraphics" + url = "https://cloud.r-project.org/src/contrib/gridGraphics_0.4-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gridGraphics" + + version('0.4-1', sha256='b770127b71664bbf67f8853a2666c071f2b9920743eddc9f3a58ecb948b923cf') diff --git a/var/spack/repos/builtin/packages/r-gsa/package.py b/var/spack/repos/builtin/packages/r-gsa/package.py index aa27d7a228..34721c7fc3 100644 --- a/var/spack/repos/builtin/packages/r-gsa/package.py +++ b/var/spack/repos/builtin/packages/r-gsa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py index 946b97b9f7..631de6ca4a 100644 --- a/var/spack/repos/builtin/packages/r-gseabase/package.py +++ b/var/spack/repos/builtin/packages/r-gseabase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,24 @@ from spack import * class RGseabase(RPackage): - """This package provides classes and methods to support Gene - Set Enrichment Analysis (GSEA).""" + """Gene set enrichment data structures and methods. - homepage = "https://www.bioconductor.org/packages/GSEABase/" + This package provides classes and methods to support Gene Set Enrichment + Analysis (GSEA).""" + + homepage = "https://bioconductor.org/packages/GSEABase" git = "https://git.bioconductor.org/packages/GSEABase.git" + version('1.46.0', commit='edce83a9256a0c03206c2bce7c90ada0d90f6622') + version('1.44.0', commit='7042ff64a98b05b9572231ee1b4f3ae4fc9c768e') + version('1.42.0', commit='5e40ce0fdd4dc0cff7601b169bbf6aa1430ae33e') + version('1.40.1', commit='3e5441708b80aab2c9642988bee709d5732831a6') version('1.38.2', commit='84c9f10c316163118ca990900a7a67555b96e75b') - depends_on('r@3.4.0:3.4.9', when='@1.38.2') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-annotate', type=('build', 'run')) - depends_on('r-graph', type=('build', 'run')) + depends_on('r@2.6.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) + depends_on('r-biobase@2.17.8:', type=('build', 'run')) + depends_on('r-annotate@1.45.3:', type=('build', 'run')) + depends_on('r-graph@1.37.2:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gss/package.py b/var/spack/repos/builtin/packages/r-gss/package.py index 02db31e599..76858c9c26 100644 --- a/var/spack/repos/builtin/packages/r-gss/package.py +++ b/var/spack/repos/builtin/packages/r-gss/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gstat/package.py b/var/spack/repos/builtin/packages/r-gstat/package.py new file mode 100644 index 0000000000..5ef91125c1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gstat/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGstat(RPackage): + """gstat: Spatial and Spatio-Temporal Geostatistical Modelling, + Predictionand Simulation""" + + homepage = "https://github.com/r-spatial/gstat/" + url = "https://cloud.r-project.org/src/contrib/gstat_2.0-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gstat" + + version('2.0-3', sha256='20a93fe6bf89221a5888de273bddf9a98187806d507cd3cd6297c2b13e7acce1') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-fnn', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-sp@0.9-72:', type=('build', 'run')) + depends_on('r-spacetime@1.0-0:', type=('build', 'run')) + depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gsubfn/package.py b/var/spack/repos/builtin/packages/r-gsubfn/package.py index a12f2bc48d..080214e0d8 100644 --- a/var/spack/repos/builtin/packages/r-gsubfn/package.py +++ b/var/spack/repos/builtin/packages/r-gsubfn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py index faff7a9e07..a0a412eddb 100644 --- a/var/spack/repos/builtin/packages/r-gtable/package.py +++ b/var/spack/repos/builtin/packages/r-gtable/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py index 3f795ad1a2..905bb5dd1d 100644 --- a/var/spack/repos/builtin/packages/r-gtools/package.py +++ b/var/spack/repos/builtin/packages/r-gtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-gtrellis/package.py b/var/spack/repos/builtin/packages/r-gtrellis/package.py index 93ccdcaebb..88a7b84b33 100644 --- a/var/spack/repos/builtin/packages/r-gtrellis/package.py +++ b/var/spack/repos/builtin/packages/r-gtrellis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,20 +7,28 @@ from spack import * class RGtrellis(RPackage): - """Genome level Trellis graph visualizes genomic data conditioned by + """Genome Level Trellis Layout. + + Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.""" - homepage = "https://bioconductor.org/packages/gtrellis/" + homepage = "https://bioconductor.org/packages/gtrellis" git = "https://git.bioconductor.org/packages/gtrellis.git" + version('1.16.1', commit='a9003ededc8f2a48c78d4545e2f214023c13a7da') + version('1.14.0', commit='93935fb34211d12b250e22291712e18a31b0208d') + version('1.12.1', commit='7f3941adddbbfa17f4cf474b703568678a38272d') + version('1.11.1', commit='ff47d99743fd697d5c724f7bb18131dfe76dee71') version('1.8.0', commit='f813b420a008c459f63a2a13e5e64c5507c4c472') + depends_on('r@3.1.2:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-circlize', type=('build', 'run')) + depends_on('r-circlize@0.3.3:', type=('build', 'run')) depends_on('r-getoptlong', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.8.0') + + depends_on('r-circlize@0.4.8:', when='@1.16.1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gviz/package.py b/var/spack/repos/builtin/packages/r-gviz/package.py index e079e4015f..3047086747 100644 --- a/var/spack/repos/builtin/packages/r-gviz/package.py +++ b/var/spack/repos/builtin/packages/r-gviz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,38 +7,43 @@ from spack import * class RGviz(RPackage): - """Genomic data analyses requires integrated visualization - of known genomic information and new experimental data. Gviz - uses the biomaRt and the rtracklayer packages to perform live - annotation queries to Ensembl and UCSC and translates this to - e.g. gene/transcript structures in viewports of the grid - graphics package. This results in genomic information plotted - together with your data.""" + """Plotting data and annotation information along genomic coordinates. - homepage = "http://bioconductor.org/packages/Gviz/" + Genomic data analyses requires integrated visualization of known genomic + information and new experimental data. Gviz uses the biomaRt and the + rtracklayer packages to perform live annotation queries to Ensembl and + UCSC and translates this to e.g. gene/transcript structures in viewports + of the grid graphics package. This results in genomic information + plotted together with your data.""" + + homepage = "https://bioconductor.org/packages/Gviz" git = "https://git.bioconductor.org/packages/Gviz.git" + version('1.28.3', commit='20b9825af144cfc888629c34aa980b5bbd65bf86') + version('1.26.5', commit='430310b9d2e098f9757a71d26a2f69871071f30c') + version('1.24.0', commit='3ee1eec97a56653c07c434a97f82cfe3c4281841') + version('1.22.3', commit='2238079d0a7017c474f010acb35d98ee7cc1c5d1') version('1.20.0', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c') - depends_on('r@3.4.0:3.4.9', when='@1.20.0') - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-xvector', type=('build', 'run')) - depends_on('r-rtracklayer', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-iranges@1.99.18:', type=('build', 'run')) + depends_on('r-genomicranges@1.17.20:', type=('build', 'run')) + depends_on('r-xvector@0.5.7:', type=('build', 'run')) + depends_on('r-rtracklayer@1.25.13:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r-biomart', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) - depends_on('r-bsgenome', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-biovizbase', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) - depends_on('r-latticeextra', type=('build', 'run')) - depends_on('r-matrixstats', type=('build', 'run')) - depends_on('r-genomicalignments', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-digest', type=('build', 'run')) + depends_on('r-biomart@2.11.0:', type=('build', 'run')) + depends_on('r-annotationdbi@1.27.5:', type=('build', 'run')) + depends_on('r-biobase@2.15.3:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.17.22:', type=('build', 'run')) + depends_on('r-bsgenome@1.33.1:', type=('build', 'run')) + depends_on('r-biostrings@2.33.11:', type=('build', 'run')) + depends_on('r-biovizbase@1.13.8:', type=('build', 'run')) + depends_on('r-rsamtools@1.17.28:', type=('build', 'run')) + depends_on('r-latticeextra@0.6-26:', type=('build', 'run')) + depends_on('r-matrixstats@0.8.14:', type=('build', 'run')) + depends_on('r-genomicalignments@1.1.16:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run')) + depends_on('r-biocgenerics@0.11.3:', type=('build', 'run')) + depends_on('r-digest@0.6.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gwmodel/package.py b/var/spack/repos/builtin/packages/r-gwmodel/package.py index 08e1cb9c1b..e1577f8f61 100644 --- a/var/spack/repos/builtin/packages/r-gwmodel/package.py +++ b/var/spack/repos/builtin/packages/r-gwmodel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-haven/package.py b/var/spack/repos/builtin/packages/r-haven/package.py index 64b626cbaf..05c1bf2e65 100644 --- a/var/spack/repos/builtin/packages/r-haven/package.py +++ b/var/spack/repos/builtin/packages/r-haven/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-hdf5array/package.py b/var/spack/repos/builtin/packages/r-hdf5array/package.py new file mode 100644 index 0000000000..0a7ed13742 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-hdf5array/package.py @@ -0,0 +1,49 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RHdf5array(RPackage): + """HDF5 backend for DelayedArray objects. + + Implements the HDF5Array and TENxMatrix classes, 2 convenient and + memory-efficient array-like containers for on-disk representation of + HDF5 datasets. HDF5Array is for datasets that use the conventional (i.e. + dense) HDF5 representation. TENxMatrix is for datasets that use the + HDF5-based sparse matrix representation from 10x Genomics (e.g. the 1.3 + Million Brain Cell Dataset). Both containers being DelayedArray + extensions, they support all operations supported by DelayedArray + objects. These operations can be either delayed or block-processed.""" + + homepage = "https://bioconductor.org/packages/HDF5Array" + git = "https://git.bioconductor.org/packages/HDF5Array.git" + + version('1.12.3', commit='21c6077f3f789748a18f2e579110576c5522e975') + version('1.10.1', commit='0b8ae1dfb56e4203dd8e14781850370df46a5e2c') + version('1.8.1', commit='3c9aa23d117bf489b6341708dc80c943bd1af11a') + version('1.6.0', commit='95f2f8d3648143abe9dc77c76340c5edf4114c82') + version('1.4.8', commit='79ab96d123c8da8f8ead81f678fe714c0958ff45') + + depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-delayedarray@0.2.4:', type=('build', 'run')) + depends_on('r-rhdf5', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + + depends_on('r-delayedarray@0.3.18:', when='@1.6.0:', type=('build', 'run')) + + depends_on('r-delayedarray@0.5.32:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.25.1:', when='@1.8.1:', type=('build', 'run')) + + depends_on('r-delayedarray@0.7.41:', when='@1.10.1:', type=('build', 'run')) + depends_on('r-rhdf5@2.25.6:', when='@1.10.1:', type=('build', 'run')) + + depends_on('r-delayedarray@0.9.3:', when='@1.12.3:', type=('build', 'run')) + depends_on('r-s4vectors@0.21.6:', when='@1.12.3:', type=('build', 'run')) + depends_on('r-rhdf5lib', when='@1.12.3:', type=('build', 'run')) + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-hdf5r/package.py b/var/spack/repos/builtin/packages/r-hdf5r/package.py index 670d1acb63..29baf0193c 100644 --- a/var/spack/repos/builtin/packages/r-hdf5r/package.py +++ b/var/spack/repos/builtin/packages/r-hdf5r/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py index a887c0c6e7..d1534b02ea 100644 --- a/var/spack/repos/builtin/packages/r-hexbin/package.py +++ b/var/spack/repos/builtin/packages/r-hexbin/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-highr/package.py b/var/spack/repos/builtin/packages/r-highr/package.py index d4445d48ce..c83f5a6427 100644 --- a/var/spack/repos/builtin/packages/r-highr/package.py +++ b/var/spack/repos/builtin/packages/r-highr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-hmisc/package.py b/var/spack/repos/builtin/packages/r-hmisc/package.py index eae2b5be52..131c3ea26c 100644 --- a/var/spack/repos/builtin/packages/r-hmisc/package.py +++ b/var/spack/repos/builtin/packages/r-hmisc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-hms/package.py b/var/spack/repos/builtin/packages/r-hms/package.py index bceece54ba..0ebcc5fbde 100644 --- a/var/spack/repos/builtin/packages/r-hms/package.py +++ b/var/spack/repos/builtin/packages/r-hms/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-hoardr/package.py b/var/spack/repos/builtin/packages/r-hoardr/package.py index cbc9806c3e..2c6f222d64 100644 --- a/var/spack/repos/builtin/packages/r-hoardr/package.py +++ b/var/spack/repos/builtin/packages/r-hoardr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-htmltable/package.py b/var/spack/repos/builtin/packages/r-htmltable/package.py index 64a0b138ce..d3876cc174 100644 --- a/var/spack/repos/builtin/packages/r-htmltable/package.py +++ b/var/spack/repos/builtin/packages/r-htmltable/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py index 914e7a5bb6..18786d763e 100644 --- a/var/spack/repos/builtin/packages/r-htmltools/package.py +++ b/var/spack/repos/builtin/packages/r-htmltools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py index f5cbf91b93..9466528f4a 100644 --- a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py +++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-httpcode/package.py b/var/spack/repos/builtin/packages/r-httpcode/package.py index ffd772eee7..52b847fda6 100644 --- a/var/spack/repos/builtin/packages/r-httpcode/package.py +++ b/var/spack/repos/builtin/packages/r-httpcode/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py index fa6721c319..f910d16e2f 100644 --- a/var/spack/repos/builtin/packages/r-httpuv/package.py +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py index fb50987c9d..3d7a2e2dbc 100644 --- a/var/spack/repos/builtin/packages/r-httr/package.py +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-hwriter/package.py b/var/spack/repos/builtin/packages/r-hwriter/package.py index 6c6cdf71c8..57d41cc87e 100644 --- a/var/spack/repos/builtin/packages/r-hwriter/package.py +++ b/var/spack/repos/builtin/packages/r-hwriter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-hypergraph/package.py b/var/spack/repos/builtin/packages/r-hypergraph/package.py index 949ba5ad9b..3240ab0c23 100644 --- a/var/spack/repos/builtin/packages/r-hypergraph/package.py +++ b/var/spack/repos/builtin/packages/r-hypergraph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,19 @@ from spack import * class RHypergraph(RPackage): - """A package that implements some simple capabilities for - representing and manipulating hypergraphs.""" + """A package providing hypergraph data structures. - homepage = "https://www.bioconductor.org/packages/hypergraph/" + A package that implements some simple capabilities for representing and + manipulating hypergraphs.""" + + homepage = "https://bioconductor.org/packages/hypergraph" git = "https://git.bioconductor.org/packages/hypergraph.git" + version('1.56.0', commit='f8b977fe068f15ecea49d30e77a871a35afcb97b') + version('1.54.0', commit='cf134b9221e9b5f6329a6786a366f57426c49e7c') + version('1.52.0', commit='3e28d8e8ab4c3facb79857b4e4cfffd65e064aca') + version('1.50.0', commit='fb3d523caf1d5791ef6962dd3c1a142742025ad5') version('1.48.0', commit='a4c19ea0b5f15204f706a7bfdea5363706382820') - depends_on('r@3.4.0:3.4.9', when='@1.48.0') + depends_on('r@2.1.0:', type=('build', 'run')) depends_on('r-graph', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ica/package.py b/var/spack/repos/builtin/packages/r-ica/package.py index d5bd431c77..7905de86b1 100644 --- a/var/spack/repos/builtin/packages/r-ica/package.py +++ b/var/spack/repos/builtin/packages/r-ica/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py index 8fbb28fad6..9ceec19052 100644 --- a/var/spack/repos/builtin/packages/r-igraph/package.py +++ b/var/spack/repos/builtin/packages/r-igraph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-illuminaio/package.py b/var/spack/repos/builtin/packages/r-illuminaio/package.py index 2803acf903..01d0f06d20 100644 --- a/var/spack/repos/builtin/packages/r-illuminaio/package.py +++ b/var/spack/repos/builtin/packages/r-illuminaio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,17 @@ from spack import * class RIlluminaio(RPackage): - """Tools for parsing Illumina's microarray output files, including - IDAT.""" + """Parsing Illumina Microarray Output Files. - homepage = "http://bioconductor.org/packages/illuminaio/" + Tools for parsing Illumina's microarray output files, including IDAT.""" + + homepage = "https://bioconductor.org/packages/illuminaio" git = "https://git.bioconductor.org/packages/illuminaio.git" + version('0.26.0', commit='40c2f94df2ea64d745d25aadd2bfb33ac3e02f81') + version('0.24.0', commit='47953c77713c2da00a610f39308f86c5b44f6c59') + version('0.22.0', commit='dbd842340999569975ea593f47d70a729b3f68f2') + version('0.20.0', commit='d226628133b2396be9e7a6bf043f0309bd70c4ec') version('0.18.0', commit='e6b8ab1f8eacb760aebdb4828e9cfbf07da06eda') depends_on('r-base64', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@0.18.0') diff --git a/var/spack/repos/builtin/packages/r-impute/package.py b/var/spack/repos/builtin/packages/r-impute/package.py index 4ec6a450a6..805a552262 100644 --- a/var/spack/repos/builtin/packages/r-impute/package.py +++ b/var/spack/repos/builtin/packages/r-impute/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,12 +7,17 @@ from spack import * class RImpute(RPackage): - """Imputation for microarray data (currently KNN only).""" + """impute: Imputation for microarray data. - homepage = "https://www.bioconductor.org/packages/impute/" + Imputation for microarray data (currently KNN only)""" + + homepage = "https://bioconductor.org/packages/impute" git = "https://git.bioconductor.org/packages/impute.git" + version('1.58.0', commit='dc17173df08d965a0d0aac9fa4ad519bd99d127e') + version('1.56.0', commit='6c037ed4dffabafceae684265f86f2a18751b559') + version('1.54.0', commit='efc61f5197e8c4baf4ae881fb556f0312beaabd8') + version('1.52.0', commit='7fa1b917a5dd60f2aaf52d9aae1fcd2c93511d63') version('1.50.1', commit='31d1cc141797afdc83743e1d95aab8a90ee19b71') - version('1.56.0', branch='RELEASE_3_8') - depends_on('r@3.4.0:3.4.9', when='@1.50.1') + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py index 9bbcd98ae9..3fc0e7aa5e 100644 --- a/var/spack/repos/builtin/packages/r-influencer/package.py +++ b/var/spack/repos/builtin/packages/r-influencer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ini/package.py b/var/spack/repos/builtin/packages/r-ini/package.py index 67edc74e65..c52e76ea7f 100644 --- a/var/spack/repos/builtin/packages/r-ini/package.py +++ b/var/spack/repos/builtin/packages/r-ini/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py index 4902ad2f4a..14d733c157 100644 --- a/var/spack/repos/builtin/packages/r-inline/package.py +++ b/var/spack/repos/builtin/packages/r-inline/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py index a6c65f8694..0d69e46c2d 100644 --- a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py +++ b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,15 +7,22 @@ from spack import * class RInteractivedisplaybase(RPackage): - """The interactiveDisplayBase package contains the the basic methods - needed to generate interactive Shiny based display methods for - Bioconductor objects.""" + """Base package for enabling powerful shiny web displays of Bioconductor + objects. - homepage = "https://bioconductor.org/packages/interactiveDisplayBase/" + The interactiveDisplayBase package contains the the basic methods needed + to generate interactive Shiny based display methods for Bioconductor + objects.""" + + homepage = "https://bioconductor.org/packages/interactiveDisplayBase" git = "https://git.bioconductor.org/packages/interactiveDisplayBase.git" + version('1.22.0', commit='4ce3cde1dabc01375c153ad614d77a5e28b96916') + version('1.20.0', commit='f40912c8af7afbaaf68c003a6e148d81cbe84df6') + version('1.18.0', commit='d07ea72a595877f27bf054f664f23e8f0304def8') + version('1.16.0', commit='a86aa586b589497f5449d36c2ce67a6b6055026d') version('1.14.0', commit='e2ccc7eefdd904e3b1032dc6b3f4a28d08c1cd40') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-shiny', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.14.0') diff --git a/var/spack/repos/builtin/packages/r-intervals/package.py b/var/spack/repos/builtin/packages/r-intervals/package.py index 52ce3e8ccf..f76684b3d1 100644 --- a/var/spack/repos/builtin/packages/r-intervals/package.py +++ b/var/spack/repos/builtin/packages/r-intervals/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-inum/package.py b/var/spack/repos/builtin/packages/r-inum/package.py index 7376f998ff..0b3cfead7f 100644 --- a/var/spack/repos/builtin/packages/r-inum/package.py +++ b/var/spack/repos/builtin/packages/r-inum/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ipred/package.py b/var/spack/repos/builtin/packages/r-ipred/package.py index 690b6b089d..ad73ee0ddb 100644 --- a/var/spack/repos/builtin/packages/r-ipred/package.py +++ b/var/spack/repos/builtin/packages/r-ipred/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py index a4313a470b..5cf6493342 100644 --- a/var/spack/repos/builtin/packages/r-iranges/package.py +++ b/var/spack/repos/builtin/packages/r-iranges/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,29 +7,34 @@ from spack import * class RIranges(RPackage): - """Provides efficient low-level and highly - reusable S4 classes for storing, - manipulating and aggregating over annotated ranges of - integers. Implements an - algebra of range operations, including efficient - algorithms for finding overlaps - and nearest neighbors. Defines efficient list-like - classes for storing, transforming - and aggregating large grouped data, - i.e., collections of atomic vectors and DataFrames.""" - - homepage = "https://www.bioconductor.org/packages/IRanges/" + """Foundation of integer range manipulation in Bioconductor. + + Provides efficient low-level and highly reusable S4 classes for storing, + manipulating and aggregating over annotated ranges of integers. + Implements an algebra of range operations, including efficient + algorithms for finding overlaps and nearest neighbors. Defines efficient + list-like classes for storing, transforming and aggregating large + grouped data, i.e., collections of atomic vectors and DataFrames.""" + + homepage = "https://bioconductor.org/packages/IRanges" git = "https://git.bioconductor.org/packages/IRanges.git" - version('2.14.10', commit='c76118a38e84c7c764141adbd66ee350d0882bc9') + version('2.18.3', commit='c98a7ba074e72f2e5ec98252dffe9d3392711972') + version('2.16.0', commit='26834c6868d7c279dd8ac1bb9daa16e6fef273c2') + version('2.14.12', commit='00af02756c14771a23df9efcf379409ab6eb3041') version('2.12.0', commit='1b1748655a8529ba87ad0f223f035ef0c08e7fcd') version('2.10.5', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614') - depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'), when='@2.10.5') - depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@2.12.0') - depends_on('r-biocgenerics@0.25.3:', type=('build', 'run'), when='@2.14.10') - depends_on('r-s4vectors@0.13.17:', type=('build', 'run'), when='@2.10.5') - depends_on('r-s4vectors@0.15.5:', type=('build', 'run'), when='@2.12.0') - depends_on('r-s4vectors@0.18.2:', type=('build', 'run'), when='@2.14.10') - depends_on('r@3.4.0:3.4.9', when='@2.10.5', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@2.14.10', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.21.1:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.17:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.23.3:', when='@2.12.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.15.5:', when='@2.12.0:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.25.3:', when='@2.14.12:', type=('build', 'run')) + depends_on('r-s4vectors@0.18.2:', when='@2.14.12:', type=('build', 'run')) + + depends_on('r-s4vectors@0.19.11:', when='@2.16.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.21.9:', when='@2.18.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-irdisplay/package.py b/var/spack/repos/builtin/packages/r-irdisplay/package.py index a78590697a..2786e6bb91 100644 --- a/var/spack/repos/builtin/packages/r-irdisplay/package.py +++ b/var/spack/repos/builtin/packages/r-irdisplay/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-irkernel/package.py b/var/spack/repos/builtin/packages/r-irkernel/package.py index 92cfbe5137..9089347e3c 100644 --- a/var/spack/repos/builtin/packages/r-irkernel/package.py +++ b/var/spack/repos/builtin/packages/r-irkernel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py index 963c572073..5e9711f74f 100644 --- a/var/spack/repos/builtin/packages/r-irlba/package.py +++ b/var/spack/repos/builtin/packages/r-irlba/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-isdparser/package.py b/var/spack/repos/builtin/packages/r-isdparser/package.py index bb5e038d04..cb7065ff23 100644 --- a/var/spack/repos/builtin/packages/r-isdparser/package.py +++ b/var/spack/repos/builtin/packages/r-isdparser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-iso/package.py b/var/spack/repos/builtin/packages/r-iso/package.py index 0ace73b5bd..4d7057b871 100644 --- a/var/spack/repos/builtin/packages/r-iso/package.py +++ b/var/spack/repos/builtin/packages/r-iso/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py index ba993dbb78..4d59c50faa 100644 --- a/var/spack/repos/builtin/packages/r-iterators/package.py +++ b/var/spack/repos/builtin/packages/r-iterators/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-janitor/package.py b/var/spack/repos/builtin/packages/r-janitor/package.py index 88e94b86eb..79c92f08d4 100644 --- a/var/spack/repos/builtin/packages/r-janitor/package.py +++ b/var/spack/repos/builtin/packages/r-janitor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-jaspar2018/package.py b/var/spack/repos/builtin/packages/r-jaspar2018/package.py index 15f6042d1e..3edc15acc1 100644 --- a/var/spack/repos/builtin/packages/r-jaspar2018/package.py +++ b/var/spack/repos/builtin/packages/r-jaspar2018/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,12 +7,15 @@ from spack import * class RJaspar2018(RPackage): - """Data package for JASPAR 2018. To search this databases, - please use the package TFBSTools (>= 1.15.6).""" + """Data package for JASPAR 2018. - homepage = "http://jaspar.genereg.net/" + Data package for JASPAR 2018. To search this databases, please use the + package TFBSTools (>= 1.15.6).""" + + homepage = "https://bioconductor.org/packages/JASPAR2018" git = "https://git.bioconductor.org/packages/JASPAR2018.git" + version('1.1.0', commit='cf8598d3c9054d85c43655cf82be17f74d800fa5') version('1.0.0', commit='4c84092b3737bb1c57ab56f4321f2f5e4b0efeaa') - depends_on('r@3.4.0:') + depends_on('r@3.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-jomo/package.py b/var/spack/repos/builtin/packages/r-jomo/package.py index 181d68285b..5a3a40f09e 100644 --- a/var/spack/repos/builtin/packages/r-jomo/package.py +++ b/var/spack/repos/builtin/packages/r-jomo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py index 4191b0dc1e..4e3d78e414 100644 --- a/var/spack/repos/builtin/packages/r-jpeg/package.py +++ b/var/spack/repos/builtin/packages/r-jpeg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index 4b3de1ddf8..68b3811d5d 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-kegg-db/package.py b/var/spack/repos/builtin/packages/r-kegg-db/package.py index 474300e0d6..693fcc7f27 100644 --- a/var/spack/repos/builtin/packages/r-kegg-db/package.py +++ b/var/spack/repos/builtin/packages/r-kegg-db/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-kegggraph/package.py b/var/spack/repos/builtin/packages/r-kegggraph/package.py index 3a75e2ef56..9feefead29 100644 --- a/var/spack/repos/builtin/packages/r-kegggraph/package.py +++ b/var/spack/repos/builtin/packages/r-kegggraph/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,26 @@ from spack import * class RKegggraph(RPackage): - """KEGGGraph is an interface between KEGG pathway and graph object as - well as a collection of tools to analyze, dissect and visualize these - graphs. It parses the regularly updated KGML (KEGG XML) files into graph - models maintaining all essential pathway attributes. The package offers - functionalities including parsing, graph operation, visualization and - etc.""" - - homepage = "https://www.bioconductor.org/packages/KEGGgraph/" + """KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor. + + KEGGGraph is an interface between KEGG pathway and graph object as well + as a collection of tools to analyze, dissect and visualize these graphs. + It parses the regularly updated KGML (KEGG XML) files into graph models + maintaining all essential pathway attributes. The package offers + functionalities including parsing, graph operation, visualization and + etc.""" + + homepage = "https://bioconductor.org/packages/KEGGgraph" git = "https://git.bioconductor.org/packages/KEGGgraph.git" + version('1.44.0', commit='2c24e8ec53fe34c72ea65f34e3c09905ab2e5c62') + version('1.42.0', commit='7d907e22a3ad7b4829a7cbaba5a8f8dc8013a609') + version('1.40.0', commit='6351a1637276f71697b01a994ebda0d3d1cf6d7a') + version('1.38.0', commit='72f102e2611e3966362cfaa43646a6e66dd2ba27') version('1.38.1', commit='dd31665beb36d5aad8ed09ed56c603633b6b2292') + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-xml@2.3-0:', type=('build', 'run')) depends_on('r-graph', type=('build', 'run')) - depends_on('r-xml', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.38.1') + + depends_on('r-rcurl', when='@1.44.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py index 44f560c40d..a422dfad36 100644 --- a/var/spack/repos/builtin/packages/r-keggrest/package.py +++ b/var/spack/repos/builtin/packages/r-keggrest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,21 +7,21 @@ from spack import * class RKeggrest(RPackage): - """This package provides functions and routines useful in the analysis - of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In - particular, functions to perform a signature analysis with known - signatures (LCD = linear combination decomposition) and a signature - analysis on stratified mutational catalogue (SMC = stratify mutational - catalogue) are provided.""" + """Client-side REST access to KEGG. - homepage = "http://bioconductor.org/packages/KEGGREST" + A package that provides a client interface to the KEGG REST server. + Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG + (python package) by Aurelien Mazurie.""" + + homepage = "https://bioconductor.org/packages/KEGGREST" git = "https://git.bioconductor.org/packages/KEGGREST.git" - version('1.18.1', commit='f6e6f1987e4db9d977a75609fab0cb710be2e2e4') - version('1.2.0', commit='ed48de0def57a909894e237fa4731c4a052d8849') + version('1.24.1', commit='bbc3ef476e02147aad8e1f33178136cc797c1b3f') + version('1.22.0', commit='4374507376be811d29416d0cbbfd9115a50494d9') + version('1.20.2', commit='62b4519367841f3548536c117e7e2bfe3fa4bf72') + version('1.18.1', commit='580c126eabc3c52145967708f67a428ca46b23b2') + version('1.16.1', commit='ed48de0def57a909894e237fa4731c4a052d8849') depends_on('r-httr', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.2.0') - depends_on('r@3.4.3:3.4.9', when='@1.18.1') diff --git a/var/spack/repos/builtin/packages/r-kernlab/package.py b/var/spack/repos/builtin/packages/r-kernlab/package.py index e1181faf39..2c7ce6bad2 100644 --- a/var/spack/repos/builtin/packages/r-kernlab/package.py +++ b/var/spack/repos/builtin/packages/r-kernlab/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-kernsmooth/package.py b/var/spack/repos/builtin/packages/r-kernsmooth/package.py index 393d71f81a..ecbf325df0 100644 --- a/var/spack/repos/builtin/packages/r-kernsmooth/package.py +++ b/var/spack/repos/builtin/packages/r-kernsmooth/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-kknn/package.py b/var/spack/repos/builtin/packages/r-kknn/package.py index 1d12e18406..9aa4c0af14 100644 --- a/var/spack/repos/builtin/packages/r-kknn/package.py +++ b/var/spack/repos/builtin/packages/r-kknn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py index af0cc893d8..bde3fe85bd 100644 --- a/var/spack/repos/builtin/packages/r-knitr/package.py +++ b/var/spack/repos/builtin/packages/r-knitr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ks/package.py b/var/spack/repos/builtin/packages/r-ks/package.py index 5ff34544a4..1fef11ef52 100644 --- a/var/spack/repos/builtin/packages/r-ks/package.py +++ b/var/spack/repos/builtin/packages/r-ks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py index 27b50786da..f3b5a3c45c 100644 --- a/var/spack/repos/builtin/packages/r-labeling/package.py +++ b/var/spack/repos/builtin/packages/r-labeling/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lambda-r/package.py b/var/spack/repos/builtin/packages/r-lambda-r/package.py index f2ff206836..1ea85260d1 100644 --- a/var/spack/repos/builtin/packages/r-lambda-r/package.py +++ b/var/spack/repos/builtin/packages/r-lambda-r/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py index 7128678cc6..f11f635ac1 100644 --- a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py +++ b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lars/package.py b/var/spack/repos/builtin/packages/r-lars/package.py index 5fd720451b..1eddbea773 100644 --- a/var/spack/repos/builtin/packages/r-lars/package.py +++ b/var/spack/repos/builtin/packages/r-lars/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-later/package.py b/var/spack/repos/builtin/packages/r-later/package.py index 1a1f2fa679..cca8c10739 100644 --- a/var/spack/repos/builtin/packages/r-later/package.py +++ b/var/spack/repos/builtin/packages/r-later/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py index c8f3ecae76..22110c6587 100644 --- a/var/spack/repos/builtin/packages/r-lattice/package.py +++ b/var/spack/repos/builtin/packages/r-lattice/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-latticeextra/package.py b/var/spack/repos/builtin/packages/r-latticeextra/package.py index 7c64d00fc6..ae74ac2c9b 100644 --- a/var/spack/repos/builtin/packages/r-latticeextra/package.py +++ b/var/spack/repos/builtin/packages/r-latticeextra/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lava/package.py b/var/spack/repos/builtin/packages/r-lava/package.py index 61dbf84081..2a7a1d2271 100644 --- a/var/spack/repos/builtin/packages/r-lava/package.py +++ b/var/spack/repos/builtin/packages/r-lava/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py index 3ce18f8cd1..7555a0890d 100644 --- a/var/spack/repos/builtin/packages/r-lazyeval/package.py +++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ldheatmap/package.py b/var/spack/repos/builtin/packages/r-ldheatmap/package.py new file mode 100644 index 0000000000..df4d181882 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ldheatmap/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RLdheatmap(RPackage): + """LDheatmap: Graphical Display of Pairwise Linkage Disequilibria Between + SNPs""" + + homepage = "https://sfustatgen.github.io/LDheatmap/" + url = "https://cloud.r-project.org/src/contrib/LDheatmap_0.99-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/LDheatmap" + + version('0.99-7', sha256='aca54c839a424506d8be7153bf03b32026aeefe7ed38f534e8e19708e34212e4') + + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-genetics', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-snpstats', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py index e6b8e3f212..0a8bcdf638 100644 --- a/var/spack/repos/builtin/packages/r-leaflet/package.py +++ b/var/spack/repos/builtin/packages/r-leaflet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-leaps/package.py b/var/spack/repos/builtin/packages/r-leaps/package.py index e4708ed234..9697c64cd3 100644 --- a/var/spack/repos/builtin/packages/r-leaps/package.py +++ b/var/spack/repos/builtin/packages/r-leaps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-learnbayes/package.py b/var/spack/repos/builtin/packages/r-learnbayes/package.py index 21f6554a18..542f02585e 100644 --- a/var/spack/repos/builtin/packages/r-learnbayes/package.py +++ b/var/spack/repos/builtin/packages/r-learnbayes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-leiden/package.py b/var/spack/repos/builtin/packages/r-leiden/package.py index 3079ce3ba6..caee6431bf 100644 --- a/var/spack/repos/builtin/packages/r-leiden/package.py +++ b/var/spack/repos/builtin/packages/r-leiden/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lhs/package.py b/var/spack/repos/builtin/packages/r-lhs/package.py index a4f295f597..ac3ff14dba 100644 --- a/var/spack/repos/builtin/packages/r-lhs/package.py +++ b/var/spack/repos/builtin/packages/r-lhs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-libcoin/package.py b/var/spack/repos/builtin/packages/r-libcoin/package.py index 69e70f4c8f..7fab441ea2 100644 --- a/var/spack/repos/builtin/packages/r-libcoin/package.py +++ b/var/spack/repos/builtin/packages/r-libcoin/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py index c4e7a04be3..fcefd3ec67 100644 --- a/var/spack/repos/builtin/packages/r-limma/package.py +++ b/var/spack/repos/builtin/packages/r-limma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,20 @@ from spack import * class RLimma(RPackage): - """Data analysis, linear models and differential expression - for microarray data.""" + """Linear Models for Microarray Data. - homepage = "https://www.bioconductor.org/packages/limma/" + Data analysis, linear models and differential expression for microarray + data.""" + + homepage = "https://bioconductor.org/packages/limma" git = "https://git.bioconductor.org/packages/limma.git" - version('3.36.2', commit='0cd5c13e22565182226bd2937ffcf8c59de1ca59') - version('3.34.9', commit='6755278a929f942a49e2441fb002a3ed393e1139') + version('3.40.6', commit='3ae0767ecf7a764030e7b7d0b1d0f292c0b24055') + version('3.38.3', commit='77b292eb150cdedaa1db704bcfb01f0bb29e9849') + version('3.36.5', commit='3148d1cb7eea9c6bdd60351d51abcfd665332d44') + version('3.34.9', commit='6755278a929f942a49e2441fb002a3ed393e1139') version('3.32.10', commit='593edf28e21fe054d64137ae271b8a52ab05bc60') - depends_on('r@3.5.0:3.5.9', when='@3.36.2') - depends_on('r@3.4.2:3.4.9', when='@3.34.9') - depends_on('r@3.4.0:3.4.9', when='@3.32.10') + depends_on('r@2.3.0:', type=('build', 'run')) + + depends_on('r@3.6.0:', when='@3.40.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-listenv/package.py b/var/spack/repos/builtin/packages/r-listenv/package.py index ef931f2612..962fc1bf6a 100644 --- a/var/spack/repos/builtin/packages/r-listenv/package.py +++ b/var/spack/repos/builtin/packages/r-listenv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py index ac77229c84..32fd1565c0 100644 --- a/var/spack/repos/builtin/packages/r-lme4/package.py +++ b/var/spack/repos/builtin/packages/r-lme4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py index 98bad18240..29bda06982 100644 --- a/var/spack/repos/builtin/packages/r-lmtest/package.py +++ b/var/spack/repos/builtin/packages/r-lmtest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-locfit/package.py b/var/spack/repos/builtin/packages/r-locfit/package.py index 2ed5f6e736..1e9b23f275 100644 --- a/var/spack/repos/builtin/packages/r-locfit/package.py +++ b/var/spack/repos/builtin/packages/r-locfit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-log4r/package.py b/var/spack/repos/builtin/packages/r-log4r/package.py index d32c4a6836..194b9c0c71 100644 --- a/var/spack/repos/builtin/packages/r-log4r/package.py +++ b/var/spack/repos/builtin/packages/r-log4r/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-loo/package.py b/var/spack/repos/builtin/packages/r-loo/package.py index 9a41eec8bc..9bbef0ee79 100644 --- a/var/spack/repos/builtin/packages/r-loo/package.py +++ b/var/spack/repos/builtin/packages/r-loo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lpsolve/package.py b/var/spack/repos/builtin/packages/r-lpsolve/package.py index dc855bc1c1..ec40ba1553 100644 --- a/var/spack/repos/builtin/packages/r-lpsolve/package.py +++ b/var/spack/repos/builtin/packages/r-lpsolve/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lsei/package.py b/var/spack/repos/builtin/packages/r-lsei/package.py index 1c4545eeb5..0b69b60b3e 100644 --- a/var/spack/repos/builtin/packages/r-lsei/package.py +++ b/var/spack/repos/builtin/packages/r-lsei/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py index 72bc815f7e..3fb1f2ddd2 100644 --- a/var/spack/repos/builtin/packages/r-lubridate/package.py +++ b/var/spack/repos/builtin/packages/r-lubridate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index 475c1dcdd9..58d39c239f 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-magick/package.py b/var/spack/repos/builtin/packages/r-magick/package.py index 66ae049615..7c314ad081 100644 --- a/var/spack/repos/builtin/packages/r-magick/package.py +++ b/var/spack/repos/builtin/packages/r-magick/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,4 +27,4 @@ class RMagick(RPackage): depends_on('r-rcpp@0.12.12:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-curl', type=('build', 'run')) - depends_on('image-magick') + depends_on('imagemagick') diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py index 2356cef2fa..1e3c697da9 100644 --- a/var/spack/repos/builtin/packages/r-magrittr/package.py +++ b/var/spack/repos/builtin/packages/r-magrittr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-makecdfenv/package.py b/var/spack/repos/builtin/packages/r-makecdfenv/package.py index ba51fcac20..8687d61be7 100644 --- a/var/spack/repos/builtin/packages/r-makecdfenv/package.py +++ b/var/spack/repos/builtin/packages/r-makecdfenv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,23 @@ from spack import * class RMakecdfenv(RPackage): - """This package has two functions. One reads a Affymetrix - chip description file (CDF) and creates a hash table environment - containing the location/probe set membership mapping. - The other creates a package that automatically loads - that environment.""" + """CDF Environment Maker. - homepage = "https://www.bioconductor.org/packages/makecdfenv/" + This package has two functions. One reads a Affymetrix chip description + file (CDF) and creates a hash table environment containing the + location/probe set membership mapping. The other creates a package that + automatically loads that environment.""" + + homepage = "https://bioconductor.org/packages/makecdfenv" git = "https://git.bioconductor.org/packages/makecdfenv.git" + version('1.60.0', commit='900ece3ecd7a0ade9f8a0374e5a03def4e079cb3') + version('1.58.0', commit='6f513e39c4920a6da10d22718fc3bf278fe5ffe2') + version('1.56.0', commit='f6b48e9a9f18598653d05bc0bdffeae7fefbb327') + version('1.54.0', commit='3ff646ddc4b028e46b1e091ff9c2d17ce77cec26') version('1.52.0', commit='b88a3e93e3b7feeeca69eda7c1fc5a0826c81120') - depends_on('r@3.4.0:3.4.9', when='@1.52.0') + depends_on('r@2.6.0:', type=('build', 'run')) depends_on('r-affyio', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-maldiquant/package.py b/var/spack/repos/builtin/packages/r-maldiquant/package.py index 74fb09d720..c032ea5d3b 100644 --- a/var/spack/repos/builtin/packages/r-maldiquant/package.py +++ b/var/spack/repos/builtin/packages/r-maldiquant/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-manipulatewidget/package.py b/var/spack/repos/builtin/packages/r-manipulatewidget/package.py index 0f04db37d9..225688abae 100644 --- a/var/spack/repos/builtin/packages/r-manipulatewidget/package.py +++ b/var/spack/repos/builtin/packages/r-manipulatewidget/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,13 @@ class RManipulatewidget(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/manipulateWidget/" version('0.10.0', sha256='3d61a3d0cedf5c8a850a3e62ed6af38c600dc3f25b44c4ff07a5093bf9ca4ffd') + version('0.9.0', sha256='5bf4bdb702263b0e156f40f3354922a06db7db544e497addcd6c98d9860bf3a3') + version('0.8.0', sha256='e7e6351b1fb8f39b9895e2536fa7c149cbc5d63d7022f67c1b25232cf0706ca7') + version('0.7.0', sha256='160ce5c68658301e00051c60ac5693701c5bc97b7344bacde0f56be4955231f6') + version('0.6.0', sha256='90aa1b30647d7034166b8d6c6185503b6855c70253e36a41742a84faa77ce0db') + version('0.5.1', sha256='5a672c2bd8ba16ec8212cd9fb620072b243e6d18c02dd3ec70bd8c2a1ff1c9c4') + version('0.5.0', sha256='2599e25f78bb0d748705160e1dfe62a673f5bb388ac5f415f3d649d2511737c8') + version('0.4.0', sha256='65cc7d28c2b2efc81fda35da019ac6e6058580cf0fdf5e31458cc96386c0c599') depends_on('r-base64enc', type=('build', 'run')) depends_on('r-codetools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mapplots/package.py b/var/spack/repos/builtin/packages/r-mapplots/package.py new file mode 100644 index 0000000000..4417d0ed14 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mapplots/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RMapplots(RPackage): + """mapplots: Data Visualisation on Maps""" + + homepage = "https://cloud.r-project.org/package=mapplots" + url = "https://cloud.r-project.org/src/contrib/mapplots_1.5.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mapplots" + + version('1.5.1', sha256='37e96d34f37922180e07bb63b4514e07d42eee5bbf0885b278286ee48cf142a3') + + depends_on('r@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py index e9afb537b1..095f251306 100644 --- a/var/spack/repos/builtin/packages/r-mapproj/package.py +++ b/var/spack/repos/builtin/packages/r-mapproj/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py index 623d0e0ead..2f8132ded3 100644 --- a/var/spack/repos/builtin/packages/r-maps/package.py +++ b/var/spack/repos/builtin/packages/r-maps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py index c5d512ad6c..e9c930e3e4 100644 --- a/var/spack/repos/builtin/packages/r-maptools/package.py +++ b/var/spack/repos/builtin/packages/r-maptools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py index 7dab7408fd..ad966e7486 100644 --- a/var/spack/repos/builtin/packages/r-markdown/package.py +++ b/var/spack/repos/builtin/packages/r-markdown/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py index fd3995f9e5..96cac84566 100644 --- a/var/spack/repos/builtin/packages/r-mass/package.py +++ b/var/spack/repos/builtin/packages/r-mass/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,7 +14,8 @@ class RMass(RPackage): url = "https://cloud.r-project.org/src/contrib/MASS_7.3-47.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/MASS" - version('7.3-51.4', sha256='9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74') + version('7.3-51.5', sha256='464c0615cef01820cde2bb8457e81575d6755ae9b3ac99f3bfaaac47d43d15cc') + version('7.3-51.4', sha256='844270a2541eaed420871dfb61d681aa67ee57126645fb6b144b436c25698eeb') version('7.3-51.3', sha256='5b0e0e7704d43a94b08dcc4b3fe600b9723d1b3e446dd393e82d39ddf66608b6') version('7.3-47', sha256='ed44cdabe84fff3553122267ade61d5cc68071c435f7645d36c8f2e4e9f9c6bf') diff --git a/var/spack/repos/builtin/packages/r-matr/package.py b/var/spack/repos/builtin/packages/r-matr/package.py index b77b3540f7..ad8bc3370a 100644 --- a/var/spack/repos/builtin/packages/r-matr/package.py +++ b/var/spack/repos/builtin/packages/r-matr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index b80ec008ba..07140d08ec 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py index 141dc23281..98de8f80c3 100644 --- a/var/spack/repos/builtin/packages/r-matrixmodels/package.py +++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-matrixstats/package.py b/var/spack/repos/builtin/packages/r-matrixstats/package.py index 2b3a5da246..9446add318 100644 --- a/var/spack/repos/builtin/packages/r-matrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-matrixstats/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mclust/package.py b/var/spack/repos/builtin/packages/r-mclust/package.py index 276c51b0b4..f0936a9e82 100644 --- a/var/spack/repos/builtin/packages/r-mclust/package.py +++ b/var/spack/repos/builtin/packages/r-mclust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py index d2d2e719d8..52f8104b40 100644 --- a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py +++ b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mco/package.py b/var/spack/repos/builtin/packages/r-mco/package.py index 39078a5b37..ec591cd8e6 100644 --- a/var/spack/repos/builtin/packages/r-mco/package.py +++ b/var/spack/repos/builtin/packages/r-mco/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mda/package.py b/var/spack/repos/builtin/packages/r-mda/package.py index 7eaeec26bf..16dd70ee59 100644 --- a/var/spack/repos/builtin/packages/r-mda/package.py +++ b/var/spack/repos/builtin/packages/r-mda/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py index 083cd1a0f8..3587dfdbfa 100644 --- a/var/spack/repos/builtin/packages/r-memoise/package.py +++ b/var/spack/repos/builtin/packages/r-memoise/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mergemaid/package.py b/var/spack/repos/builtin/packages/r-mergemaid/package.py index f85fa253fe..5d02468dcb 100644 --- a/var/spack/repos/builtin/packages/r-mergemaid/package.py +++ b/var/spack/repos/builtin/packages/r-mergemaid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,23 +7,29 @@ from spack import * class RMergemaid(RPackage): - """The functions in this R extension are intended for cross-study - comparison of gene expression array data. Required from the user is - gene expression matrices, their corresponding gene-id vectors and - other useful information, and they could be 'list','matrix', or - 'ExpressionSet'. The main function is 'mergeExprs' which transforms - the input objects into data in the merged format, such that common - genes in different datasets can be easily found. And the function - 'intcor' calculate the correlation coefficients. Other functions use - the output from 'modelOutcome' to graphically display the results and - cross-validate associations of gene expression data with survival.""" + """Merge Maid. - homepage = "https://www.bioconductor.org/packages/MergeMaid/" + The functions in this R extension are intended for cross-study + comparison of gene expression array data. Required from the user is gene + expression matrices, their corresponding gene-id vectors and other + useful information, and they could be 'list','matrix', or + 'ExpressionSet'. The main function is 'mergeExprs' which transforms the + input objects into data in the merged format, such that common genes in + different datasets can be easily found. And the function 'intcor' + calculate the correlation coefficients. Other functions use the output + from 'modelOutcome' to graphically display the results and cross- + validate associations of gene expression data with survival.""" + + homepage = "https://bioconductor.org/packages/MergeMaid" git = "https://git.bioconductor.org/packages/MergeMaid.git" + version('2.56.0', commit='c510d1d85bb39476e8397b24c4bc127780a17686') + version('2.54.0', commit='8e79bd2bd06b25138b3c5107681c89d714a3b194') + version('2.52.0', commit='88a1ddfd9cdbe902ba40fae0f39ee5665ac33a74') + version('2.50.0', commit='b77d7fcb8ac8cf9ee71303bb193ef1a36a7f6049') version('2.48.0', commit='aee89c523fcafff4c166ff3db4fff90df16a1ed4') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.48.0') diff --git a/var/spack/repos/builtin/packages/r-metap/package.py b/var/spack/repos/builtin/packages/r-metap/package.py index 2b9ee109a6..c910da734e 100644 --- a/var/spack/repos/builtin/packages/r-metap/package.py +++ b/var/spack/repos/builtin/packages/r-metap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py index a15b1f0865..5a12096785 100644 --- a/var/spack/repos/builtin/packages/r-mgcv/package.py +++ b/var/spack/repos/builtin/packages/r-mgcv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mgraster/package.py b/var/spack/repos/builtin/packages/r-mgraster/package.py index 688993d6cc..a3bcf11d7e 100644 --- a/var/spack/repos/builtin/packages/r-mgraster/package.py +++ b/var/spack/repos/builtin/packages/r-mgraster/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mice/package.py b/var/spack/repos/builtin/packages/r-mice/package.py index cdf57abd6c..583e6cae8d 100644 --- a/var/spack/repos/builtin/packages/r-mice/package.py +++ b/var/spack/repos/builtin/packages/r-mice/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py index bc64eabd3e..1c795c905d 100644 --- a/var/spack/repos/builtin/packages/r-mime/package.py +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py index 0f6e1af6f8..b786dd2129 100644 --- a/var/spack/repos/builtin/packages/r-minfi/package.py +++ b/var/spack/repos/builtin/packages/r-minfi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,21 +7,27 @@ from spack import * class RMinfi(RPackage): - """Tools to analyze & visualize Illumina Infinium methylation arrays.""" + """Analyze Illumina Infinium DNA methylation arrays. - homepage = "https://bioconductor.org/packages/minfi/" + Tools to analyze & visualize Illumina Infinium methylation arrays.""" + + homepage = "https://bioconductor.org/packages/minfi" git = "https://git.bioconductor.org/packages/minfi.git" + version('1.30.0', commit='a4c28e9388fe3b35e7d21a9669e39250ed6dcbcd') + version('1.28.4', commit='b5125b2f3e05d37d519eeb6fd44a60efdad388e7') + version('1.26.2', commit='ebb07b728b2453998d46e4e53d4fbf873e8e81fc') + version('1.24.0', commit='a4df428588ea86a1c79ddba76132014f0a39644e') version('1.22.1', commit='b2faf84bcbb291e32d470a0e029450093527545b') - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.3:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-summarizedexperiment', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.1.6:', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-bumphunter', type=('build', 'run')) + depends_on('r-bumphunter@1.1.9:', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) + depends_on('r-biobase@2.33.2:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-beanplot', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) @@ -31,7 +37,7 @@ class RMinfi(RPackage): depends_on('r-limma', type=('build', 'run')) depends_on('r-preprocesscore', type=('build', 'run')) depends_on('r-illuminaio', type=('build', 'run')) - depends_on('r-matrixstats', type=('build', 'run')) + depends_on('r-matrixstats@0.50.0:', type=('build', 'run')) depends_on('r-mclust', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) @@ -40,4 +46,14 @@ class RMinfi(RPackage): depends_on('r-quadprog', type=('build', 'run')) depends_on('r-data-table', type=('build', 'run')) depends_on('r-geoquery', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.22.1') + + depends_on('r-delayedmatrixstats', when='@1.26.2:', type=('build', 'run')) + depends_on('r-delayedarray@0.5.23:', when='@1.26.2:', type=('build', 'run')) + depends_on('r-hdf5array', when='@1.26.2:', type=('build', 'run')) + depends_on('r-biocparallel', when='@1.26.2:', type=('build', 'run')) + + depends_on('r-illuminaio@0.23.2:', when='@1.28.4:', type=('build', 'run')) + depends_on('r-delayedmatrixstats@1.3.4:', when='@1.28.4:', type=('build', 'run')) + depends_on('r-delayedarray@0.7.38:', when='@1.28.4:', type=('build', 'run')) + + depends_on('r-delayedarray@0.9.8:', when='@1.30.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-miniui/package.py b/var/spack/repos/builtin/packages/r-miniui/package.py index 5b7de8ba85..71761dffd3 100644 --- a/var/spack/repos/builtin/packages/r-miniui/package.py +++ b/var/spack/repos/builtin/packages/r-miniui/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py index 0f585121c8..efdd719932 100644 --- a/var/spack/repos/builtin/packages/r-minqa/package.py +++ b/var/spack/repos/builtin/packages/r-minqa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-misc3d/package.py b/var/spack/repos/builtin/packages/r-misc3d/package.py index 0bf82caa20..7d4a1c63fa 100644 --- a/var/spack/repos/builtin/packages/r-misc3d/package.py +++ b/var/spack/repos/builtin/packages/r-misc3d/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mitml/package.py b/var/spack/repos/builtin/packages/r-mitml/package.py index 8bb251f1b8..f46d8a497a 100644 --- a/var/spack/repos/builtin/packages/r-mitml/package.py +++ b/var/spack/repos/builtin/packages/r-mitml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mitools/package.py b/var/spack/repos/builtin/packages/r-mitools/package.py index 45a9f80c6e..264e20c811 100644 --- a/var/spack/repos/builtin/packages/r-mitools/package.py +++ b/var/spack/repos/builtin/packages/r-mitools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mixtools/package.py b/var/spack/repos/builtin/packages/r-mixtools/package.py index 2472b945a3..7558cc02ab 100644 --- a/var/spack/repos/builtin/packages/r-mixtools/package.py +++ b/var/spack/repos/builtin/packages/r-mixtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mlbench/package.py b/var/spack/repos/builtin/packages/r-mlbench/package.py index 45eef32331..6b75828c71 100644 --- a/var/spack/repos/builtin/packages/r-mlbench/package.py +++ b/var/spack/repos/builtin/packages/r-mlbench/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py index 0d37551de5..4a2e45585b 100644 --- a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py +++ b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,20 +7,31 @@ from spack import * class RMlinterfaces(RPackage): - """This package provides uniform interfaces to machine learning - code for data in R and Bioconductor containers.""" + """Uniform interfaces to R machine learning procedures for data in + Bioconductor containers. - homepage = "https://www.bioconductor.org/packages/MLInterfaces/" + This package provides uniform interfaces to machine learning code for + data in R and Bioconductor containers.""" + + homepage = "https://bioconductor.org/packages/MLInterfaces" git = "https://git.bioconductor.org/packages/MLInterfaces.git" + version('1.64.1', commit='0b081112d87771248bc33b3b82d5ca4685f986a1') + version('1.62.1', commit='6cf59a90b14779cf57a0b36f1087304082ae50fe') + version('1.60.1', commit='019e9ed44923e5d845a4800246aa044ddd59d548') + version('1.58.1', commit='4e2b5efa019fcb677dc82a58a1668c8a00cdfe07') version('1.56.0', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f') - depends_on('r@3.4.0:3.4.9', when='@1.56.0') - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r@2.9:', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.11:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) + depends_on('r-annotate', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) depends_on('r-gdata', type=('build', 'run')) depends_on('r-pls', type=('build', 'run')) depends_on('r-sfsmisc', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-rpart', type=('build', 'run')) depends_on('r-rda', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-fpc', type=('build', 'run')) @@ -29,5 +40,7 @@ class RMlinterfaces(RPackage): depends_on('r-gbm', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-hwriter', type=('build', 'run')) - depends_on('r-threejs', type=('build', 'run')) + depends_on('r-threejs@0.2.2:', type=('build', 'run')) depends_on('r-mlbench', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.60.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlr/package.py b/var/spack/repos/builtin/packages/r-mlr/package.py index cbbf4d1c88..306d8ff92a 100644 --- a/var/spack/repos/builtin/packages/r-mlr/package.py +++ b/var/spack/repos/builtin/packages/r-mlr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mlrmbo/package.py b/var/spack/repos/builtin/packages/r-mlrmbo/package.py index d0bc16c752..ba8cb37abf 100644 --- a/var/spack/repos/builtin/packages/r-mlrmbo/package.py +++ b/var/spack/repos/builtin/packages/r-mlrmbo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mmwrweek/package.py b/var/spack/repos/builtin/packages/r-mmwrweek/package.py index c4be88a804..40f6bf1c77 100644 --- a/var/spack/repos/builtin/packages/r-mmwrweek/package.py +++ b/var/spack/repos/builtin/packages/r-mmwrweek/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mnormt/package.py b/var/spack/repos/builtin/packages/r-mnormt/package.py index 7bbea16619..ae94319f8c 100644 --- a/var/spack/repos/builtin/packages/r-mnormt/package.py +++ b/var/spack/repos/builtin/packages/r-mnormt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-modelmetrics/package.py b/var/spack/repos/builtin/packages/r-modelmetrics/package.py index f26f4bc4db..67404cc234 100644 --- a/var/spack/repos/builtin/packages/r-modelmetrics/package.py +++ b/var/spack/repos/builtin/packages/r-modelmetrics/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-modelr/package.py b/var/spack/repos/builtin/packages/r-modelr/package.py index 609266d475..a3c3232e1d 100644 --- a/var/spack/repos/builtin/packages/r-modelr/package.py +++ b/var/spack/repos/builtin/packages/r-modelr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-modeltools/package.py b/var/spack/repos/builtin/packages/r-modeltools/package.py index 61087e9b68..73fdd643bf 100644 --- a/var/spack/repos/builtin/packages/r-modeltools/package.py +++ b/var/spack/repos/builtin/packages/r-modeltools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mpm/package.py b/var/spack/repos/builtin/packages/r-mpm/package.py index f5b5b40235..dd831ffd27 100644 --- a/var/spack/repos/builtin/packages/r-mpm/package.py +++ b/var/spack/repos/builtin/packages/r-mpm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-msnbase/package.py b/var/spack/repos/builtin/packages/r-msnbase/package.py index b617d077ed..932372681c 100644 --- a/var/spack/repos/builtin/packages/r-msnbase/package.py +++ b/var/spack/repos/builtin/packages/r-msnbase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,19 +7,27 @@ from spack import * class RMsnbase(RPackage): - """Manipulation, processing and visualisation of mass spectrometry and - proteomics data.""" + """Base Functions and Classes for Mass Spectrometry and Proteomics. - homepage = "https://www.bioconductor.org/packages/MSnbase/" + MSnbase provides infrastructure for manipulation, processing and + visualisation of mass spectrometry and proteomics data, ranging from raw + to quantitative and annotated data.""" + + homepage = "https://bioconductor.org/packages/MSnbase" git = "https://git.bioconductor.org/packages/MSnbase.git" + version('2.10.1', commit='4d5899bc9c714f0b1a70cddd537cd4621b2b53b0') + version('2.8.3', commit='ef883752c5e92d445647bc5b5d23d5df320db415') + version('2.6.4', commit='46836860ce0281eef135303f2e2948303d67f68c') + version('2.4.2', commit='c045d65daa730c7837852e6343a05cae9644ab5e') version('2.2.0', commit='d6e8fb7f106d05096fa9074da0f829ac8f02c197') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-mzr', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.7.1:', type=('build', 'run')) + depends_on('r-biobase@2.15.2:', type=('build', 'run')) + depends_on('r-mzr@2.7.6:', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) - depends_on('r-protgenerics', type=('build', 'run')) + depends_on('r-protgenerics@1.5.1:', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-preprocesscore', type=('build', 'run')) @@ -27,12 +35,23 @@ class RMsnbase(RPackage): depends_on('r-affy', type=('build', 'run')) depends_on('r-impute', type=('build', 'run')) depends_on('r-pcamethods', type=('build', 'run')) - depends_on('r-mzid', type=('build', 'run')) - depends_on('r-maldiquant', type=('build', 'run')) + depends_on('r-mzid@1.5.2:', type=('build', 'run')) + depends_on('r-maldiquant@1.16:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.2.0') + + depends_on('r-mzr@2.11.11:', when='@2.4.2:', type=('build', 'run')) + depends_on('r-protgenerics@1.9.1:', when='@2.4.2:', type=('build', 'run')) + + depends_on('r-mzr@2.13.6:', when='@2.6.4:', type=('build', 'run')) + depends_on('r-iranges@2.13.28:', when='@2.6.4:', type=('build', 'run')) + depends_on('r-scales', when='@2.6.4:', type=('build', 'run')) + depends_on('r-mass', when='@2.6.4:', type=('build', 'run')) + + depends_on('r-mzr@2.15.1:', when='@2.8.3:', type=('build', 'run')) + + depends_on('r-mzr@2.17.3:', when='@2.10.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py index e66d05cd25..d0566c2004 100644 --- a/var/spack/repos/builtin/packages/r-multcomp/package.py +++ b/var/spack/repos/builtin/packages/r-multcomp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-multicool/package.py b/var/spack/repos/builtin/packages/r-multicool/package.py index c4e322f678..fc87206d73 100644 --- a/var/spack/repos/builtin/packages/r-multicool/package.py +++ b/var/spack/repos/builtin/packages/r-multicool/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-multitaper/package.py b/var/spack/repos/builtin/packages/r-multitaper/package.py index 8e31a39c39..52f8a05b2c 100644 --- a/var/spack/repos/builtin/packages/r-multitaper/package.py +++ b/var/spack/repos/builtin/packages/r-multitaper/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-multtest/package.py b/var/spack/repos/builtin/packages/r-multtest/package.py index ce4b5502c3..3e8667de9f 100644 --- a/var/spack/repos/builtin/packages/r-multtest/package.py +++ b/var/spack/repos/builtin/packages/r-multtest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,37 @@ from spack import * class RMulttest(RPackage): - """Resampling-based multiple hypothesis testing""" + """Resampling-based multiple hypothesis testing. - homepage = "https://www.bioconductor.org/packages/multtest/" + Non-parametric bootstrap and permutation resampling-based multiple + testing procedures (including empirical Bayes methods) for controlling + the family-wise error rate (FWER), generalized family-wise error rate + (gFWER), tail probability of the proportion of false positives (TPPFP), + and false discovery rate (FDR). Several choices of bootstrap-based null + distribution are implemented (centered, centered and scaled, quantile- + transformed). Single-step and step-wise methods are available. Tests + based on a variety of t- and F-statistics (including t-statistics based + on regression parameters from linear and survival models as well as + those based on correlation parameters) are included. When probing + hypotheses with t-statistics, users may also select a potentially faster + null distribution which is multivariate normal with mean zero and + variance covariance matrix derived from the vector influence function. + Results are reported in terms of adjusted p-values, confidence regions + and test statistic cutoffs. The procedures are directly applicable to + identifying differentially expressed genes in DNA microarray + experiments.""" + + homepage = "https://bioconductor.org/packages/multtest" git = "https://git.bioconductor.org/packages/multtest.git" + version('2.40.0', commit='5f00017c2d3a31e05e1cfe06d9f7afdee19f8473') + version('2.38.0', commit='4dfe71cecfb298a94521088fb7bd83c5498d2915') + version('2.36.0', commit='babb15e8d110eb72300ad59cf7e53386237a4198') + version('2.34.0', commit='6ef873e05e6c93ede54f3421424f56eda057cd54') version('2.32.0', commit='c5e890dfbffcc3a3f107303a24b6085614312f4a') - depends_on('r@3.4.0:3.4.9', when='@2.32.0') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py index efff472a17..64637d9779 100644 --- a/var/spack/repos/builtin/packages/r-munsell/package.py +++ b/var/spack/repos/builtin/packages/r-munsell/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py index bf27761914..b4a10009f1 100644 --- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py +++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-mzid/package.py b/var/spack/repos/builtin/packages/r-mzid/package.py index 321ef53455..68f2a2c440 100644 --- a/var/spack/repos/builtin/packages/r-mzid/package.py +++ b/var/spack/repos/builtin/packages/r-mzid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,15 +7,21 @@ from spack import * class RMzid(RPackage): - """A parser for mzIdentML files implemented using the XML package. The + """An mzIdentML parser for R. + + A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.""" - homepage = "https://www.bioconductor.org/packages/mzID/" + homepage = "https://bioconductor.org/packages/mzID" git = "https://git.bioconductor.org/packages/mzID.git" + version('1.22.0', commit='382d9cf11f0cba996911a9d79e193d28f3ac6042') + version('1.20.1', commit='819582646944440ddd9ed3724ae964841573e54c') + version('1.18.0', commit='7d8924ae95585eb8cf472d21619a7603d291d652') + version('1.16.0', commit='fc203832a4cbbbe20f6dd826c6bf2128f2c271c4') version('1.14.0', commit='1c53aa6523ae61d3ebb13381381fc119d6cc6115') depends_on('r-xml', type=('build', 'run')) @@ -24,4 +30,3 @@ class RMzid(RPackage): depends_on('r-foreach', type=('build', 'run')) depends_on('r-iterators', type=('build', 'run')) depends_on('r-protgenerics', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.14.0') diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py index 5ccf4dd6cd..3f11e98fe3 100644 --- a/var/spack/repos/builtin/packages/r-mzr/package.py +++ b/var/spack/repos/builtin/packages/r-mzr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,22 +7,34 @@ from spack import * class RMzr(RPackage): - """mzR provides a unified API to the common file formats and parsers + """parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass + spectrometry data). + + mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.""" - homepage = "https://www.bioconductor.org/packages/mzR/" + homepage = "https://bioconductor.org/packages/mzR" git = "https://git.bioconductor.org/packages/mzR.git" + version('2.18.1', commit='13f9f9b1149859c3e29cfce941d958cc4f680546') + version('2.16.2', commit='22d7dad98f46b5bed7f6f7b3a703dcdf5997f709') + version('2.14.0', commit='bf1154bc45101d95b5a67c66980856a779b84bd4') + version('2.12.0', commit='f05eb27ae31c3d019cca10fc3b9ee513cbcdfc5a') version('2.10.0', commit='a6168b68e48c281e88de9647254a8db1e21df388') + depends_on('r-rcpp@0.10.1:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.6:', type=('build', 'run')) depends_on('r-protgenerics', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('netcdf') - depends_on('r@3.4.0:3.4.9', when='@2.10.0') + + depends_on('r-protgenerics@1.9.1:', when='@2.12.0:', type=('build', 'run')) + depends_on('r-rhdf5lib@1.1.4:', when='@2.14.0:', type=('build', 'run')) + + depends_on('r-ncdf4', when='@2.16.2:', type=('build', 'run')) + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-nanotime/package.py b/var/spack/repos/builtin/packages/r-nanotime/package.py index 61cd98ba9f..845f6dcd7a 100644 --- a/var/spack/repos/builtin/packages/r-nanotime/package.py +++ b/var/spack/repos/builtin/packages/r-nanotime/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ncbit/package.py b/var/spack/repos/builtin/packages/r-ncbit/package.py index b84ff8c961..021bb6cfbb 100644 --- a/var/spack/repos/builtin/packages/r-ncbit/package.py +++ b/var/spack/repos/builtin/packages/r-ncbit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py index 14e1273381..2e06ef22df 100644 --- a/var/spack/repos/builtin/packages/r-ncdf4/package.py +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,4 +30,4 @@ class RNcdf4(RPackage): version('1.16', sha256='edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253') version('1.15', sha256='d58298f4317c6c80a041a70216126492fd09ba8ecde9da09d5145ae26f324d4d') - depends_on('netcdf@4.1:') + depends_on('netcdf-c@4.1:') diff --git a/var/spack/repos/builtin/packages/r-network/package.py b/var/spack/repos/builtin/packages/r-network/package.py index dad4a541a2..82279fc8a4 100644 --- a/var/spack/repos/builtin/packages/r-network/package.py +++ b/var/spack/repos/builtin/packages/r-network/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py index 633b2580fc..bcef714f11 100644 --- a/var/spack/repos/builtin/packages/r-networkd3/package.py +++ b/var/spack/repos/builtin/packages/r-networkd3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-nleqslv/package.py b/var/spack/repos/builtin/packages/r-nleqslv/package.py index 75dda5930d..37968fe777 100644 --- a/var/spack/repos/builtin/packages/r-nleqslv/package.py +++ b/var/spack/repos/builtin/packages/r-nleqslv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py index 59fc2342a9..483cc68a75 100644 --- a/var/spack/repos/builtin/packages/r-nlme/package.py +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py index 9607bd1faa..2e95081b91 100644 --- a/var/spack/repos/builtin/packages/r-nloptr/package.py +++ b/var/spack/repos/builtin/packages/r-nloptr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py index 95346b8290..480451367f 100644 --- a/var/spack/repos/builtin/packages/r-nmf/package.py +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,7 +15,7 @@ class RNmf(RPackage): computations on multicore machines..""" homepage = "http://renozao.github.io/NMF" - url = "https://cloud.r-project.org/src/contrib/NMF_0.20.6.tar.gz" + url = "https://cloud.r-project.org/src/contrib/NMF_0.21.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/NMF" version('0.21.0', sha256='3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3') diff --git a/var/spack/repos/builtin/packages/r-nmof/package.py b/var/spack/repos/builtin/packages/r-nmof/package.py index ccd3061f12..1e43a1faeb 100644 --- a/var/spack/repos/builtin/packages/r-nmof/package.py +++ b/var/spack/repos/builtin/packages/r-nmof/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py index aea3a898a3..4e03f0032f 100644 --- a/var/spack/repos/builtin/packages/r-nnet/package.py +++ b/var/spack/repos/builtin/packages/r-nnet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-nnls/package.py b/var/spack/repos/builtin/packages/r-nnls/package.py index 6966bbde46..fff636f8a9 100644 --- a/var/spack/repos/builtin/packages/r-nnls/package.py +++ b/var/spack/repos/builtin/packages/r-nnls/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-nor1mix/package.py b/var/spack/repos/builtin/packages/r-nor1mix/package.py index 1bb824bada..8c9a234766 100644 --- a/var/spack/repos/builtin/packages/r-nor1mix/package.py +++ b/var/spack/repos/builtin/packages/r-nor1mix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-nortest/package.py b/var/spack/repos/builtin/packages/r-nortest/package.py index c93b8b79bb..112071de5d 100644 --- a/var/spack/repos/builtin/packages/r-nortest/package.py +++ b/var/spack/repos/builtin/packages/r-nortest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py index e20a04d681..57c9b8c21c 100644 --- a/var/spack/repos/builtin/packages/r-np/package.py +++ b/var/spack/repos/builtin/packages/r-np/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-npsurv/package.py b/var/spack/repos/builtin/packages/r-npsurv/package.py index 6ef60c6345..1f9d5c63c7 100644 --- a/var/spack/repos/builtin/packages/r-npsurv/package.py +++ b/var/spack/repos/builtin/packages/r-npsurv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-numderiv/package.py b/var/spack/repos/builtin/packages/r-numderiv/package.py index cdad79a700..925987a0f1 100644 --- a/var/spack/repos/builtin/packages/r-numderiv/package.py +++ b/var/spack/repos/builtin/packages/r-numderiv/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-oligoclasses/package.py b/var/spack/repos/builtin/packages/r-oligoclasses/package.py index 1ed8e1d4d3..ff553e2a6a 100644 --- a/var/spack/repos/builtin/packages/r-oligoclasses/package.py +++ b/var/spack/repos/builtin/packages/r-oligoclasses/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,25 +7,36 @@ from spack import * class ROligoclasses(RPackage): - """This package contains class definitions, validity checks, - and initialization methods for classes used by the oligo and - crlmm packages.""" + """Classes for high-throughput arrays supported by oligo and crlmm. - homepage = "https://www.bioconductor.org/packages/oligoClasses/" + This package contains class definitions, validity checks, and + initialization methods for classes used by the oligo and crlmm + packages.""" + + homepage = "https://bioconductor.org/packages/oligoClasses" git = "https://git.bioconductor.org/packages/oligoClasses.git" + version('1.46.0', commit='325684f66fc92f778098f24bcfbef0ce3da9717c') + version('1.44.0', commit='d3e1134cdbea5f95b83215dc66e5f7b6a1cd0638') + version('1.42.0', commit='ef125700d487b470281a9c1e985390633c4dd2bd') + version('1.40.0', commit='32f40617e62d05c457baaebc7e27585b852848ed') version('1.38.0', commit='fe2bb7f02c7ed3cbd338254c27ceba6ff829a962') - depends_on('r@3.4.0:3.4.9', when='@1.38.0') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r@2.14:', type=('build', 'run')) + depends_on('r-biocgenerics@0.3.2:', type=('build', 'run')) + depends_on('r-biobase@2.17.8:', type=('build', 'run')) + depends_on('r-iranges@2.5.17:', type=('build', 'run')) + depends_on('r-genomicranges@1.23.7:', type=('build', 'run')) depends_on('r-summarizedexperiment', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-affyio', type=('build', 'run')) + depends_on('r-biostrings@2.23.6:', type=('build', 'run')) + depends_on('r-affyio@1.23.2:', type=('build', 'run')) depends_on('r-ff', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) - depends_on('r-biocinstaller', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-biocinstaller', when='@1.38.0:1.42.0', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) + + depends_on('r-dbi', when='@1.40.0:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.27.1:', when='@1.44.0:', type=('build', 'run')) + depends_on('r-biocmanager', when='@1.44.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py index de7782cf42..36ddd5ed7d 100644 --- a/var/spack/repos/builtin/packages/r-openssl/package.py +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-openxlsx/package.py b/var/spack/repos/builtin/packages/r-openxlsx/package.py index cd375247e5..9c7d4326e5 100644 --- a/var/spack/repos/builtin/packages/r-openxlsx/package.py +++ b/var/spack/repos/builtin/packages/r-openxlsx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-optparse/package.py b/var/spack/repos/builtin/packages/r-optparse/package.py index 1dec5d57bb..ae987142db 100644 --- a/var/spack/repos/builtin/packages/r-optparse/package.py +++ b/var/spack/repos/builtin/packages/r-optparse/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ordinal/package.py b/var/spack/repos/builtin/packages/r-ordinal/package.py index ad837a3411..0345f8f040 100644 --- a/var/spack/repos/builtin/packages/r-ordinal/package.py +++ b/var/spack/repos/builtin/packages/r-ordinal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py index 0677d405f1..d0ce1a26e0 100644 --- a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py +++ b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -8,12 +8,16 @@ from spack import * class ROrgHsEgDb(RPackage): """Genome wide annotation for Human, primarily based on mapping - using Entrez Gene identifiers.""" + using Entrez Gene identifiers.""" homepage = "https://bioconductor.org/packages/org.Hs.eg.db/" url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz" + version('3.8.2', sha256='a0a16b7428f9e3d6ba54ebf4e05cd97a7bd298510ec4cf46ed2bed3e8f80db02', + url='https://www.bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Hs.eg.db_3.8.2.tar.gz') version('3.4.1', sha256='0f87b3f1925a1d7007e5ad9200bdf511788bd1d7cb76f1121feeb109889c2b00') - depends_on('r@3.4.0:3.4.9', when='@3.4.1') - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.7.0:', when='@3.4.1:', type=('build', 'run')) + + depends_on('r-annotationdbi@1.37.4:', when='@3.4.1:', type=('build', 'run')) + depends_on('r-annotationdbi@1.43.1:', when='@3.8.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-organismdbi/package.py b/var/spack/repos/builtin/packages/r-organismdbi/package.py index f9b4b68769..3fe6243c6a 100644 --- a/var/spack/repos/builtin/packages/r-organismdbi/package.py +++ b/var/spack/repos/builtin/packages/r-organismdbi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,24 +7,35 @@ from spack import * class ROrganismdbi(RPackage): - """The package enables a simple unified interface to several annotation + """Software to enable the smooth interfacing of different database + packages. + + The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.""" - homepage = "https://bioconductor.org/packages/OrganismDbi/" + homepage = "https://bioconductor.org/packages/OrganismDbi" git = "https://git.bioconductor.org/packages/OrganismDbi.git" + version('1.26.0', commit='495b4a8f8264d06d827537d43b3c6cc705244bb5') + version('1.24.0', commit='3428952dc0f267a01e256a1c0873656cfbfde7f8') + version('1.22.0', commit='24e953eb3847222d8018103b79b9fc72483cc513') + version('1.20.0', commit='d42e06a24777e5ffb966ad5addb4f46dfffa2269') version('1.18.1', commit='ba2d1237256805e935d9534a0c6f1ded07b42e95') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) + depends_on('r-annotationdbi@1.33.15:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.23.31:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-biocinstaller', type=('build', 'run')) + depends_on('r-biocinstaller', when='@1.18.1:1.22.0', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-graph', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-rbgl', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.18.1') + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.13:', when='@1.22.0:', type=('build', 'run')) + + depends_on('r-biocmanager', when='@1.24.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py index 9ddd728b04..500de7626b 100644 --- a/var/spack/repos/builtin/packages/r-packrat/package.py +++ b/var/spack/repos/builtin/packages/r-packrat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pacman/package.py b/var/spack/repos/builtin/packages/r-pacman/package.py index ae4627cf27..41e75f06ca 100644 --- a/var/spack/repos/builtin/packages/r-pacman/package.py +++ b/var/spack/repos/builtin/packages/r-pacman/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-paleotree/package.py b/var/spack/repos/builtin/packages/r-paleotree/package.py index f14ea30f0c..2464042e3b 100644 --- a/var/spack/repos/builtin/packages/r-paleotree/package.py +++ b/var/spack/repos/builtin/packages/r-paleotree/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pamr/package.py b/var/spack/repos/builtin/packages/r-pamr/package.py index d61717c0fd..c7cb41c6d1 100644 --- a/var/spack/repos/builtin/packages/r-pamr/package.py +++ b/var/spack/repos/builtin/packages/r-pamr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pan/package.py b/var/spack/repos/builtin/packages/r-pan/package.py index ef42bcf6b7..f39d8f9fee 100644 --- a/var/spack/repos/builtin/packages/r-pan/package.py +++ b/var/spack/repos/builtin/packages/r-pan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-parallelmap/package.py b/var/spack/repos/builtin/packages/r-parallelmap/package.py index e6c46c5149..a0d047ace2 100644 --- a/var/spack/repos/builtin/packages/r-parallelmap/package.py +++ b/var/spack/repos/builtin/packages/r-parallelmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-paramhelpers/package.py b/var/spack/repos/builtin/packages/r-paramhelpers/package.py index 2a422c6fdc..779df9f898 100644 --- a/var/spack/repos/builtin/packages/r-paramhelpers/package.py +++ b/var/spack/repos/builtin/packages/r-paramhelpers/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-party/package.py b/var/spack/repos/builtin/packages/r-party/package.py index 4ca371f37e..18303c3b1b 100644 --- a/var/spack/repos/builtin/packages/r-party/package.py +++ b/var/spack/repos/builtin/packages/r-party/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-partykit/package.py b/var/spack/repos/builtin/packages/r-partykit/package.py index 039949f867..f6ad1cf369 100644 --- a/var/spack/repos/builtin/packages/r-partykit/package.py +++ b/var/spack/repos/builtin/packages/r-partykit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pathview/package.py b/var/spack/repos/builtin/packages/r-pathview/package.py index cb753e51d8..80b6a1aebd 100644 --- a/var/spack/repos/builtin/packages/r-pathview/package.py +++ b/var/spack/repos/builtin/packages/r-pathview/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,26 +7,32 @@ from spack import * class RPathview(RPackage): - """Pathview is a tool set for pathway based data integration and - visualization. It maps and renders a wide variety of biological data on - relevant pathway graphs. All users need is to supply their data and - specify the target pathway. Pathview automatically downloads the pathway - graph data, parses the data file, maps user data to the pathway, and - render pathway graph with the mapped data. In addition, Pathview also - seamlessly integrates with pathway and gene set (enrichment) analysis - tools for large-scale and fully automated analysis.""" + """a tool set for pathway based data integration and visualization. - homepage = "https://www.bioconductor.org/packages/pathview/" + Pathview is a tool set for pathway based data integration and + visualization. It maps and renders a wide variety of biological data on + relevant pathway graphs. All users need is to supply their data and + specify the target pathway. Pathview automatically downloads the pathway + graph data, parses the data file, maps user data to the pathway, and + render pathway graph with the mapped data. In addition, Pathview also + seamlessly integrates with pathway and gene set (enrichment) analysis + tools for large-scale and fully automated analysis.""" + + homepage = "https://bioconductor.org/packages/pathview" git = "https://git.bioconductor.org/packages/pathview.git" + version('1.24.0', commit='e4401c1425c980ce2e6e478a4602a9f6d36ccd8d') + version('1.22.3', commit='ff86f9e166a5b03bbed1a0ad276778958c3045ce') + version('1.20.0', commit='a195afa6ba6c7917af2c7f77170f0644c46880c7') + version('1.18.2', commit='d2048981696564ec75f661ed665977d3a6e09188') version('1.16.7', commit='fc560ed15ef7393a73d35e714716cc24dc835339') - depends_on('r-keggrest', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-org-hs-eg-db', type=('build', 'run')) + depends_on('r-kegggraph', type=('build', 'run')) + depends_on('r-xml', type=('build', 'run')) + depends_on('r-rgraphviz', type=('build', 'run')) + depends_on('r-graph', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-graph', type=('build', 'run')) - depends_on('r-rgraphviz', type=('build', 'run')) - depends_on('r-xml', type=('build', 'run')) - depends_on('r-kegggraph', type=('build', 'run')) - depends_on('r-org-hs-eg-db', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.16.7') + depends_on('r-keggrest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pbapply/package.py b/var/spack/repos/builtin/packages/r-pbapply/package.py index f8457b7452..f63552328f 100644 --- a/var/spack/repos/builtin/packages/r-pbapply/package.py +++ b/var/spack/repos/builtin/packages/r-pbapply/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py index 4ec6ee9055..e58328adf3 100644 --- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py +++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,4 +27,4 @@ class RPbdzmq(RPackage): depends_on('r@3.0.0:', when='@:0.2-5', type=('build', 'run')) depends_on('r@3.2.0:', when='@0.2-6:', type=('build', 'run')) depends_on('r-r6', when='@:0.2-6', type=('build', 'run')) - depends_on('zeromq@4.0.4:') + depends_on('libzmq@4.0.4:') diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py index fd0ba857df..c7b7be8c42 100644 --- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py +++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pcamethods/package.py b/var/spack/repos/builtin/packages/r-pcamethods/package.py index a61b08a850..9981212244 100644 --- a/var/spack/repos/builtin/packages/r-pcamethods/package.py +++ b/var/spack/repos/builtin/packages/r-pcamethods/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,23 +7,28 @@ from spack import * class RPcamethods(RPackage): - """Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse - Non-Linear PCA and the conventional SVD PCA. A cluster based method for - missing value estimation is included for comparison. BPCA, PPCA and - NipalsPCA may be used to perform PCA on incomplete data as well as for - accurate missing value estimation. A set of methods for printing and - plotting the results is also provided. All PCA methods make use of the - same data structure (pcaRes) to provide a common interface to the PCA - results. Initiated at the Max-Planck Institute for Molecular Plant - Physiology, Golm, Germany.""" + """A collection of PCA methods. - homepage = "http://bioconductor.org/packages/pcaMethods/" + Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear + PCA and the conventional SVD PCA. A cluster based method for missing + value estimation is included for comparison. BPCA, PPCA and NipalsPCA + may be used to perform PCA on incomplete data as well as for accurate + missing value estimation. A set of methods for printing and plotting the + results is also provided. All PCA methods make use of the same data + structure (pcaRes) to provide a common interface to the PCA results. + Initiated at the Max-Planck Institute for Molecular Plant Physiology, + Golm, Germany.""" + + homepage = "https://bioconductor.org/packages/pcaMethods" git = "https://git.bioconductor.org/packages/pcaMethods.git" + version('1.76.0', commit='5db995330ced37dfd5ddad6ad1d90b4815d3127a') + version('1.74.0', commit='1b8f0a5cdfe3664119d0d7e926a2e0fe7320133c') + version('1.72.0', commit='1bb8c7d056645e62ee5179f6bb30b6594ebf3bfd') + version('1.70.0', commit='3368fad48ea930775505fd26e4179d7714d633d8') version('1.68.0', commit='c8d7c93dcaf7ef728f3d089ae5d55771b320bdab') depends_on('r-biobase', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.3:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.68.0') diff --git a/var/spack/repos/builtin/packages/r-pcapp/package.py b/var/spack/repos/builtin/packages/r-pcapp/package.py index fe62e5a714..299beee233 100644 --- a/var/spack/repos/builtin/packages/r-pcapp/package.py +++ b/var/spack/repos/builtin/packages/r-pcapp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-permute/package.py b/var/spack/repos/builtin/packages/r-permute/package.py index 9a3b0aa97f..b181976baa 100644 --- a/var/spack/repos/builtin/packages/r-permute/package.py +++ b/var/spack/repos/builtin/packages/r-permute/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pfam-db/package.py b/var/spack/repos/builtin/packages/r-pfam-db/package.py index 67d06960ae..df7d456787 100644 --- a/var/spack/repos/builtin/packages/r-pfam-db/package.py +++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,10 @@ class RPfamDb(RPackage): homepage = "https://www.bioconductor.org/packages/PFAM.db/" url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz" + version('3.10.0', sha256='038888f95ce69230ac0e0b08aa3bcb09965682415520d437a7fb0a031eefe158') version('3.4.1', sha256='fc45a0d53139daf85873f67bd3f1b68f2d883617f4447caddbd2d7dcc58a393f') - depends_on('r@3.4.0:3.4.9', when='@3.4.1') - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.7.0:', when='@3.4.1:', type=('build', 'run')) + depends_on('r-annotationdbi@1.37.4:', when='@3.4.1:', type=('build', 'run')) + + depends_on('r-annotationdbi@1.47.1:', when='@3.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-phangorn/package.py b/var/spack/repos/builtin/packages/r-phangorn/package.py index a285315885..c7acba152f 100644 --- a/var/spack/repos/builtin/packages/r-phangorn/package.py +++ b/var/spack/repos/builtin/packages/r-phangorn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py index e1825092c1..dd11719596 100644 --- a/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py +++ b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,5 +26,5 @@ class RPhantompeakqualtools(RPackage): conflicts('%gcc@6:') - def setup_environment(self, spack_env, run_env): - spack_env.set('BOOST_ROOT', self.spec['boost'].prefix) + def setup_build_environment(self, env): + env.set('BOOST_ROOT', self.spec['boost'].prefix) diff --git a/var/spack/repos/builtin/packages/r-phyloseq/package.py b/var/spack/repos/builtin/packages/r-phyloseq/package.py index 1a9016bcb1..84ebc98ba4 100644 --- a/var/spack/repos/builtin/packages/r-phyloseq/package.py +++ b/var/spack/repos/builtin/packages/r-phyloseq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,28 +7,43 @@ from spack import * class RPhyloseq(RPackage): - """phyloseq provides a set of classes and tools to facilitate the import, - storage, analysis, and graphical display of microbiome census data.""" + """Handling and analysis of high-throughput microbiome census data. - homepage = "https://www.bioconductor.org/packages/phyloseq/" + phyloseq provides a set of classes and tools to facilitate the import, + storage, analysis, and graphical display of microbiome census data.""" + + homepage = "https://bioconductor.org/packages/phyloseq" git = "https://git.bioconductor.org/packages/phyloseq.git" + version('1.28.0', commit='a86ed1e0a650fdf80bee5a0a5a82aaa5a276178d') + version('1.26.1', commit='a084072bc9e057b90adfbd59e27db2a1ecee151c') + version('1.24.2', commit='829992f88c79de48bb8749678624e2bbd3b66645') + version('1.22.3', commit='c695323f2963636d16acda9f05a583bd58e31344') version('1.20.0', commit='107d1d5e3437a6e33982c06a548d3cc91df2a7e0') - depends_on('r@3.4.0:3.4.9', when='@1.20.0') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-ade4', type=('build', 'run')) - depends_on('r-ape', type=('build', 'run')) - depends_on('r-biomformat', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-cluster', type=('build', 'run')) - depends_on('r-data-table', type=('build', 'run')) - depends_on('r-foreach', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-igraph', type=('build', 'run')) - depends_on('r-multtest', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-reshape2', type=('build', 'run')) - depends_on('r-scales', type=('build', 'run')) - depends_on('r-vegan', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.18.0:', type=('build', 'run')) + depends_on('r-ade4@1.7.4:', type=('build', 'run')) + depends_on('r-ape@3.4:', type=('build', 'run')) + depends_on('r-biomformat@1.0.0:', type=('build', 'run')) + depends_on('r-biostrings@2.40.0:', type=('build', 'run')) + depends_on('r-cluster@2.0.4:', type=('build', 'run')) + depends_on('r-data-table@1.9.6:', type=('build', 'run')) + depends_on('r-foreach@1.4.3:', type=('build', 'run')) + depends_on('r-ggplot2@2.1.0:', type=('build', 'run')) + depends_on('r-igraph@1.0.1:', type=('build', 'run')) + depends_on('r-multtest@2.28.0:', type=('build', 'run')) + depends_on('r-plyr@1.8.3:', type=('build', 'run')) + depends_on('r-reshape2@1.4.1:', type=('build', 'run')) + depends_on('r-scales@0.4.0:', type=('build', 'run')) + depends_on('r-vegan@2.3.5:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-ape@5.0:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-biobase@2.36.2:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-biocgenerics@0.22.0:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-data-table@1.10.4:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-vegan@2.4:', when='@1.22.3:', type=('build', 'run')) + + depends_on('r-vegan@2.5:', when='@1.24.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-phylostratr/package.py b/var/spack/repos/builtin/packages/r-phylostratr/package.py index 2fc3198551..a84c4333a9 100644 --- a/var/spack/repos/builtin/packages/r-phylostratr/package.py +++ b/var/spack/repos/builtin/packages/r-phylostratr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-phytools/package.py b/var/spack/repos/builtin/packages/r-phytools/package.py index 718e54cb4b..6bae38dbf9 100644 --- a/var/spack/repos/builtin/packages/r-phytools/package.py +++ b/var/spack/repos/builtin/packages/r-phytools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-picante/package.py b/var/spack/repos/builtin/packages/r-picante/package.py index 10ed4c0329..1eec2c274d 100644 --- a/var/spack/repos/builtin/packages/r-picante/package.py +++ b/var/spack/repos/builtin/packages/r-picante/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pillar/package.py b/var/spack/repos/builtin/packages/r-pillar/package.py index 213a2658db..325d40c4da 100644 --- a/var/spack/repos/builtin/packages/r-pillar/package.py +++ b/var/spack/repos/builtin/packages/r-pillar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pkgbuild/package.py b/var/spack/repos/builtin/packages/r-pkgbuild/package.py index 2e4dedfa1b..33ca13d095 100644 --- a/var/spack/repos/builtin/packages/r-pkgbuild/package.py +++ b/var/spack/repos/builtin/packages/r-pkgbuild/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pkgconfig/package.py b/var/spack/repos/builtin/packages/r-pkgconfig/package.py index bda85a518d..6e28f7cb15 100644 --- a/var/spack/repos/builtin/packages/r-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/r-pkgconfig/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pkgload/package.py b/var/spack/repos/builtin/packages/r-pkgload/package.py index fa6d0aa635..324584a242 100644 --- a/var/spack/repos/builtin/packages/r-pkgload/package.py +++ b/var/spack/repos/builtin/packages/r-pkgload/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py index e400f1228f..e40752c2fd 100644 --- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ class RPkgmaker(RPackage): changes in the interface(s) are more than likely to happen.""" homepage = "https://renozao.github.io/pkgmaker" - url = "https://cloud.r-project.org/src/contrib/pkgmaker_0.22.tar.gz" + url = "https://cloud.r-project.org/src/contrib/pkgmaker_0.27.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgmaker" version('0.27', sha256='17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a') diff --git a/var/spack/repos/builtin/packages/r-plogr/package.py b/var/spack/repos/builtin/packages/r-plogr/package.py index fbcdbee52a..7e062a210e 100644 --- a/var/spack/repos/builtin/packages/r-plogr/package.py +++ b/var/spack/repos/builtin/packages/r-plogr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-plot3d/package.py b/var/spack/repos/builtin/packages/r-plot3d/package.py index 6a8ed0ac0a..4b0fc46f94 100644 --- a/var/spack/repos/builtin/packages/r-plot3d/package.py +++ b/var/spack/repos/builtin/packages/r-plot3d/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-plotly/package.py b/var/spack/repos/builtin/packages/r-plotly/package.py index f6be7e55bd..173787f6d2 100644 --- a/var/spack/repos/builtin/packages/r-plotly/package.py +++ b/var/spack/repos/builtin/packages/r-plotly/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-plotmo/package.py b/var/spack/repos/builtin/packages/r-plotmo/package.py new file mode 100644 index 0000000000..8bec6e3d51 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-plotmo/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RPlotmo(RPackage): + """plotmo: Plot a Model's Residuals, Response, and Partial Dependence + Plots. + + Plot model surfaces for a wide variety of models using partial dependence + plots and other techniques. Also plot model residuals and other information + on the model.""" + + homepage = "http://www.milbo.users.sonic.net/" + url = "https://cloud.r-project.org/src/contrib/plotmo_3.5.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/plotmo" + + version('3.5.6', sha256='78f08dc897136d21fa8ade2acb6290351b569d29eb0592c7074c0be3cf2aa594') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-formula@1.2-3:', type=('build', 'run')) + depends_on('r-plotrix', type=('build', 'run')) + depends_on('r-teachingdemos', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py index edb9c9f0d2..26da98bbf7 100644 --- a/var/spack/repos/builtin/packages/r-plotrix/package.py +++ b/var/spack/repos/builtin/packages/r-plotrix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pls/package.py b/var/spack/repos/builtin/packages/r-pls/package.py index 28977bfa95..7a82c84cd0 100644 --- a/var/spack/repos/builtin/packages/r-pls/package.py +++ b/var/spack/repos/builtin/packages/r-pls/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py index c51d358124..041d02841a 100644 --- a/var/spack/repos/builtin/packages/r-plyr/package.py +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pmcmr/package.py b/var/spack/repos/builtin/packages/r-pmcmr/package.py index 505927ce05..1cd813915f 100644 --- a/var/spack/repos/builtin/packages/r-pmcmr/package.py +++ b/var/spack/repos/builtin/packages/r-pmcmr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py index d43ccb7314..025edb46c7 100644 --- a/var/spack/repos/builtin/packages/r-png/package.py +++ b/var/spack/repos/builtin/packages/r-png/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-polyclip/package.py b/var/spack/repos/builtin/packages/r-polyclip/package.py new file mode 100644 index 0000000000..947b290bcd --- /dev/null +++ b/var/spack/repos/builtin/packages/r-polyclip/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RPolyclip(RPackage): + """polyclip: Polygon Clipping""" + + homepage = "https://cloud.r-project.org/package=polyclip" + url = "https://cloud.r-project.org/src/contrib/polyclip_1.10-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/polyclip" + + version('1.10-0', sha256='74dabc0dfe5a527114f0bb8f3d22f5d1ae694e6ea9345912909bae885525d34b') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-polynom/package.py b/var/spack/repos/builtin/packages/r-polynom/package.py index 4244a2a4ea..3822185641 100644 --- a/var/spack/repos/builtin/packages/r-polynom/package.py +++ b/var/spack/repos/builtin/packages/r-polynom/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-popgenome/package.py b/var/spack/repos/builtin/packages/r-popgenome/package.py index 70ca45e3b4..1db5b5fbf1 100644 --- a/var/spack/repos/builtin/packages/r-popgenome/package.py +++ b/var/spack/repos/builtin/packages/r-popgenome/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-popvar/package.py b/var/spack/repos/builtin/packages/r-popvar/package.py index 15e1c03645..220b133f9f 100644 --- a/var/spack/repos/builtin/packages/r-popvar/package.py +++ b/var/spack/repos/builtin/packages/r-popvar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-powerlaw/package.py b/var/spack/repos/builtin/packages/r-powerlaw/package.py index 1f2382d6f7..b38b9cd1ad 100644 --- a/var/spack/repos/builtin/packages/r-powerlaw/package.py +++ b/var/spack/repos/builtin/packages/r-powerlaw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-prabclus/package.py b/var/spack/repos/builtin/packages/r-prabclus/package.py index 7ed08e4f1e..80f90ba0ba 100644 --- a/var/spack/repos/builtin/packages/r-prabclus/package.py +++ b/var/spack/repos/builtin/packages/r-prabclus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py index 706c23ee6a..543962196f 100644 --- a/var/spack/repos/builtin/packages/r-praise/package.py +++ b/var/spack/repos/builtin/packages/r-praise/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py index bed1fa0fc0..91a47310d0 100644 --- a/var/spack/repos/builtin/packages/r-preprocesscore/package.py +++ b/var/spack/repos/builtin/packages/r-preprocesscore/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,12 +7,15 @@ from spack import * class RPreprocesscore(RPackage): - """A library of core preprocessing routines""" + """A collection of pre-processing functions. - homepage = "https://bioconductor.org/packages/preprocessCore/" + A library of core preprocessing routines.""" + + homepage = "https://bioconductor.org/packages/preprocessCore" git = "https://git.bioconductor.org/packages/preprocessCore.git" + version('1.46.0', commit='8cfc3938c1b08424587f437ed6cd2ec43512500e') + version('1.44.0', commit='dc1dc61fc562aaff3fd9b11ab0d48c2d6b3a5b81') + version('1.42.0', commit='2e3a8baeacfaa1526d51252642772ea951015bba') + version('1.40.0', commit='969bb0e5cbd63d569502ae4e6eaadc1e216646dd') version('1.38.1', commit='c58cb4c720eda0f1c733b989b14912093a7c5fbc') - version('1.44.0', branch='RELEASE_3_8') - - depends_on('r@3.4.0:3.4.9', when='@1.38.1') diff --git a/var/spack/repos/builtin/packages/r-prettyunits/package.py b/var/spack/repos/builtin/packages/r-prettyunits/package.py index 4d57055ef1..283a538c2c 100644 --- a/var/spack/repos/builtin/packages/r-prettyunits/package.py +++ b/var/spack/repos/builtin/packages/r-prettyunits/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-processx/package.py b/var/spack/repos/builtin/packages/r-processx/package.py index d6661875b4..88b4e95a38 100644 --- a/var/spack/repos/builtin/packages/r-processx/package.py +++ b/var/spack/repos/builtin/packages/r-processx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-prodlim/package.py b/var/spack/repos/builtin/packages/r-prodlim/package.py index 022f3a6f61..97105f4c6c 100644 --- a/var/spack/repos/builtin/packages/r-prodlim/package.py +++ b/var/spack/repos/builtin/packages/r-prodlim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-progress/package.py b/var/spack/repos/builtin/packages/r-progress/package.py index 13f2217c49..ffe455a611 100644 --- a/var/spack/repos/builtin/packages/r-progress/package.py +++ b/var/spack/repos/builtin/packages/r-progress/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-promises/package.py b/var/spack/repos/builtin/packages/r-promises/package.py index 6b0f6bf679..9c21434a2f 100644 --- a/var/spack/repos/builtin/packages/r-promises/package.py +++ b/var/spack/repos/builtin/packages/r-promises/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-protgenerics/package.py b/var/spack/repos/builtin/packages/r-protgenerics/package.py index 2bd18088ca..fed08cdd6d 100644 --- a/var/spack/repos/builtin/packages/r-protgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-protgenerics/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,11 +7,15 @@ from spack import * class RProtgenerics(RPackage): - """S4 generic functions needed by Bioconductor proteomics packages.""" + """S4 generic functions for Bioconductor proteomics infrastructure. - homepage = "https://bioconductor.org/packages/ProtGenerics/" + S4 generic functions needed by Bioconductor proteomics packages.""" + + homepage = "https://bioconductor.org/packages/ProtGenerics" git = "https://git.bioconductor.org/packages/ProtGenerics.git" + version('1.16.0', commit='960a5fdc586898513b5ae9c48fffba5c5d703723') + version('1.14.0', commit='c85940b70a16ad69275c4facb3ef673d20a1c998') + version('1.12.0', commit='e84382a4b1730409f572fb681b5070017d00d30d') + version('1.10.0', commit='9ae2c3710b77381571900f0f25c6c8fda65795ac') version('1.8.0', commit='b2b3bb0938e20f58fca905f6870de7dbc9dfd7a3') - - depends_on('r@3.4.0:3.4.9', when='@1.8.0') diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py index 346cf3cf92..4c834fa39c 100644 --- a/var/spack/repos/builtin/packages/r-proto/package.py +++ b/var/spack/repos/builtin/packages/r-proto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-proxy/package.py b/var/spack/repos/builtin/packages/r-proxy/package.py index 93063a3fc8..79841fc9ab 100644 --- a/var/spack/repos/builtin/packages/r-proxy/package.py +++ b/var/spack/repos/builtin/packages/r-proxy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-pryr/package.py b/var/spack/repos/builtin/packages/r-pryr/package.py index 81a59b02c8..b8666bf622 100644 --- a/var/spack/repos/builtin/packages/r-pryr/package.py +++ b/var/spack/repos/builtin/packages/r-pryr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ps/package.py b/var/spack/repos/builtin/packages/r-ps/package.py index 6c75998ed5..d5279b1afe 100644 --- a/var/spack/repos/builtin/packages/r-ps/package.py +++ b/var/spack/repos/builtin/packages/r-ps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-psych/package.py b/var/spack/repos/builtin/packages/r-psych/package.py index fcabd1e0c9..79c171ca9c 100644 --- a/var/spack/repos/builtin/packages/r-psych/package.py +++ b/var/spack/repos/builtin/packages/r-psych/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ptw/package.py b/var/spack/repos/builtin/packages/r-ptw/package.py index 19c11a51d7..424bb0fb10 100644 --- a/var/spack/repos/builtin/packages/r-ptw/package.py +++ b/var/spack/repos/builtin/packages/r-ptw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-purrr/package.py b/var/spack/repos/builtin/packages/r-purrr/package.py index b948f733fa..da5220dfef 100644 --- a/var/spack/repos/builtin/packages/r-purrr/package.py +++ b/var/spack/repos/builtin/packages/r-purrr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-qtl/package.py b/var/spack/repos/builtin/packages/r-qtl/package.py index 010b95665c..43db132843 100644 --- a/var/spack/repos/builtin/packages/r-qtl/package.py +++ b/var/spack/repos/builtin/packages/r-qtl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-quadprog/package.py b/var/spack/repos/builtin/packages/r-quadprog/package.py index 7296854f12..063b7a91a5 100644 --- a/var/spack/repos/builtin/packages/r-quadprog/package.py +++ b/var/spack/repos/builtin/packages/r-quadprog/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py index 717dccfd2d..c173d4a783 100644 --- a/var/spack/repos/builtin/packages/r-quantmod/package.py +++ b/var/spack/repos/builtin/packages/r-quantmod/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py index f96d0bf704..6f1fe145a7 100644 --- a/var/spack/repos/builtin/packages/r-quantreg/package.py +++ b/var/spack/repos/builtin/packages/r-quantreg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-quantro/package.py b/var/spack/repos/builtin/packages/r-quantro/package.py index 637d741ecb..b56af1b419 100644 --- a/var/spack/repos/builtin/packages/r-quantro/package.py +++ b/var/spack/repos/builtin/packages/r-quantro/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,25 @@ from spack import * class RQuantro(RPackage): - """A data-driven test for the assumptions of quantile normalization using + """A test for when to use quantile normalization. + + A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, - MethylSet). Group level information about each sample (such as - Tumor / Normal status) must also be provided because the test assesses - if there are global differences in the distributions between the - user-defined groups.""" + MethylSet). Group level information about each sample (such as Tumor / + Normal status) must also be provided because the test assesses if there + are global differences in the distributions between the user-defined + groups.""" - homepage = "https://www.bioconductor.org/packages/quantro/" + homepage = "https://bioconductor.org/packages/quantro" git = "https://git.bioconductor.org/packages/quantro.git" + version('1.18.0', commit='f6553c2296289eed31e4b2f32a082e990bdb8359') + version('1.16.0', commit='cfc2e853bdc3cc90fd35e153fe243892d50d61c6') + version('1.14.0', commit='2d43264b2a95ae8ca51a69d7768fe43b9f1b77bb') + version('1.12.0', commit='1cfcc73875cf4ecc2618e5e45fda89bd075a5d12') version('1.10.0', commit='111337c0aba052aa49c3d2e2d3042794b28858c9') + depends_on('r@3.1.3:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-minfi', type=('build', 'run')) depends_on('r-doparallel', type=('build', 'run')) @@ -26,4 +33,3 @@ class RQuantro(RPackage): depends_on('r-iterators', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.10.0') diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py index 2e1b8e56b3..740a6cc996 100644 --- a/var/spack/repos/builtin/packages/r-qvalue/package.py +++ b/var/spack/repos/builtin/packages/r-qvalue/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,27 +7,29 @@ from spack import * class RQvalue(RPackage): - """This package takes a list of p-values resulting from the - simultaneous testing of many hypotheses and estimates their - q-values and local FDR values. The q-value of a test measures - the proportion of false positives incurred (called the false - discovery rate) when that particular test is called significant. - The local FDR measures the posterior probability the null - hypothesis is true given the test's p-value. Various plots are - automatically generated, allowing one to make sensible - significance cut-offs. Several mathematical results have - recently been shown on the conservative accuracy of the - estimated q-values from this software. The software can be - applied to problems in genomics, brain imaging, astrophysics, - and data mining.""" + """Q-value estimation for false discovery rate control. - homepage = "https://www.bioconductor.org/packages/qvalue/" + This package takes a list of p-values resulting from the simultaneous + testing of many hypotheses and estimates their q-values and local FDR + values. The q-value of a test measures the proportion of false positives + incurred (called the false discovery rate) when that particular test is + called significant. The local FDR measures the posterior probability the + null hypothesis is true given the test's p-value. Various plots are + automatically generated, allowing one to make sensible significance cut- + offs. Several mathematical results have recently been shown on the + conservative accuracy of the estimated q-values from this software. The + software can be applied to problems in genomics, brain imaging, + astrophysics, and data mining.""" + + homepage = "https://bioconductor.org/packages/qvalue" git = "https://git.bioconductor.org/packages/qvalue.git" + version('2.16.0', commit='5efbe20ef522a45a7a04b681f72bb9a12e2747ae') + version('2.14.1', commit='b694e4b264f25250eb1d1115e70c07f65767c20e') version('2.12.0', commit='7df64ebfcbe69dcbf8b88cb6ef0068bf16979673') + version('2.10.0', commit='581e5664b4356440a96310897398f01a98ceb81b') version('2.8.0', commit='c7bf3315619d42d800f57a36670c25a7495ded72') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.8.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@2.12.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-r-methodss3/package.py b/var/spack/repos/builtin/packages/r-r-methodss3/package.py index 585e4cdd6b..5dc58406cc 100644 --- a/var/spack/repos/builtin/packages/r-r-methodss3/package.py +++ b/var/spack/repos/builtin/packages/r-r-methodss3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-r-oo/package.py b/var/spack/repos/builtin/packages/r-r-oo/package.py index cc2d2b1f02..e25e515b7f 100644 --- a/var/spack/repos/builtin/packages/r-r-oo/package.py +++ b/var/spack/repos/builtin/packages/r-r-oo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-r-utils/package.py b/var/spack/repos/builtin/packages/r-r-utils/package.py index eb8a18b5db..a1e3743c97 100644 --- a/var/spack/repos/builtin/packages/r-r-utils/package.py +++ b/var/spack/repos/builtin/packages/r-r-utils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-r6/package.py b/var/spack/repos/builtin/packages/r-r6/package.py index 3b2c3867a0..43429dc5c4 100644 --- a/var/spack/repos/builtin/packages/r-r6/package.py +++ b/var/spack/repos/builtin/packages/r-r6/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-randomfields/package.py b/var/spack/repos/builtin/packages/r-randomfields/package.py index 42be2728a1..7856afa835 100644 --- a/var/spack/repos/builtin/packages/r-randomfields/package.py +++ b/var/spack/repos/builtin/packages/r-randomfields/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py index f8420eebb0..aadecfe47b 100644 --- a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py +++ b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,7 @@ class RRandomfieldsutils(RPackage): Furthermore, it includes the Struve functions.""" homepage = "https://cloud.r-project.org/package=RandomFieldsUtils" - url = "https://cloud.r-project.org/src/contrib/RandomFieldsUtils_0.3.25.tar.gz" + url = "https://cloud.r-project.org/src/contrib/RandomFieldsUtils_0.5.3.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/RandomFieldsUtils" version('0.5.3', sha256='ea823cba2e254a9f534efb4b772c0aeef2039ee9ef99744e077b969a87f8031d') diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py index d20c4d32c4..78245e4aac 100644 --- a/var/spack/repos/builtin/packages/r-randomforest/package.py +++ b/var/spack/repos/builtin/packages/r-randomforest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-randomglm/package.py b/var/spack/repos/builtin/packages/r-randomglm/package.py index 817d6467b4..461fa43d36 100644 --- a/var/spack/repos/builtin/packages/r-randomglm/package.py +++ b/var/spack/repos/builtin/packages/r-randomglm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ranger/package.py b/var/spack/repos/builtin/packages/r-ranger/package.py index b16c2e2ead..eec92d0ac1 100644 --- a/var/spack/repos/builtin/packages/r-ranger/package.py +++ b/var/spack/repos/builtin/packages/r-ranger/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rann/package.py b/var/spack/repos/builtin/packages/r-rann/package.py index bbe014ee45..c4ee212e10 100644 --- a/var/spack/repos/builtin/packages/r-rann/package.py +++ b/var/spack/repos/builtin/packages/r-rann/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rappdirs/package.py b/var/spack/repos/builtin/packages/r-rappdirs/package.py index 25644aa1f2..e00f35597f 100644 --- a/var/spack/repos/builtin/packages/r-rappdirs/package.py +++ b/var/spack/repos/builtin/packages/r-rappdirs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py index 80e83d79c2..58ad440060 100644 --- a/var/spack/repos/builtin/packages/r-raster/package.py +++ b/var/spack/repos/builtin/packages/r-raster/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rbgl/package.py b/var/spack/repos/builtin/packages/r-rbgl/package.py index d5390e9a5b..b4f816d24b 100644 --- a/var/spack/repos/builtin/packages/r-rbgl/package.py +++ b/var/spack/repos/builtin/packages/r-rbgl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,20 @@ from spack import * class RRbgl(RPackage): - """A fairly extensive and comprehensive interface to the graph - algorithms contained in the BOOST library.""" + """An interface to the BOOST graph library. - homepage = "https://www.bioconductor.org/packages/RBGL/" + A fairly extensive and comprehensive interface to the graph algorithms + contained in the BOOST library.""" + + homepage = "https://bioconductor.org/packages/RBGL" git = "https://git.bioconductor.org/packages/RBGL.git" version('1.60.0', commit='ef24c17c411659b8f030602bd9781c534d6ec93b') + version('1.58.2', commit='086ad0c6bab7be29311b6ae14fd39df7a21331a6') + version('1.56.0', commit='a1fa9d89c6a3401892c5dd1493df6a14031f0912') + version('1.54.0', commit='e9c743d380e83c155495cb8732102f01f213c905') version('1.52.0', commit='93e8fcfafec8f1cd5638fe30dc0f9506d15b49c0') - depends_on('r@3.4.0:3.4.9', when='@1.52.0') - depends_on('r@3.6.0:', when='@1.60.0', type=('build', 'run')) - depends_on('r-bh', when='@1.60.0', type=('build', 'run')) depends_on('r-graph', type=('build', 'run')) + + depends_on('r-bh', when='@1.60.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rbokeh/package.py b/var/spack/repos/builtin/packages/r-rbokeh/package.py index 619e67050c..7b0c75d974 100644 --- a/var/spack/repos/builtin/packages/r-rbokeh/package.py +++ b/var/spack/repos/builtin/packages/r-rbokeh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcmdcheck/package.py b/var/spack/repos/builtin/packages/r-rcmdcheck/package.py index c64a59bc97..b1fc06071d 100644 --- a/var/spack/repos/builtin/packages/r-rcmdcheck/package.py +++ b/var/spack/repos/builtin/packages/r-rcmdcheck/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py index d3770d93b5..f49aaa4893 100644 --- a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py +++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index 5053b32ce1..4d9b6dae2c 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcppannoy/package.py b/var/spack/repos/builtin/packages/r-rcppannoy/package.py index 64ee9a72aa..e65c96ed49 100644 --- a/var/spack/repos/builtin/packages/r-rcppannoy/package.py +++ b/var/spack/repos/builtin/packages/r-rcppannoy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py index 6250468572..2c9dd4d30f 100644 --- a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py +++ b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcppblaze/package.py b/var/spack/repos/builtin/packages/r-rcppblaze/package.py index b043f054eb..4838083e49 100644 --- a/var/spack/repos/builtin/packages/r-rcppblaze/package.py +++ b/var/spack/repos/builtin/packages/r-rcppblaze/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcppcctz/package.py b/var/spack/repos/builtin/packages/r-rcppcctz/package.py index 7948218f5e..4acfe804ea 100644 --- a/var/spack/repos/builtin/packages/r-rcppcctz/package.py +++ b/var/spack/repos/builtin/packages/r-rcppcctz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py index 822092a103..e86e6c0994 100644 --- a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py +++ b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py index 1095229c21..8b6ed5cc49 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcpphnsw/package.py b/var/spack/repos/builtin/packages/r-rcpphnsw/package.py new file mode 100644 index 0000000000..9196583bf5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcpphnsw/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRcpphnsw(RPackage): + """RcppHNSW: 'Rcpp' Bindings for 'hnswlib', a Library for Approximate + NearestNeighbors""" + + homepage = "https://cloud.r-project.org/package=RcppHNSW" + url = "https://cloud.r-project.org/src/contrib/RcppHNSW_0.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppHNSW" + + version('0.1.0', sha256='75a54c30953845dec685764c7b3b4cd7315197c91aef4ab3b4eb0a6293010a95') + + depends_on('r-rcpp@0.11.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppparallel/package.py b/var/spack/repos/builtin/packages/r-rcppparallel/package.py index ad723a0de5..0e172ca491 100644 --- a/var/spack/repos/builtin/packages/r-rcppparallel/package.py +++ b/var/spack/repos/builtin/packages/r-rcppparallel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcppprogress/package.py b/var/spack/repos/builtin/packages/r-rcppprogress/package.py index 618bd87ece..c0ed65f86f 100644 --- a/var/spack/repos/builtin/packages/r-rcppprogress/package.py +++ b/var/spack/repos/builtin/packages/r-rcppprogress/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rcurl/package.py b/var/spack/repos/builtin/packages/r-rcurl/package.py index 3014977be6..4fe4b6454e 100644 --- a/var/spack/repos/builtin/packages/r-rcurl/package.py +++ b/var/spack/repos/builtin/packages/r-rcurl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rda/package.py b/var/spack/repos/builtin/packages/r-rda/package.py index f5d0a08bf6..06c40411a4 100644 --- a/var/spack/repos/builtin/packages/r-rda/package.py +++ b/var/spack/repos/builtin/packages/r-rda/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rdpack/package.py b/var/spack/repos/builtin/packages/r-rdpack/package.py index 2febe78186..77b290c72c 100644 --- a/var/spack/repos/builtin/packages/r-rdpack/package.py +++ b/var/spack/repos/builtin/packages/r-rdpack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-readr/package.py b/var/spack/repos/builtin/packages/r-readr/package.py index 7020c1e2fc..f618df980b 100644 --- a/var/spack/repos/builtin/packages/r-readr/package.py +++ b/var/spack/repos/builtin/packages/r-readr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-readxl/package.py b/var/spack/repos/builtin/packages/r-readxl/package.py index 6d97196aa2..a4dbb70c4f 100644 --- a/var/spack/repos/builtin/packages/r-readxl/package.py +++ b/var/spack/repos/builtin/packages/r-readxl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-recipes/package.py b/var/spack/repos/builtin/packages/r-recipes/package.py index 12c00f6613..2bd58e60cf 100644 --- a/var/spack/repos/builtin/packages/r-recipes/package.py +++ b/var/spack/repos/builtin/packages/r-recipes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py index f8f204f0a1..d2a190b7fa 100644 --- a/var/spack/repos/builtin/packages/r-registry/package.py +++ b/var/spack/repos/builtin/packages/r-registry/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rematch/package.py b/var/spack/repos/builtin/packages/r-rematch/package.py index d4172c70da..00117f87a9 100644 --- a/var/spack/repos/builtin/packages/r-rematch/package.py +++ b/var/spack/repos/builtin/packages/r-rematch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-remotes/package.py b/var/spack/repos/builtin/packages/r-remotes/package.py index 9c4a790dcb..ca51212143 100644 --- a/var/spack/repos/builtin/packages/r-remotes/package.py +++ b/var/spack/repos/builtin/packages/r-remotes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-reordercluster/package.py b/var/spack/repos/builtin/packages/r-reordercluster/package.py index 3c85ee3503..bf1951f3ca 100644 --- a/var/spack/repos/builtin/packages/r-reordercluster/package.py +++ b/var/spack/repos/builtin/packages/r-reordercluster/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py index de4930c4c8..17d6ef9200 100644 --- a/var/spack/repos/builtin/packages/r-reportingtools/package.py +++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,42 +7,45 @@ from spack import * class RReportingtools(RPackage): - """The ReportingTools software package enables users to easily - display reports of analysis results generated from sources such - as microarray and sequencing data. The package allows users to - create HTML pages that may be viewed on a web browser such as - Safari, or in other formats readable by programs such as Excel. - Users can generate tables with sortable and filterable columns, - make and display plots, and link table entries to other data - sources such as NCBI or larger plots within the HTML page. Using - the package, users can also produce a table of contents page to - link various reports together for a particular project that can - be viewed in a web browser. For more examples, please visit our - site: http:// research-pub.gene.com/ReportingTools.""" + """Tools for making reports in various formats. - homepage = "https://bioconductor.org/packages/ReportingTools/" + The ReportingTools software package enables users to easily display + reports of analysis results generated from sources such as microarray + and sequencing data. The package allows users to create HTML pages that + may be viewed on a web browser such as Safari, or in other formats + readable by programs such as Excel. Users can generate tables with + sortable and filterable columns, make and display plots, and link table + entries to other data sources such as NCBI or larger plots within the + HTML page. Using the package, users can also produce a table of contents + page to link various reports together for a particular project that can + be viewed in a web browser. For more examples, please visit our site: + http:// research-pub.gene.com/ReportingTools.""" + + homepage = "https://bioconductor.org/packages/ReportingTools" git = "https://git.bioconductor.org/packages/ReportingTools.git" + version('2.24.0', commit='d114c658affba9b682a37b4e2caf4341cf8da6cf') + version('2.22.1', commit='dce6af6c6a1cddff077fe61368f2c13e5a0e7bab') + version('2.20.0', commit='77e14ae13fdc16654300852dfd94e6cef58009da') + version('2.17.3', commit='b2e379cd5b813d8ccca37ec25f0660deec943622') version('2.16.0', commit='b1aa0ea302da7f2993ce8087b1d09c11ddf03663') - depends_on('r@3.4.0:3.4.9', when='@2.16.0') depends_on('r-knitr', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-hwriter', type=('build', 'run')) depends_on('r-category', type=('build', 'run')) depends_on('r-gostats', type=('build', 'run')) - depends_on('r-limma', type=('build', 'run')) - depends_on('r-limma', type=('build', 'run')) + depends_on('r-limma@3.17.5:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-edger', type=('build', 'run')) depends_on('r-annotate', type=('build', 'run')) depends_on('r-pfam-db', type=('build', 'run')) depends_on('r-gseabase', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.6:', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) depends_on('r-r-utils', type=('build', 'run')) - depends_on('r-deseq2', type=('build', 'run')) + depends_on('r-deseq2@1.3.41:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-ggbio', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-repr/package.py b/var/spack/repos/builtin/packages/r-repr/package.py index 925ab477ea..f9dde095a7 100644 --- a/var/spack/repos/builtin/packages/r-repr/package.py +++ b/var/spack/repos/builtin/packages/r-repr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-reprex/package.py b/var/spack/repos/builtin/packages/r-reprex/package.py index 9c9206e9a6..4c215d4f4e 100644 --- a/var/spack/repos/builtin/packages/r-reprex/package.py +++ b/var/spack/repos/builtin/packages/r-reprex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-reshape/package.py b/var/spack/repos/builtin/packages/r-reshape/package.py index 9ef32d2fb6..c5b61c71bc 100644 --- a/var/spack/repos/builtin/packages/r-reshape/package.py +++ b/var/spack/repos/builtin/packages/r-reshape/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py index 4feabd2e1d..b4b43a892f 100644 --- a/var/spack/repos/builtin/packages/r-reshape2/package.py +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-reticulate/package.py b/var/spack/repos/builtin/packages/r-reticulate/package.py index f1dc039491..378134032f 100644 --- a/var/spack/repos/builtin/packages/r-reticulate/package.py +++ b/var/spack/repos/builtin/packages/r-reticulate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rex/package.py b/var/spack/repos/builtin/packages/r-rex/package.py index 168aced530..26066e8bdc 100644 --- a/var/spack/repos/builtin/packages/r-rex/package.py +++ b/var/spack/repos/builtin/packages/r-rex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rgdal/package.py b/var/spack/repos/builtin/packages/r-rgdal/package.py index 156781d24a..c25fd9120b 100644 --- a/var/spack/repos/builtin/packages/r-rgdal/package.py +++ b/var/spack/repos/builtin/packages/r-rgdal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rgenoud/package.py b/var/spack/repos/builtin/packages/r-rgenoud/package.py index 46875cffeb..19e9bd26f6 100644 --- a/var/spack/repos/builtin/packages/r-rgenoud/package.py +++ b/var/spack/repos/builtin/packages/r-rgenoud/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rgeos/package.py b/var/spack/repos/builtin/packages/r-rgeos/package.py index 248a5b1760..a6fea66172 100644 --- a/var/spack/repos/builtin/packages/r-rgeos/package.py +++ b/var/spack/repos/builtin/packages/r-rgeos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rgexf/package.py b/var/spack/repos/builtin/packages/r-rgexf/package.py index 3a98d90035..137a4baf6a 100644 --- a/var/spack/repos/builtin/packages/r-rgexf/package.py +++ b/var/spack/repos/builtin/packages/r-rgexf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rgl/package.py b/var/spack/repos/builtin/packages/r-rgl/package.py index fcd18eb22f..c890df70d9 100644 --- a/var/spack/repos/builtin/packages/r-rgl/package.py +++ b/var/spack/repos/builtin/packages/r-rgl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,6 +20,7 @@ class RRgl(RPackage): version('0.100.26', sha256='e1889c2723ad458b39fdf9366fdaf590d7657d3762748f8534a8491ef754e740') version('0.100.24', sha256='1233a7bdc5a2b908fc64d5f56e92a0e123e8f7c0b9bac93dfd005608b78fa35a') + version('0.100.19', sha256='50630702554e422e0603f27d499aad3b6f822de5a73da7fdf70404ac50df7025') version('0.99.16', sha256='692a545ed2ff0f5e15289338736f0e3c092667574c43ac358d8004901d7a1a61') version('0.98.1', sha256='5f49bed9e092e672f73c8a1a5365cdffcda06db0315ac087e95ab9c9c71a6986') diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py index bd24f77056..1938aa41fe 100644 --- a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py +++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rgraphviz/package.py b/var/spack/repos/builtin/packages/r-rgraphviz/package.py index 34936da7e3..f0e986190e 100644 --- a/var/spack/repos/builtin/packages/r-rgraphviz/package.py +++ b/var/spack/repos/builtin/packages/r-rgraphviz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,21 @@ from spack import * class RRgraphviz(RPackage): - """Interfaces R with the AT and T graphviz library for plotting - R graph objects from the graph package.""" + """Provides plotting capabilities for R graph objects. - homepage = "http://bioconductor.org/packages/Rgraphviz/" + Interfaces R with the AT and T graphviz library for plotting R graph + objects from the graph package.""" + + homepage = "https://bioconductor.org/packages/Rgraphviz" git = "https://git.bioconductor.org/packages/Rgraphviz.git" + version('2.28.0', commit='c1f57c11f037c977f1d17f227f12a09a999e8c0b') + version('2.26.0', commit='e9b08c77121a45c65129d94a12b5c0b31c65617f') + version('2.24.0', commit='7d1fb00afed0d44e32b4a46f10137ab34f100577') + version('2.22.0', commit='5b8ebbf9b38574c08959dd4632e802b3fbccc121') version('2.20.0', commit='eface6298150667bb22eac672f1a45e52fbf8c90') - depends_on('r@3.4.0:3.4.9', when='@2.20.0') + depends_on('r@2.6.0:', type=('build', 'run')) depends_on('r-graph', type=('build', 'run')) + + depends_on('graphviz@2.16:', type='run') diff --git a/var/spack/repos/builtin/packages/r-rhdf5/package.py b/var/spack/repos/builtin/packages/r-rhdf5/package.py index 0f86da44f3..932d1c342c 100644 --- a/var/spack/repos/builtin/packages/r-rhdf5/package.py +++ b/var/spack/repos/builtin/packages/r-rhdf5/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,30 @@ from spack import * class RRhdf5(RPackage): - """This R/Bioconductor package provides an interface between HDF5 - and R. HDF5's main features are the ability to store and access very - large and/or complex datasets and a wide variety of metadata on mass - storage (disk) through a completely portable file format. The rhdf5 - package is thus suited for the exchange of large and/or complex - datasets between R and other software package, and for letting R - applications work on datasets that are larger than the available RAM.""" - - homepage = "https://www.bioconductor.org/packages/rhdf5/" + """R Interface to HDF5. + + This package provides an interface between HDF5 and R. HDF5's main + features are the ability to store and access very large and/or complex + datasets and a wide variety of metadata on mass storage (disk) through a + completely portable file format. The rhdf5 package is thus suited for + the exchange of large and/or complex datasets between R and other + software package, and for letting R applications work on datasets that + are larger than the available RAM.""" + + homepage = "https://bioconductor.org/packages/rhdf5" git = "https://git.bioconductor.org/packages/rhdf5.git" + version('2.28.1', commit='e230fa34d6f3e97dd4e6065115675baf5e8213bb') + version('2.26.2', commit='81e11258db493661a19cf83e142b690ecac4e6cf') + version('2.24.0', commit='e926e8ce4e77082781afb943324a1e6745385b48') + version('2.22.0', commit='4431bdc0a2bcbb8086ee08a0f2300129b808d1be') version('2.20.0', commit='37b5165325062728bbec9167f89f5f4b794f30bc') - depends_on('r@3.4.0:3.4.9', when='@2.20.0') depends_on('r-zlibbioc', type=('build', 'run')) + + depends_on('r-rhdf5lib', when='@2.24.0:', type=('build', 'run')) + + depends_on('r@3.5.0:', when='@2.26.2:', type=('build', 'run')) + depends_on('r-rhdf5lib@1.3.2:', when='@2.26.2:', type=('build', 'run')) + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rhdf5lib/package.py b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py new file mode 100644 index 0000000000..266bb4859f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRhdf5lib(RPackage): + """hdf5 library as an R package. + + Provides C and C++ hdf5 libraries.""" + + homepage = "https://bioconductor.org/packages/Rhdf5lib" + git = "https://git.bioconductor.org/packages/Rhdf5lib.git" + + version('1.6.3', commit='11ac3069f28b0068002db9c645817401f6c5b3c4') + version('1.4.3', commit='f6be8c2659b2daa17541506058917b7981490d65') + version('1.2.1', commit='dbf85dbedb736d5a696794d52875729c8514494e') + version('1.0.0', commit='79608038c2016a518ba747fe6a2bf02ce53a75f9') + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rhmmer/package.py b/var/spack/repos/builtin/packages/r-rhmmer/package.py index 23854fb2b1..ab00ef0bad 100644 --- a/var/spack/repos/builtin/packages/r-rhmmer/package.py +++ b/var/spack/repos/builtin/packages/r-rhmmer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rhtslib/package.py b/var/spack/repos/builtin/packages/r-rhtslib/package.py index e2286b4847..2ee01f0ac9 100644 --- a/var/spack/repos/builtin/packages/r-rhtslib/package.py +++ b/var/spack/repos/builtin/packages/r-rhtslib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,26 @@ from spack import * class RRhtslib(RPackage): - """This package provides version 1.1 of the 'HTSlib' C library - for high-throughput sequence analysis. The package is primarily - useful to developers of other R packages who wish to make use - of HTSlib. Motivation and instructions for use of this package - are in the vignette, vignette(package="Rhtslib", "Rhtslib").""" + """HTSlib high-throughput sequencing library as an R package. - homepage = "https://www.bioconductor.org/packages/Rhtslib/" + This package provides version 1.7 of the 'HTSlib' C library for high- + throughput sequence analysis. The package is primarily useful to + developers of other R packages who wish to make use of HTSlib. + Motivation and instructions for use of this package are in the vignette, + vignette(package="Rhtslib", "Rhtslib").""" + + homepage = "https://bioconductor.org/packages/Rhtslib" git = "https://git.bioconductor.org/packages/Rhtslib.git" + version('1.16.3', commit='3ed0b5db2ee3cf0df1c6096fde8855c8485eebd4') + version('1.14.1', commit='4be260720f845a34d0ac838278fce1363f645230') + version('1.12.1', commit='e3487b1355995d09b28fde5d0a7504a3e79a7203') + version('1.10.0', commit='53dcf7dfe35d735283956c77c011a97ca3f4eb26') version('1.8.0', commit='3b5493473bed42958614091c58c739932ffcfa79') - depends_on('r@3.4.0:3.4.9', when='@1.8.0') depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('autoconf@2.67:', type='build') + + depends_on('bzip2', type=('build', 'link', 'run')) + depends_on('xz', type=('build', 'link', 'run')) + depends_on('curl', type=('build', 'link', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rinside/package.py b/var/spack/repos/builtin/packages/r-rinside/package.py index f540a83bf8..5b2b99e161 100644 --- a/var/spack/repos/builtin/packages/r-rinside/package.py +++ b/var/spack/repos/builtin/packages/r-rinside/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rio/package.py b/var/spack/repos/builtin/packages/r-rio/package.py index 5b4934f429..4472501133 100644 --- a/var/spack/repos/builtin/packages/r-rio/package.py +++ b/var/spack/repos/builtin/packages/r-rio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rjags/package.py b/var/spack/repos/builtin/packages/r-rjags/package.py index c2a70c8dc3..7a74f65ba3 100644 --- a/var/spack/repos/builtin/packages/r-rjags/package.py +++ b/var/spack/repos/builtin/packages/r-rjags/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py index 59cbde505f..762836e685 100644 --- a/var/spack/repos/builtin/packages/r-rjava/package.py +++ b/var/spack/repos/builtin/packages/r-rjava/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py index ae0dbac3f4..a2084273c4 100644 --- a/var/spack/repos/builtin/packages/r-rjson/package.py +++ b/var/spack/repos/builtin/packages/r-rjson/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py index 17a6b7251e..b38fe5c17d 100644 --- a/var/spack/repos/builtin/packages/r-rjsonio/package.py +++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rlang/package.py b/var/spack/repos/builtin/packages/r-rlang/package.py index 5136c13061..ae099f7b9a 100644 --- a/var/spack/repos/builtin/packages/r-rlang/package.py +++ b/var/spack/repos/builtin/packages/r-rlang/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rmarkdown/package.py b/var/spack/repos/builtin/packages/r-rmarkdown/package.py index c059b57ce5..52f76a7a56 100644 --- a/var/spack/repos/builtin/packages/r-rmarkdown/package.py +++ b/var/spack/repos/builtin/packages/r-rmarkdown/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rminer/package.py b/var/spack/repos/builtin/packages/r-rminer/package.py index 84f86a813d..5d4a97f247 100644 --- a/var/spack/repos/builtin/packages/r-rminer/package.py +++ b/var/spack/repos/builtin/packages/r-rminer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rmpfr/package.py b/var/spack/repos/builtin/packages/r-rmpfr/package.py index 72e232adc1..e01eeefbd1 100644 --- a/var/spack/repos/builtin/packages/r-rmpfr/package.py +++ b/var/spack/repos/builtin/packages/r-rmpfr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rmpi/package.py b/var/spack/repos/builtin/packages/r-rmpi/package.py index a029dfba27..b1e4bdccfa 100644 --- a/var/spack/repos/builtin/packages/r-rmpi/package.py +++ b/var/spack/repos/builtin/packages/r-rmpi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rmutil/package.py b/var/spack/repos/builtin/packages/r-rmutil/package.py index 58bb7c4154..202cf10571 100644 --- a/var/spack/repos/builtin/packages/r-rmutil/package.py +++ b/var/spack/repos/builtin/packages/r-rmutil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py index 6f02466d06..7c161a60cb 100644 --- a/var/spack/repos/builtin/packages/r-rmysql/package.py +++ b/var/spack/repos/builtin/packages/r-rmysql/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rnaseqmap/package.py b/var/spack/repos/builtin/packages/r-rnaseqmap/package.py new file mode 100644 index 0000000000..361e11a8f1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rnaseqmap/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRnaseqmap(RPackage): + """rnaSeq secondary analyses. + + The rnaSeqMap library provides classes and functions to analyze the RNA- + sequencing data using the coverage profiles in multiple samples at a + time""" + + homepage = "https://bioconductor.org/packages/rnaSeqMap" + git = "https://git.bioconductor.org/packages/rnaSeqMap.git" + + version('2.42.0', commit='3a3a1030cc38d79d04536e0ab16114e4fa6721cf') + version('2.40.1', commit='c122d645b3503fb1a061f5515e4f8cf2863b3ba3') + version('2.38.0', commit='5eb9583bfacd375161739a8ae6057204487f8b9e') + version('2.36.0', commit='69c46fa467be0ac30776ede85a521f7622539b7e') + version('2.34.0', commit='7881bc00600ed824ac437edf3cfba35573261e46') + + depends_on('r@2.11.0:', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-rsamtools', type=('build', 'run')) + depends_on('r-genomicalignments', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-edger', type=('build', 'run')) + depends_on('r-deseq', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py index c4b52c3437..ac7e0fd8e6 100644 --- a/var/spack/repos/builtin/packages/r-rngtools/package.py +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,7 +14,7 @@ class RRngtools(RPackage): the way current RNG settings can be changed.""" homepage = "https://renozao.github.io/rngtools" - url = "https://cloud.r-project.org/src/contrib/rngtools_1.2.4.tar.gz" + url = "https://cloud.r-project.org/src/contrib/rngtools_1.4.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/rngtools" version('1.4', sha256='3aa92366e5d0500537964302f5754a750aff6b169a27611725e7d84552913bce') diff --git a/var/spack/repos/builtin/packages/r-rnoaa/package.py b/var/spack/repos/builtin/packages/r-rnoaa/package.py index 7434fb58ba..bdaee96de1 100644 --- a/var/spack/repos/builtin/packages/r-rnoaa/package.py +++ b/var/spack/repos/builtin/packages/r-rnoaa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-robust/package.py b/var/spack/repos/builtin/packages/r-robust/package.py index b49de8879f..fafba06909 100644 --- a/var/spack/repos/builtin/packages/r-robust/package.py +++ b/var/spack/repos/builtin/packages/r-robust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-robustbase/package.py b/var/spack/repos/builtin/packages/r-robustbase/package.py index 84bbafc83f..4afc35894c 100644 --- a/var/spack/repos/builtin/packages/r-robustbase/package.py +++ b/var/spack/repos/builtin/packages/r-robustbase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rocr/package.py b/var/spack/repos/builtin/packages/r-rocr/package.py index f7df3a0836..44b95183fa 100644 --- a/var/spack/repos/builtin/packages/r-rocr/package.py +++ b/var/spack/repos/builtin/packages/r-rocr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py index 187d218583..8db227f82a 100644 --- a/var/spack/repos/builtin/packages/r-rodbc/package.py +++ b/var/spack/repos/builtin/packages/r-rodbc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rook/package.py b/var/spack/repos/builtin/packages/r-rook/package.py index 4d3b1dbda9..c440de3446 100644 --- a/var/spack/repos/builtin/packages/r-rook/package.py +++ b/var/spack/repos/builtin/packages/r-rook/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rots/package.py b/var/spack/repos/builtin/packages/r-rots/package.py index 32564c1fe7..339d92893c 100644 --- a/var/spack/repos/builtin/packages/r-rots/package.py +++ b/var/spack/repos/builtin/packages/r-rots/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,14 +7,20 @@ from spack import * class RRots(RPackage): - """Calculates the Reproducibility-Optimized Test Statistic (ROTS) - for differential testing in omics data.""" + """Reproducibility-Optimized Test Statistic. - homepage = "https://bioconductor.org/packages/release/bioc/html/ROTS.html" + Calculates the Reproducibility-Optimized Test Statistic (ROTS) for + differential testing in omics data.""" + + homepage = "https://bioconductor.org/packages/ROTS" git = "https://git.bioconductor.org/packages/ROTS.git" + version('1.12.0', commit='7e2c96fd8fd36710321498745f24cc6b59ac02f0') + version('1.10.1', commit='1733d3f868cef4d81af6edfc102221d80793937b') version('1.8.0', commit='02e3c6455bb1afe7c4cc59ad6d4d8bae7b01428b') + version('1.6.0', commit='3567ac1142ba97770b701ee8e5f9e3e6c781bd56') + version('1.4.0', commit='2e656514a4bf5a837ee6e14ce9b28a61dab955e7') - depends_on('r@3.5.0:3.5.9', when='@1.8.0:', type=('build', 'run')) + depends_on('r@3.3:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py index e686f380c5..bd129a375e 100644 --- a/var/spack/repos/builtin/packages/r-roxygen2/package.py +++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rpart-plot/package.py b/var/spack/repos/builtin/packages/r-rpart-plot/package.py index cf854fce3e..e18f72efe8 100644 --- a/var/spack/repos/builtin/packages/r-rpart-plot/package.py +++ b/var/spack/repos/builtin/packages/r-rpart-plot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rpart/package.py b/var/spack/repos/builtin/packages/r-rpart/package.py index ef57ad9b3c..8964a28517 100644 --- a/var/spack/repos/builtin/packages/r-rpart/package.py +++ b/var/spack/repos/builtin/packages/r-rpart/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py index 08417089cc..01467dfac2 100644 --- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rprojroot/package.py b/var/spack/repos/builtin/packages/r-rprojroot/package.py index 5388cff895..63df595741 100644 --- a/var/spack/repos/builtin/packages/r-rprojroot/package.py +++ b/var/spack/repos/builtin/packages/r-rprojroot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rrblup/package.py b/var/spack/repos/builtin/packages/r-rrblup/package.py index b165e2a527..1f978f84a1 100644 --- a/var/spack/repos/builtin/packages/r-rrblup/package.py +++ b/var/spack/repos/builtin/packages/r-rrblup/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rrcov/package.py b/var/spack/repos/builtin/packages/r-rrcov/package.py index 7b1d3bd74a..b1843d025e 100644 --- a/var/spack/repos/builtin/packages/r-rrcov/package.py +++ b/var/spack/repos/builtin/packages/r-rrcov/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rrpp/package.py b/var/spack/repos/builtin/packages/r-rrpp/package.py index a2448a3636..629f5b2300 100644 --- a/var/spack/repos/builtin/packages/r-rrpp/package.py +++ b/var/spack/repos/builtin/packages/r-rrpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py index 7292fcf1cd..d988fbb9a8 100644 --- a/var/spack/repos/builtin/packages/r-rsamtools/package.py +++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,33 +7,41 @@ from spack import * class RRsamtools(RPackage): - """This package provides an interface to the 'samtools', 'bcftools', and - 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence - Alignment / Map), FASTA, binary variant call (BCF) and compressed - indexed tab-delimited (tabix) files.""" + """Binary alignment (BAM), FASTA, variant call (BCF), and tabix file + import. - homepage = "https://bioconductor.org/packages/Rsamtools/" + This package provides an interface to the 'samtools', 'bcftools', and + 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), + FASTA, binary variant call (BCF) and compressed indexed tab-delimited + (tabix) files.""" + + homepage = "https://bioconductor.org/packages/Rsamtools" git = "https://git.bioconductor.org/packages/Rsamtools.git" - version('1.32.2', commit='2b3254ccdeb24dc6ad95a93c2eb527021631797e') + version('2.0.3', commit='17d254cc026574d20db67474260944bf60befd70') + version('1.34.1', commit='0ec1d45c7a14b51d019c3e20c4aa87c6bd2b0d0c') + version('1.32.3', commit='0aa3f134143b045aa423894de81912becf64e4c2') + version('1.30.0', commit='61b365fe3762e796b3808cec7238944b7f68d7a6') version('1.28.0', commit='dfa5b6abef68175586f21add7927174786412472') - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomeinfodb@1.1.3:', when='@1.32.2', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-genomicranges@1.31.8:', when='@1.32.2', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-biostrings@2.47.6:', when='@1.32.2', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.25.1:', when='@1.32.2', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.25:', when='@1.32.2', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.12:', when='@1.32.2', type=('build', 'run')) - depends_on('r-xvector', type=('build', 'run')) - depends_on('r-xvector@0.19.7:', when='@1.32.2', type=('build', 'run')) + depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.21.6:', type=('build', 'run')) + depends_on('r-biostrings@2.37.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.3:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.8:', type=('build', 'run')) + depends_on('r-iranges@2.3.7:', type=('build', 'run')) + depends_on('r-xvector@0.15.1:', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) depends_on('r-bitops', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.28.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.32.2', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.8:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-biocgenerics@0.25.1:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run')) + + depends_on('r-rhtslib@1.16.3:', when='@2.0.3:', type=('build', 'run')) + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rsnns/package.py b/var/spack/repos/builtin/packages/r-rsnns/package.py index c6df54a481..094efe1729 100644 --- a/var/spack/repos/builtin/packages/r-rsnns/package.py +++ b/var/spack/repos/builtin/packages/r-rsnns/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rsolnp/package.py b/var/spack/repos/builtin/packages/r-rsolnp/package.py index 891c70632e..1180de0f46 100644 --- a/var/spack/repos/builtin/packages/r-rsolnp/package.py +++ b/var/spack/repos/builtin/packages/r-rsolnp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rspectra/package.py b/var/spack/repos/builtin/packages/r-rspectra/package.py index 460a649c25..8d9958a424 100644 --- a/var/spack/repos/builtin/packages/r-rspectra/package.py +++ b/var/spack/repos/builtin/packages/r-rspectra/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py index c84e712ba5..c09613dcea 100644 --- a/var/spack/repos/builtin/packages/r-rsqlite/package.py +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py index 30df716358..5167998e1e 100644 --- a/var/spack/repos/builtin/packages/r-rstan/package.py +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rstantools/package.py b/var/spack/repos/builtin/packages/r-rstantools/package.py index 08f2e968bb..1566e05de2 100644 --- a/var/spack/repos/builtin/packages/r-rstantools/package.py +++ b/var/spack/repos/builtin/packages/r-rstantools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py index a14069e90c..e9c73695aa 100644 --- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rsvd/package.py b/var/spack/repos/builtin/packages/r-rsvd/package.py index 554824aea5..232cffdb47 100644 --- a/var/spack/repos/builtin/packages/r-rsvd/package.py +++ b/var/spack/repos/builtin/packages/r-rsvd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py index e272d6a80d..0020bf75b2 100644 --- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py +++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,39 +7,48 @@ from spack import * class RRtracklayer(RPackage): - """Extensible framework for interacting with multiple genome browsers + """R interface to genome annotation files and the UCSC genome browser. + + Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.""" - homepage = "http://bioconductor.org/packages/rtracklayer/" + homepage = "https://bioconductor.org/packages/rtracklayer" git = "https://git.bioconductor.org/packages/rtracklayer.git" - version('1.40.5', commit='4e5b06daccd0bca1ddcd93052deca896ade58fd6') + version('1.44.4', commit='aec96e85daf53b5c5eb2e89250d2755352be4de3') + version('1.42.2', commit='76702f671faea736807d54aeecfbadcd152d94c5') + version('1.40.6', commit='ba9a6e711504a702147383bc7abfcc36eb304df7') + version('1.38.3', commit='f20db703c09dc7e808c09e9b78c15aec9e546248') version('1.36.6', commit='8c0ac7230f94e0c5a981acbb178c8de70e968131') - depends_on('r-xml', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.25.1:', when='@1.40.5', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.25:', when='@1.40.5', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.13:', when='@1.40.5', type=('build', 'run')) - depends_on('r-xvector', type=('build', 'run')) - depends_on('r-xvector@0.19.7:', when='@1.40.5', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomeinfodb@1.15.2:', when='@1.40.5', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-biostrings@2.47.6:', when='@1.40.5', type=('build', 'run')) + depends_on('r@3.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.21.20:', type=('build', 'run')) + depends_on('r-xml@1.98-0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-iranges@2.3.7:', type=('build', 'run')) + depends_on('r-xvector@0.9.4:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.3.14:', type=('build', 'run')) + depends_on('r-biostrings@2.43.7:', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('r-rcurl', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) - depends_on('r-rsamtools@1.31.2:', when='@1.40.5', type=('build', 'run')) - depends_on('r-genomicalignments', type=('build', 'run')) - depends_on('r-genomicalignments@1.15.6:', when='@1.40.5', type=('build', 'run')) - depends_on('r-genomicranges@1.21.20:', when='@1.36.3', type=('build', 'run')) - depends_on('r-genomicranges@1.31.8:', when='@1.40.5', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.36.6', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.40.5', type=('build', 'run')) + depends_on('r-rcurl@1.4-2:', type=('build', 'run')) + depends_on('r-rsamtools@1.17.8:', type=('build', 'run')) + depends_on('r-genomicalignments@1.5.4:', type=('build', 'run')) + + depends_on('r-iranges@2.11.12:', when='@1.38.3:', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.8:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-biocgenerics@0.25.1:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-iranges@2.13.13:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-genomicalignments@1.15.6:', when='@1.40.6:', type=('build', 'run')) + + depends_on('r-s4vectors@0.19.22:', when='@1.42.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rtsne/package.py b/var/spack/repos/builtin/packages/r-rtsne/package.py index be9dc73336..f0acd005fc 100644 --- a/var/spack/repos/builtin/packages/r-rtsne/package.py +++ b/var/spack/repos/builtin/packages/r-rtsne/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-runit/package.py b/var/spack/repos/builtin/packages/r-runit/package.py index 03452d630e..e922f74fdf 100644 --- a/var/spack/repos/builtin/packages/r-runit/package.py +++ b/var/spack/repos/builtin/packages/r-runit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rvcheck/package.py b/var/spack/repos/builtin/packages/r-rvcheck/package.py index b0727ab380..33bfef6de5 100644 --- a/var/spack/repos/builtin/packages/r-rvcheck/package.py +++ b/var/spack/repos/builtin/packages/r-rvcheck/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rvest/package.py b/var/spack/repos/builtin/packages/r-rvest/package.py index ede298ee4c..96de5d7090 100644 --- a/var/spack/repos/builtin/packages/r-rvest/package.py +++ b/var/spack/repos/builtin/packages/r-rvest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py index aeaa990a45..68b46c102d 100644 --- a/var/spack/repos/builtin/packages/r-rzmq/package.py +++ b/var/spack/repos/builtin/packages/r-rzmq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -19,4 +19,4 @@ class RRzmq(RPackage): version('0.7.7', sha256='bdbaf77a0e04c5b6d6ce79ab2747848a5044355eed2e2c4d39c4ba16f97dc83d') depends_on('r@3.1.0:', when='@0.9.0:', type=('build', 'run')) - depends_on('zeromq@3.0.0:') + depends_on('libzmq@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py index 1a4ca70513..132218b109 100644 --- a/var/spack/repos/builtin/packages/r-s4vectors/package.py +++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,23 +7,27 @@ from spack import * class RS4vectors(RPackage): - """The S4Vectors package defines the Vector and List virtual classes and - a set of generic functions that extend the semantic of ordinary - vectors and lists in R. Package developers can easily implement - vector-like or list-like objects as concrete subclasses of Vector or - List. In addition, a few low-level concrete subclasses of general - interest (e.g. DataFrame, Rle, and Hits) are implemented in the - S4Vectors package itself (many more are implemented in the IRanges - package and in other Bioconductor infrastructure packages).""" - - homepage = "https://bioconductor.org/packages/S4Vectors/" + """Foundation of vector-like and list-like containers in Bioconductor. + + The S4Vectors package defines the Vector and List virtual classes and a + set of generic functions that extend the semantic of ordinary vectors + and lists in R. Package developers can easily implement vector-like or + list-like objects as concrete subclasses of Vector or List. In addition, + a few low-level concrete subclasses of general interest (e.g. DataFrame, + Rle, and Hits) are implemented in the S4Vectors package itself (many + more are implemented in the IRanges package and in other Bioconductor + infrastructure packages).""" + + homepage = "https://bioconductor.org/packages/S4Vectors" git = "https://git.bioconductor.org/packages/S4Vectors.git" + version('0.22.1', commit='d25e517b48ca4184a4c2ee1f8223c148a55a8b8a') + version('0.20.1', commit='1878b2909086941e556c5ea953c6fd86aebe9b02') version('0.18.3', commit='d6804f94ad3663828440914920ac933b934aeff1') version('0.16.0', commit='00fec03fcbcb7cff37917fab0da28d91fdf9dc3d') version('0.14.7', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23') - depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'), when='@0.14.7') - depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@0.16.0:') - depends_on('r@3.4.0:3.4.9', when='@0.14.7', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@0.18.3', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.21.1:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.23.3:', when='@0.16.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-samr/package.py b/var/spack/repos/builtin/packages/r-samr/package.py index 98171dfcb4..d776f6b10b 100644 --- a/var/spack/repos/builtin/packages/r-samr/package.py +++ b/var/spack/repos/builtin/packages/r-samr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py index 00f508c0e5..4afd68d4a6 100644 --- a/var/spack/repos/builtin/packages/r-sandwich/package.py +++ b/var/spack/repos/builtin/packages/r-sandwich/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py index 46fcef15b0..4949d18917 100644 --- a/var/spack/repos/builtin/packages/r-scales/package.py +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-scater/package.py b/var/spack/repos/builtin/packages/r-scater/package.py new file mode 100644 index 0000000000..ca8d49f67e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scater/package.py @@ -0,0 +1,63 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RScater(RPackage): + """Single-Cell Analysis Toolkit for Gene Expression Data in R. + + A collection of tools for doing various analyses of single-cell RNA-seq + gene expression data, with a focus on quality control and + visualization.""" + + homepage = "https://bioconductor.org/packages/scater" + git = "https://git.bioconductor.org/packages/scater.git" + + version('1.12.2', commit='1518dc27a87c79181c34107d639e95fe55e55092') + version('1.10.1', commit='2e6694af2929092f263c2b0830d48b3f9632e70c') + version('1.8.4', commit='d560a9a378541d53d17990d2aa2cd28874df3dcd') + version('1.6.3', commit='964effb4e883102d7c8cae627dbac4ba5d216a75') + version('1.4.0', commit='90a2eab66ff82ba6dd7fbb33e41cd0ded20fa218') + + depends_on('r@3.3:', when='@1.4.0', type=('build', 'run')) + depends_on('r-biobase', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-biomart', when='@1.4.0:1.6.3', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-data-table', when='@1.4.0:1.6.3', type=('build', 'run')) + depends_on('r-dplyr', when='@1.4.0:1.12.2', type=('build', 'run')) + depends_on('r-edger', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-ggbeeswarm', type=('build', 'run')) + depends_on('r-limma', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-matrixstats', when='@1.4.0:1.6.3', type=('build', 'run')) + depends_on('r-plyr', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-reshape2', when='@1.4.0:1.10.1', type=('build', 'run')) + depends_on('r-rhdf5', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-rjson', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-shiny', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-shinydashboard', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-tximport', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-viridis', type=('build', 'run')) + + depends_on('r@3.4:', when='@1.6.3', type=('build', 'run')) + depends_on('r-singlecellexperiment', when='@1.6.3:', type=('build', 'run')) + depends_on('r-summarizedexperiment', when='@1.6.3:', type=('build', 'run')) + depends_on('r-s4vectors', when='@1.6.3:', type=('build', 'run')) + depends_on('r-rcpp', when='@1.6.3:', type=('build', 'run')) + depends_on('r-rhdf5lib', when='@1.6.3:1.10.1', type=('build', 'run')) + depends_on('r-beachmat', when='@1.6.3:', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.8.4', type=('build', 'run')) + depends_on('r-delayedmatrixstats', when='@1.8.4:', type=('build', 'run')) + depends_on('r-rcpp@0.12.14:', when='@1.8.4:', type=('build', 'run')) + depends_on('r-delayedarray', when='@1.8.4:', type=('build', 'run')) + + depends_on('r-biocparallel', when='@1.10.1:', type=('build', 'run')) + + depends_on('r@3.6:', when='@1.12.2', type=('build', 'run')) + depends_on('r-biocneighbors', when='@1.12.2:', type=('build', 'run')) + depends_on('r-biocsingular', when='@1.12.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py index 1772ff5014..c624cc62e2 100644 --- a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py +++ b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-scrime/package.py b/var/spack/repos/builtin/packages/r-scrime/package.py new file mode 100644 index 0000000000..6f839435ed --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scrime/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RScrime(RPackage): + """scrime: Analysis of High-Dimensional Categorical Data Such as SNP + Data""" + + homepage = "https://cloud.r-project.org/package=scrime" + url = "https://cloud.r-project.org/src/contrib/scrime_1.3.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/scrime" + + version('1.3.5', sha256='5d97d3e57d8eb30709340fe572746029fd139456d7a955421c4e3aa75d825578') diff --git a/var/spack/repos/builtin/packages/r-sctransform/package.py b/var/spack/repos/builtin/packages/r-sctransform/package.py index 7dd0b4e703..65d733fe25 100644 --- a/var/spack/repos/builtin/packages/r-sctransform/package.py +++ b/var/spack/repos/builtin/packages/r-sctransform/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-sdmtools/package.py b/var/spack/repos/builtin/packages/r-sdmtools/package.py index bf1d228b58..1d46c4961a 100644 --- a/var/spack/repos/builtin/packages/r-sdmtools/package.py +++ b/var/spack/repos/builtin/packages/r-sdmtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-segmented/package.py b/var/spack/repos/builtin/packages/r-segmented/package.py index c6e8e2616a..922c779b57 100644 --- a/var/spack/repos/builtin/packages/r-segmented/package.py +++ b/var/spack/repos/builtin/packages/r-segmented/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-selectr/package.py b/var/spack/repos/builtin/packages/r-selectr/package.py index f26c706974..5f306470c2 100644 --- a/var/spack/repos/builtin/packages/r-selectr/package.py +++ b/var/spack/repos/builtin/packages/r-selectr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-seqinr/package.py b/var/spack/repos/builtin/packages/r-seqinr/package.py index 7bba7601eb..5d3a46fe70 100644 --- a/var/spack/repos/builtin/packages/r-seqinr/package.py +++ b/var/spack/repos/builtin/packages/r-seqinr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-seqlogo/package.py b/var/spack/repos/builtin/packages/r-seqlogo/package.py index b264ad50e8..bd03c3a5f4 100644 --- a/var/spack/repos/builtin/packages/r-seqlogo/package.py +++ b/var/spack/repos/builtin/packages/r-seqlogo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,17 @@ from spack import * class RSeqlogo(RPackage): - """seqLogo takes the position weight matrix of a DNA sequence motif and + """Sequence logos for DNA sequence alignments. + + seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).""" - homepage = "https://bioconductor.org/packages/seqLogo/" + homepage = "https://bioconductor.org/packages/seqLogo" git = "https://git.bioconductor.org/packages/seqLogo.git" + version('1.50.0', commit='57986221c90c3920f9829756c4b3ee566dc1e14d') + version('1.48.0', commit='dde85582e7fd0c08c5b8bc73f9aed8f23b727d9d') + version('1.46.0', commit='e78be03db5f6a516138aeea6aa9512685633a4a2') version('1.44.0', commit='4cac14ff29f413d6de1a9944eb5d21bfe5045fac') - - depends_on('r@3.4.3:3.4.9', when='@1.44.0') + version('1.42.0', commit='d7e04726c813282aa3f47a9ee98c5e1cec9bdddd') diff --git a/var/spack/repos/builtin/packages/r-sessioninfo/package.py b/var/spack/repos/builtin/packages/r-sessioninfo/package.py index f8770c7f19..48f238ef25 100644 --- a/var/spack/repos/builtin/packages/r-sessioninfo/package.py +++ b/var/spack/repos/builtin/packages/r-sessioninfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-seurat/package.py b/var/spack/repos/builtin/packages/r-seurat/package.py index a00cc72c99..32a66852e2 100644 --- a/var/spack/repos/builtin/packages/r-seurat/package.py +++ b/var/spack/repos/builtin/packages/r-seurat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-sf/package.py b/var/spack/repos/builtin/packages/r-sf/package.py index b9b382d7df..f04ff3fc03 100644 --- a/var/spack/repos/builtin/packages/r-sf/package.py +++ b/var/spack/repos/builtin/packages/r-sf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-sfsmisc/package.py b/var/spack/repos/builtin/packages/r-sfsmisc/package.py index 86d2b0267b..7cf91c64da 100644 --- a/var/spack/repos/builtin/packages/r-sfsmisc/package.py +++ b/var/spack/repos/builtin/packages/r-sfsmisc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-shape/package.py b/var/spack/repos/builtin/packages/r-shape/package.py index 7ee9940289..26142b242b 100644 --- a/var/spack/repos/builtin/packages/r-shape/package.py +++ b/var/spack/repos/builtin/packages/r-shape/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py index a35f37a4b4..f2774ecefa 100644 --- a/var/spack/repos/builtin/packages/r-shiny/package.py +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-shinydashboard/package.py b/var/spack/repos/builtin/packages/r-shinydashboard/package.py index 8958f7bb1a..ad63f2ade0 100644 --- a/var/spack/repos/builtin/packages/r-shinydashboard/package.py +++ b/var/spack/repos/builtin/packages/r-shinydashboard/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-shinyfiles/package.py b/var/spack/repos/builtin/packages/r-shinyfiles/package.py index 70b4864f40..7c969cd4e4 100644 --- a/var/spack/repos/builtin/packages/r-shinyfiles/package.py +++ b/var/spack/repos/builtin/packages/r-shinyfiles/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py index b42f2b715f..22ae509299 100644 --- a/var/spack/repos/builtin/packages/r-shortread/package.py +++ b/var/spack/repos/builtin/packages/r-shortread/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,30 +7,46 @@ from spack import * class RShortread(RPackage): - """This package implements sampling, iteration, and input of FASTQ - files. The package includes functions for filtering and trimming - reads, and for generating a quality assessment report. Data are - represented as DNAStringSet-derived objects, and easily manipulated - for a diversity of purposes. The package also contains legacy support - for early single-end, ungapped alignment formats.""" - - homepage = "https://www.bioconductor.org/packages/ShortRead/" + """FASTQ input and manipulation. + + This package implements sampling, iteration, and input of FASTQ files. + The package includes functions for filtering and trimming reads, and for + generating a quality assessment report. Data are represented as + DNAStringSet-derived objects, and easily manipulated for a diversity of + purposes. The package also contains legacy support for early single-end, + ungapped alignment formats.""" + + homepage = "https://bioconductor.org/packages/ShortRead" git = "https://git.bioconductor.org/packages/ShortRead.git" + version('1.42.0', commit='daa2576a48278460caf87f42c022c796652f4908') + version('1.40.0', commit='0cbe4b62b0be4c5f2e2670da17493423446e008f') + version('1.38.0', commit='e9498f04b7b4bf0212bbb10ec7e3de2d7699f4bf') + version('1.36.1', commit='176c34eddf4a416d30c69cb4ac197141ba42e66f') version('1.34.2', commit='25daac63b301df66a8ef6e98cc2977522c6786cd') - depends_on('r@3.4.0:3.4.9', when='@1.34.2') - depends_on('r-latticeextra', type=('build', 'run')) - depends_on('r-lattice', type=('build', 'run')) - depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('r-hwriter', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-genomicalignments', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-biocgenerics@0.22.1:', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biostrings@2.37.1:', type=('build', 'run')) + depends_on('r-rsamtools@1.21.4:', type=('build', 'run')) + depends_on('r-genomicalignments@1.5.4:', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-s4vectors@0.13.8:', type=('build', 'run')) + depends_on('r-iranges@2.3.7:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.1.19:', type=('build', 'run')) + depends_on('r-genomicranges@1.21.6:', type=('build', 'run')) + depends_on('r-hwriter', type=('build', 'run')) + depends_on('r-zlibbioc', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-latticeextra', type=('build', 'run')) + depends_on('r-xvector', type=('build', 'run')) + + depends_on('r-biocgenerics@0.23.3:', when='@1.36.1:', type=('build', 'run')) + + depends_on('r-biostrings@2.47.6:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-genomicalignments@1.15.6:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.8:', when='@1.38.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-siggenes/package.py b/var/spack/repos/builtin/packages/r-siggenes/package.py index a619f1902c..395a07bdb6 100644 --- a/var/spack/repos/builtin/packages/r-siggenes/package.py +++ b/var/spack/repos/builtin/packages/r-siggenes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,23 @@ from spack import * class RSiggenes(RPackage): - """Identification of differentially expressed genes and estimation of the + """Multiple Testing using SAM and Efron's Empirical Bayes Approaches. + + Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).""" - homepage = "http://bioconductor.org/packages/siggenes/" + homepage = "https://bioconductor.org/packages/siggenes" git = "https://git.bioconductor.org/packages/siggenes.git" + version('1.58.0', commit='69500158d69942cf7c62f583830933cf8baf89a1') + version('1.56.0', commit='3e929feaa76311be07ff51ad807e657b0b521f6f') + version('1.54.0', commit='1630e42652192e3e4e48e9e78e53665a120cfc7f') + version('1.52.0', commit='dc46cf4b6053ea99c6c841d661f97390653c2e71') version('1.50.0', commit='b1818f26e1449005ffd971df6bda8da0303080bc') depends_on('r-biobase', type=('build', 'run')) depends_on('r-multtest', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.50.0') + + depends_on('r-scrime@1.2.5:', when='@1.58.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-simpleaffy/package.py b/var/spack/repos/builtin/packages/r-simpleaffy/package.py index a5798e0575..489318cde0 100644 --- a/var/spack/repos/builtin/packages/r-simpleaffy/package.py +++ b/var/spack/repos/builtin/packages/r-simpleaffy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,20 +7,26 @@ from spack import * class RSimpleaffy(RPackage): - """Provides high level functions for reading Affy .CEL files, - phenotypic data, and then computing simple things with it, such as - t-tests, fold changes and the like. Makes heavy use of the affy - library. Also has some basic scatter plot functions and mechanisms - for generating high resolution journal figures...""" + """Very simple high level analysis of Affymetrix data. - homepage = "http://bioconductor.org/packages/simpleaffy/" + Provides high level functions for reading Affy .CEL files, phenotypic + data, and then computing simple things with it, such as t-tests, fold + changes and the like. Makes heavy use of the affy library. Also has some + basic scatter plot functions and mechanisms for generating high + resolution journal figures...""" + + homepage = "https://bioconductor.org/packages/simpleaffy" git = "https://git.bioconductor.org/packages/simpleaffy.git" + version('2.60.0', commit='b32b5e7d5c65e43c10f98ab8684a1086a06d04f9') + version('2.58.0', commit='70cf1199bad620f60eaa288279632110bb571200') + version('2.56.0', commit='a05d768180b8713ad9e1dc46d491b7ef389b299d') + version('2.54.0', commit='6876e028d412b14504ad3915cbec1a189e9c6478') version('2.52.0', commit='f2b43fb9b8e6fa4c03fe28b4efb3144a0a42a385') - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r@2.0.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.12:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-affy', type=('build', 'run')) + depends_on('r-affy@1.33.6:', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-gcrma', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.52.0') diff --git a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py new file mode 100644 index 0000000000..c6b4665352 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSinglecellexperiment(RPackage): + """S4 Classes for Single Cell Data. + + Defines a S4 class for storing data from single-cell experiments. This + includes specialized methods to store and retrieve spike-in information, + dimensionality reduction coordinates and size factors for each cell, + along with the usual metadata for genes and libraries.""" + + homepage = "https://bioconductor.org/packages/SingleCellExperiment" + git = "https://git.bioconductor.org/packages/SingleCellExperiment.git" + + version('1.6.0', commit='baa51d77a8dacd2a22e7293095a8cffaaa3293b4') + version('1.4.1', commit='b1efcb338e9176ae6829bb897957aa37e74d4870') + version('1.2.0', commit='fe512259da79e0c660b322b5387e9bb16f2e6321') + version('1.0.0', commit='545e974aa7ca7855e039bf9e3030290cd71d9031') + + depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-summarizedexperiment', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sitmo/package.py b/var/spack/repos/builtin/packages/r-sitmo/package.py index eab70f5ac4..fd7c1df3cc 100644 --- a/var/spack/repos/builtin/packages/r-sitmo/package.py +++ b/var/spack/repos/builtin/packages/r-sitmo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-sm/package.py b/var/spack/repos/builtin/packages/r-sm/package.py index 29a46acd05..ff2e4cb335 100644 --- a/var/spack/repos/builtin/packages/r-sm/package.py +++ b/var/spack/repos/builtin/packages/r-sm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-smoof/package.py b/var/spack/repos/builtin/packages/r-smoof/package.py index 1214c8f5ef..40979fa30b 100644 --- a/var/spack/repos/builtin/packages/r-smoof/package.py +++ b/var/spack/repos/builtin/packages/r-smoof/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-sn/package.py b/var/spack/repos/builtin/packages/r-sn/package.py index 8f15910324..0ba4183ea0 100644 --- a/var/spack/repos/builtin/packages/r-sn/package.py +++ b/var/spack/repos/builtin/packages/r-sn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-snakecase/package.py b/var/spack/repos/builtin/packages/r-snakecase/package.py index fddcd2c56c..55c3592a2b 100644 --- a/var/spack/repos/builtin/packages/r-snakecase/package.py +++ b/var/spack/repos/builtin/packages/r-snakecase/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-snow/package.py b/var/spack/repos/builtin/packages/r-snow/package.py index ac4d2a3b4b..393ca50444 100644 --- a/var/spack/repos/builtin/packages/r-snow/package.py +++ b/var/spack/repos/builtin/packages/r-snow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-snowfall/package.py b/var/spack/repos/builtin/packages/r-snowfall/package.py index 36cb71c9a2..57686af15e 100644 --- a/var/spack/repos/builtin/packages/r-snowfall/package.py +++ b/var/spack/repos/builtin/packages/r-snowfall/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-snprelate/package.py b/var/spack/repos/builtin/packages/r-snprelate/package.py index a78a59236c..9877ffe52b 100644 --- a/var/spack/repos/builtin/packages/r-snprelate/package.py +++ b/var/spack/repos/builtin/packages/r-snprelate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,27 +7,34 @@ from spack import * class RSnprelate(RPackage): - """Genome-wide association studies (GWAS) are widely used to investigate + """Parallel Computing Toolset for Relatedness and Principal Component + Analysis of SNP Data. + + Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many - computational challenges. We developed an R package SNPRelate to - provide a binary format for single-nucleotide polymorphism (SNP) data - in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. - The GDS format offers the efficient operations specifically designed - for integers with two bits, since a SNP could occupy only two bits. + computational challenges. We developed an R package SNPRelate to provide + a binary format for single-nucleotide polymorphism (SNP) data in GWAS + utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS + format offers the efficient operations specifically designed for + integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 - classes and generic functions. The extended GDS format is implemented - in the SeqArray package to support the storage of single nucleotide + classes and generic functions. The extended GDS format is implemented in + the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls.""" homepage = "https://bioconductor.org/packages/SNPRelate" git = "https://git.bioconductor.org/packages/SNPRelate.git" + version('1.18.1', commit='81c581bf76392efdc8ba237ca2e42ca1dba788ca') + version('1.16.0', commit='0e38e8df4af87dff6c27a23af2867661998c0d85') + version('1.14.0', commit='9501cbfc411aa320e58654a865fda2e9077977af') version('1.12.2', commit='dce2e2b6f36483a9f905bb5df6ae834a9f1136fe') + version('1.10.2', commit='3f5c4010871df742e7a460586b38ad0c2fd37aeb') - depends_on('r@3.4.0:3.4.9', when='@1.12.2') + depends_on('r@2.15:', type=('build', 'run')) depends_on('r-gdsfmt@1.8.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-snpstats/package.py b/var/spack/repos/builtin/packages/r-snpstats/package.py new file mode 100644 index 0000000000..2705246582 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-snpstats/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSnpstats(RPackage): + """SnpMatrix and XSnpMatrix classes and methods. + + Classes and statistical methods for large SNP association studies. This + extends the earlier snpMatrix package, allowing for uncertainty in + genotypes.""" + + homepage = "https://bioconductor.org/packages/snpStats" + git = "https://git.bioconductor.org/packages/snpStats.git" + + version('1.34.0', commit='e31cdfb18a9e12d70d6a3e8e6fbf7cf8faa3ea5b') + version('1.32.0', commit='7c31158183b4e39da6dc30c7da275acc36b2e32f') + version('1.30.0', commit='0dc1e4246f015feaf2579d60268b10ab5149ce09') + version('1.28.0', commit='8df9f4188f720dfbb4f4f4ec255cd2e22f3f4426') + version('1.26.0', commit='7c9b3304073e0556d694a8531882b349822fdda8') + + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-zlibbioc', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-som/package.py b/var/spack/repos/builtin/packages/r-som/package.py index 0be184ed1e..eed2ca8fc8 100644 --- a/var/spack/repos/builtin/packages/r-som/package.py +++ b/var/spack/repos/builtin/packages/r-som/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py index 7a1c8b2ca3..a955110c1d 100644 --- a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py +++ b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,23 @@ from spack import * class RSomaticsignatures(RPackage): - """The SomaticSignatures package identifies mutational signatures of - single nucleotide variants (SNVs). It provides a infrastructure related - to the methodology described in Nik-Zainal (2012, Cell), with - flexibility in the matrix decomposition algorithms.""" + """Somatic Signatures. - homepage = "https://bioconductor.org/packages/SomaticSignatures/" + The SomaticSignatures package identifies mutational signatures of single + nucleotide variants (SNVs). It provides a infrastructure related to the + methodology described in Nik-Zainal (2012, Cell), with flexibility in + the matrix decomposition algorithms.""" + + homepage = "https://bioconductor.org/packages/SomaticSignatures" git = "https://git.bioconductor.org/packages/SomaticSignatures.git" + version('2.20.0', commit='dbedc30d92b600b3a17de596ebe38d15982c70c6') + version('2.18.0', commit='facccd67eee5202fcbe6ad32e667546546e7ccff') + version('2.16.0', commit='4ae348d9fa096c0ec307df95149991edf6044977') + version('2.14.0', commit='b12d24f86e96a7c6a17cbbad21ca14fa3aa7c60f') version('2.12.1', commit='932298c6877d076004de5541cec85a14e819517a') + depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-variantannotation', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-nmf', type=('build', 'run')) @@ -30,4 +37,3 @@ class RSomaticsignatures(RPackage): depends_on('r-pcamethods', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-proxy', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.12.1') diff --git a/var/spack/repos/builtin/packages/r-sourcetools/package.py b/var/spack/repos/builtin/packages/r-sourcetools/package.py index 404c04c8b6..22a8c75836 100644 --- a/var/spack/repos/builtin/packages/r-sourcetools/package.py +++ b/var/spack/repos/builtin/packages/r-sourcetools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py index 1a953994d6..dbcb6e8dac 100644 --- a/var/spack/repos/builtin/packages/r-sp/package.py +++ b/var/spack/repos/builtin/packages/r-sp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-spacetime/package.py b/var/spack/repos/builtin/packages/r-spacetime/package.py index e12bd4cc0b..e7fe2eefcf 100644 --- a/var/spack/repos/builtin/packages/r-spacetime/package.py +++ b/var/spack/repos/builtin/packages/r-spacetime/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-spam/package.py b/var/spack/repos/builtin/packages/r-spam/package.py new file mode 100644 index 0000000000..0d5544124b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-spam/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSpam(RPackage): + """spam: SPArse Matrix""" + + homepage = "https://www.math.uzh.ch/pages/spam/" + url = "https://cloud.r-project.org/src/contrib/spam_2.3-0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/spam" + + version('2.3-0.2', sha256='848fa95c0a71ac82af6344539af7b1c33563c687f06ead42851a68b621fff533') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-dotcall64', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py index 15ca85f544..18db3c27d7 100644 --- a/var/spack/repos/builtin/packages/r-sparsem/package.py +++ b/var/spack/repos/builtin/packages/r-sparsem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-spatial/package.py b/var/spack/repos/builtin/packages/r-spatial/package.py index 6673560c04..b2fc45f406 100644 --- a/var/spack/repos/builtin/packages/r-spatial/package.py +++ b/var/spack/repos/builtin/packages/r-spatial/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-spatialreg/package.py b/var/spack/repos/builtin/packages/r-spatialreg/package.py index bcbadc07a1..1a0065f528 100644 --- a/var/spack/repos/builtin/packages/r-spatialreg/package.py +++ b/var/spack/repos/builtin/packages/r-spatialreg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-spdata/package.py b/var/spack/repos/builtin/packages/r-spdata/package.py index 0cfa061db6..d541d1d253 100644 --- a/var/spack/repos/builtin/packages/r-spdata/package.py +++ b/var/spack/repos/builtin/packages/r-spdata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-spdep/package.py b/var/spack/repos/builtin/packages/r-spdep/package.py index 24073cbcde..159b39fedd 100644 --- a/var/spack/repos/builtin/packages/r-spdep/package.py +++ b/var/spack/repos/builtin/packages/r-spdep/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-speedglm/package.py b/var/spack/repos/builtin/packages/r-speedglm/package.py index d3b87fd29d..080d7071c4 100644 --- a/var/spack/repos/builtin/packages/r-speedglm/package.py +++ b/var/spack/repos/builtin/packages/r-speedglm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-spem/package.py b/var/spack/repos/builtin/packages/r-spem/package.py index c5417ffa2b..6abc2823a7 100644 --- a/var/spack/repos/builtin/packages/r-spem/package.py +++ b/var/spack/repos/builtin/packages/r-spem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,14 +7,20 @@ from spack import * class RSpem(RPackage): - """This package can optimize the parameter in S-system models given time - series data""" + """S-system parameter estimation method. - homepage = "https://bioconductor.org/packages/SPEM/" + This package can optimize the parameter in S-system models given time + series data""" + + homepage = "https://bioconductor.org/packages/SPEM" git = "https://git.bioconductor.org/packages/SPEM.git" + version('1.24.0', commit='537ed19e466008f2972a246479b327c95177a99e') + version('1.22.0', commit='fddb7cd1f81e47eae603724ea149c2adca5b3eb4') + version('1.20.0', commit='b0e1049c61a35da00882d21026f4c1eb03b17517') version('1.18.0', commit='3ab425dd9889885eac328d26b73366a875cd250b') + version('1.16.0', commit='9c0a96374086765db9c81e36a662999067fa4cc7') + depends_on('r@2.15.1:', type=('build', 'run')) depends_on('r-rsolnp', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r@3.4.3:3.4.9', when='@1.18.0') diff --git a/var/spack/repos/builtin/packages/r-splancs/package.py b/var/spack/repos/builtin/packages/r-splancs/package.py index 9b3726a2b7..58306eee5e 100644 --- a/var/spack/repos/builtin/packages/r-splancs/package.py +++ b/var/spack/repos/builtin/packages/r-splancs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-splitstackshape/package.py b/var/spack/repos/builtin/packages/r-splitstackshape/package.py index d4ce79870f..f63ed5959d 100644 --- a/var/spack/repos/builtin/packages/r-splitstackshape/package.py +++ b/var/spack/repos/builtin/packages/r-splitstackshape/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-sqldf/package.py b/var/spack/repos/builtin/packages/r-sqldf/package.py index c7ffa1786c..6402080162 100644 --- a/var/spack/repos/builtin/packages/r-sqldf/package.py +++ b/var/spack/repos/builtin/packages/r-sqldf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-squarem/package.py b/var/spack/repos/builtin/packages/r-squarem/package.py index a4f0e9de36..6ffebf4168 100644 --- a/var/spack/repos/builtin/packages/r-squarem/package.py +++ b/var/spack/repos/builtin/packages/r-squarem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-squash/package.py b/var/spack/repos/builtin/packages/r-squash/package.py index fbd4ac1545..31db085fb5 100644 --- a/var/spack/repos/builtin/packages/r-squash/package.py +++ b/var/spack/repos/builtin/packages/r-squash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-sseq/package.py b/var/spack/repos/builtin/packages/r-sseq/package.py index fb36786018..a5238639d5 100644 --- a/var/spack/repos/builtin/packages/r-sseq/package.py +++ b/var/spack/repos/builtin/packages/r-sseq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,13 +7,28 @@ from spack import * class RSseq(RPackage): - """Shrinkage estimation of dispersion in Negative Binomial models for - RNA-seq experiments with small sample size""" + """Shrinkage estimation of dispersion in Negative Binomial models for RNA- + seq experiments with small sample size. - homepage = "https://www.bioconductor.org/packages/sSeq/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/sSeq_1.20.0.tar.gz" + The purpose of this package is to discover the genes that are + differentially expressed between two conditions in RNA-seq experiments. + Gene expression is measured in counts of transcripts and modeled with + the Negative Binomial (NB) distribution using a shrinkage approach for + dispersion estimation. The method of moment (MM) estimates for + dispersion are shrunk towards an estimated target, which minimizes the + average squared difference between the shrinkage estimates and the + initial estimates. The exact per-gene probability under the NB model is + calculated, and used to test the hypothesis that the expected expression + of a gene in two conditions identically follow a NB distribution.""" - version('1.20.0', sha256='0fddcb238a6c401987843debe5b46dc03c22a1ee04df670f0d502e86a4f2144f') + homepage = "https://bioconductor.org/packages/sSeq" + git = "https://git.bioconductor.org/packages/sSeq.git" + + version('1.22.0', commit='fa3895c9578edddca17b5d13a2678ee5830b85cc') + version('1.20.1', commit='91f31440323612cb04beb44404ab0a1bcb3ad87d') + version('1.18.0', commit='1f65e5a55ce0d51672b785450031872e6db5ca0f') + version('1.16.0', commit='b7f2b99dbd4a12ee9d18b0ec9898f13f1038479e') + version('1.14.0', commit='20ccffeb60196914975aa1feef902ddba659c571') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-catools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py index 374cd8e67f..d561f2e8ff 100644 --- a/var/spack/repos/builtin/packages/r-stanheaders/package.py +++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-stargazer/package.py b/var/spack/repos/builtin/packages/r-stargazer/package.py new file mode 100644 index 0000000000..fff3c6ece2 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-stargazer/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RStargazer(RPackage): + """stargazer: Well-Formatted Regression and Summary Statistics Tables""" + + homepage = "https://cloud.r-project.org/package=stargazer" + url = "https://cloud.r-project.org/src/contrib/stargazer_5.2.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/stargazer" + + version('5.2.2', sha256='70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de') diff --git a/var/spack/repos/builtin/packages/r-statmod/package.py b/var/spack/repos/builtin/packages/r-statmod/package.py index 14b8c62feb..f95c996a77 100644 --- a/var/spack/repos/builtin/packages/r-statmod/package.py +++ b/var/spack/repos/builtin/packages/r-statmod/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-statnet-common/package.py b/var/spack/repos/builtin/packages/r-statnet-common/package.py index 5c032da353..1683197747 100644 --- a/var/spack/repos/builtin/packages/r-statnet-common/package.py +++ b/var/spack/repos/builtin/packages/r-statnet-common/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py index 3ddca99716..a02c9584bb 100644 --- a/var/spack/repos/builtin/packages/r-stringi/package.py +++ b/var/spack/repos/builtin/packages/r-stringi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py index cc1812e7bb..7ff1aad0d7 100644 --- a/var/spack/repos/builtin/packages/r-stringr/package.py +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-strucchange/package.py b/var/spack/repos/builtin/packages/r-strucchange/package.py index debf0a73b9..ab24deeb75 100644 --- a/var/spack/repos/builtin/packages/r-strucchange/package.py +++ b/var/spack/repos/builtin/packages/r-strucchange/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-subplex/package.py b/var/spack/repos/builtin/packages/r-subplex/package.py index 1d057dc046..7a28b6e60e 100644 --- a/var/spack/repos/builtin/packages/r-subplex/package.py +++ b/var/spack/repos/builtin/packages/r-subplex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py index d9aaa00ee7..2d4ffdf571 100644 --- a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py +++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,31 +7,39 @@ from spack import * class RSummarizedexperiment(RPackage): - """The SummarizedExperiment container contains one or more assays, each + """SummarizedExperiment container. + + The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows - typically represent genomic ranges of interest and the columns - represent samples.""" + typically represent genomic ranges of interest and the columns represent + samples.""" - homepage = "https://bioconductor.org/packages/SummarizedExperiment/" + homepage = "https://bioconductor.org/packages/SummarizedExperiment" git = "https://git.bioconductor.org/packages/SummarizedExperiment.git" - version('1.10.0', commit='7ad2e991c8285bfc4b2e15b29d94cc86d07f8f2b') + version('1.14.1', commit='2c68d99e11c7345e5ed388370822ea48395c64a4') + version('1.12.0', commit='5f8416864636add121ec1d6737ebb89a42227fd7') + version('1.10.1', commit='7ad2e991c8285bfc4b2e15b29d94cc86d07f8f2b') version('1.8.1', commit='9d8a29aa9c78bbc7dcc6472537e13fc0d11dc1f7') version('1.6.5', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0') - depends_on('r-genomicranges@1.27.22:', when='@1.6.5', type=('build', 'run')) - depends_on('r-genomicranges@1.29.14:', when='@1.8.1', type=('build', 'run')) - depends_on('r-genomicranges@1.31.17:', when='@1.10.0', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.22:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-delayedarray@0.1.9:', when='@1.6.5', type=('build', 'run')) - depends_on('r-delayedarray@0.3.20:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-delayedarray@0.1.9:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.25:', when='@1.10.0', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.16:', when='@1.10.0', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomeinfodb@1.13.1:', when='@1.10.0', type=('build', 'run')) - depends_on('r-biocgenerics@0.15.3:', when='@1.6.5:', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.6.5:1.9.9', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.10.0', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.3:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-iranges@2.7.2:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + + depends_on('r-genomicranges@1.29.14:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-delayedarray@0.3.20:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-iranges@2.11.17:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.8.1:', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.17:', when='@1.10.1:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.10.1:', type=('build', 'run')) + depends_on('r-iranges@2.13.16:', when='@1.10.1:', type=('build', 'run')) + + depends_on('r-genomicranges@1.33.6:', when='@1.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py index e3a2c69b1b..c07a9ce22c 100644 --- a/var/spack/repos/builtin/packages/r-survey/package.py +++ b/var/spack/repos/builtin/packages/r-survey/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py index bea175b3ec..c7d81fc02c 100644 --- a/var/spack/repos/builtin/packages/r-survival/package.py +++ b/var/spack/repos/builtin/packages/r-survival/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-sva/package.py b/var/spack/repos/builtin/packages/r-sva/package.py index e6ec8b9715..79ecbaea3c 100644 --- a/var/spack/repos/builtin/packages/r-sva/package.py +++ b/var/spack/repos/builtin/packages/r-sva/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,14 +7,37 @@ from spack import * class RSva(RPackage): - """Surrogate Variable Analysis.""" + """Surrogate Variable Analysis. - homepage = "https://www.bioconductor.org/packages/sva/" + The sva package contains functions for removing batch effects and other + unwanted variation in high-throughput experiment. Specifically, the sva + package contains functions for the identifying and building surrogate + variables for high-dimensional data sets. Surrogate variables are + covariates constructed directly from high-dimensional data (like gene + expression/RNA sequencing/methylation/brain imaging data) that can be + used in subsequent analyses to adjust for unknown, unmodeled, or latent + sources of noise. The sva package can be used to remove artifacts in + three ways: (1) identifying and estimating surrogate variables for + unknown sources of variation in high-throughput experiments (Leek and + Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch + effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) + removing batch effects with known control probes (Leek 2014 biorXiv). + Removing batch effects and using surrogate variables in differential + expression analysis have been shown to reduce dependence, stabilize + error rate estimates, and improve reproducibility, see (Leek and Storey + 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews + Genetics).""" + + homepage = "https://bioconductor.org/packages/sva" git = "https://git.bioconductor.org/packages/sva.git" + version('3.32.1', commit='1b8286734d00533b49d9f1456b6523cc778bb744') + version('3.30.1', commit='fdb98bc2299dc5213c62d83cb7c0b1c1b4912f0c') + version('3.28.0', commit='dd4937229dbccd2f383a04d5237fe147a884728d') + version('3.26.0', commit='3cc5e75413c35ed5511892f5c36a8b5cb454937e') version('3.24.4', commit='ed2ebb6e33374dc9ec50e6ea97cc1d9aef836c73') - depends_on('r@3.4.0:3.4.9', when='@3.24.4') + depends_on('r@3.2:', type=('build', 'run')) depends_on('r-mgcv', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sys/package.py b/var/spack/repos/builtin/packages/r-sys/package.py index af8fb3ebbd..bd9aff9519 100644 --- a/var/spack/repos/builtin/packages/r-sys/package.py +++ b/var/spack/repos/builtin/packages/r-sys/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py index a219d3b5c5..2aac0efab2 100644 --- a/var/spack/repos/builtin/packages/r-tarifx/package.py +++ b/var/spack/repos/builtin/packages/r-tarifx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-taxizedb/package.py b/var/spack/repos/builtin/packages/r-taxizedb/package.py index 973d75262b..3002e6e8f5 100644 --- a/var/spack/repos/builtin/packages/r-taxizedb/package.py +++ b/var/spack/repos/builtin/packages/r-taxizedb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tclust/package.py b/var/spack/repos/builtin/packages/r-tclust/package.py index 5f6d169c9c..393e56e84b 100644 --- a/var/spack/repos/builtin/packages/r-tclust/package.py +++ b/var/spack/repos/builtin/packages/r-tclust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-teachingdemos/package.py b/var/spack/repos/builtin/packages/r-teachingdemos/package.py new file mode 100644 index 0000000000..b1d5d8e3a7 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-teachingdemos/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RTeachingdemos(RPackage): + """TeachingDemos: Demonstrations for Teaching and Learning. + + Demonstration functions that can be used in a classroom to demonstrate + statistical concepts, or on your own to better understand the concepts + or the programming.""" + + homepage = "https://cloud.r-project.org/package=TeachingDemos" + url = "https://cloud.r-project.org/src/contrib/TeachingDemos_2.10.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/TeachingDemos" + + version('2.10', sha256='2ef4c2e36ba13e32f66000e84281a3616584c86b255bca8643ff3fe4f78ed704') diff --git a/var/spack/repos/builtin/packages/r-tensora/package.py b/var/spack/repos/builtin/packages/r-tensora/package.py index fdcd057365..20cc9794a4 100644 --- a/var/spack/repos/builtin/packages/r-tensora/package.py +++ b/var/spack/repos/builtin/packages/r-tensora/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-testit/package.py b/var/spack/repos/builtin/packages/r-testit/package.py index ed72ba336f..dfc7b59d5c 100644 --- a/var/spack/repos/builtin/packages/r-testit/package.py +++ b/var/spack/repos/builtin/packages/r-testit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py index a9128acb3e..e0712387bd 100644 --- a/var/spack/repos/builtin/packages/r-testthat/package.py +++ b/var/spack/repos/builtin/packages/r-testthat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tfbstools/package.py b/var/spack/repos/builtin/packages/r-tfbstools/package.py index 393071cb67..4017c71219 100644 --- a/var/spack/repos/builtin/packages/r-tfbstools/package.py +++ b/var/spack/repos/builtin/packages/r-tfbstools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,25 +7,25 @@ from spack import * class RTfbstools(RPackage): - """TFBSTools is a package for the analysis and manipulation of - transcription factor binding sites. + """Software Package for Transcription Factor Binding Site (TFBS) Analysis. - It includes matrices conversion between Position Frequency Matirx (PFM), - Position Weight Matirx (PWM) and Information Content Matrix (ICM). It - can also scan putative TFBS from sequence/alignment, query JASPAR - database and provides a wrapper of de novo motif discovery software. TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS - from sequence/alignment, query JASPAR database and provides a wrapper - of de novo motif discovery software.""" + from sequence/alignment, query JASPAR database and provides a wrapper of + de novo motif discovery software.""" - homepage = "http://bioconductor.org/packages/TFBSTools/" + homepage = "https://bioconductor.org/packages/TFBSTools" git = "https://git.bioconductor.org/packages/TFBSTools.git" + version('1.22.0', commit='613d3567fd662b65269bd200c5aa5f87ac6a4612') + version('1.20.0', commit='74035fc6beb1af82f171c11ef2b0a8817714c5bc') + version('1.18.0', commit='17e12b9f3dcb9059d414307ec0bc23ed1ee33294') version('1.16.0', commit='565436a5a674d4dea7279e796a20c5bd2034f65a') + version('1.14.2', commit='e429fdefb6f7ee4585dd2a8ca3d0ced7a5bed4ff') + depends_on('r@3.2.2:', type=('build', 'run')) depends_on('r-biobase@2.28:', type=('build', 'run')) depends_on('r-biostrings@2.36.4:', type=('build', 'run')) depends_on('r-biocgenerics@0.14.0:', type=('build', 'run')) @@ -46,4 +46,3 @@ class RTfbstools(RPackage): depends_on('r-tfmpvalue@0.0.5:', type=('build', 'run')) depends_on('r-xml@3.98-1.3:', type=('build', 'run')) depends_on('r-xvector@0.8.0:', type=('build', 'run')) - depends_on('r@3.4.3:3.4.9', when='@1.16.0') diff --git a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py index 52597e6153..f0b354cca6 100644 --- a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py +++ b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-th-data/package.py b/var/spack/repos/builtin/packages/r-th-data/package.py index 20c163164e..8457465bf1 100644 --- a/var/spack/repos/builtin/packages/r-th-data/package.py +++ b/var/spack/repos/builtin/packages/r-th-data/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py index a6e2c603e7..b73e450f51 100644 --- a/var/spack/repos/builtin/packages/r-threejs/package.py +++ b/var/spack/repos/builtin/packages/r-threejs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py index 950f336df2..fe8190c219 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tidycensus/package.py b/var/spack/repos/builtin/packages/r-tidycensus/package.py index 87cc13bd5c..1d7269612b 100644 --- a/var/spack/repos/builtin/packages/r-tidycensus/package.py +++ b/var/spack/repos/builtin/packages/r-tidycensus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tidygraph/package.py b/var/spack/repos/builtin/packages/r-tidygraph/package.py new file mode 100644 index 0000000000..07fe0442de --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tidygraph/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RTidygraph(RPackage): + """tidygraph: A Tidy API for Graph Manipulation. + + A graph, while not "tidy" in itself, can be thought of as two tidy data + frames describing node and edge data respectively. 'tidygraph' provides an + approach to manipulate these two virtual data frames using the API defined + in the 'dplyr' package, as well as provides tidy interfaces to a lot of + common graph algorithms.""" + + homepage = "https://github.com/thomasp85/tidygraph" + url = "https://cloud.r-project.org/src/contrib/tidygraph_1.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tidygraph" + + version('1.1.2', sha256='5642001d4cccb122d66481b7c61a06c724c02007cbd356ee61cb29726a56fafe') + + depends_on('r-tibble', type=('build', 'run')) + depends_on('r-dplyr@0.8:', type=('build', 'run')) + depends_on('r-igraph', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-tidyr', type=('build', 'run')) + depends_on('r-pillar', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py index 5f3b471b58..ac089a646b 100644 --- a/var/spack/repos/builtin/packages/r-tidyr/package.py +++ b/var/spack/repos/builtin/packages/r-tidyr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tidyselect/package.py b/var/spack/repos/builtin/packages/r-tidyselect/package.py index ef33042330..eec8929ee3 100644 --- a/var/spack/repos/builtin/packages/r-tidyselect/package.py +++ b/var/spack/repos/builtin/packages/r-tidyselect/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tidyverse/package.py b/var/spack/repos/builtin/packages/r-tidyverse/package.py index 671d8a7856..6b27c90934 100644 --- a/var/spack/repos/builtin/packages/r-tidyverse/package.py +++ b/var/spack/repos/builtin/packages/r-tidyverse/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tiff/package.py b/var/spack/repos/builtin/packages/r-tiff/package.py index 44779dde90..91e7f261c2 100644 --- a/var/spack/repos/builtin/packages/r-tiff/package.py +++ b/var/spack/repos/builtin/packages/r-tiff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tigris/package.py b/var/spack/repos/builtin/packages/r-tigris/package.py index 3d7bd60769..dfa9230ace 100644 --- a/var/spack/repos/builtin/packages/r-tigris/package.py +++ b/var/spack/repos/builtin/packages/r-tigris/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-timedate/package.py b/var/spack/repos/builtin/packages/r-timedate/package.py index bb5fb25a0a..86a5d27fc1 100644 --- a/var/spack/repos/builtin/packages/r-timedate/package.py +++ b/var/spack/repos/builtin/packages/r-timedate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tinytex/package.py b/var/spack/repos/builtin/packages/r-tinytex/package.py index e8384c0285..d17b71ef9e 100644 --- a/var/spack/repos/builtin/packages/r-tinytex/package.py +++ b/var/spack/repos/builtin/packages/r-tinytex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py index 0ac49d576e..03ee54b2e0 100644 --- a/var/spack/repos/builtin/packages/r-tmixclust/package.py +++ b/var/spack/repos/builtin/packages/r-tmixclust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,24 @@ from spack import * class RTmixclust(RPackage): - """Implementation of a clustering method for time series gene expression - data based on mixed-effects models with Gaussian variables and - non-parametric cubic splines estimation. The method can robustly account - for the high levels of noise present in typical gene expression time - series datasets.""" + """Time Series Clustering of Gene Expression with Gaussian Mixed-Effects + Models and Smoothing Splines. - homepage = "https://bioconductor.org/packages/TMixClust/" + Implementation of a clustering method for time series gene expression + data based on mixed-effects models with Gaussian variables and non- + parametric cubic splines estimation. The method can robustly account for + the high levels of noise present in typical gene expression time series + datasets.""" + + homepage = "https://bioconductor.org/packages/TMixClust" git = "https://git.bioconductor.org/packages/TMixClust.git" + version('1.6.0', commit='9f5f78e52538d15f402c8f6e4c60f7212c7bc548') + version('1.4.0', commit='a52fcae6e7a5dd41e7afbe128f35397e8bc8cb12') + version('1.2.0', commit='0250c0b238f08077b5b9ff17c2f3b7633c67dc3c') version('1.0.1', commit='0ac800210e3eb9da911767a80fb5582ab33c0cad') + depends_on('r@3.4:', type=('build', 'run')) depends_on('r-gss', type=('build', 'run')) depends_on('r-mvtnorm', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) @@ -26,4 +33,3 @@ class RTmixclust(RPackage): depends_on('r-flexclust', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-spem', type=('build', 'run')) - depends_on('r@3.4.3:3.4.9', when='@1.0.1') diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py index 7822f1f543..e1a7d922cd 100644 --- a/var/spack/repos/builtin/packages/r-topgo/package.py +++ b/var/spack/repos/builtin/packages/r-topgo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,24 +7,29 @@ from spack import * class RTopgo(RPackage): - """topGO package provides tools for testing GO terms while accounting - for the topology of the GO graph. Different test statistics and - different methods for eliminating local similarities and dependencies - between GO terms can be implemented and applied.""" + """Enrichment Analysis for Gene Ontology. - homepage = "https://www.bioconductor.org/packages/topGO/" + topGO package provides tools for testing GO terms while accounting for + the topology of the GO graph. Different test statistics and different + methods for eliminating local similarities and dependencies between GO + terms can be implemented and applied.""" + + homepage = "https://bioconductor.org/packages/topGO" git = "https://git.bioconductor.org/packages/topGO.git" + version('2.36.0', commit='c2f6c187b41c4aa44cc92ac781fdd878491a4019') + version('2.34.0', commit='44cb5eaba515b365b7b2a8c22df0a45883db6b4d') + version('2.32.0', commit='78ce3068fc06ae38d55219759fa177e2fcb3f596') version('2.30.1', commit='b1469ce1d198ccb73ef79ca22cab81659e16dbaa') version('2.28.0', commit='066a975d460046cce33fb27e74e6a0ebc33fd716') - depends_on('r@3.4.0:3.4.9') - depends_on('r-dbi', type=('build', 'run')) - depends_on('r-matrixstats', type=('build', 'run')) - depends_on('r-lattice', type=('build', 'run')) - depends_on('r-sparsem@0.73:', type=('build', 'run')) - depends_on('r-annotationdbi@1.7.19:', type=('build', 'run')) - depends_on('r-go-db@2.3.0:', type=('build', 'run')) - depends_on('r-biobase@2.0.0:', type=('build', 'run')) - depends_on('r-graph@1.14.0:', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-biocgenerics@0.13.6:', type=('build', 'run')) + depends_on('r-graph@1.14.0:', type=('build', 'run')) + depends_on('r-biobase@2.0.0:', type=('build', 'run')) + depends_on('r-go-db@2.3.0:', type=('build', 'run')) + depends_on('r-annotationdbi@1.7.19:', type=('build', 'run')) + depends_on('r-sparsem@0.73:', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-matrixstats', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-triebeard/package.py b/var/spack/repos/builtin/packages/r-triebeard/package.py index a3521c9c1b..002ee655ca 100644 --- a/var/spack/repos/builtin/packages/r-triebeard/package.py +++ b/var/spack/repos/builtin/packages/r-triebeard/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-trimcluster/package.py b/var/spack/repos/builtin/packages/r-trimcluster/package.py index ccd0d8980d..c23abf948d 100644 --- a/var/spack/repos/builtin/packages/r-trimcluster/package.py +++ b/var/spack/repos/builtin/packages/r-trimcluster/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-truncnorm/package.py b/var/spack/repos/builtin/packages/r-truncnorm/package.py index d307bccdb5..8ffad56a3f 100644 --- a/var/spack/repos/builtin/packages/r-truncnorm/package.py +++ b/var/spack/repos/builtin/packages/r-truncnorm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-trust/package.py b/var/spack/repos/builtin/packages/r-trust/package.py index 3acc3c4796..90ec0c4059 100644 --- a/var/spack/repos/builtin/packages/r-trust/package.py +++ b/var/spack/repos/builtin/packages/r-trust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tseries/package.py b/var/spack/repos/builtin/packages/r-tseries/package.py index ef00918fb7..4c67387fcc 100644 --- a/var/spack/repos/builtin/packages/r-tseries/package.py +++ b/var/spack/repos/builtin/packages/r-tseries/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tsne/package.py b/var/spack/repos/builtin/packages/r-tsne/package.py index 1ef92be922..98c3e47ebe 100644 --- a/var/spack/repos/builtin/packages/r-tsne/package.py +++ b/var/spack/repos/builtin/packages/r-tsne/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py index a137c21bd5..3e895bcee6 100644 --- a/var/spack/repos/builtin/packages/r-ttr/package.py +++ b/var/spack/repos/builtin/packages/r-ttr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-tweenr/package.py b/var/spack/repos/builtin/packages/r-tweenr/package.py new file mode 100644 index 0000000000..a3838289e2 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tweenr/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RTweenr(RPackage): + """tweenr: Interpolate Data for Smooth Animations""" + + homepage = "https://github.com/thomasp85/tweenr" + url = "https://cloud.r-project.org/src/contrib/tweenr_1.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tweenr" + + version('1.0.1', sha256='efd68162cd6d5a4f6d833dbf785a2bbce1cb7b9f90ba3fb060931a4bd705096b') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-farver', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-rcpp@0.12.3:', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tximport/package.py b/var/spack/repos/builtin/packages/r-tximport/package.py new file mode 100644 index 0000000000..8e36f5b518 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tximport/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RTximport(RPackage): + """Import and summarize transcript-level estimates for transcript- and + gene-level analysis. + + Imports transcript-level abundance, estimated counts and transcript + lengths, and summarizes into matrices for use with downstream gene-level + analysis packages. Average transcript length, weighted by sample- + specific transcript abundance estimates, is provided as a matrix which + can be used as an offset for different expression of gene-level + counts.""" + + homepage = "https://bioconductor.org/packages/tximport" + git = "https://git.bioconductor.org/packages/tximport.git" + + version('1.12.3', commit='acbdead961471c3b910d720f73bd0af1b7a07c57') + version('1.10.1', commit='cd8f81cf7140f61d4a4f25f89451fb49e2cd4bd3') + version('1.8.0', commit='cc91b8389ca4c16b0f588bdeb63d051a11e8a705') + version('1.6.0', commit='0b1ba6c6622e02b954812c88454c28e8efb75e0b') + version('1.4.0', commit='bfbd2436eca21acf212b76a658b49cfb5e116d6b') diff --git a/var/spack/repos/builtin/packages/r-ucminf/package.py b/var/spack/repos/builtin/packages/r-ucminf/package.py index a0ddaaa7b1..e3a26f33e4 100644 --- a/var/spack/repos/builtin/packages/r-ucminf/package.py +++ b/var/spack/repos/builtin/packages/r-ucminf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-udunits2/package.py b/var/spack/repos/builtin/packages/r-udunits2/package.py index 551455471f..eda9137d8e 100644 --- a/var/spack/repos/builtin/packages/r-udunits2/package.py +++ b/var/spack/repos/builtin/packages/r-udunits2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,4 +16,4 @@ class RUdunits2(RPackage): version('0.13', sha256='d155d3c07f6202b65dec4075ffd1e1c3f4f35f5fdece8cfb319d39256a3e5b79') depends_on('r@2.10.0:', type=('build', 'run')) - depends_on('udunits2') + depends_on('udunits') diff --git a/var/spack/repos/builtin/packages/r-units/package.py b/var/spack/repos/builtin/packages/r-units/package.py index c6b4ce8f19..bac5d4637a 100644 --- a/var/spack/repos/builtin/packages/r-units/package.py +++ b/var/spack/repos/builtin/packages/r-units/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -25,4 +25,4 @@ class RUnits(RPackage): depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-udunits2@0.13:', when='@:0.5-1', type=('build', 'run')) depends_on('r-rcpp@0.12.10:', type=('build', 'run')) - depends_on('udunits2', when='@0.6-0:') + depends_on('udunits', when='@0.6-0:') diff --git a/var/spack/repos/builtin/packages/r-upsetr/package.py b/var/spack/repos/builtin/packages/r-upsetr/package.py new file mode 100644 index 0000000000..405bf7994a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-upsetr/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RUpsetr(RPackage): + """UpSetR: A More Scalable Alternative to Venn and Euler Diagrams + forVisualizing Intersecting Sets""" + + homepage = "http://github.com/hms-dbmi/UpSetR" + url = "https://cloud.r-project.org/src/contrib/UpSetR_1.4.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/UpSetR" + + version('1.4.0', sha256='351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100') + + depends_on('r@3.0:', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-gridextra', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-urca/package.py b/var/spack/repos/builtin/packages/r-urca/package.py index 1dc5753a43..364482b5c3 100644 --- a/var/spack/repos/builtin/packages/r-urca/package.py +++ b/var/spack/repos/builtin/packages/r-urca/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-urltools/package.py b/var/spack/repos/builtin/packages/r-urltools/package.py index 5187a31288..479e201fbb 100644 --- a/var/spack/repos/builtin/packages/r-urltools/package.py +++ b/var/spack/repos/builtin/packages/r-urltools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-usethis/package.py b/var/spack/repos/builtin/packages/r-usethis/package.py index 4f7cfc743c..e82085b541 100644 --- a/var/spack/repos/builtin/packages/r-usethis/package.py +++ b/var/spack/repos/builtin/packages/r-usethis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-utf8/package.py b/var/spack/repos/builtin/packages/r-utf8/package.py index 8a00a26db6..f35800cb5f 100644 --- a/var/spack/repos/builtin/packages/r-utf8/package.py +++ b/var/spack/repos/builtin/packages/r-utf8/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-uuid/package.py b/var/spack/repos/builtin/packages/r-uuid/package.py index 2e502658cc..f696d52f9b 100644 --- a/var/spack/repos/builtin/packages/r-uuid/package.py +++ b/var/spack/repos/builtin/packages/r-uuid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-uwot/package.py b/var/spack/repos/builtin/packages/r-uwot/package.py index 092288646d..294e36b692 100644 --- a/var/spack/repos/builtin/packages/r-uwot/package.py +++ b/var/spack/repos/builtin/packages/r-uwot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-variantannotation/package.py b/var/spack/repos/builtin/packages/r-variantannotation/package.py index 5293b84150..d1037acc7a 100644 --- a/var/spack/repos/builtin/packages/r-variantannotation/package.py +++ b/var/spack/repos/builtin/packages/r-variantannotation/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,28 +7,53 @@ from spack import * class RVariantannotation(RPackage): - """Annotate variants, compute amino acid coding changes, predict coding + """Annotation of Genetic Variants. + + Annotate variants, compute amino acid coding changes, predict coding outcomes.""" - homepage = "https://www.bioconductor.org/packages/VariantAnnotation/" + homepage = "https://bioconductor.org/packages/VariantAnnotation" git = "https://git.bioconductor.org/packages/VariantAnnotation.git" + version('1.30.1', commit='fb1ab00872570afb280522c4663e347dafc07a9e') + version('1.28.13', commit='0393347b8ce2d5edf1a61589be93e6a93eda3419') + version('1.26.1', commit='60ae67598cc3d7ed20ee6417920f8c209085faaf') + version('1.24.5', commit='468d7f53fd743e04c9af853d58e871b4cc13a090') version('1.22.3', commit='3a91b6d4297aa416d5f056dec6f8925eb1a8eaee') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-summarizedexperiment', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) + depends_on('r@2.8.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.3:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.6:', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run')) + depends_on('r-rsamtools@1.23.10:', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-xvector', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-bsgenome', type=('build', 'run')) - depends_on('r-rtracklayer', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.22.3') + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-iranges@2.3.25:', type=('build', 'run')) + depends_on('r-xvector@0.5.6:', type=('build', 'run')) + depends_on('r-biostrings@2.33.5:', type=('build', 'run')) + depends_on('r-annotationdbi@1.27.9:', type=('build', 'run')) + depends_on('r-bsgenome@1.37.6:', type=('build', 'run')) + depends_on('r-rtracklayer@1.25.16:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.27.4:', type=('build', 'run')) + + depends_on('r-genomeinfodb@1.15.2:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.8:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.9.9:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.24:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-iranges@2.13.13:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-rtracklayer@1.39.7:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-bsgenome@1.47.3:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.31.3:', when='@1.26.1:', type=('build', 'run')) + + depends_on('r-rsamtools@1.33.6:', when='@1.28.13:', type=('build', 'run')) + + depends_on('r-rsamtools@1.99.0:', when='@1.30.1:', type=('build', 'run')) + depends_on('r-rhtslib', when='@1.30.1:', type=('build', 'run')) + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-varselrf/package.py b/var/spack/repos/builtin/packages/r-varselrf/package.py index 090d6d90bb..1bc5e7b4b7 100644 --- a/var/spack/repos/builtin/packages/r-varselrf/package.py +++ b/var/spack/repos/builtin/packages/r-varselrf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py index 150adb9248..cb8e90e46a 100644 --- a/var/spack/repos/builtin/packages/r-vcd/package.py +++ b/var/spack/repos/builtin/packages/r-vcd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-vctrs/package.py b/var/spack/repos/builtin/packages/r-vctrs/package.py index 0dc05227c5..ad1fea5dc2 100644 --- a/var/spack/repos/builtin/packages/r-vctrs/package.py +++ b/var/spack/repos/builtin/packages/r-vctrs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-vegan/package.py b/var/spack/repos/builtin/packages/r-vegan/package.py index 59c851dbab..adbfe7869e 100644 --- a/var/spack/repos/builtin/packages/r-vegan/package.py +++ b/var/spack/repos/builtin/packages/r-vegan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-vfs/package.py b/var/spack/repos/builtin/packages/r-vfs/package.py index d6c52c2c50..a43566b888 100644 --- a/var/spack/repos/builtin/packages/r-vfs/package.py +++ b/var/spack/repos/builtin/packages/r-vfs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-vgam/package.py b/var/spack/repos/builtin/packages/r-vgam/package.py index d496816056..b0a8c9a253 100644 --- a/var/spack/repos/builtin/packages/r-vgam/package.py +++ b/var/spack/repos/builtin/packages/r-vgam/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-vioplot/package.py b/var/spack/repos/builtin/packages/r-vioplot/package.py new file mode 100644 index 0000000000..451e5cf5b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-vioplot/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RVioplot(RPackage): + """vioplot: Violin Plot""" + + homepage = "https://cloud.r-project.org/package=vioplot" + url = "https://cloud.r-project.org/src/contrib/vioplot_0.3.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/vioplot" + + version('0.3.2', sha256='7b51d0876903a3c315744cb051ac61920eeaa1f0694814959edfae43ce956e8e') + + depends_on('r-sm', type=('build', 'run')) + depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vipor/package.py b/var/spack/repos/builtin/packages/r-vipor/package.py index a4fe8257f1..232a59cc48 100644 --- a/var/spack/repos/builtin/packages/r-vipor/package.py +++ b/var/spack/repos/builtin/packages/r-vipor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-viridis/package.py b/var/spack/repos/builtin/packages/r-viridis/package.py index 50b6683a8d..42ec7cfdf0 100644 --- a/var/spack/repos/builtin/packages/r-viridis/package.py +++ b/var/spack/repos/builtin/packages/r-viridis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-viridislite/package.py b/var/spack/repos/builtin/packages/r-viridislite/package.py index e81c7b2ef0..6b0a3fda03 100644 --- a/var/spack/repos/builtin/packages/r-viridislite/package.py +++ b/var/spack/repos/builtin/packages/r-viridislite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py index 5c68597a7f..07b18d82d6 100644 --- a/var/spack/repos/builtin/packages/r-visnetwork/package.py +++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py index 5db8fec045..b3a45677aa 100644 --- a/var/spack/repos/builtin/packages/r-vsn/package.py +++ b/var/spack/repos/builtin/packages/r-vsn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,28 +7,36 @@ from spack import * class RVsn(RPackage): - """The package implements a method for normalising microarray intensities, - and works for single- and multiple-color arrays. It can also be used - for data from other technologies, as long as they have similar format. - The method uses a robust variant of the maximum-likelihood estimator - for an additive-multiplicative error model and affine calibration. The - model incorporates data calibration step (a.k.a. normalization), a - model for the dependence of the variance on the mean intensity and a - variance stabilizing data transformation. Differences between - transformed intensities are analogous to "normalized log-ratios". - However, in contrast to the latter, their variance is independent of - the mean, and they are usually more sensitive and specific in detecting - differential transcription.""" - - homepage = "https://www.bioconductor.org/packages/vsn/" + """Variance stabilization and calibration for microarray data. + + The package implements a method for normalising microarray intensities, + and works for single- and multiple-color arrays. It can also be used for + data from other technologies, as long as they have similar format. The + method uses a robust variant of the maximum-likelihood estimator for an + additive-multiplicative error model and affine calibration. The model + incorporates data calibration step (a.k.a. normalization), a model for + the dependence of the variance on the mean intensity and a variance + stabilizing data transformation. Differences between transformed + intensities are analogous to "normalized log-ratios". However, in + contrast to the latter, their variance is independent of the mean, and + they are usually more sensitive and specific in detecting differential + transcription.""" + + homepage = "https://bioconductor.org/packages/vsn" git = "https://git.bioconductor.org/packages/vsn.git" + version('3.52.0', commit='e80642d850ae93bc141654200a8970b561a94fbe') + version('3.50.0', commit='ad49fcc288c6065d0f04040acd688e7f0d7d927e') + version('3.48.1', commit='d57f64112004b1d73b3be625949830209de027eb') + version('3.46.0', commit='7ecfd20452348da27d6fcc052cbff2b9be777792') version('3.44.0', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-hexbin', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@3.44.0') + depends_on('r-hexbin', when='@3.44.0', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@3.46.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-webshot/package.py b/var/spack/repos/builtin/packages/r-webshot/package.py index 987dd60c2c..bcf2997ddc 100644 --- a/var/spack/repos/builtin/packages/r-webshot/package.py +++ b/var/spack/repos/builtin/packages/r-webshot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-wgcna/package.py b/var/spack/repos/builtin/packages/r-wgcna/package.py index 7b21e756ed..4af76c78ad 100644 --- a/var/spack/repos/builtin/packages/r-wgcna/package.py +++ b/var/spack/repos/builtin/packages/r-wgcna/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class RWgcna(RPackage): """WGCNA: Weighted Correlation Network Analysis""" homepage = "https://cloud.r-project.org/package=WGCNA" - url = "https://cloud.r-project.org/src/contrib/WGCNA_1.66.tar.gz" + url = "https://cloud.r-project.org/src/contrib/WGCNA_1.68.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/WGCNA/" version('1.68', sha256='0a04f15a20817f9260ae1896eda3be83a7f4855a27a348df85c7f4d376f1efe8') diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py index 3a1f67657c..cecb1eb2af 100644 --- a/var/spack/repos/builtin/packages/r-whisker/package.py +++ b/var/spack/repos/builtin/packages/r-whisker/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py index b8f6606ea3..a1fbce55b1 100644 --- a/var/spack/repos/builtin/packages/r-withr/package.py +++ b/var/spack/repos/builtin/packages/r-withr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xde/package.py b/var/spack/repos/builtin/packages/r-xde/package.py index f36835b58c..928503c1d5 100644 --- a/var/spack/repos/builtin/packages/r-xde/package.py +++ b/var/spack/repos/builtin/packages/r-xde/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,26 @@ from spack import * class RXde(RPackage): - """Multi-level model for cross-study detection of differential gene - expression.""" + """XDE: a Bayesian hierarchical model for cross-study analysis of + differential gene expression.""" - homepage = "https://www.bioconductor.org/packages/XDE/" + homepage = "https://bioconductor.org/packages/XDE" git = "https://git.bioconductor.org/packages/XDE.git" + version('2.30.0', commit='058af6f1e431522778f970bf61f834620d3d7dd7') + version('2.28.0', commit='b8cc7d0840ce1324644e8b4a750fbb964884498b') + version('2.26.0', commit='7bf6368037937c53542447175061c2e2059ee3be') + version('2.24.0', commit='fd5f245f82893657dc36e5a67a1d3b8255772462') version('2.22.0', commit='25bcec965ae42a410dd285a9db9be46d112d8e81') - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-biobase@2.5.5:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-gtools', type=('build', 'run')) depends_on('r-mergemaid', type=('build', 'run')) depends_on('r-mvtnorm', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.22.0') + + depends_on('r-rcolorbrewer', when='@2.24.0:', type=('build', 'run')) + depends_on('r-genemeta', when='@2.24.0:', type=('build', 'run')) + depends_on('r-siggenes', when='@2.24.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xfun/package.py b/var/spack/repos/builtin/packages/r-xfun/package.py index 9ffb8f618e..af92291d52 100644 --- a/var/spack/repos/builtin/packages/r-xfun/package.py +++ b/var/spack/repos/builtin/packages/r-xfun/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xgboost/package.py b/var/spack/repos/builtin/packages/r-xgboost/package.py index 50b7c0f880..825e24eef5 100644 --- a/var/spack/repos/builtin/packages/r-xgboost/package.py +++ b/var/spack/repos/builtin/packages/r-xgboost/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py index 33cce26177..9d1b8732b3 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py index 0dce0584cf..3c6fabd9d0 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index ee0f934447..694a347a0c 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class RXlsx(RPackage): 97/2000/XP/2003 file formats.""" homepage = "http://code.google.com/p/rexcel/" - url = "https://cloud.r-project.org/src/contrib/xlsx_0.5.7.tar.gz" + url = "https://cloud.r-project.org/src/contrib/xlsx_0.6.1.tar.gz" listurl = "https://cloud.r-project.org/src/contrib/Archive/xlsx" version('0.6.1', sha256='a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4') diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py index 0de4e08d24..45202b1ea0 100644 --- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xmapbridge/package.py b/var/spack/repos/builtin/packages/r-xmapbridge/package.py index 661017ba75..69680fb6de 100644 --- a/var/spack/repos/builtin/packages/r-xmapbridge/package.py +++ b/var/spack/repos/builtin/packages/r-xmapbridge/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,12 +7,18 @@ from spack import * class RXmapbridge(RPackage): - """xmapBridge can plot graphs in the X:Map genome browser. This package + """Export plotting files to the xmapBridge for visualisation in X:Map. + + xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.""" - homepage = "https://www.bioconductor.org/packages/xmapbridge/" + homepage = "https://bioconductor.org/packages/xmapbridge" git = "https://git.bioconductor.org/packages/xmapbridge.git" + version('1.42.0', commit='d79c80dfc1a0ed3fd6d3e7a7c3a4aff778537ca9') + version('1.40.0', commit='00a2993863f28711e237bc937fa0ba2d05f81684') + version('1.38.0', commit='08138f00385fa0c669ff4cc33d7eac3d29cd615d') + version('1.36.0', commit='e44f648c9da9eaa130849a738d90dc11685050e2') version('1.34.0', commit='f162e1f72ead5f5a1aede69032d5771a6572d965') - depends_on('r@3.4.0:3.4.9', when='@1.34.0') + depends_on('r@2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py index ebe512ea63..948ed81dfa 100644 --- a/var/spack/repos/builtin/packages/r-xml/package.py +++ b/var/spack/repos/builtin/packages/r-xml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xml2/package.py b/var/spack/repos/builtin/packages/r-xml2/package.py index 5ade615aef..55edf949ea 100644 --- a/var/spack/repos/builtin/packages/r-xml2/package.py +++ b/var/spack/repos/builtin/packages/r-xml2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xnomial/package.py b/var/spack/repos/builtin/packages/r-xnomial/package.py index 609340c966..eb26c95c70 100644 --- a/var/spack/repos/builtin/packages/r-xnomial/package.py +++ b/var/spack/repos/builtin/packages/r-xnomial/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xopen/package.py b/var/spack/repos/builtin/packages/r-xopen/package.py index 4365dff7e1..362553401a 100644 --- a/var/spack/repos/builtin/packages/r-xopen/package.py +++ b/var/spack/repos/builtin/packages/r-xopen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py index 68a11ea0f5..bc92f22721 100644 --- a/var/spack/repos/builtin/packages/r-xtable/package.py +++ b/var/spack/repos/builtin/packages/r-xtable/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py index 95732f19a3..69c2ea107f 100644 --- a/var/spack/repos/builtin/packages/r-xts/package.py +++ b/var/spack/repos/builtin/packages/r-xts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py index 9623be17c0..1ee264a373 100644 --- a/var/spack/repos/builtin/packages/r-xvector/package.py +++ b/var/spack/repos/builtin/packages/r-xvector/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,21 +7,33 @@ from spack import * class RXvector(RPackage): - """Memory efficient S4 classes for storing sequences "externally" (behind - an R external pointer, or on disk).""" + """Foundation of external vector representation and manipulation in + Bioconductor. - homepage = "https://bioconductor.org/packages/XVector/" + Provides memory efficient S4 classes for storing sequences "externally" + (e.g. behind an R external pointer, or on disk).""" + + homepage = "https://bioconductor.org/packages/XVector" git = "https://git.bioconductor.org/packages/XVector.git" + version('0.24.0', commit='e5109cb2687724b9fddddf296c07a82bae4c551d') + version('0.22.0', commit='b5e107a5fd719e18374eb836eb498b529afa4473') version('0.20.0', commit='a83a7ea01f6a710f0ba7d9fb021cfa795b291cb4') + version('0.18.0', commit='27acf47282c9880b54d04dff46c1e50f0c87fa6b') version('0.16.0', commit='54615888e1a559da4a81de33e934fc0f1c3ad99f') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.19.2:', when='@0.20.0', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.24:', when='@0.20.0', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.16:', when='@0.20.0', type=('build', 'run')) + depends_on('r@2.8.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.19.2:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-iranges@2.9.18:', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@0.16.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@0.20.0', type=('build', 'run')) + + depends_on('r-s4vectors@0.15.14:', when='@0.18.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.24:', when='@0.20.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.16:', when='@0.20.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.19.15:', when='@0.22.0:', type=('build', 'run')) + depends_on('r-iranges@2.15.12:', when='@0.22.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.21.13:', when='@0.24.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py index 260e3d82bf..60b5fab154 100644 --- a/var/spack/repos/builtin/packages/r-yaml/package.py +++ b/var/spack/repos/builtin/packages/r-yaml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py index c41dca0f4d..a6facc807d 100644 --- a/var/spack/repos/builtin/packages/r-yapsa/package.py +++ b/var/spack/repos/builtin/packages/r-yapsa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,18 +7,25 @@ from spack import * class RYapsa(RPackage): - """This package provides functions and routines useful in the analysis of + """Yet Another Package for Signature Analysis. + + This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.""" - homepage = "http://bioconductor.org/packages/YAPSA/" + homepage = "https://bioconductor.org/packages/YAPSA" git = "https://git.bioconductor.org/packages/YAPSA.git" + version('1.10.0', commit='06af18e424868eb0f0be6c80e90cbab1eabf3d73') + version('1.8.0', commit='402f3f7774fdf8afc7883579ad651c26df0f8fdb') + version('1.6.0', commit='2455d272b076835ddb36ad21c01ef15af66abc36') + version('1.4.0', commit='6f24150a0689d5215983975ece96c8c205923c72') version('1.2.0', commit='320809b69e470e30a777a383f8341f93064ec24d') + depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-lsei', type=('build', 'run')) @@ -30,8 +37,8 @@ class RYapsa(RPackage): depends_on('r-corrplot', type=('build', 'run')) depends_on('r-dendextend', type=('build', 'run')) depends_on('r-getoptlong', type=('build', 'run')) + depends_on('r-circlize', type=('build', 'run')) depends_on('r-gtrellis', type=('build', 'run')) depends_on('r-pmcmr', type=('build', 'run')) depends_on('r-complexheatmap', type=('build', 'run')) depends_on('r-keggrest', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.2.0') diff --git a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py index 342fea2b18..eb5ac5f82c 100644 --- a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py +++ b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,14 +7,19 @@ from spack import * class RYaqcaffy(RPackage): - """Quality control of Affymetrix GeneChip expression data and + """Affymetrix expression data quality control and reproducibility analysis. + + Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.""" - homepage = "http://bioconductor.org/packages/yaqcaffy/" + homepage = "https://bioconductor.org/packages/yaqcaffy" git = "https://git.bioconductor.org/packages/yaqcaffy.git" + version('1.44.0', commit='00898f3ec9ac0beadbcf57bda3d3c1c99fb0c3c0') + version('1.42.0', commit='a4af673774165e087499ecc35f96aab6bbfbeea1') + version('1.40.0', commit='0c78f8ff8f675305f6fa4b052d2482e9aee551bb') + version('1.38.0', commit='d57100862c2dc0f5e7684f318b9ceda7349352be') version('1.36.0', commit='4d46fe77b2c8de2230a77b0c07dd5dd726e3abd6') - depends_on('r-simpleaffy', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.36.0') + depends_on('r-simpleaffy@2.19.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py index 12ffca6910..8cec9b3612 100644 --- a/var/spack/repos/builtin/packages/r-yarn/package.py +++ b/var/spack/repos/builtin/packages/r-yarn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,16 +7,22 @@ from spack import * class RYarn(RPackage): - """Expedite large RNA-Seq analyses using a combination of previously + """YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization. + + Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.""" - homepage = "https://bioconductor.org/packages/yarn/" + homepage = "https://bioconductor.org/packages/yarn" git = "https://git.bioconductor.org/packages/yarn.git" + version('1.10.0', commit='36ffe84148eb871e93bc8f9e697475319b5ea472') + version('1.8.1', commit='ee0723d4dbf082b4469ca9c22cce4f1a2ac81c04') + version('1.6.0', commit='19d1b2ef275f294bd318b86e0d237c271880117d') + version('1.4.0', commit='36100f40b9e520c072d0d5ebf963723b813f7db0') version('1.2.0', commit='28af616ef8c27dcadf6568e276dea8465486a697') depends_on('r-biobase', type=('build', 'run')) @@ -30,4 +36,3 @@ class RYarn(RPackage): depends_on('r-readr', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-quantro', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.2.0') diff --git a/var/spack/repos/builtin/packages/r-zeallot/package.py b/var/spack/repos/builtin/packages/r-zeallot/package.py index 7276bff255..67c0a8b27c 100644 --- a/var/spack/repos/builtin/packages/r-zeallot/package.py +++ b/var/spack/repos/builtin/packages/r-zeallot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-zip/package.py b/var/spack/repos/builtin/packages/r-zip/package.py index 13270d7b32..dc5a2341c9 100644 --- a/var/spack/repos/builtin/packages/r-zip/package.py +++ b/var/spack/repos/builtin/packages/r-zip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py index 3b36a02b16..2e4f8175ea 100644 --- a/var/spack/repos/builtin/packages/r-zlibbioc/package.py +++ b/var/spack/repos/builtin/packages/r-zlibbioc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,17 +7,18 @@ from spack import * class RZlibbioc(RPackage): - """This package uses the source code of zlib-1.2.5 to create libraries - for systems that do not have these available via other means (most - Linux and Mac users should have system-level access to zlib, and no - direct need for this package). See the vignette for instructions - on use.""" + """An R packaged zlib-1.2.5. - homepage = "http://bioconductor.org/packages/release/bioc/html/zlibbioc.html" + This package uses the source code of zlib-1.2.5 to create libraries for + systems that do not have these available via other means (most Linux and + Mac users should have system-level access to zlib, and no direct need + for this package). See the vignette for instructions on use.""" + + homepage = "https://bioconductor.org/packages/zlibbioc" git = "https://git.bioconductor.org/packages/zlibbioc.git" + version('1.30.0', commit='99eae5b05968bf6abc9b54b9031afd93517381e0') + version('1.28.0', commit='b825b042742ba45455fc284b988ff4cd2a33222c') version('1.26.0', commit='2e3ab097caa09a5e3ddaa3469b13e19a7224da0d') + version('1.24.0', commit='2990059338d1b987d098c009b0bfa806bd24afec') version('1.22.0', commit='30377f830af2bc1ff17bbf3fdd2cb6442015fea5') - - depends_on('r@3.4.0:3.4.9', when='@1.22.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.26.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py index 43a4069adf..6c12d29e21 100644 --- a/var/spack/repos/builtin/packages/r-zoo/package.py +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py index 3755fb594f..6489a8585c 100644 --- a/var/spack/repos/builtin/packages/r/package.py +++ b/var/spack/repos/builtin/packages/r/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,6 +21,7 @@ class R(AutotoolsPackage): extendable = True + version('3.6.2', sha256='bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954') version('3.6.1', sha256='5baa9ebd3e71acecdcc3da31d9042fb174d55a42829f8315f2457080978b1389') version('3.6.0', sha256='36fcac3e452666158e62459c6fc810adc247c7109ed71c5b6c3ad5fc2bf57509') version('3.5.3', sha256='2bfa37b7bd709f003d6b8a172ddfb6d03ddd2d672d6096439523039f7a8e678c') @@ -109,18 +110,25 @@ class R(AutotoolsPackage): prefix = self.prefix tcl_config_path = join_path(spec['tcl'].prefix.lib, 'tclConfig.sh') + if not os.path.exists(tcl_config_path): + tcl_config_path = join_path(spec['tcl'].prefix, + 'lib64', 'tclConfig.sh') config_args = [ '--libdir={0}'.format(join_path(prefix, 'rlib')), '--enable-R-shlib', '--enable-BLAS-shlib', '--enable-R-framework=no', + '--without-recommended-packages', '--with-tcl-config={0}'.format(tcl_config_path), 'LDFLAGS=-L{0} -Wl,-rpath,{0}'.format(join_path(prefix, 'rlib', 'R', 'lib')), ] if '^tk' in spec: tk_config_path = join_path(spec['tk'].prefix.lib, 'tkConfig.sh') + if not os.path.exists(tk_config_path): + tk_config_path = join_path(spec['tk'].prefix, + 'lib64', 'tkConfig.sh') config_args.append('--with-tk-config={0}'.format(tk_config_path)) if '+external-lapack' in spec: diff --git a/var/spack/repos/builtin/packages/r3d/package.py b/var/spack/repos/builtin/packages/r3d/package.py index 6e2984253c..228a0dbaa6 100644 --- a/var/spack/repos/builtin/packages/r3d/package.py +++ b/var/spack/repos/builtin/packages/r3d/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,11 +11,11 @@ class R3d(MakefilePackage): conservative voxelization.""" homepage = "https://github.com/devonmpowell/r3d" - url = "https://github.com/devonmpowell/r3d.git" + git = "https://github.com/devonmpowell/r3d.git" - version('2019-04-24', git=url, commit='86cea79c124c6a8edd8c8cdea61e3e923acb0b22') - version('2018-12-19', git=url, commit='47308f68c782ed3227d3dab1eff24d41f6421f21') - version('2018-01-07', git=url, commit='d6799a582256a120ef3bd7e18959e96cba0e5495') + version('2019-04-24', commit='86cea79c124c6a8edd8c8cdea61e3e923acb0b22') + version('2018-12-19', commit='47308f68c782ed3227d3dab1eff24d41f6421f21') + version('2018-01-07', commit='d6799a582256a120ef3bd7e18959e96cba0e5495') variant("test", default=False, description="Build R3D regression tests") diff --git a/var/spack/repos/builtin/packages/rabbitmq/package.py b/var/spack/repos/builtin/packages/rabbitmq/package.py new file mode 100644 index 0000000000..e496af820c --- /dev/null +++ b/var/spack/repos/builtin/packages/rabbitmq/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Rabbitmq(Package): + """ + RabbitMQ is lightweight and easy to deploy on premises and in the cloud. + It supports multiple messaging protocols. RabbitMQ can be deployed in + distributed and federated configurations to meet high-scale, + high-availability requirements. + """ + + homepage = "http://www.rabbitmq.com/" + url = "http://www.rabbitmq.com/releases/rabbitmq-server/v3.6.15/rabbitmq-server-generic-unix-3.6.15.tar.xz" + + version('3.6.15', sha256='04e6a291642f80e87fc892d5e8ea309fb3fab85ebb64a79a70dfe6c6cfde36fb') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/racon/aarch64.patch b/var/spack/repos/builtin/packages/racon/aarch64.patch new file mode 100644 index 0000000000..332be1179d --- /dev/null +++ b/var/spack/repos/builtin/packages/racon/aarch64.patch @@ -0,0 +1,2806 @@ +diff --git a/vendor/spoa/include/arch/aarch64/sse2neon.h b/vendor/spoa/include/arch/aarch64/sse2neon.h +new file mode 100644 +index 0000000..1477ae1 +--- /dev/null ++++ b/vendor/spoa/include/arch/aarch64/sse2neon.h +@@ -0,0 +1,2783 @@ ++#ifndef SSE2NEON_H ++#define SSE2NEON_H ++ ++// This header file provides a simple API translation layer ++// between SSE intrinsics to their corresponding Arm/Aarch64 NEON versions ++// ++// This header file does not yet translate all of the SSE intrinsics. ++// ++// Contributors to this work are: ++// John W. Ratcliff <jratcliffscarab@gmail.com> ++// Brandon Rowlett <browlett@nvidia.com> ++// Ken Fast <kfast@gdeb.com> ++// Eric van Beurden <evanbeurden@nvidia.com> ++// Alexander Potylitsin <apotylitsin@nvidia.com> ++// Hasindu Gamaarachchi <hasindu2008@gmail.com> ++// Jim Huang <jserv@biilabs.io> ++// Mark Cheng <marktwtn@biilabs.io> ++// Malcolm James MacLeod <malcolm@gulden.com> ++ ++/* ++ * The MIT license: ++ * ++ * Permission is hereby granted, free of charge, to any person obtaining a copy ++ * of this software and associated documentation files (the "Software"), to deal ++ * in the Software without restriction, including without limitation the rights ++ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell ++ * copies of the Software, and to permit persons to whom the Software is ++ * furnished to do so, subject to the following conditions: ++ * ++ * The above copyright notice and this permission notice shall be included in ++ * all copies or substantial portions of the Software. ++ * ++ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR ++ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, ++ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE ++ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER ++ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, ++ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE ++ * SOFTWARE. ++ */ ++ ++#if defined(__GNUC__) || defined(__clang__) ++ ++#pragma push_macro("FORCE_INLINE") ++#pragma push_macro("ALIGN_STRUCT") ++#define FORCE_INLINE static inline __attribute__((always_inline)) ++#define ALIGN_STRUCT(x) __attribute__((aligned(x))) ++ ++#else ++ ++#error "Macro name collisions may happens with unknown compiler" ++#ifdef FORCE_INLINE ++#undef FORCE_INLINE ++#endif ++#define FORCE_INLINE static inline ++#ifndef ALIGN_STRUCT ++#define ALIGN_STRUCT(x) __declspec(align(x)) ++#endif ++ ++#endif ++ ++#include <stdint.h> ++ ++#include "arm_neon.h" ++ ++/** ++ * MACRO for shuffle parameter for _mm_shuffle_ps(). ++ * Argument fp3 is a digit[0123] that represents the fp from argument "b" ++ * of mm_shuffle_ps that will be placed in fp3 of result. fp2 is the same ++ * for fp2 in result. fp1 is a digit[0123] that represents the fp from ++ * argument "a" of mm_shuffle_ps that will be places in fp1 of result. ++ * fp0 is the same for fp0 of result. ++ */ ++#define _MM_SHUFFLE(fp3, fp2, fp1, fp0) \ ++ (((fp3) << 6) | ((fp2) << 4) | ((fp1) << 2) | ((fp0))) ++ ++/* indicate immediate constant argument in a given range */ ++#define __constrange(a, b) const ++ ++typedef float32x2_t __m64; ++typedef float32x4_t __m128; ++typedef int32x4_t __m128i; ++ ++// ****************************************** ++// type-safe casting between types ++// ****************************************** ++ ++#define vreinterpretq_m128_f16(x) vreinterpretq_f32_f16(x) ++#define vreinterpretq_m128_f32(x) (x) ++#define vreinterpretq_m128_f64(x) vreinterpretq_f32_f64(x) ++ ++#define vreinterpretq_m128_u8(x) vreinterpretq_f32_u8(x) ++#define vreinterpretq_m128_u16(x) vreinterpretq_f32_u16(x) ++#define vreinterpretq_m128_u32(x) vreinterpretq_f32_u32(x) ++#define vreinterpretq_m128_u64(x) vreinterpretq_f32_u64(x) ++ ++#define vreinterpretq_m128_s8(x) vreinterpretq_f32_s8(x) ++#define vreinterpretq_m128_s16(x) vreinterpretq_f32_s16(x) ++#define vreinterpretq_m128_s32(x) vreinterpretq_f32_s32(x) ++#define vreinterpretq_m128_s64(x) vreinterpretq_f32_s64(x) ++ ++#define vreinterpretq_f16_m128(x) vreinterpretq_f16_f32(x) ++#define vreinterpretq_f32_m128(x) (x) ++#define vreinterpretq_f64_m128(x) vreinterpretq_f64_f32(x) ++ ++#define vreinterpretq_u8_m128(x) vreinterpretq_u8_f32(x) ++#define vreinterpretq_u16_m128(x) vreinterpretq_u16_f32(x) ++#define vreinterpretq_u32_m128(x) vreinterpretq_u32_f32(x) ++#define vreinterpretq_u64_m128(x) vreinterpretq_u64_f32(x) ++ ++#define vreinterpretq_s8_m128(x) vreinterpretq_s8_f32(x) ++#define vreinterpretq_s16_m128(x) vreinterpretq_s16_f32(x) ++#define vreinterpretq_s32_m128(x) vreinterpretq_s32_f32(x) ++#define vreinterpretq_s64_m128(x) vreinterpretq_s64_f32(x) ++ ++#define vreinterpretq_m128i_s8(x) vreinterpretq_s32_s8(x) ++#define vreinterpretq_m128i_s16(x) vreinterpretq_s32_s16(x) ++#define vreinterpretq_m128i_s32(x) (x) ++#define vreinterpretq_m128i_s64(x) vreinterpretq_s32_s64(x) ++ ++#define vreinterpretq_m128i_u8(x) vreinterpretq_s32_u8(x) ++#define vreinterpretq_m128i_u16(x) vreinterpretq_s32_u16(x) ++#define vreinterpretq_m128i_u32(x) vreinterpretq_s32_u32(x) ++#define vreinterpretq_m128i_u64(x) vreinterpretq_s32_u64(x) ++ ++#define vreinterpretq_s8_m128i(x) vreinterpretq_s8_s32(x) ++#define vreinterpretq_s16_m128i(x) vreinterpretq_s16_s32(x) ++#define vreinterpretq_s32_m128i(x) (x) ++#define vreinterpretq_s64_m128i(x) vreinterpretq_s64_s32(x) ++ ++#define vreinterpretq_u8_m128i(x) vreinterpretq_u8_s32(x) ++#define vreinterpretq_u16_m128i(x) vreinterpretq_u16_s32(x) ++#define vreinterpretq_u32_m128i(x) vreinterpretq_u32_s32(x) ++#define vreinterpretq_u64_m128i(x) vreinterpretq_u64_s32(x) ++ ++// A struct is defined in this header file called 'SIMDVec' which can be used ++// by applications which attempt to access the contents of an _m128 struct ++// directly. It is important to note that accessing the __m128 struct directly ++// is bad coding practice by Microsoft: @see: ++// https://msdn.microsoft.com/en-us/library/ayeb3ayc.aspx ++// ++// However, some legacy source code may try to access the contents of an __m128 ++// struct directly so the developer can use the SIMDVec as an alias for it. Any ++// casting must be done manually by the developer, as you cannot cast or ++// otherwise alias the base NEON data type for intrinsic operations. ++// ++// union intended to allow direct access to an __m128 variable using the names ++// that the MSVC compiler provides. This union should really only be used when ++// trying to access the members of the vector as integer values. GCC/clang ++// allow native access to the float members through a simple array access ++// operator (in C since 4.6, in C++ since 4.8). ++// ++// Ideally direct accesses to SIMD vectors should not be used since it can cause ++// a performance hit. If it really is needed however, the original __m128 ++// variable can be aliased with a pointer to this union and used to access ++// individual components. The use of this union should be hidden behind a macro ++// that is used throughout the codebase to access the members instead of always ++// declaring this type of variable. ++typedef union ALIGN_STRUCT(16) SIMDVec { ++ float ++ m128_f32[4]; // as floats - do not to use this. Added for convenience. ++ int8_t m128_i8[16]; // as signed 8-bit integers. ++ int16_t m128_i16[8]; // as signed 16-bit integers. ++ int32_t m128_i32[4]; // as signed 32-bit integers. ++ int64_t m128_i64[2]; // as signed 64-bit integers. ++ uint8_t m128_u8[16]; // as unsigned 8-bit integers. ++ uint16_t m128_u16[8]; // as unsigned 16-bit integers. ++ uint32_t m128_u32[4]; // as unsigned 32-bit integers. ++ uint64_t m128_u64[2]; // as unsigned 64-bit integers. ++} SIMDVec; ++ ++// casting using SIMDVec ++#define vreinterpretq_nth_u64_m128i(x, n) (((SIMDVec *) &x)->m128_u64[n]) ++#define vreinterpretq_nth_u32_m128i(x, n) (((SIMDVec *) &x)->m128_u32[n]) ++ ++ ++// ****************************************** ++// Backwards compatibility for compilers with lack of specific type support ++// ****************************************** ++ ++// Older gcc does not define vld1q_u8_x4 type ++#if defined(__GNUC__) && !defined(__clang__) ++#if __GNUC__ < 9 || (__GNUC__ == 9 && (__GNUC_MINOR__ <= 2)) ++FORCE_INLINE uint8x16x4_t vld1q_u8_x4(const uint8_t *p) ++{ ++ uint8x16x4_t ret; ++ ret.val[0] = vld1q_u8(p + 0); ++ ret.val[1] = vld1q_u8(p + 16); ++ ret.val[2] = vld1q_u8(p + 32); ++ ret.val[3] = vld1q_u8(p + 48); ++ return ret; ++} ++#endif ++#endif ++ ++ ++// ****************************************** ++// Set/get methods ++// ****************************************** ++ ++// Loads one cache line of data from address p to a location closer to the ++// processor. https://msdn.microsoft.com/en-us/library/84szxsww(v=vs.100).aspx ++FORCE_INLINE void _mm_prefetch(const void *p, int i) ++{ ++ __builtin_prefetch(p); ++} ++ ++// extracts the lower order floating point value from the parameter : ++// https://msdn.microsoft.com/en-us/library/bb514059%28v=vs.120%29.aspx?f=255&MSPPError=-2147217396 ++FORCE_INLINE float _mm_cvtss_f32(__m128 a) ++{ ++ return vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++} ++ ++// Sets the 128-bit value to zero ++// https://msdn.microsoft.com/en-us/library/vstudio/ys7dw0kh(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_setzero_si128(void) ++{ ++ return vreinterpretq_m128i_s32(vdupq_n_s32(0)); ++} ++ ++// Clears the four single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/vstudio/tk1t2tbz(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_setzero_ps(void) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(0)); ++} ++ ++// Sets the four single-precision, floating-point values to w. ++// ++// r0 := r1 := r2 := r3 := w ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/2x1se8ha(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_set1_ps(float _w) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(_w)); ++} ++ ++// Sets the four single-precision, floating-point values to w. ++// https://msdn.microsoft.com/en-us/library/vstudio/2x1se8ha(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_set_ps1(float _w) ++{ ++ return vreinterpretq_m128_f32(vdupq_n_f32(_w)); ++} ++ ++// Sets the four single-precision, floating-point values to the four inputs. ++// https://msdn.microsoft.com/en-us/library/vstudio/afh0zf75(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_set_ps(float w, float z, float y, float x) ++{ ++ float __attribute__((aligned(16))) data[4] = {x, y, z, w}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++} ++ ++// Sets the four single-precision, floating-point values to the four inputs in ++// reverse order. ++// https://msdn.microsoft.com/en-us/library/vstudio/d2172ct3(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_setr_ps(float w, float z, float y, float x) ++{ ++ float __attribute__((aligned(16))) data[4] = {w, z, y, x}; ++ return vreinterpretq_m128_f32(vld1q_f32(data)); ++} ++ ++// Sets the 8 signed 16-bit integer values in reverse order. ++// ++// Return Value ++// r0 := w0 ++// r1 := w1 ++// ... ++// r7 := w7 ++FORCE_INLINE __m128i _mm_setr_epi16(short w0, ++ short w1, ++ short w2, ++ short w3, ++ short w4, ++ short w5, ++ short w6, ++ short w7) ++{ ++ int16_t __attribute__((aligned(16))) ++ data[8] = {w0, w1, w2, w3, w4, w5, w6, w7}; ++ return vreinterpretq_m128i_s16(vld1q_s16((int16_t *) data)); ++} ++ ++// Sets the 4 signed 32-bit integer values in reverse order ++// https://technet.microsoft.com/en-us/library/security/27yb3ee5(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_setr_epi32(int i3, int i2, int i1, int i0) ++{ ++ int32_t __attribute__((aligned(16))) data[4] = {i3, i2, i1, i0}; ++ return vreinterpretq_m128i_s32(vld1q_s32(data)); ++} ++ ++// Sets the 16 signed 8-bit integer values to b. ++// ++// r0 := b ++// r1 := b ++// ... ++// r15 := b ++// ++// https://msdn.microsoft.com/en-us/library/6e14xhyf(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_set1_epi8(char w) ++{ ++ return vreinterpretq_m128i_s8(vdupq_n_s8(w)); ++} ++ ++// Sets the 8 signed 16-bit integer values to w. ++// ++// r0 := w ++// r1 := w ++// ... ++// r7 := w ++// ++// https://msdn.microsoft.com/en-us/library/k0ya3x0e(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_set1_epi16(short w) ++{ ++ return vreinterpretq_m128i_s16(vdupq_n_s16(w)); ++} ++ ++// Sets the 16 signed 8-bit integer values. ++// https://msdn.microsoft.com/en-us/library/x0cx8zd3(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_set_epi8(char b15, ++ char b14, ++ char b13, ++ char b12, ++ char b11, ++ char b10, ++ char b9, ++ char b8, ++ char b7, ++ char b6, ++ char b5, ++ char b4, ++ char b3, ++ char b2, ++ char b1, ++ char b0) ++{ ++ int8_t __attribute__((aligned(16))) ++ data[16] = {(int8_t) b0, (int8_t) b1, (int8_t) b2, (int8_t) b3, ++ (int8_t) b4, (int8_t) b5, (int8_t) b6, (int8_t) b7, ++ (int8_t) b8, (int8_t) b9, (int8_t) b10, (int8_t) b11, ++ (int8_t) b12, (int8_t) b13, (int8_t) b14, (int8_t) b15}; ++ return (__m128i) vld1q_s8(data); ++} ++ ++// Sets the 8 signed 16-bit integer values. ++// https://msdn.microsoft.com/en-au/library/3e0fek84(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_set_epi16(short i7, ++ short i6, ++ short i5, ++ short i4, ++ short i3, ++ short i2, ++ short i1, ++ short i0) ++{ ++ int16_t __attribute__((aligned(16))) ++ data[8] = {i0, i1, i2, i3, i4, i5, i6, i7}; ++ return vreinterpretq_m128i_s16(vld1q_s16(data)); ++} ++ ++// Sets the 16 signed 8-bit integer values in reverse order. ++// https://msdn.microsoft.com/en-us/library/2khb9c7k(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_setr_epi8(char b0, ++ char b1, ++ char b2, ++ char b3, ++ char b4, ++ char b5, ++ char b6, ++ char b7, ++ char b8, ++ char b9, ++ char b10, ++ char b11, ++ char b12, ++ char b13, ++ char b14, ++ char b15) ++{ ++ int8_t __attribute__((aligned(16))) ++ data[16] = {(int8_t) b0, (int8_t) b1, (int8_t) b2, (int8_t) b3, ++ (int8_t) b4, (int8_t) b5, (int8_t) b6, (int8_t) b7, ++ (int8_t) b8, (int8_t) b9, (int8_t) b10, (int8_t) b11, ++ (int8_t) b12, (int8_t) b13, (int8_t) b14, (int8_t) b15}; ++ return (__m128i) vld1q_s8(data); ++} ++ ++// Sets the 4 signed 32-bit integer values to i. ++// ++// r0 := i ++// r1 := i ++// r2 := i ++// r3 := I ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/h4xscxat(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_set1_epi32(int _i) ++{ ++ return vreinterpretq_m128i_s32(vdupq_n_s32(_i)); ++} ++ ++// Sets the 4 signed 64-bit integer values to i. ++// https://msdn.microsoft.com/en-us/library/vstudio/h4xscxat(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_set1_epi64(int64_t _i) ++{ ++ return vreinterpretq_m128i_s64(vdupq_n_s64(_i)); ++} ++ ++// Sets the 4 signed 32-bit integer values. ++// https://msdn.microsoft.com/en-us/library/vstudio/019beekt(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_set_epi32(int i3, int i2, int i1, int i0) ++{ ++ int32_t __attribute__((aligned(16))) data[4] = {i0, i1, i2, i3}; ++ return vreinterpretq_m128i_s32(vld1q_s32(data)); ++} ++ ++// Returns the __m128i structure with its two 64-bit integer values ++// initialized to the values of the two 64-bit integers passed in. ++// https://msdn.microsoft.com/en-us/library/dk2sdw0h(v=vs.120).aspx ++FORCE_INLINE __m128i _mm_set_epi64x(int64_t i1, int64_t i2) ++{ ++ int64_t __attribute__((aligned(16))) data[2] = {i2, i1}; ++ return vreinterpretq_m128i_s64(vld1q_s64(data)); ++} ++ ++// Stores four single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/vstudio/s3h4ay6y(v=vs.100).aspx ++FORCE_INLINE void _mm_store_ps(float *p, __m128 a) ++{ ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++} ++ ++// Stores four single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/44e30x22(v=vs.100).aspx ++FORCE_INLINE void _mm_storeu_ps(float *p, __m128 a) ++{ ++ vst1q_f32(p, vreinterpretq_f32_m128(a)); ++} ++ ++// Stores four 32-bit integer values as (as a __m128i value) at the address p. ++// https://msdn.microsoft.com/en-us/library/vstudio/edk11s13(v=vs.100).aspx ++FORCE_INLINE void _mm_store_si128(__m128i *p, __m128i a) ++{ ++ vst1q_s32((int32_t *) p, vreinterpretq_s32_m128i(a)); ++} ++ ++// Stores four 32-bit integer values as (as a __m128i value) at the address p. ++// https://msdn.microsoft.com/en-us/library/vstudio/edk11s13(v=vs.100).aspx ++FORCE_INLINE void _mm_storeu_si128(__m128i *p, __m128i a) ++{ ++ vst1q_s32((int32_t *) p, vreinterpretq_s32_m128i(a)); ++} ++ ++// Stores the lower single - precision, floating - point value. ++// https://msdn.microsoft.com/en-us/library/tzz10fbx(v=vs.100).aspx ++FORCE_INLINE void _mm_store_ss(float *p, __m128 a) ++{ ++ vst1q_lane_f32(p, vreinterpretq_f32_m128(a), 0); ++} ++ ++// Reads the lower 64 bits of b and stores them into the lower 64 bits of a. ++// https://msdn.microsoft.com/en-us/library/hhwf428f%28v=vs.90%29.aspx ++FORCE_INLINE void _mm_storel_epi64(__m128i *a, __m128i b) ++{ ++ uint64x1_t hi = vget_high_u64(vreinterpretq_u64_m128i(*a)); ++ uint64x1_t lo = vget_low_u64(vreinterpretq_u64_m128i(b)); ++ *a = vreinterpretq_m128i_u64(vcombine_u64(lo, hi)); ++} ++ ++// Stores the lower two single-precision floating point values of a to the ++// address p. ++// ++// *p0 := b0 ++// *p1 := b1 ++// ++// https://msdn.microsoft.com/en-us/library/h54t98ks(v=vs.90).aspx ++FORCE_INLINE void _mm_storel_pi(__m64 *p, __m128 a) ++{ ++ *p = vget_low_f32(a); ++} ++ ++// Loads a single single-precision, floating-point value, copying it into all ++// four words ++// https://msdn.microsoft.com/en-us/library/vstudio/5cdkf716(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_load1_ps(const float *p) ++{ ++ return vreinterpretq_m128_f32(vld1q_dup_f32(p)); ++} ++#define _mm_load_ps1 _mm_load1_ps ++ ++// Sets the lower two single-precision, floating-point values with 64 ++// bits of data loaded from the address p; the upper two values are passed ++// through from a. ++// ++// Return Value ++// r0 := *p0 ++// r1 := *p1 ++// r2 := a2 ++// r3 := a3 ++// ++// https://msdn.microsoft.com/en-us/library/s57cyak2(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_loadl_pi(__m128 a, __m64 const *b) ++{ ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vld1_f32((const float32_t *) b), vget_high_f32(a))); ++} ++ ++// Loads four single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/vstudio/zzd50xxt(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_load_ps(const float *p) ++{ ++ return vreinterpretq_m128_f32(vld1q_f32(p)); ++} ++ ++// Loads four single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/x1b16s7z%28v=vs.90%29.aspx ++FORCE_INLINE __m128 _mm_loadu_ps(const float *p) ++{ ++ // for neon, alignment doesn't matter, so _mm_load_ps and _mm_loadu_ps are ++ // equivalent for neon ++ return vreinterpretq_m128_f32(vld1q_f32(p)); ++} ++ ++// Loads an single - precision, floating - point value into the low word and ++// clears the upper three words. ++// https://msdn.microsoft.com/en-us/library/548bb9h4%28v=vs.90%29.aspx ++FORCE_INLINE __m128 _mm_load_ss(const float *p) ++{ ++ return vreinterpretq_m128_f32(vsetq_lane_f32(*p, vdupq_n_f32(0), 0)); ++} ++ ++FORCE_INLINE __m128i _mm_loadl_epi64(__m128i const *p) ++{ ++ /* Load the lower 64 bits of the value pointed to by p into the ++ * lower 64 bits of the result, zeroing the upper 64 bits of the result. ++ */ ++ return vcombine_s32(vld1_s32((int32_t const *) p), vcreate_s32(0)); ++} ++ ++// ****************************************** ++// Logic/Binary operations ++// ****************************************** ++ ++// Compares for inequality. ++// https://msdn.microsoft.com/en-us/library/sf44thbx(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmpneq_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32(vmvnq_u32( ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)))); ++} ++ ++// Computes the bitwise AND-NOT of the four single-precision, floating-point ++// values of a and b. ++// ++// r0 := ~a0 & b0 ++// r1 := ~a1 & b1 ++// r2 := ~a2 & b2 ++// r3 := ~a3 & b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/68h7wd02(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_andnot_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vbicq_s32(vreinterpretq_s32_m128(b), ++ vreinterpretq_s32_m128(a))); // *NOTE* argument swap ++} ++ ++// Computes the bitwise AND of the 128-bit value in b and the bitwise NOT of the ++// 128-bit value in a. ++// ++// r := (~a) & b ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/1beaceh8(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_andnot_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vbicq_s32(vreinterpretq_s32_m128i(b), ++ vreinterpretq_s32_m128i(a))); // *NOTE* argument swap ++} ++ ++// Computes the bitwise AND of the 128-bit value in a and the 128-bit value in ++// b. ++// ++// r := a & b ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/6d1txsa8(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_and_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vandq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Computes the bitwise AND of the four single-precision, floating-point values ++// of a and b. ++// ++// r0 := a0 & b0 ++// r1 := a1 & b1 ++// r2 := a2 & b2 ++// r3 := a3 & b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/73ck1xc5(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_and_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vandq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++// Computes the bitwise OR of the four single-precision, floating-point values ++// of a and b. ++// https://msdn.microsoft.com/en-us/library/vstudio/7ctdsyy0(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_or_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ vorrq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++// Computes bitwise EXOR (exclusive-or) of the four single-precision, ++// floating-point values of a and b. ++// https://msdn.microsoft.com/en-us/library/ss6k3wk8(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_xor_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_s32( ++ veorq_s32(vreinterpretq_s32_m128(a), vreinterpretq_s32_m128(b))); ++} ++ ++// Computes the bitwise OR of the 128-bit value in a and the 128-bit value in b. ++// ++// r := a | b ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/ew8ty0db(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_or_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vorrq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Computes the bitwise XOR of the 128-bit value in a and the 128-bit value in ++// b. https://msdn.microsoft.com/en-us/library/fzt08www(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_xor_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ veorq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Moves the upper two values of B into the lower two values of A. ++// ++// r3 := a3 ++// r2 := a2 ++// r1 := b3 ++// r0 := b2 ++FORCE_INLINE __m128 _mm_movehl_ps(__m128 __A, __m128 __B) ++{ ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(__A)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(__B)); ++ return vreinterpretq_m128_f32(vcombine_f32(b32, a32)); ++} ++ ++// Moves the lower two values of B into the upper two values of A. ++// ++// r3 := b1 ++// r2 := b0 ++// r1 := a1 ++// r0 := a0 ++FORCE_INLINE __m128 _mm_movelh_ps(__m128 __A, __m128 __B) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(__A)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(__B)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b10)); ++} ++ ++// NEON does not provide this method ++// Creates a 4-bit mask from the most significant bits of the four ++// single-precision, floating-point values. ++// https://msdn.microsoft.com/en-us/library/vstudio/4490ys29(v=vs.100).aspx ++FORCE_INLINE int _mm_movemask_ps(__m128 a) ++{ ++#if 0 /* C version */ ++ uint32x4_t &ia = *(uint32x4_t *) &a; ++ return (ia[0] >> 31) | ((ia[1] >> 30) & 2) | ((ia[2] >> 29) & 4) | ++ ((ia[3] >> 28) & 8); ++#endif ++ static const uint32x4_t movemask = {1, 2, 4, 8}; ++ static const uint32x4_t highbit = {0x80000000, 0x80000000, 0x80000000, ++ 0x80000000}; ++ uint32x4_t t0 = vreinterpretq_u32_m128(a); ++ uint32x4_t t1 = vtstq_u32(t0, highbit); ++ uint32x4_t t2 = vandq_u32(t1, movemask); ++ uint32x2_t t3 = vorr_u32(vget_low_u32(t2), vget_high_u32(t2)); ++ return vget_lane_u32(t3, 0) | vget_lane_u32(t3, 1); ++} ++ ++FORCE_INLINE __m128i _mm_abs_epi32(__m128i a) ++{ ++ return vqabsq_s32(a); ++} ++ ++FORCE_INLINE __m128i _mm_abs_epi16(__m128i a) ++{ ++ return vreinterpretq_s32_s16(vqabsq_s16(vreinterpretq_s16_s32(a))); ++} ++ ++// Takes the upper 64 bits of a and places it in the low end of the result ++// Takes the lower 64 bits of b and places it into the high end of the result. ++FORCE_INLINE __m128 _mm_shuffle_ps_1032(__m128 a, __m128 b) ++{ ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a32, b10)); ++} ++ ++// takes the lower two 32-bit values from a and swaps them and places in high ++// end of result takes the higher two 32 bit values from b and swaps them and ++// places in low end of result. ++FORCE_INLINE __m128 _mm_shuffle_ps_2301(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b23 = vrev64_f32(vget_high_f32(vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b23)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0321(__m128 a, __m128 b) ++{ ++ float32x2_t a21 = vget_high_f32( ++ vextq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 3)); ++ float32x2_t b03 = vget_low_f32( ++ vextq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b), 3)); ++ return vreinterpretq_m128_f32(vcombine_f32(a21, b03)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2103(__m128 a, __m128 b) ++{ ++ float32x2_t a03 = vget_low_f32( ++ vextq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a), 3)); ++ float32x2_t b21 = vget_high_f32( ++ vextq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b), 3)); ++ return vreinterpretq_m128_f32(vcombine_f32(a03, b21)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1010(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b10)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1001(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b10)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0101(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32x2_t b01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b01)); ++} ++ ++// keeps the low 64 bits of b in the low and puts the high 64 bits of a in the ++// high ++FORCE_INLINE __m128 _mm_shuffle_ps_3210(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b32)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0011(__m128 a, __m128 b) ++{ ++ float32x2_t a11 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(a)), 1); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a11, b00)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_0022(__m128 a, __m128 b) ++{ ++ float32x2_t a22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a22, b00)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2200(__m128 a, __m128 b) ++{ ++ float32x2_t a00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t b22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32(vcombine_f32(a00, b22)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_3202(__m128 a, __m128 b) ++{ ++ float32_t a0 = vgetq_lane_f32(vreinterpretq_f32_m128(a), 0); ++ float32x2_t a22 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 0); ++ float32x2_t a02 = vset_lane_f32(a0, a22, 1); /* TODO: use vzip ?*/ ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32(vcombine_f32(a02, b32)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_1133(__m128 a, __m128 b) ++{ ++ float32x2_t a33 = ++ vdup_lane_f32(vget_high_f32(vreinterpretq_f32_m128(a)), 1); ++ float32x2_t b11 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a33, b11)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2010(__m128 a, __m128 b) ++{ ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32_t b2 = vgetq_lane_f32(vreinterpretq_f32_m128(b), 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a10, b20)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2001(__m128 a, __m128 b) ++{ ++ float32x2_t a01 = vrev64_f32(vget_low_f32(vreinterpretq_f32_m128(a))); ++ float32_t b2 = vgetq_lane_f32(b, 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a01, b20)); ++} ++ ++FORCE_INLINE __m128 _mm_shuffle_ps_2032(__m128 a, __m128 b) ++{ ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32_t b2 = vgetq_lane_f32(b, 2); ++ float32x2_t b00 = vdup_lane_f32(vget_low_f32(vreinterpretq_f32_m128(b)), 0); ++ float32x2_t b20 = vset_lane_f32(b2, b00, 1); ++ return vreinterpretq_m128_f32(vcombine_f32(a32, b20)); ++} ++ ++// NEON does not support a general purpose permute intrinsic ++// Selects four specific single-precision, floating-point values from a and b, ++// based on the mask i. ++// https://msdn.microsoft.com/en-us/library/vstudio/5f0858x0(v=vs.100).aspx ++#if 0 /* C version */ ++FORCE_INLINE __m128 _mm_shuffle_ps_default(__m128 a, ++ __m128 b, ++ __constrange(0, 255) int imm) ++{ ++ __m128 ret; ++ ret[0] = a[imm & 0x3]; ++ ret[1] = a[(imm >> 2) & 0x3]; ++ ret[2] = b[(imm >> 4) & 0x03]; ++ ret[3] = b[(imm >> 6) & 0x03]; ++ return ret; ++} ++#endif ++#define _mm_shuffle_ps_default(a, b, imm) \ ++ ({ \ ++ float32x4_t ret; \ ++ ret = vmovq_n_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(a), (imm) &0x3)); \ ++ ret = vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(a), ((imm) >> 2) & 0x3), \ ++ ret, 1); \ ++ ret = vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(b), ((imm) >> 4) & 0x3), \ ++ ret, 2); \ ++ ret = vsetq_lane_f32( \ ++ vgetq_lane_f32(vreinterpretq_f32_m128(b), ((imm) >> 6) & 0x3), \ ++ ret, 3); \ ++ vreinterpretq_m128_f32(ret); \ ++ }) ++ ++// FORCE_INLINE __m128 _mm_shuffle_ps(__m128 a, __m128 b, __constrange(0,255) ++// int imm) ++#define _mm_shuffle_ps(a, b, imm) \ ++ ({ \ ++ __m128 ret; \ ++ switch (imm) { \ ++ case _MM_SHUFFLE(1, 0, 3, 2): \ ++ ret = _mm_shuffle_ps_1032((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 3, 0, 1): \ ++ ret = _mm_shuffle_ps_2301((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 3, 2, 1): \ ++ ret = _mm_shuffle_ps_0321((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 1, 0, 3): \ ++ ret = _mm_shuffle_ps_2103((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 1, 0): \ ++ ret = _mm_movelh_ps((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 0, 1): \ ++ ret = _mm_shuffle_ps_1001((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 0, 1): \ ++ ret = _mm_shuffle_ps_0101((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 1, 0): \ ++ ret = _mm_shuffle_ps_3210((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 1, 1): \ ++ ret = _mm_shuffle_ps_0011((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 2, 2): \ ++ ret = _mm_shuffle_ps_0022((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 0, 0): \ ++ ret = _mm_shuffle_ps_2200((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 0, 2): \ ++ ret = _mm_shuffle_ps_3202((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(3, 2, 3, 2): \ ++ ret = _mm_movehl_ps((b), (a)); \ ++ break; \ ++ case _MM_SHUFFLE(1, 1, 3, 3): \ ++ ret = _mm_shuffle_ps_1133((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 1, 0): \ ++ ret = _mm_shuffle_ps_2010((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 0, 1): \ ++ ret = _mm_shuffle_ps_2001((a), (b)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 0, 3, 2): \ ++ ret = _mm_shuffle_ps_2032((a), (b)); \ ++ break; \ ++ default: \ ++ ret = _mm_shuffle_ps_default((a), (b), (imm)); \ ++ break; \ ++ } \ ++ ret; \ ++ }) ++ ++// Takes the upper 64 bits of a and places it in the low end of the result ++// Takes the lower 64 bits of a and places it into the high end of the result. ++FORCE_INLINE __m128i _mm_shuffle_epi_1032(__m128i a) ++{ ++ int32x2_t a32 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a32, a10)); ++} ++ ++// takes the lower two 32-bit values from a and swaps them and places in low end ++// of result takes the higher two 32 bit values from a and swaps them and places ++// in high end of result. ++FORCE_INLINE __m128i _mm_shuffle_epi_2301(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ int32x2_t a23 = vrev64_s32(vget_high_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a23)); ++} ++ ++// rotates the least significant 32 bits into the most signficant 32 bits, and ++// shifts the rest down ++FORCE_INLINE __m128i _mm_shuffle_epi_0321(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vextq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(a), 1)); ++} ++ ++// rotates the most significant 32 bits into the least signficant 32 bits, and ++// shifts the rest up ++FORCE_INLINE __m128i _mm_shuffle_epi_2103(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vextq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(a), 3)); ++} ++ ++// gets the lower 64 bits of a, and places it in the upper 64 bits ++// gets the lower 64 bits of a and places it in the lower 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_1010(__m128i a) ++{ ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a10, a10)); ++} ++ ++// gets the lower 64 bits of a, swaps the 0 and 1 elements, and places it in the ++// lower 64 bits gets the lower 64 bits of a, and places it in the upper 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_1001(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ int32x2_t a10 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a10)); ++} ++ ++// gets the lower 64 bits of a, swaps the 0 and 1 elements and places it in the ++// upper 64 bits gets the lower 64 bits of a, swaps the 0 and 1 elements, and ++// places it in the lower 64 bits ++FORCE_INLINE __m128i _mm_shuffle_epi_0101(__m128i a) ++{ ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a01, a01)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_2211(__m128i a) ++{ ++ int32x2_t a11 = vdup_lane_s32(vget_low_s32(vreinterpretq_s32_m128i(a)), 1); ++ int32x2_t a22 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 0); ++ return vreinterpretq_m128i_s32(vcombine_s32(a11, a22)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_0122(__m128i a) ++{ ++ int32x2_t a22 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 0); ++ int32x2_t a01 = vrev64_s32(vget_low_s32(vreinterpretq_s32_m128i(a))); ++ return vreinterpretq_m128i_s32(vcombine_s32(a22, a01)); ++} ++ ++FORCE_INLINE __m128i _mm_shuffle_epi_3332(__m128i a) ++{ ++ int32x2_t a32 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t a33 = vdup_lane_s32(vget_high_s32(vreinterpretq_s32_m128i(a)), 1); ++ return vreinterpretq_m128i_s32(vcombine_s32(a32, a33)); ++} ++ ++// Shuffle packed 8-bit integers in a according to shuffle control mask in the ++// corresponding 8-bit element of b, and store the results in dst. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_shuffle_epi8&expand=5146 ++FORCE_INLINE __m128i _mm_shuffle_epi8(__m128i a, __m128i b) ++{ ++#if __aarch64__ ++ int8x16_t tbl = vreinterpretq_s8_m128i(a); // input a ++ uint8x16_t idx = vreinterpretq_u8_m128i(b); // input b ++ uint8_t __attribute__((aligned(16))) ++ mask[16] = {0x8F, 0x8F, 0x8F, 0x8F, 0x8F, 0x8F, 0x8F, 0x8F, ++ 0x8F, 0x8F, 0x8F, 0x8F, 0x8F, 0x8F, 0x8F, 0x8F}; ++ uint8x16_t idx_masked = ++ vandq_u8(idx, vld1q_u8(mask)); // avoid using meaningless bits ++ ++ return vreinterpretq_m128i_s8(vqtbl1q_s8(tbl, idx_masked)); ++#else ++ uint8_t *tbl = (uint8_t *) &a; // input a ++ uint8_t *idx = (uint8_t *) &b; // input b ++ int32_t r[4]; ++ ++ r[0] = ((idx[3] & 0x80) ? 0 : tbl[idx[3] % 16]) << 24; ++ r[0] |= ((idx[2] & 0x80) ? 0 : tbl[idx[2] % 16]) << 16; ++ r[0] |= ((idx[1] & 0x80) ? 0 : tbl[idx[1] % 16]) << 8; ++ r[0] |= ((idx[0] & 0x80) ? 0 : tbl[idx[0] % 16]); ++ ++ r[1] = ((idx[7] & 0x80) ? 0 : tbl[idx[7] % 16]) << 24; ++ r[1] |= ((idx[6] & 0x80) ? 0 : tbl[idx[6] % 16]) << 16; ++ r[1] |= ((idx[5] & 0x80) ? 0 : tbl[idx[5] % 16]) << 8; ++ r[1] |= ((idx[4] & 0x80) ? 0 : tbl[idx[4] % 16]); ++ ++ r[2] = ((idx[11] & 0x80) ? 0 : tbl[idx[11] % 16]) << 24; ++ r[2] |= ((idx[10] & 0x80) ? 0 : tbl[idx[10] % 16]) << 16; ++ r[2] |= ((idx[9] & 0x80) ? 0 : tbl[idx[9] % 16]) << 8; ++ r[2] |= ((idx[8] & 0x80) ? 0 : tbl[idx[8] % 16]); ++ ++ r[3] = ((idx[15] & 0x80) ? 0 : tbl[idx[15] % 16]) << 24; ++ r[3] |= ((idx[14] & 0x80) ? 0 : tbl[idx[14] % 16]) << 16; ++ r[3] |= ((idx[13] & 0x80) ? 0 : tbl[idx[13] % 16]) << 8; ++ r[3] |= ((idx[12] & 0x80) ? 0 : tbl[idx[12] % 16]); ++ ++ return vld1q_s32(r); ++#endif ++} ++ ++ ++#if 0 /* C version */ ++FORCE_INLINE __m128i _mm_shuffle_epi32_default(__m128i a, ++ __constrange(0, 255) int imm) ++{ ++ __m128i ret; ++ ret[0] = a[imm & 0x3]; ++ ret[1] = a[(imm >> 2) & 0x3]; ++ ret[2] = a[(imm >> 4) & 0x03]; ++ ret[3] = a[(imm >> 6) & 0x03]; ++ return ret; ++} ++#endif ++#define _mm_shuffle_epi32_default(a, imm) \ ++ ({ \ ++ int32x4_t ret; \ ++ ret = vmovq_n_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), (imm) &0x3)); \ ++ ret = vsetq_lane_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), ((imm) >> 2) & 0x3), \ ++ ret, 1); \ ++ ret = vsetq_lane_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), ((imm) >> 4) & 0x3), \ ++ ret, 2); \ ++ ret = vsetq_lane_s32( \ ++ vgetq_lane_s32(vreinterpretq_s32_m128i(a), ((imm) >> 6) & 0x3), \ ++ ret, 3); \ ++ vreinterpretq_m128i_s32(ret); \ ++ }) ++ ++// FORCE_INLINE __m128i _mm_shuffle_epi32_splat(__m128i a, __constrange(0,255) ++// int imm) ++#if defined(__aarch64__) ++#define _mm_shuffle_epi32_splat(a, imm) \ ++ ({ \ ++ vreinterpretq_m128i_s32( \ ++ vdupq_laneq_s32(vreinterpretq_s32_m128i(a), (imm))); \ ++ }) ++#else ++#define _mm_shuffle_epi32_splat(a, imm) \ ++ ({ \ ++ vreinterpretq_m128i_s32( \ ++ vdupq_n_s32(vgetq_lane_s32(vreinterpretq_s32_m128i(a), (imm)))); \ ++ }) ++#endif ++ ++// Shuffles the 4 signed or unsigned 32-bit integers in a as specified by imm. ++// https://msdn.microsoft.com/en-us/library/56f67xbk%28v=vs.90%29.aspx ++// FORCE_INLINE __m128i _mm_shuffle_epi32(__m128i a, __constrange(0,255) int ++// imm) ++#define _mm_shuffle_epi32(a, imm) \ ++ ({ \ ++ __m128i ret; \ ++ switch (imm) { \ ++ case _MM_SHUFFLE(1, 0, 3, 2): \ ++ ret = _mm_shuffle_epi_1032((a)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 3, 0, 1): \ ++ ret = _mm_shuffle_epi_2301((a)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 3, 2, 1): \ ++ ret = _mm_shuffle_epi_0321((a)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 1, 0, 3): \ ++ ret = _mm_shuffle_epi_2103((a)); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 1, 0): \ ++ ret = _mm_shuffle_epi_1010((a)); \ ++ break; \ ++ case _MM_SHUFFLE(1, 0, 0, 1): \ ++ ret = _mm_shuffle_epi_1001((a)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 0, 1): \ ++ ret = _mm_shuffle_epi_0101((a)); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 1, 1): \ ++ ret = _mm_shuffle_epi_2211((a)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 1, 2, 2): \ ++ ret = _mm_shuffle_epi_0122((a)); \ ++ break; \ ++ case _MM_SHUFFLE(3, 3, 3, 2): \ ++ ret = _mm_shuffle_epi_3332((a)); \ ++ break; \ ++ case _MM_SHUFFLE(0, 0, 0, 0): \ ++ ret = _mm_shuffle_epi32_splat((a), 0); \ ++ break; \ ++ case _MM_SHUFFLE(1, 1, 1, 1): \ ++ ret = _mm_shuffle_epi32_splat((a), 1); \ ++ break; \ ++ case _MM_SHUFFLE(2, 2, 2, 2): \ ++ ret = _mm_shuffle_epi32_splat((a), 2); \ ++ break; \ ++ case _MM_SHUFFLE(3, 3, 3, 3): \ ++ ret = _mm_shuffle_epi32_splat((a), 3); \ ++ break; \ ++ default: \ ++ ret = _mm_shuffle_epi32_default((a), (imm)); \ ++ break; \ ++ } \ ++ ret; \ ++ }) ++ ++// Shuffles the upper 4 signed or unsigned 16 - bit integers in a as specified ++// by imm. https://msdn.microsoft.com/en-us/library/13ywktbs(v=vs.100).aspx ++// FORCE_INLINE __m128i _mm_shufflehi_epi16_function(__m128i a, ++// __constrange(0,255) int imm) ++#define _mm_shufflelo_epi16_function(a, imm) \ ++ ({ \ ++ int16x8_t ret = vreinterpretq_s16_s32(a); \ ++ int16x4_t lowBits = vget_low_s16(ret); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, (imm) &0x3), ret, 4); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 2) & 0x3), ret, \ ++ 5); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 4) & 0x3), ret, \ ++ 6); \ ++ ret = vsetq_lane_s16(vget_lane_s16(lowBits, ((imm) >> 6) & 0x3), ret, \ ++ 7); \ ++ vreinterpretq_s32_s16(ret); \ ++ }) ++ ++// FORCE_INLINE __m128i _mm_shufflehi_epi16(__m128i a, __constrange(0,255) int ++// imm) ++#define _mm_shufflelo_epi16(a, imm) _mm_shufflehi_epi16_function((a), (imm)) ++ ++// Shuffles the upper 4 signed or unsigned 16 - bit integers in a as specified ++// by imm. https://msdn.microsoft.com/en-us/library/13ywktbs(v=vs.100).aspx ++// FORCE_INLINE __m128i _mm_shufflehi_epi16_function(__m128i a, ++// __constrange(0,255) int imm) ++#define _mm_shufflehi_epi16_function(a, imm) \ ++ ({ \ ++ int16x8_t ret = vreinterpretq_s16_s32(a); \ ++ int16x4_t highBits = vget_high_s16(ret); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, (imm) &0x3), ret, 4); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 2) & 0x3), ret, \ ++ 5); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 4) & 0x3), ret, \ ++ 6); \ ++ ret = vsetq_lane_s16(vget_lane_s16(highBits, ((imm) >> 6) & 0x3), ret, \ ++ 7); \ ++ vreinterpretq_s32_s16(ret); \ ++ }) ++ ++// FORCE_INLINE __m128i _mm_shufflehi_epi16(__m128i a, __constrange(0,255) int ++// imm) ++#define _mm_shufflehi_epi16(a, imm) _mm_shufflehi_epi16_function((a), (imm)) ++ ++// Shifts the 4 signed 32-bit integers in a right by count bits while shifting ++// in the sign bit. ++// ++// r0 := a0 >> count ++// r1 := a1 >> count ++// r2 := a2 >> count ++// r3 := a3 >> count immediate ++FORCE_INLINE __m128i _mm_srai_epi32(__m128i a, int count) ++{ ++ return vshlq_s32(a, vdupq_n_s32(-count)); ++} ++ ++// Shifts the 8 signed 16-bit integers in a right by count bits while shifting ++// in the sign bit. ++// ++// r0 := a0 >> count ++// r1 := a1 >> count ++// ... ++// r7 := a7 >> count ++FORCE_INLINE __m128i _mm_srai_epi16(__m128i a, int count) ++{ ++ return (__m128i) vshlq_s16((int16x8_t) a, vdupq_n_s16(-count)); ++} ++ ++// Shifts the 8 signed or unsigned 16-bit integers in a left by count bits while ++// shifting in zeros. ++// ++// r0 := a0 << count ++// r1 := a1 << count ++// ... ++// r7 := a7 << count ++// ++// https://msdn.microsoft.com/en-us/library/es73bcsy(v=vs.90).aspx ++#define _mm_slli_epi16(a, imm) \ ++ ({ \ ++ __m128i ret; \ ++ if ((imm) <= 0) { \ ++ ret = a; \ ++ } else if ((imm) > 31) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_s16( \ ++ vshlq_n_s16(vreinterpretq_s16_m128i(a), (imm))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shifts the 4 signed or unsigned 32-bit integers in a left by count bits while ++// shifting in zeros. : ++// https://msdn.microsoft.com/en-us/library/z2k3bbtb%28v=vs.90%29.aspx ++// FORCE_INLINE __m128i _mm_slli_epi32(__m128i a, __constrange(0,255) int imm) ++#define _mm_slli_epi32(a, imm) \ ++ ({ \ ++ __m128i ret; \ ++ if ((imm) <= 0) { \ ++ ret = a; \ ++ } else if ((imm) > 31) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_s32( \ ++ vshlq_n_s32(vreinterpretq_s32_m128i(a), (imm))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shift packed 64-bit integers in a left by imm8 while shifting in zeros, and ++// store the results in dst. ++#define _mm_slli_epi64(a, imm) \ ++ ({ \ ++ __m128i ret; \ ++ if ((imm) <= 0) { \ ++ ret = a; \ ++ } else if ((imm) > 63) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_s64( \ ++ vshlq_n_s64(vreinterpretq_s64_m128i(a), (imm))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shifts the 8 signed or unsigned 16-bit integers in a right by count bits ++// while shifting in zeros. ++// ++// r0 := srl(a0, count) ++// r1 := srl(a1, count) ++// ... ++// r7 := srl(a7, count) ++// ++// https://msdn.microsoft.com/en-us/library/6tcwd38t(v=vs.90).aspx ++#define _mm_srli_epi16(a, imm) \ ++ ({ \ ++ __m128i ret; \ ++ if ((imm) <= 0) { \ ++ ret = a; \ ++ } else if ((imm) > 31) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u16( \ ++ vshrq_n_u16(vreinterpretq_u16_m128i(a), (imm))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shifts the 4 signed or unsigned 32-bit integers in a right by count bits ++// while shifting in zeros. ++// https://msdn.microsoft.com/en-us/library/w486zcfa(v=vs.100).aspx FORCE_INLINE ++// __m128i _mm_srli_epi32(__m128i a, __constrange(0,255) int imm) ++#define _mm_srli_epi32(a, imm) \ ++ ({ \ ++ __m128i ret; \ ++ if ((imm) <= 0) { \ ++ ret = a; \ ++ } else if ((imm) > 31) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u32( \ ++ vshrq_n_u32(vreinterpretq_u32_m128i(a), (imm))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shift packed 64-bit integers in a right by imm8 while shifting in zeros, and ++// store the results in dst. ++#define _mm_srli_epi64(a, imm) \ ++ ({ \ ++ __m128i ret; \ ++ if ((imm) <= 0) { \ ++ ret = a; \ ++ } else if ((imm) > 63) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_u64( \ ++ vshrq_n_u64(vreinterpretq_u64_m128i(a), (imm))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shifts the 4 signed 32 - bit integers in a right by count bits while shifting ++// in the sign bit. ++// https://msdn.microsoft.com/en-us/library/z1939387(v=vs.100).aspx ++// FORCE_INLINE __m128i _mm_srai_epi32(__m128i a, __constrange(0,255) int imm) ++#define _mm_srai_epi32(a, imm) \ ++ ({ \ ++ __m128i ret; \ ++ if ((imm) <= 0) { \ ++ ret = a; \ ++ } else if ((imm) > 31) { \ ++ ret = vreinterpretq_m128i_s32( \ ++ vshrq_n_s32(vreinterpretq_s32_m128i(a), 16)); \ ++ ret = vreinterpretq_m128i_s32( \ ++ vshrq_n_s32(vreinterpretq_s32_m128i(ret), 16)); \ ++ } else { \ ++ ret = vreinterpretq_m128i_s32( \ ++ vshrq_n_s32(vreinterpretq_s32_m128i(a), (imm))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shifts the 128 - bit value in a right by imm bytes while shifting in ++// zeros.imm must be an immediate. ++// ++// r := srl(a, imm*8) ++// ++// https://msdn.microsoft.com/en-us/library/305w28yz(v=vs.100).aspx ++// FORCE_INLINE _mm_srli_si128(__m128i a, __constrange(0,255) int imm) ++#define _mm_srli_si128(a, imm) \ ++ ({ \ ++ __m128i ret; \ ++ if ((imm) <= 0) { \ ++ ret = a; \ ++ } else if ((imm) > 15) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_s8( \ ++ vextq_s8(vreinterpretq_s8_m128i(a), vdupq_n_s8(0), (imm))); \ ++ } \ ++ ret; \ ++ }) ++ ++// Shifts the 128-bit value in a left by imm bytes while shifting in zeros. imm ++// must be an immediate. ++// ++// r := a << (imm * 8) ++// ++// https://msdn.microsoft.com/en-us/library/34d3k2kt(v=vs.100).aspx ++// FORCE_INLINE __m128i _mm_slli_si128(__m128i a, __constrange(0,255) int imm) ++#define _mm_slli_si128(a, imm) \ ++ ({ \ ++ __m128i ret; \ ++ if ((imm) <= 0) { \ ++ ret = a; \ ++ } else if ((imm) > 15) { \ ++ ret = _mm_setzero_si128(); \ ++ } else { \ ++ ret = vreinterpretq_m128i_s8(vextq_s8( \ ++ vdupq_n_s8(0), vreinterpretq_s8_m128i(a), 16 - (imm))); \ ++ } \ ++ ret; \ ++ }) ++ ++// NEON does not provide a version of this function, here is an article about ++// some ways to repro the results. ++// http://stackoverflow.com/questions/11870910/sse-mm-movemask-epi8-equivalent-method-for-arm-neon ++// Creates a 16-bit mask from the most significant bits of the 16 signed or ++// unsigned 8-bit integers in a and zero extends the upper bits. ++// https://msdn.microsoft.com/en-us/library/vstudio/s090c8fk(v=vs.100).aspx ++FORCE_INLINE int _mm_movemask_epi8(__m128i _a) ++{ ++ uint8x16_t input = vreinterpretq_u8_m128i(_a); ++ static const int8_t __attribute__((aligned(16))) ++ xr[8] = {-7, -6, -5, -4, -3, -2, -1, 0}; ++ uint8x8_t mask_and = vdup_n_u8(0x80); ++ int8x8_t mask_shift = vld1_s8(xr); ++ ++ uint8x8_t lo = vget_low_u8(input); ++ uint8x8_t hi = vget_high_u8(input); ++ ++ lo = vand_u8(lo, mask_and); ++ lo = vshl_u8(lo, mask_shift); ++ ++ hi = vand_u8(hi, mask_and); ++ hi = vshl_u8(hi, mask_shift); ++ ++ lo = vpadd_u8(lo, lo); ++ lo = vpadd_u8(lo, lo); ++ lo = vpadd_u8(lo, lo); ++ ++ hi = vpadd_u8(hi, hi); ++ hi = vpadd_u8(hi, hi); ++ hi = vpadd_u8(hi, hi); ++ ++ return ((hi[0] << 8) | (lo[0] & 0xFF)); ++} ++ ++// Compute the bitwise AND of 128 bits (representing integer data) in a and ++// mask, and return 1 if the result is zero, otherwise return 0. ++// https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_test_all_zeros&expand=5871 ++FORCE_INLINE int _mm_test_all_zeros(__m128i a, __m128i mask) ++{ ++ int64x2_t a_and_mask = ++ vandq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(mask)); ++ return (vgetq_lane_s64(a_and_mask, 0) | vgetq_lane_s64(a_and_mask, 1)) ? 0 ++ : 1; ++} ++ ++// ****************************************** ++// Math operations ++// ****************************************** ++ ++// Subtracts the four single-precision, floating-point values of a and b. ++// ++// r0 := a0 - b0 ++// r1 := a1 - b1 ++// r2 := a2 - b2 ++// r3 := a3 - b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/1zad2k61(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_sub_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vsubq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Subtract 2 packed 64-bit integers in b from 2 packed 64-bit integers in a, ++// and store the results in dst. ++// r0 := a0 - b0 ++// r1 := a1 - b1 ++FORCE_INLINE __m128i _mm_sub_epi64(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s64( ++ vsubq_s64(vreinterpretq_s64_m128i(a), vreinterpretq_s64_m128i(b))); ++} ++ ++// Subtracts the 4 signed or unsigned 32-bit integers of b from the 4 signed or ++// unsigned 32-bit integers of a. ++// ++// r0 := a0 - b0 ++// r1 := a1 - b1 ++// r2 := a2 - b2 ++// r3 := a3 - b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/fhh866h0(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_sub_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128_f32( ++ vsubq_s32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++FORCE_INLINE __m128i _mm_sub_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vsubq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++FORCE_INLINE __m128i _mm_sub_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vsubq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Subtracts the 8 unsigned 16-bit integers of bfrom the 8 unsigned 16-bit ++// integers of a and saturates.. ++// https://technet.microsoft.com/en-us/subscriptions/index/f44y0s19(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_subs_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vqsubq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++// Subtracts the 16 unsigned 8-bit integers of b from the 16 unsigned 8-bit ++// integers of a and saturates. ++// ++// r0 := UnsignedSaturate(a0 - b0) ++// r1 := UnsignedSaturate(a1 - b1) ++// ... ++// r15 := UnsignedSaturate(a15 - b15) ++// ++// https://technet.microsoft.com/en-us/subscriptions/yadkxc18(v=vs.90) ++FORCE_INLINE __m128i _mm_subs_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vqsubq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Subtracts the 8 signed 16-bit integers of b from the 8 signed 16-bit integers ++// of a and saturates. ++// ++// r0 := SignedSaturate(a0 - b0) ++// r1 := SignedSaturate(a1 - b1) ++// ... ++// r7 := SignedSaturate(a7 - b7) ++FORCE_INLINE __m128i _mm_subs_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vqsubq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++FORCE_INLINE __m128i _mm_adds_epu16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vqaddq_u16(vreinterpretq_u16_m128i(a), vreinterpretq_u16_m128i(b))); ++} ++ ++FORCE_INLINE __m128i _mm_sign_epi32(__m128i a, __m128i b) ++{ ++ __m128i zer0 = vdupq_n_s32(0); ++ __m128i ltMask = vreinterpretq_s32_u32(vcltq_s32(b, zer0)); ++ __m128i gtMask = vreinterpretq_s32_u32(vcgtq_s32(b, zer0)); ++ __m128i neg = vnegq_s32(a); ++ __m128i tmp = vandq_s32(a, gtMask); ++ return vorrq_s32(tmp, vandq_s32(neg, ltMask)); ++} ++ ++FORCE_INLINE __m128i _mm_sign_epi16(__m128i a, __m128i b) ++{ ++ int16x8_t zer0 = vdupq_n_s16(0); ++ int16x8_t ltMask = ++ vreinterpretq_s16_u16(vcltq_s16(vreinterpretq_s16_s32(b), zer0)); ++ int16x8_t gtMask = ++ vreinterpretq_s16_u16(vcgtq_s16(vreinterpretq_s16_s32(b), zer0)); ++ int16x8_t neg = vnegq_s16(vreinterpretq_s16_s32(a)); ++ int16x8_t tmp = vandq_s16(vreinterpretq_s16_s32(a), gtMask); ++ return vreinterpretq_s32_s16(vorrq_s16(tmp, vandq_s16(neg, ltMask))); ++} ++ ++// Adds the four single-precision, floating-point values of a and b. ++// ++// r0 := a0 + b0 ++// r1 := a1 + b1 ++// r2 := a2 + b2 ++// r3 := a3 + b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/c9848chc(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_add_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vaddq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// adds the scalar single-precision floating point values of a and b. ++// https://msdn.microsoft.com/en-us/library/be94x2y6(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_add_ss(__m128 a, __m128 b) ++{ ++ float32_t b0 = vgetq_lane_f32(vreinterpretq_f32_m128(b), 0); ++ float32x4_t value = vsetq_lane_f32(b0, vdupq_n_f32(0), 0); ++ // the upper values in the result must be the remnants of <a>. ++ return vreinterpretq_m128_f32(vaddq_f32(a, value)); ++} ++ ++// Adds the 4 signed or unsigned 64-bit integers in a to the 4 signed or ++// unsigned 32-bit integers in b. ++// https://msdn.microsoft.com/en-us/library/vstudio/09xs4fkk(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_add_epi64(__m128i a, __m128i b) ++{ ++ return vreinterpretq_s32_s64( ++ vaddq_s64(vreinterpretq_s64_s32(a), vreinterpretq_s64_s32(b))); ++} ++ ++// Adds the 4 signed or unsigned 32-bit integers in a to the 4 signed or ++// unsigned 32-bit integers in b. ++// ++// r0 := a0 + b0 ++// r1 := a1 + b1 ++// r2 := a2 + b2 ++// r3 := a3 + b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/09xs4fkk(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_add_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vaddq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Adds the 8 signed or unsigned 16-bit integers in a to the 8 signed or ++// unsigned 16-bit integers in b. ++// https://msdn.microsoft.com/en-us/library/fceha5k4(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_add_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vaddq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Adds the 16 signed or unsigned 8-bit integers in a to the 16 signed or ++// unsigned 8-bit integers in b. ++// https://technet.microsoft.com/en-us/subscriptions/yc7tcyzs(v=vs.90) ++FORCE_INLINE __m128i _mm_add_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vaddq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Adds the 8 signed 16-bit integers in a to the 8 signed 16-bit integers in b ++// and saturates. ++// ++// r0 := SignedSaturate(a0 + b0) ++// r1 := SignedSaturate(a1 + b1) ++// ... ++// r7 := SignedSaturate(a7 + b7) ++// ++// https://msdn.microsoft.com/en-us/library/1a306ef8(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_adds_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vqaddq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Adds the 16 unsigned 8-bit integers in a to the 16 unsigned 8-bit integers in ++// b and saturates.. ++// https://msdn.microsoft.com/en-us/library/9hahyddy(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_adds_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vqaddq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Multiplies the 8 signed or unsigned 16-bit integers from a by the 8 signed or ++// unsigned 16-bit integers from b. ++// ++// r0 := (a0 * b0)[15:0] ++// r1 := (a1 * b1)[15:0] ++// ... ++// r7 := (a7 * b7)[15:0] ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/9ks1472s(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_mullo_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vmulq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Multiplies the 4 signed or unsigned 32-bit integers from a by the 4 signed or ++// unsigned 32-bit integers from b. ++// https://msdn.microsoft.com/en-us/library/vstudio/bb531409(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_mullo_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vmulq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Multiplies the four single-precision, floating-point values of a and b. ++// ++// r0 := a0 * b0 ++// r1 := a1 * b1 ++// r2 := a2 * b2 ++// r3 := a3 * b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/22kbk6t9(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_mul_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vmulq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Multiply the low unsigned 32-bit integers from each packed 64-bit element in ++// a and b, and store the unsigned 64-bit results in dst. ++// ++// r0 := (uint32_t*)a0 * (uint32_t*)b0 ++// r1 := (uint32_t*)a2 * (uint32_t*)b2 ++#if 1 /* C version */ ++FORCE_INLINE __m128i _mm_mul_epu32(__m128i a, __m128i b) ++{ ++ __m128i d; ++ vreinterpretq_nth_u64_m128i(d, 0) = ++ (uint64_t)(vreinterpretq_nth_u32_m128i(a, 0)) * ++ (uint64_t)(vreinterpretq_nth_u32_m128i(b, 0)); ++ vreinterpretq_nth_u64_m128i(d, 1) = ++ (uint64_t)(vreinterpretq_nth_u32_m128i(a, 2)) * ++ (uint64_t)(vreinterpretq_nth_u32_m128i(b, 2)); ++ return d; ++} ++#else /* Neon version */ ++// Default to c version until casting can be sorted out on neon version. ++// (Otherwise requires compiling with -fpermissive) Also unclear whether neon ++// version actually performs better. ++FORCE_INLINE __m128i _mm_mul_epu32(__m128i a, __m128i b) ++{ ++ // shuffle: 0, 1, 2, 3 -> 0, 2, 1, 3 */ ++ __m128i const a_shuf = ++ *(__m128i *) (&vzip_u32(vget_low_u32(vreinterpretq_u32_m128i(a)), ++ vget_high_u32(vreinterpretq_u32_m128i(a)))); ++ __m128i const b_shuf = ++ *(__m128i *) (&vzip_u32(vget_low_u32(vreinterpretq_u32_m128i(b)), ++ vget_high_u32(vreinterpretq_u32_m128i(b)))); ++ // Multiply low word (32 bit) against low word (32 bit) and high word (32 ++ // bit) against high word (32 bit). Pack both results (64 bit) into 128 bit ++ // register and return result. ++ return vreinterpretq_m128i_u64( ++ vmull_u32(vget_low_u32(vreinterpretq_u32_m128i(a_shuf)), ++ vget_low_u32(vreinterpretq_u32_m128i(b_shuf)))); ++} ++#endif ++ ++// Multiplies the 8 signed 16-bit integers from a by the 8 signed 16-bit ++// integers from b. ++// ++// r0 := (a0 * b0) + (a1 * b1) ++// r1 := (a2 * b2) + (a3 * b3) ++// r2 := (a4 * b4) + (a5 * b5) ++// r3 := (a6 * b6) + (a7 * b7) ++// https://msdn.microsoft.com/en-us/library/yht36sa6(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_madd_epi16(__m128i a, __m128i b) ++{ ++ int32x4_t low = vmull_s16(vget_low_s16(vreinterpretq_s16_m128i(a)), ++ vget_low_s16(vreinterpretq_s16_m128i(b))); ++ int32x4_t high = vmull_s16(vget_high_s16(vreinterpretq_s16_m128i(a)), ++ vget_high_s16(vreinterpretq_s16_m128i(b))); ++ ++ int32x2_t low_sum = vpadd_s32(vget_low_s32(low), vget_high_s32(low)); ++ int32x2_t high_sum = vpadd_s32(vget_low_s32(high), vget_high_s32(high)); ++ ++ return vreinterpretq_s32_m128i(vcombine_s32(low_sum, high_sum)); ++} ++ ++// Computes the absolute difference of the 16 unsigned 8-bit integers from a ++// and the 16 unsigned 8-bit integers from b. ++// ++// Return Value ++// Sums the upper 8 differences and lower 8 differences and packs the ++// resulting 2 unsigned 16-bit integers into the upper and lower 64-bit ++// elements. ++// ++// r0 := abs(a0 - b0) + abs(a1 - b1) +...+ abs(a7 - b7) ++// r1 := 0x0 ++// r2 := 0x0 ++// r3 := 0x0 ++// r4 := abs(a8 - b8) + abs(a9 - b9) +...+ abs(a15 - b15) ++// r5 := 0x0 ++// r6 := 0x0 ++// r7 := 0x0 ++FORCE_INLINE __m128i _mm_sad_epu8(__m128i a, __m128i b) ++{ ++ uint16x8_t t = vpaddlq_u8(vabdq_u8((uint8x16_t) a, (uint8x16_t) b)); ++ uint16_t r0 = t[0] + t[1] + t[2] + t[3]; ++ uint16_t r4 = t[4] + t[5] + t[6] + t[7]; ++ uint16x8_t r = vsetq_lane_u16(r0, vdupq_n_u16(0), 0); ++ return (__m128i) vsetq_lane_u16(r4, r, 4); ++} ++ ++// Divides the four single-precision, floating-point values of a and b. ++// ++// r0 := a0 / b0 ++// r1 := a1 / b1 ++// r2 := a2 / b2 ++// r3 := a3 / b3 ++// ++// https://msdn.microsoft.com/en-us/library/edaw8147(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_div_ps(__m128 a, __m128 b) ++{ ++ float32x4_t recip0 = vrecpeq_f32(vreinterpretq_f32_m128(b)); ++ float32x4_t recip1 = ++ vmulq_f32(recip0, vrecpsq_f32(recip0, vreinterpretq_f32_m128(b))); ++ return vreinterpretq_m128_f32(vmulq_f32(vreinterpretq_f32_m128(a), recip1)); ++} ++ ++// Divides the scalar single-precision floating point value of a by b. ++// https://msdn.microsoft.com/en-us/library/4y73xa49(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_div_ss(__m128 a, __m128 b) ++{ ++ float32_t value = ++ vgetq_lane_f32(vreinterpretq_f32_m128(_mm_div_ps(a, b)), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// This version does additional iterations to improve accuracy. Between 1 and 4 ++// recommended. Computes the approximations of reciprocals of the four ++// single-precision, floating-point values of a. ++// https://msdn.microsoft.com/en-us/library/vstudio/796k1tty(v=vs.100).aspx ++FORCE_INLINE __m128 recipq_newton(__m128 in, int n) ++{ ++ int i; ++ float32x4_t recip = vrecpeq_f32(vreinterpretq_f32_m128(in)); ++ for (i = 0; i < n; ++i) { ++ recip = ++ vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(in))); ++ } ++ return vreinterpretq_m128_f32(recip); ++} ++ ++// Computes the approximations of reciprocals of the four single-precision, ++// floating-point values of a. ++// https://msdn.microsoft.com/en-us/library/vstudio/796k1tty(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_rcp_ps(__m128 in) ++{ ++ float32x4_t recip = vrecpeq_f32(vreinterpretq_f32_m128(in)); ++ recip = vmulq_f32(recip, vrecpsq_f32(recip, vreinterpretq_f32_m128(in))); ++ return vreinterpretq_m128_f32(recip); ++} ++ ++// Computes the approximations of square roots of the four single-precision, ++// floating-point values of a. First computes reciprocal square roots and then ++// reciprocals of the four values. ++// ++// r0 := sqrt(a0) ++// r1 := sqrt(a1) ++// r2 := sqrt(a2) ++// r3 := sqrt(a3) ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/8z67bwwk(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_sqrt_ps(__m128 in) ++{ ++ float32x4_t recipsq = vrsqrteq_f32(vreinterpretq_f32_m128(in)); ++ float32x4_t sq = vrecpeq_f32(recipsq); ++ // ??? use step versions of both sqrt and recip for better accuracy? ++ return vreinterpretq_m128_f32(sq); ++} ++ ++// Computes the approximation of the square root of the scalar single-precision ++// floating point value of in. ++// https://msdn.microsoft.com/en-us/library/ahfsc22d(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_sqrt_ss(__m128 in) ++{ ++ float32_t value = ++ vgetq_lane_f32(vreinterpretq_f32_m128(_mm_sqrt_ps(in)), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(in), 0)); ++} ++ ++// Computes the approximations of the reciprocal square roots of the four ++// single-precision floating point values of in. ++// https://msdn.microsoft.com/en-us/library/22hfsh53(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_rsqrt_ps(__m128 in) ++{ ++ return vreinterpretq_m128_f32(vrsqrteq_f32(vreinterpretq_f32_m128(in))); ++} ++ ++// Computes the maximums of the four single-precision, floating-point values of ++// a and b. ++// https://msdn.microsoft.com/en-us/library/vstudio/ff5d607a(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_max_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vmaxq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Computes the minima of the four single-precision, floating-point values of a ++// and b. ++// https://msdn.microsoft.com/en-us/library/vstudio/wh13kadz(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_min_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_f32( ++ vminq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Computes the maximum of the two lower scalar single-precision floating point ++// values of a and b. ++// https://msdn.microsoft.com/en-us/library/s6db5esz(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_max_ss(__m128 a, __m128 b) ++{ ++ float32_t value = vgetq_lane_f32( ++ vmaxq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Computes the minimum of the two lower scalar single-precision floating point ++// values of a and b. ++// https://msdn.microsoft.com/en-us/library/0a9y7xaa(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_min_ss(__m128 a, __m128 b) ++{ ++ float32_t value = vgetq_lane_f32( ++ vminq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)), 0); ++ return vreinterpretq_m128_f32( ++ vsetq_lane_f32(value, vreinterpretq_f32_m128(a), 0)); ++} ++ ++// Computes the pairwise maxima of the 16 unsigned 8-bit integers from a and the ++// 16 unsigned 8-bit integers from b. ++// https://msdn.microsoft.com/en-us/library/st6634za(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_max_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vmaxq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Computes the pairwise minima of the 16 unsigned 8-bit integers from a and the ++// 16 unsigned 8-bit integers from b. ++// https://msdn.microsoft.com/ko-kr/library/17k8cf58(v=vs.100).aspxx ++FORCE_INLINE __m128i _mm_min_epu8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vminq_u8(vreinterpretq_u8_m128i(a), vreinterpretq_u8_m128i(b))); ++} ++ ++// Computes the pairwise minima of the 8 signed 16-bit integers from a and the 8 ++// signed 16-bit integers from b. ++// https://msdn.microsoft.com/en-us/library/vstudio/6te997ew(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_min_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vminq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Computes the pairwise maxima of the 8 signed 16-bit integers from a and the 8 ++// signed 16-bit integers from b. ++// https://msdn.microsoft.com/en-us/LIBRary/3x060h7c(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_max_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vmaxq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// epi versions of min/max ++// Computes the pariwise maximums of the four signed 32-bit integer values of a ++// and b. ++// ++// A 128-bit parameter that can be defined with the following equations: ++// r0 := (a0 > b0) ? a0 : b0 ++// r1 := (a1 > b1) ? a1 : b1 ++// r2 := (a2 > b2) ? a2 : b2 ++// r3 := (a3 > b3) ? a3 : b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/bb514055(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_max_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vmaxq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Computes the pariwise minima of the four signed 32-bit integer values of a ++// and b. ++// ++// A 128-bit parameter that can be defined with the following equations: ++// r0 := (a0 < b0) ? a0 : b0 ++// r1 := (a1 < b1) ? a1 : b1 ++// r2 := (a2 < b2) ? a2 : b2 ++// r3 := (a3 < b3) ? a3 : b3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/bb531476(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_min_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s32( ++ vminq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Multiplies the 8 signed 16-bit integers from a by the 8 signed 16-bit ++// integers from b. ++// ++// r0 := (a0 * b0)[31:16] ++// r1 := (a1 * b1)[31:16] ++// ... ++// r7 := (a7 * b7)[31:16] ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/59hddw1d(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_mulhi_epi16(__m128i a, __m128i b) ++{ ++ /* FIXME: issue with large values because of result saturation */ ++ // int16x8_t ret = vqdmulhq_s16(vreinterpretq_s16_m128i(a), ++ // vreinterpretq_s16_m128i(b)); /* =2*a*b */ return ++ // vreinterpretq_m128i_s16(vshrq_n_s16(ret, 1)); ++ int16x4_t a3210 = vget_low_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b3210 = vget_low_s16(vreinterpretq_s16_m128i(b)); ++ int32x4_t ab3210 = vmull_s16(a3210, b3210); /* 3333222211110000 */ ++ int16x4_t a7654 = vget_high_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b7654 = vget_high_s16(vreinterpretq_s16_m128i(b)); ++ int32x4_t ab7654 = vmull_s16(a7654, b7654); /* 7777666655554444 */ ++ uint16x8x2_t r = ++ vuzpq_u16(vreinterpretq_u16_s32(ab3210), vreinterpretq_u16_s32(ab7654)); ++ return vreinterpretq_m128i_u16(r.val[1]); ++} ++ ++// Computes pairwise add of each argument as single-precision, floating-point ++// values a and b. ++// https://msdn.microsoft.com/en-us/library/yd9wecaa.aspx ++FORCE_INLINE __m128 _mm_hadd_ps(__m128 a, __m128 b) ++{ ++#if defined(__aarch64__) ++ return vreinterpretq_m128_f32(vpaddq_f32( ++ vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); // AArch64 ++#else ++ float32x2_t a10 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t a32 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b10 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ float32x2_t b32 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_f32( ++ vcombine_f32(vpadd_f32(a10, a32), vpadd_f32(b10, b32))); ++#endif ++} ++ ++// ****************************************** ++// Compare operations ++// ****************************************** ++ ++// Compares for less than ++// https://msdn.microsoft.com/en-us/library/vstudio/f330yhc8(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmplt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compares for greater than. ++// ++// r0 := (a0 > b0) ? 0xffffffff : 0x0 ++// r1 := (a1 > b1) ? 0xffffffff : 0x0 ++// r2 := (a2 > b2) ? 0xffffffff : 0x0 ++// r3 := (a3 > b3) ? 0xffffffff : 0x0 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/11dy102s(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmpgt_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compares for greater than or equal. ++// https://msdn.microsoft.com/en-us/library/vstudio/fs813y2t(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmpge_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compares for less than or equal. ++// ++// r0 := (a0 <= b0) ? 0xffffffff : 0x0 ++// r1 := (a1 <= b1) ? 0xffffffff : 0x0 ++// r2 := (a2 <= b2) ? 0xffffffff : 0x0 ++// r3 := (a3 <= b3) ? 0xffffffff : 0x0 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/1s75w83z(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmple_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compares for equality. ++// https://msdn.microsoft.com/en-us/library/vstudio/36aectz5(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cmpeq_ps(__m128 a, __m128 b) ++{ ++ return vreinterpretq_m128_u32( ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++} ++ ++// Compares the 16 signed or unsigned 8-bit integers in a and the 16 signed or ++// unsigned 8-bit integers in b for equality. ++// https://msdn.microsoft.com/en-us/library/windows/desktop/bz5xk21a(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_cmpeq_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vceqq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compares the 8 signed or unsigned 16-bit integers in a and the 8 signed or ++// unsigned 16-bit integers in b for equality. ++// https://msdn.microsoft.com/en-us/library/2ay060te(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmpeq_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vceqq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++// Compare packed 32-bit integers in a and b for equality, and store the results ++// in dst ++FORCE_INLINE __m128i _mm_cmpeq_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vceqq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compares the 16 signed 8-bit integers in a and the 16 signed 8-bit integers ++// in b for lesser than. ++// https://msdn.microsoft.com/en-us/library/windows/desktop/9s46csht(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_cmplt_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcltq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compares the 16 signed 8-bit integers in a and the 16 signed 8-bit integers ++// in b for greater than. ++// ++// r0 := (a0 > b0) ? 0xff : 0x0 ++// r1 := (a1 > b1) ? 0xff : 0x0 ++// ... ++// r15 := (a15 > b15) ? 0xff : 0x0 ++// ++// https://msdn.microsoft.com/zh-tw/library/wf45zt2b(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmpgt_epi8(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcgtq_s8(vreinterpretq_s8_m128i(a), vreinterpretq_s8_m128i(b))); ++} ++ ++// Compares the 8 signed 16-bit integers in a and the 8 signed 16-bit integers ++// in b for greater than. ++// ++// r0 := (a0 > b0) ? 0xffff : 0x0 ++// r1 := (a1 > b1) ? 0xffff : 0x0 ++// ... ++// r7 := (a7 > b7) ? 0xffff : 0x0 ++// ++// https://technet.microsoft.com/en-us/library/xd43yfsa(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmpgt_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u16( ++ vcgtq_s16(vreinterpretq_s16_m128i(a), vreinterpretq_s16_m128i(b))); ++} ++ ++ ++// Compares the 4 signed 32-bit integers in a and the 4 signed 32-bit integers ++// in b for less than. ++// https://msdn.microsoft.com/en-us/library/vstudio/4ak0bf5d(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmplt_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vcltq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compares the 4 signed 32-bit integers in a and the 4 signed 32-bit integers ++// in b for greater than. ++// https://msdn.microsoft.com/en-us/library/vstudio/1s9f2z0y(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cmpgt_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_u32( ++ vcgtq_s32(vreinterpretq_s32_m128i(a), vreinterpretq_s32_m128i(b))); ++} ++ ++// Compares the four 32-bit floats in a and b to check if any values are NaN. ++// Ordered compare between each value returns true for "orderable" and false for ++// "not orderable" (NaN). ++// https://msdn.microsoft.com/en-us/library/vstudio/0h9w00fx(v=vs.100).aspx see ++// also: ++// http://stackoverflow.com/questions/8627331/what-does-ordered-unordered-comparison-mean ++// http://stackoverflow.com/questions/29349621/neon-isnanval-intrinsics ++FORCE_INLINE __m128 _mm_cmpord_ps(__m128 a, __m128 b) ++{ ++ // Note: NEON does not have ordered compare builtin ++ // Need to compare a eq a and b eq b to check for NaN ++ // Do AND of results to get final ++ uint32x4_t ceqaa = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t ceqbb = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ return vreinterpretq_m128_u32(vandq_u32(ceqaa, ceqbb)); ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using a less than operation. : ++// https://msdn.microsoft.com/en-us/library/2kwe606b(v=vs.90).aspx Important ++// note!! The documentation on MSDN is incorrect! If either of the values is a ++// NAN the docs say you will get a one, but in fact, it will return a zero!! ++FORCE_INLINE int _mm_comilt_ss(__m128 a, __m128 b) ++{ ++ uint32x4_t a_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t b_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ uint32x4_t a_and_b_not_nan = vandq_u32(a_not_nan, b_not_nan); ++ uint32x4_t a_lt_b = ++ vcltq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return (vgetq_lane_u32(vandq_u32(a_and_b_not_nan, a_lt_b), 0) != 0) ? 1 : 0; ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using a greater than operation. : ++// https://msdn.microsoft.com/en-us/library/b0738e0t(v=vs.100).aspx ++FORCE_INLINE int _mm_comigt_ss(__m128 a, __m128 b) ++{ ++ // return vgetq_lane_u32(vcgtq_f32(vreinterpretq_f32_m128(a), ++ // vreinterpretq_f32_m128(b)), 0); ++ uint32x4_t a_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t b_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ uint32x4_t a_and_b_not_nan = vandq_u32(a_not_nan, b_not_nan); ++ uint32x4_t a_gt_b = ++ vcgtq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return (vgetq_lane_u32(vandq_u32(a_and_b_not_nan, a_gt_b), 0) != 0) ? 1 : 0; ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using a less than or equal operation. : ++// https://msdn.microsoft.com/en-us/library/1w4t7c57(v=vs.90).aspx ++FORCE_INLINE int _mm_comile_ss(__m128 a, __m128 b) ++{ ++ // return vgetq_lane_u32(vcleq_f32(vreinterpretq_f32_m128(a), ++ // vreinterpretq_f32_m128(b)), 0); ++ uint32x4_t a_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t b_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ uint32x4_t a_and_b_not_nan = vandq_u32(a_not_nan, b_not_nan); ++ uint32x4_t a_le_b = ++ vcleq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return (vgetq_lane_u32(vandq_u32(a_and_b_not_nan, a_le_b), 0) != 0) ? 1 : 0; ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using a greater than or equal operation. : ++// https://msdn.microsoft.com/en-us/library/8t80des6(v=vs.100).aspx ++FORCE_INLINE int _mm_comige_ss(__m128 a, __m128 b) ++{ ++ // return vgetq_lane_u32(vcgeq_f32(vreinterpretq_f32_m128(a), ++ // vreinterpretq_f32_m128(b)), 0); ++ uint32x4_t a_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t b_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ uint32x4_t a_and_b_not_nan = vandq_u32(a_not_nan, b_not_nan); ++ uint32x4_t a_ge_b = ++ vcgeq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return (vgetq_lane_u32(vandq_u32(a_and_b_not_nan, a_ge_b), 0) != 0) ? 1 : 0; ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using an equality operation. : ++// https://msdn.microsoft.com/en-us/library/93yx2h2b(v=vs.100).aspx ++FORCE_INLINE int _mm_comieq_ss(__m128 a, __m128 b) ++{ ++ // return vgetq_lane_u32(vceqq_f32(vreinterpretq_f32_m128(a), ++ // vreinterpretq_f32_m128(b)), 0); ++ uint32x4_t a_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t b_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ uint32x4_t a_and_b_not_nan = vandq_u32(a_not_nan, b_not_nan); ++ uint32x4_t a_eq_b = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b)); ++ return (vgetq_lane_u32(vandq_u32(a_and_b_not_nan, a_eq_b), 0) != 0) ? 1 : 0; ++} ++ ++// Compares the lower single-precision floating point scalar values of a and b ++// using an inequality operation. : ++// https://msdn.microsoft.com/en-us/library/bafh5e0a(v=vs.90).aspx ++FORCE_INLINE int _mm_comineq_ss(__m128 a, __m128 b) ++{ ++ // return !vgetq_lane_u32(vceqq_f32(vreinterpretq_f32_m128(a), ++ // vreinterpretq_f32_m128(b)), 0); ++ uint32x4_t a_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(a)); ++ uint32x4_t b_not_nan = ++ vceqq_f32(vreinterpretq_f32_m128(b), vreinterpretq_f32_m128(b)); ++ uint32x4_t a_or_b_nan = vmvnq_u32(vandq_u32(a_not_nan, b_not_nan)); ++ uint32x4_t a_neq_b = vmvnq_u32( ++ vceqq_f32(vreinterpretq_f32_m128(a), vreinterpretq_f32_m128(b))); ++ return (vgetq_lane_u32(vorrq_u32(a_or_b_nan, a_neq_b), 0) != 0) ? 1 : 0; ++} ++ ++// according to the documentation, these intrinsics behave the same as the ++// non-'u' versions. We'll just alias them here. ++#define _mm_ucomilt_ss _mm_comilt_ss ++#define _mm_ucomile_ss _mm_comile_ss ++#define _mm_ucomigt_ss _mm_comigt_ss ++#define _mm_ucomige_ss _mm_comige_ss ++#define _mm_ucomieq_ss _mm_comieq_ss ++#define _mm_ucomineq_ss _mm_comineq_ss ++ ++// ****************************************** ++// Conversions ++// ****************************************** ++ ++// Converts the four single-precision, floating-point values of a to signed ++// 32-bit integer values using truncate. ++// https://msdn.microsoft.com/en-us/library/vstudio/1h005y6x(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_cvttps_epi32(__m128 a) ++{ ++ return vreinterpretq_m128i_s32(vcvtq_s32_f32(vreinterpretq_f32_m128(a))); ++} ++ ++// Converts the four signed 32-bit integer values of a to single-precision, ++// floating-point values ++// https://msdn.microsoft.com/en-us/library/vstudio/36bwxcx5(v=vs.100).aspx ++FORCE_INLINE __m128 _mm_cvtepi32_ps(__m128i a) ++{ ++ return vreinterpretq_m128_f32(vcvtq_f32_s32(vreinterpretq_s32_m128i(a))); ++} ++ ++// Converts the four unsigned 8-bit integers in the lower 32 bits to four ++// unsigned 32-bit integers. ++// https://msdn.microsoft.com/en-us/library/bb531467%28v=vs.100%29.aspx ++FORCE_INLINE __m128i _mm_cvtepu8_epi32(__m128i a) ++{ ++ uint8x16_t u8x16 = vreinterpretq_u8_s32(a); /* xxxx xxxx xxxx DCBA */ ++ uint16x8_t u16x8 = vmovl_u8(vget_low_u8(u8x16)); /* 0x0x 0x0x 0D0C 0B0A */ ++ uint32x4_t u32x4 = vmovl_u16(vget_low_u16(u16x8)); /* 000D 000C 000B 000A */ ++ return vreinterpretq_s32_u32(u32x4); ++} ++ ++// Converts the four signed 16-bit integers in the lower 64 bits to four signed ++// 32-bit integers. ++// https://msdn.microsoft.com/en-us/library/bb514079%28v=vs.100%29.aspx ++FORCE_INLINE __m128i _mm_cvtepi16_epi32(__m128i a) ++{ ++ return vreinterpretq_m128i_s32( ++ vmovl_s16(vget_low_s16(vreinterpretq_s16_m128i(a)))); ++} ++ ++// Converts the four single-precision, floating-point values of a to signed ++// 32-bit integer values. ++// ++// r0 := (int) a0 ++// r1 := (int) a1 ++// r2 := (int) a2 ++// r3 := (int) a3 ++// ++// https://msdn.microsoft.com/en-us/library/vstudio/xdc42k5e(v=vs.100).aspx ++// *NOTE*. The default rounding mode on SSE is 'round to even', which ArmV7-A ++// does not support! It is supported on ARMv8-A however. ++FORCE_INLINE __m128i _mm_cvtps_epi32(__m128 a) ++{ ++#if defined(__aarch64__) ++ return vcvtnq_s32_f32(a); ++#else ++ uint32x4_t signmask = vdupq_n_u32(0x80000000); ++ float32x4_t half = vbslq_f32(signmask, vreinterpretq_f32_m128(a), ++ vdupq_n_f32(0.5f)); /* +/- 0.5 */ ++ int32x4_t r_normal = vcvtq_s32_f32(vaddq_f32( ++ vreinterpretq_f32_m128(a), half)); /* round to integer: [a + 0.5]*/ ++ int32x4_t r_trunc = ++ vcvtq_s32_f32(vreinterpretq_f32_m128(a)); /* truncate to integer: [a] */ ++ int32x4_t plusone = vreinterpretq_s32_u32(vshrq_n_u32( ++ vreinterpretq_u32_s32(vnegq_s32(r_trunc)), 31)); /* 1 or 0 */ ++ int32x4_t r_even = vbicq_s32(vaddq_s32(r_trunc, plusone), ++ vdupq_n_s32(1)); /* ([a] + {0,1}) & ~1 */ ++ float32x4_t delta = vsubq_f32( ++ vreinterpretq_f32_m128(a), ++ vcvtq_f32_s32(r_trunc)); /* compute delta: delta = (a - [a]) */ ++ uint32x4_t is_delta_half = vceqq_f32(delta, half); /* delta == +/- 0.5 */ ++ return vreinterpretq_m128i_s32(vbslq_s32(is_delta_half, r_even, r_normal)); ++#endif ++} ++ ++// Moves the least significant 32 bits of a to a 32-bit integer. ++// https://msdn.microsoft.com/en-us/library/5z7a9642%28v=vs.90%29.aspx ++FORCE_INLINE int _mm_cvtsi128_si32(__m128i a) ++{ ++ return vgetq_lane_s32(vreinterpretq_s32_m128i(a), 0); ++} ++ ++// Extracts the low order 64-bit integer from the parameter. ++// https://msdn.microsoft.com/en-us/library/bb531384(v=vs.120).aspx ++FORCE_INLINE uint64_t _mm_cvtsi128_si64(__m128i a) ++{ ++ return vgetq_lane_s64(vreinterpretq_s64_m128i(a), 0); ++} ++ ++// Moves 32-bit integer a to the least significant 32 bits of an __m128 object, ++// zero extending the upper bits. ++// ++// r0 := a ++// r1 := 0x0 ++// r2 := 0x0 ++// r3 := 0x0 ++// ++// https://msdn.microsoft.com/en-us/library/ct3539ha%28v=vs.90%29.aspx ++FORCE_INLINE __m128i _mm_cvtsi32_si128(int a) ++{ ++ return vreinterpretq_m128i_s32(vsetq_lane_s32(a, vdupq_n_s32(0), 0)); ++} ++ ++// Applies a type cast to reinterpret four 32-bit floating point values passed ++// in as a 128-bit parameter as packed 32-bit integers. ++// https://msdn.microsoft.com/en-us/library/bb514099.aspx ++FORCE_INLINE __m128i _mm_castps_si128(__m128 a) ++{ ++ return vreinterpretq_m128i_s32(vreinterpretq_s32_m128(a)); ++} ++ ++// Applies a type cast to reinterpret four 32-bit integers passed in as a ++// 128-bit parameter as packed 32-bit floating point values. ++// https://msdn.microsoft.com/en-us/library/bb514029.aspx ++FORCE_INLINE __m128 _mm_castsi128_ps(__m128i a) ++{ ++ return vreinterpretq_m128_s32(vreinterpretq_s32_m128i(a)); ++} ++ ++// Loads 128-bit value. : ++// https://msdn.microsoft.com/en-us/library/atzzad1h(v=vs.80).aspx ++FORCE_INLINE __m128i _mm_load_si128(const __m128i *p) ++{ ++ return vreinterpretq_m128i_s32(vld1q_s32((const int32_t *) p)); ++} ++ ++// Loads 128-bit value. : ++// https://msdn.microsoft.com/zh-cn/library/f4k12ae8(v=vs.90).aspx ++FORCE_INLINE __m128i _mm_loadu_si128(const __m128i *p) ++{ ++ return vreinterpretq_m128i_s32(vld1q_s32((const int32_t *) p)); ++} ++ ++// ****************************************** ++// Miscellaneous Operations ++// ****************************************** ++ ++// Packs the 16 signed 16-bit integers from a and b into 8-bit integers and ++// saturates. ++// https://msdn.microsoft.com/en-us/library/k4y4f7w5%28v=vs.90%29.aspx ++FORCE_INLINE __m128i _mm_packs_epi16(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s8( ++ vcombine_s8(vqmovn_s16(vreinterpretq_s16_m128i(a)), ++ vqmovn_s16(vreinterpretq_s16_m128i(b)))); ++} ++ ++// Packs the 16 signed 16 - bit integers from a and b into 8 - bit unsigned ++// integers and saturates. ++// ++// r0 := UnsignedSaturate(a0) ++// r1 := UnsignedSaturate(a1) ++// ... ++// r7 := UnsignedSaturate(a7) ++// r8 := UnsignedSaturate(b0) ++// r9 := UnsignedSaturate(b1) ++// ... ++// r15 := UnsignedSaturate(b7) ++// ++// https://msdn.microsoft.com/en-us/library/07ad1wx4(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_packus_epi16(const __m128i a, const __m128i b) ++{ ++ return vreinterpretq_m128i_u8( ++ vcombine_u8(vqmovun_s16(vreinterpretq_s16_m128i(a)), ++ vqmovun_s16(vreinterpretq_s16_m128i(b)))); ++} ++ ++// Packs the 8 signed 32-bit integers from a and b into signed 16-bit integers ++// and saturates. ++// ++// r0 := SignedSaturate(a0) ++// r1 := SignedSaturate(a1) ++// r2 := SignedSaturate(a2) ++// r3 := SignedSaturate(a3) ++// r4 := SignedSaturate(b0) ++// r5 := SignedSaturate(b1) ++// r6 := SignedSaturate(b2) ++// r7 := SignedSaturate(b3) ++// ++// https://msdn.microsoft.com/en-us/library/393t56f9%28v=vs.90%29.aspx ++FORCE_INLINE __m128i _mm_packs_epi32(__m128i a, __m128i b) ++{ ++ return vreinterpretq_m128i_s16( ++ vcombine_s16(vqmovn_s32(vreinterpretq_s32_m128i(a)), ++ vqmovn_s32(vreinterpretq_s32_m128i(b)))); ++} ++ ++// Interleaves the lower 8 signed or unsigned 8-bit integers in a with the lower ++// 8 signed or unsigned 8-bit integers in b. ++// ++// r0 := a0 ++// r1 := b0 ++// r2 := a1 ++// r3 := b1 ++// ... ++// r14 := a7 ++// r15 := b7 ++// ++// https://msdn.microsoft.com/en-us/library/xf7k860c%28v=vs.90%29.aspx ++FORCE_INLINE __m128i _mm_unpacklo_epi8(__m128i a, __m128i b) ++{ ++ int8x8_t a1 = vreinterpret_s8_s16(vget_low_s16(vreinterpretq_s16_m128i(a))); ++ int8x8_t b1 = vreinterpret_s8_s16(vget_low_s16(vreinterpretq_s16_m128i(b))); ++ int8x8x2_t result = vzip_s8(a1, b1); ++ return vreinterpretq_m128i_s8(vcombine_s8(result.val[0], result.val[1])); ++} ++ ++// Interleaves the lower 4 signed or unsigned 16-bit integers in a with the ++// lower 4 signed or unsigned 16-bit integers in b. ++// ++// r0 := a0 ++// r1 := b0 ++// r2 := a1 ++// r3 := b1 ++// r4 := a2 ++// r5 := b2 ++// r6 := a3 ++// r7 := b3 ++// ++// https://msdn.microsoft.com/en-us/library/btxb17bw%28v=vs.90%29.aspx ++FORCE_INLINE __m128i _mm_unpacklo_epi16(__m128i a, __m128i b) ++{ ++ int16x4_t a1 = vget_low_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b1 = vget_low_s16(vreinterpretq_s16_m128i(b)); ++ int16x4x2_t result = vzip_s16(a1, b1); ++ return vreinterpretq_m128i_s16(vcombine_s16(result.val[0], result.val[1])); ++} ++ ++// Interleaves the lower 2 signed or unsigned 32 - bit integers in a with the ++// lower 2 signed or unsigned 32 - bit integers in b. ++// ++// r0 := a0 ++// r1 := b0 ++// r2 := a1 ++// r3 := b1 ++// ++// https://msdn.microsoft.com/en-us/library/x8atst9d(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_unpacklo_epi32(__m128i a, __m128i b) ++{ ++ int32x2_t a1 = vget_low_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t b1 = vget_low_s32(vreinterpretq_s32_m128i(b)); ++ int32x2x2_t result = vzip_s32(a1, b1); ++ return vreinterpretq_m128i_s32(vcombine_s32(result.val[0], result.val[1])); ++} ++ ++FORCE_INLINE __m128i _mm_unpacklo_epi64(__m128i a, __m128i b) ++{ ++ int64x1_t a_l = vget_low_s64(vreinterpretq_s64_m128i(a)); ++ int64x1_t b_l = vget_low_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vcombine_s64(a_l, b_l)); ++} ++ ++// Selects and interleaves the lower two single-precision, floating-point values ++// from a and b. ++// ++// r0 := a0 ++// r1 := b0 ++// r2 := a1 ++// r3 := b1 ++// ++// https://msdn.microsoft.com/en-us/library/25st103b%28v=vs.90%29.aspx ++FORCE_INLINE __m128 _mm_unpacklo_ps(__m128 a, __m128 b) ++{ ++ float32x2_t a1 = vget_low_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b1 = vget_low_f32(vreinterpretq_f32_m128(b)); ++ float32x2x2_t result = vzip_f32(a1, b1); ++ return vreinterpretq_m128_f32(vcombine_f32(result.val[0], result.val[1])); ++} ++ ++// Selects and interleaves the upper two single-precision, floating-point values ++// from a and b. ++// ++// r0 := a2 ++// r1 := b2 ++// r2 := a3 ++// r3 := b3 ++// ++// https://msdn.microsoft.com/en-us/library/skccxx7d%28v=vs.90%29.aspx ++FORCE_INLINE __m128 _mm_unpackhi_ps(__m128 a, __m128 b) ++{ ++ float32x2_t a1 = vget_high_f32(vreinterpretq_f32_m128(a)); ++ float32x2_t b1 = vget_high_f32(vreinterpretq_f32_m128(b)); ++ float32x2x2_t result = vzip_f32(a1, b1); ++ return vreinterpretq_m128_f32(vcombine_f32(result.val[0], result.val[1])); ++} ++ ++// Interleaves the upper 8 signed or unsigned 8-bit integers in a with the upper ++// 8 signed or unsigned 8-bit integers in b. ++// ++// r0 := a8 ++// r1 := b8 ++// r2 := a9 ++// r3 := b9 ++// ... ++// r14 := a15 ++// r15 := b15 ++// ++// https://msdn.microsoft.com/en-us/library/t5h7783k(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_unpackhi_epi8(__m128i a, __m128i b) ++{ ++ int8x8_t a1 = ++ vreinterpret_s8_s16(vget_high_s16(vreinterpretq_s16_m128i(a))); ++ int8x8_t b1 = ++ vreinterpret_s8_s16(vget_high_s16(vreinterpretq_s16_m128i(b))); ++ int8x8x2_t result = vzip_s8(a1, b1); ++ return vreinterpretq_m128i_s8(vcombine_s8(result.val[0], result.val[1])); ++} ++ ++// Interleaves the upper 4 signed or unsigned 16-bit integers in a with the ++// upper 4 signed or unsigned 16-bit integers in b. ++// ++// r0 := a4 ++// r1 := b4 ++// r2 := a5 ++// r3 := b5 ++// r4 := a6 ++// r5 := b6 ++// r6 := a7 ++// r7 := b7 ++// ++// https://msdn.microsoft.com/en-us/library/03196cz7(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_unpackhi_epi16(__m128i a, __m128i b) ++{ ++ int16x4_t a1 = vget_high_s16(vreinterpretq_s16_m128i(a)); ++ int16x4_t b1 = vget_high_s16(vreinterpretq_s16_m128i(b)); ++ int16x4x2_t result = vzip_s16(a1, b1); ++ return vreinterpretq_m128i_s16(vcombine_s16(result.val[0], result.val[1])); ++} ++ ++// Interleaves the upper 2 signed or unsigned 32-bit integers in a with the ++// upper 2 signed or unsigned 32-bit integers in b. ++// https://msdn.microsoft.com/en-us/library/65sa7cbs(v=vs.100).aspx ++FORCE_INLINE __m128i _mm_unpackhi_epi32(__m128i a, __m128i b) ++{ ++ int32x2_t a1 = vget_high_s32(vreinterpretq_s32_m128i(a)); ++ int32x2_t b1 = vget_high_s32(vreinterpretq_s32_m128i(b)); ++ int32x2x2_t result = vzip_s32(a1, b1); ++ return vreinterpretq_m128i_s32(vcombine_s32(result.val[0], result.val[1])); ++} ++ ++// Interleaves the upper signed or unsigned 64-bit integer in a with the ++// upper signed or unsigned 64-bit integer in b. ++// ++// r0 := a1 ++// r1 := b1 ++FORCE_INLINE __m128i _mm_unpackhi_epi64(__m128i a, __m128i b) ++{ ++ int64x1_t a_h = vget_high_s64(vreinterpretq_s64_m128i(a)); ++ int64x1_t b_h = vget_high_s64(vreinterpretq_s64_m128i(b)); ++ return vreinterpretq_m128i_s64(vcombine_s64(a_h, b_h)); ++} ++ ++// shift to right ++// https://msdn.microsoft.com/en-us/library/bb514041(v=vs.120).aspx ++// http://blog.csdn.net/hemmingway/article/details/44828303 ++FORCE_INLINE __m128i _mm_alignr_epi8(__m128i a, __m128i b, const int c) ++{ ++ return (__m128i) vextq_s8((int8x16_t) a, (int8x16_t) b, c); ++} ++ ++// Extracts the selected signed or unsigned 16-bit integer from a and zero ++// extends. https://msdn.microsoft.com/en-us/library/6dceta0c(v=vs.100).aspx ++// FORCE_INLINE int _mm_extract_epi16(__m128i a, __constrange(0,8) int imm) ++#define _mm_extract_epi16(a, imm) \ ++ ({ (vgetq_lane_s16(vreinterpretq_s16_m128i(a), (imm)) & 0x0000ffffUL); }) ++ ++// Inserts the least significant 16 bits of b into the selected 16-bit integer ++// of a. https://msdn.microsoft.com/en-us/library/kaze8hz1%28v=vs.100%29.aspx ++// FORCE_INLINE __m128i _mm_insert_epi16(__m128i a, const int b, ++// __constrange(0,8) int imm) ++#define _mm_insert_epi16(a, b, imm) \ ++ ({ \ ++ vreinterpretq_m128i_s16( \ ++ vsetq_lane_s16((b), vreinterpretq_s16_m128i(a), (imm))); \ ++ }) ++ ++// ****************************************** ++// Crypto Extensions ++// ****************************************** ++#if !defined(__ARM_FEATURE_CRYPTO) && defined(__aarch64__) ++// In the absence of crypto extensions, implement aesenc using regular neon ++// intrinsics instead. See: ++// http://www.workofard.com/2017/01/accelerated-aes-for-the-arm64-linux-kernel/ ++// http://www.workofard.com/2017/07/ghash-for-low-end-cores/ and ++// https://github.com/ColinIanKing/linux-next-mirror/blob/b5f466091e130caaf0735976648f72bd5e09aa84/crypto/aegis128-neon-inner.c#L52 ++// for more information Reproduced with permission of the author. ++FORCE_INLINE __m128i _mm_aesenc_si128(__m128i EncBlock, __m128i RoundKey) ++{ ++ static const uint8_t crypto_aes_sbox[256] = { ++ 0x63, 0x7c, 0x77, 0x7b, 0xf2, 0x6b, 0x6f, 0xc5, 0x30, 0x01, 0x67, 0x2b, ++ 0xfe, 0xd7, 0xab, 0x76, 0xca, 0x82, 0xc9, 0x7d, 0xfa, 0x59, 0x47, 0xf0, ++ 0xad, 0xd4, 0xa2, 0xaf, 0x9c, 0xa4, 0x72, 0xc0, 0xb7, 0xfd, 0x93, 0x26, ++ 0x36, 0x3f, 0xf7, 0xcc, 0x34, 0xa5, 0xe5, 0xf1, 0x71, 0xd8, 0x31, 0x15, ++ 0x04, 0xc7, 0x23, 0xc3, 0x18, 0x96, 0x05, 0x9a, 0x07, 0x12, 0x80, 0xe2, ++ 0xeb, 0x27, 0xb2, 0x75, 0x09, 0x83, 0x2c, 0x1a, 0x1b, 0x6e, 0x5a, 0xa0, ++ 0x52, 0x3b, 0xd6, 0xb3, 0x29, 0xe3, 0x2f, 0x84, 0x53, 0xd1, 0x00, 0xed, ++ 0x20, 0xfc, 0xb1, 0x5b, 0x6a, 0xcb, 0xbe, 0x39, 0x4a, 0x4c, 0x58, 0xcf, ++ 0xd0, 0xef, 0xaa, 0xfb, 0x43, 0x4d, 0x33, 0x85, 0x45, 0xf9, 0x02, 0x7f, ++ 0x50, 0x3c, 0x9f, 0xa8, 0x51, 0xa3, 0x40, 0x8f, 0x92, 0x9d, 0x38, 0xf5, ++ 0xbc, 0xb6, 0xda, 0x21, 0x10, 0xff, 0xf3, 0xd2, 0xcd, 0x0c, 0x13, 0xec, ++ 0x5f, 0x97, 0x44, 0x17, 0xc4, 0xa7, 0x7e, 0x3d, 0x64, 0x5d, 0x19, 0x73, ++ 0x60, 0x81, 0x4f, 0xdc, 0x22, 0x2a, 0x90, 0x88, 0x46, 0xee, 0xb8, 0x14, ++ 0xde, 0x5e, 0x0b, 0xdb, 0xe0, 0x32, 0x3a, 0x0a, 0x49, 0x06, 0x24, 0x5c, ++ 0xc2, 0xd3, 0xac, 0x62, 0x91, 0x95, 0xe4, 0x79, 0xe7, 0xc8, 0x37, 0x6d, ++ 0x8d, 0xd5, 0x4e, 0xa9, 0x6c, 0x56, 0xf4, 0xea, 0x65, 0x7a, 0xae, 0x08, ++ 0xba, 0x78, 0x25, 0x2e, 0x1c, 0xa6, 0xb4, 0xc6, 0xe8, 0xdd, 0x74, 0x1f, ++ 0x4b, 0xbd, 0x8b, 0x8a, 0x70, 0x3e, 0xb5, 0x66, 0x48, 0x03, 0xf6, 0x0e, ++ 0x61, 0x35, 0x57, 0xb9, 0x86, 0xc1, 0x1d, 0x9e, 0xe1, 0xf8, 0x98, 0x11, ++ 0x69, 0xd9, 0x8e, 0x94, 0x9b, 0x1e, 0x87, 0xe9, 0xce, 0x55, 0x28, 0xdf, ++ 0x8c, 0xa1, 0x89, 0x0d, 0xbf, 0xe6, 0x42, 0x68, 0x41, 0x99, 0x2d, 0x0f, ++ 0xb0, 0x54, 0xbb, 0x16}; ++ static const uint8_t shift_rows[] = {0x0, 0x5, 0xa, 0xf, 0x4, 0x9, ++ 0xe, 0x3, 0x8, 0xd, 0x2, 0x7, ++ 0xc, 0x1, 0x6, 0xb}; ++ static const uint8_t ror32by8[] = {0x1, 0x2, 0x3, 0x0, 0x5, 0x6, 0x7, 0x4, ++ 0x9, 0xa, 0xb, 0x8, 0xd, 0xe, 0xf, 0xc}; ++ ++ uint8x16_t v; ++ uint8x16_t w = vreinterpretq_u8_m128i(EncBlock); ++ ++ // shift rows ++ w = vqtbl1q_u8(w, vld1q_u8(shift_rows)); ++ ++ // sub bytes ++ v = vqtbl4q_u8(vld1q_u8_x4(crypto_aes_sbox), w); ++ v = vqtbx4q_u8(v, vld1q_u8_x4(crypto_aes_sbox + 0x40), w - 0x40); ++ v = vqtbx4q_u8(v, vld1q_u8_x4(crypto_aes_sbox + 0x80), w - 0x80); ++ v = vqtbx4q_u8(v, vld1q_u8_x4(crypto_aes_sbox + 0xc0), w - 0xc0); ++ ++ // mix columns ++ w = (v << 1) ^ (uint8x16_t)(((int8x16_t) v >> 7) & 0x1b); ++ w ^= (uint8x16_t) vrev32q_u16((uint16x8_t) v); ++ w ^= vqtbl1q_u8(v ^ w, vld1q_u8(ror32by8)); ++ ++ // add round key ++ return vreinterpretq_m128i_u8(w) ^ RoundKey; ++} ++#elif defined(__ARM_FEATURE_CRYPTO) ++// Implements equivalent of 'aesenc' by combining AESE (with an empty key) and ++// AESMC and then manually applying the real key as an xor operation This ++// unfortunately means an additional xor op; the compiler should be able to ++// optimise this away for repeated calls however See ++// https://blog.michaelbrase.com/2018/05/08/emulating-x86-aes-intrinsics-on-armv8-a ++// for more details. ++inline __m128i _mm_aesenc_si128(__m128i a, __m128i b) ++{ ++ return vreinterpretq_s32_u8( ++ vaesmcq_u8(vaeseq_u8(vreinterpretq_u8_s32(a), uint8x16_t{})) ^ ++ vreinterpretq_u8_s32(b)); ++} ++#endif ++ ++// ****************************************** ++// Streaming Extensions ++// ****************************************** ++ ++// Guarantees that every preceding store is globally visible before any ++// subsequent store. ++// https://msdn.microsoft.com/en-us/library/5h2w73d1%28v=vs.90%29.aspx ++FORCE_INLINE void _mm_sfence(void) ++{ ++ __sync_synchronize(); ++} ++ ++// Stores the data in a to the address p without polluting the caches. If the ++// cache line containing address p is already in the cache, the cache will be ++// updated.Address p must be 16 - byte aligned. ++// https://msdn.microsoft.com/en-us/library/ba08y07y%28v=vs.90%29.aspx ++FORCE_INLINE void _mm_stream_si128(__m128i *p, __m128i a) ++{ ++ vst1q_s32((int32_t *) p, a); ++} ++ ++// Cache line containing p is flushed and invalidated from all caches in the ++// coherency domain. : ++// https://msdn.microsoft.com/en-us/library/ba08y07y(v=vs.100).aspx ++FORCE_INLINE void _mm_clflush(void const *p) ++{ ++ // no corollary for Neon? ++} ++ ++#if defined(__GNUC__) || defined(__clang__) ++#pragma pop_macro("ALIGN_STRUCT") ++#pragma pop_macro("FORCE_INLINE") ++#endif ++ ++#endif +diff --git a/vendor/spoa/src/simd_alignment_engine.cpp b/vendor/spoa/src/simd_alignment_engine.cpp +index 3e5815a..2fd10d7 100644 +--- a/vendor/spoa/src/simd_alignment_engine.cpp ++++ b/vendor/spoa/src/simd_alignment_engine.cpp +@@ -7,9 +7,12 @@ + #include <algorithm> + #include <limits> + ++#include "arch/aarch64/sse2neon.h" ++/* + extern "C" { + #include <immintrin.h> // AVX2 and lower + } ++*/ + + #include "spoa/graph.hpp" + #include "simd_alignment_engine.hpp" diff --git a/var/spack/repos/builtin/packages/racon/package.py b/var/spack/repos/builtin/packages/racon/package.py index 50b92e668a..1e661b4bd7 100644 --- a/var/spack/repos/builtin/packages/racon/package.py +++ b/var/spack/repos/builtin/packages/racon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,6 +14,10 @@ class Racon(CMakePackage): homepage = "https://github.com/isovic/racon" url = "https://github.com/isovic/racon/releases/download/1.2.1/racon-v1.2.1.tar.gz" + version('1.4.3', sha256='dfce0bae8234c414ef72b690247701b4299e39a2593bcda548a7a864f51de7f2') + version('1.4.2', sha256='b36d8b767e0fc9acdd3e9d34c99a8bbc02a3aae7a953c57923d935ebdf332700') + version('1.4.0', sha256='3e1e97388f428326342dead3f8500e72b1986f292bdfd4d1be4a0d2a21f4cc61') + version('1.3.3', sha256='174afde420ed2e187e57c1a6e9fc6a414aa26723b4ae83c3904640fc84941e66') version('1.3.2', sha256='7c99380a0f1091f5ee138b559e318d7e9463d3145eac026bf236751c2c4b92c7') version('1.3.1', sha256='7ce3b1ce6abdb6c6a63d50755b1fc55d5a4d2ab8f86a1df81890d4a7842d9b75') version('1.3.0', sha256='f2331fb88eae5c54227dc16651607af6f045ae1ccccc1d117011762927d4606a') @@ -25,10 +29,8 @@ class Racon(CMakePackage): conflicts('%gcc@:4.7') conflicts('%clang@:3.1') + patch('aarch64.patch', when='target=aarch64:') + def cmake_args(self): args = ['-Dracon_build_wrapper=ON'] return args - - def install(self, spec, prefix): - install_tree('spack-build/bin', prefix.bin) - install_tree('spack-build/lib', prefix.lib) diff --git a/var/spack/repos/builtin/packages/raft/package.py b/var/spack/repos/builtin/packages/raft/package.py index fda2e02a50..d164cc9c1f 100644 --- a/var/spack/repos/builtin/packages/raft/package.py +++ b/var/spack/repos/builtin/packages/raft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ragel/package.py b/var/spack/repos/builtin/packages/ragel/package.py index 586bbac28c..cff731ef75 100644 --- a/var/spack/repos/builtin/packages/ragel/package.py +++ b/var/spack/repos/builtin/packages/ragel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py index 4eb7dcbd1e..0f9951fe49 100644 --- a/var/spack/repos/builtin/packages/raja/package.py +++ b/var/spack/repos/builtin/packages/raja/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/randfold/package.py b/var/spack/repos/builtin/packages/randfold/package.py index b28035d195..bfb1ee80a9 100644 --- a/var/spack/repos/builtin/packages/randfold/package.py +++ b/var/spack/repos/builtin/packages/randfold/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/random123/package.py b/var/spack/repos/builtin/packages/random123/package.py index 6afd7a3168..48df03fee8 100644 --- a/var/spack/repos/builtin/packages/random123/package.py +++ b/var/spack/repos/builtin/packages/random123/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/randrproto/package.py b/var/spack/repos/builtin/packages/randrproto/package.py index 6b6a2de5af..c3315568f1 100644 --- a/var/spack/repos/builtin/packages/randrproto/package.py +++ b/var/spack/repos/builtin/packages/randrproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/range-v3/package.py b/var/spack/repos/builtin/packages/range-v3/package.py index ee3933df26..261922ceb7 100644 --- a/var/spack/repos/builtin/packages/range-v3/package.py +++ b/var/spack/repos/builtin/packages/range-v3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rankstr/package.py b/var/spack/repos/builtin/packages/rankstr/package.py index c72c46b54a..6cf2dc42f9 100644 --- a/var/spack/repos/builtin/packages/rankstr/package.py +++ b/var/spack/repos/builtin/packages/rankstr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class Rankstr(CMakePackage): """Assign one-to-one mapping of MPI ranks to strings""" homepage = "https://github.com/ECP-VeloC/rankstr" - url = "https://github.com/ECP-VeloC/rankstr/archive/v0.0.1.zip" + url = "https://github.com/ECP-VeloC/rankstr/archive/v0.0.2.zip" git = "https://github.com/ecp-veloc/rankstr.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/rapidjson/package.py b/var/spack/repos/builtin/packages/rapidjson/package.py index 028b1b007f..12e2498a23 100644 --- a/var/spack/repos/builtin/packages/rapidjson/package.py +++ b/var/spack/repos/builtin/packages/rapidjson/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -22,3 +22,6 @@ class Rapidjson(CMakePackage): patch('0001-turn-off-Werror.patch') patch('arm.patch', when='@1.1.0 target=aarch64: %gcc@:5.9') + + # Not correspond to define '-march=native' with Fujitsu compiler. + patch('remove_march.patch', when='%fj') diff --git a/var/spack/repos/builtin/packages/rapidjson/remove_march.patch b/var/spack/repos/builtin/packages/rapidjson/remove_march.patch new file mode 100644 index 0000000000..99276fdae5 --- /dev/null +++ b/var/spack/repos/builtin/packages/rapidjson/remove_march.patch @@ -0,0 +1,11 @@ +--- spack-src/CMakeLists.txt.org 2020-01-08 17:39:08.831616711 +0900 ++++ spack-src/CMakeLists.txt 2020-01-08 17:39:27.431716190 +0900 +@@ -73,7 +73,7 @@ + endif() + endif() + elseif (CMAKE_CXX_COMPILER_ID MATCHES "Clang") +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native -Wall -Wextra -Wno-missing-field-initializers") ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-missing-field-initializers") + if (RAPIDJSON_BUILD_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() diff --git a/var/spack/repos/builtin/packages/ravel/package.py b/var/spack/repos/builtin/packages/ravel/package.py index 43fb415ff4..e9a3abb0e6 100644 --- a/var/spack/repos/builtin/packages/ravel/package.py +++ b/var/spack/repos/builtin/packages/ravel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/raxml/package.py b/var/spack/repos/builtin/packages/raxml/package.py index ec4a3b5680..08d99e6b16 100644 --- a/var/spack/repos/builtin/packages/raxml/package.py +++ b/var/spack/repos/builtin/packages/raxml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ray/package.py b/var/spack/repos/builtin/packages/ray/package.py index 6c7a9c463e..f737ee8063 100644 --- a/var/spack/repos/builtin/packages/ray/package.py +++ b/var/spack/repos/builtin/packages/ray/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rclone/package.py b/var/spack/repos/builtin/packages/rclone/package.py index 00a5221ef9..8e043319f8 100644 --- a/var/spack/repos/builtin/packages/rclone/package.py +++ b/var/spack/repos/builtin/packages/rclone/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,13 +13,19 @@ class Rclone(Package): homepage = "http://rclone.org" url = "https://github.com/ncw/rclone/releases/download/v1.43/rclone-v1.43.tar.gz" + version('1.51.0', sha256='3eb5b7ffce17e56fadb29bf854666723a14c93fedc02046c7f34c792dbd227ee') + version('1.50.2', sha256='6dd8998a72514d3820d241ae46dc609c0305b742aee3db6aaf6017b46c996091') + version('1.50.1', sha256='48d6c80883427469682b4d97099d7631cf3b67aa85e652c254423bd1422ce216') + version('1.50.0', sha256='f901fd1752aae6116d94fd08d010a70d94535257c2d23caa505e631cce1e802a') + version('1.49.5', sha256='abd2c83d71c63a4b0a30b1980b942868e707d05e14ae76ad39abf5cc5a5fde63') + version('1.49.4', sha256='070afc85e4e9921151d7cb67247db8f0ff2f06fcf2652c43a42fa6e1e35847af') version('1.43', sha256='d30527b00cecb4e5e7188dddb78e5cec62d67cf2422dab82190db58512b5a4e3') depends_on("go", type='build') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Point GOPATH at the top of the staging dir for the build step. - spack_env.prepend_path('GOPATH', self.stage.path) + env.prepend_path('GOPATH', self.stage.path) def install(self, spec, prefix): go('build') diff --git a/var/spack/repos/builtin/packages/rdma-core/package.py b/var/spack/repos/builtin/packages/rdma-core/package.py index 2a36cd2fce..9069dec49f 100644 --- a/var/spack/repos/builtin/packages/rdma-core/package.py +++ b/var/spack/repos/builtin/packages/rdma-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rdp-classifier/package.py b/var/spack/repos/builtin/packages/rdp-classifier/package.py index f2f0f254fb..8c182d323a 100644 --- a/var/spack/repos/builtin/packages/rdp-classifier/package.py +++ b/var/spack/repos/builtin/packages/rdp-classifier/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rdptools/package.py b/var/spack/repos/builtin/packages/rdptools/package.py index 22644f6606..5f5957c8b1 100644 --- a/var/spack/repos/builtin/packages/rdptools/package.py +++ b/var/spack/repos/builtin/packages/rdptools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/re2c/package.py b/var/spack/repos/builtin/packages/re2c/package.py index 5b64b2ec66..976fc17d39 100644 --- a/var/spack/repos/builtin/packages/re2c/package.py +++ b/var/spack/repos/builtin/packages/re2c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/readfq/package.py b/var/spack/repos/builtin/packages/readfq/package.py index 542d7a2fdc..ce06114ba2 100644 --- a/var/spack/repos/builtin/packages/readfq/package.py +++ b/var/spack/repos/builtin/packages/readfq/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py index 74cd4b661b..c73a08daab 100644 --- a/var/spack/repos/builtin/packages/readline/package.py +++ b/var/spack/repos/builtin/packages/readline/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Readline(AutotoolsPackage): +class Readline(AutotoolsPackage, GNUMirrorPackage): """The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library @@ -16,7 +16,7 @@ class Readline(AutotoolsPackage): homepage = "http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html" # URL must remain http:// so Spack can bootstrap curl - url = "http://ftpmirror.gnu.org/readline/readline-8.0.tar.gz" + gnu_mirror_path = "readline/readline-8.0.tar.gz" version('8.0', sha256='e339f51971478d369f8a053a330a190781acb9864cf4c541060f12078948e461') version('7.0', sha256='750d437185286f40a369e1e4f4764eda932b9459b5ec9a731628393dd3d32334') diff --git a/var/spack/repos/builtin/packages/recon/package.py b/var/spack/repos/builtin/packages/recon/package.py index 860e2b7ba0..68f3c37f98 100644 --- a/var/spack/repos/builtin/packages/recon/package.py +++ b/var/spack/repos/builtin/packages/recon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/recordproto/package.py b/var/spack/repos/builtin/packages/recordproto/package.py index 30eb222936..c70d539abc 100644 --- a/var/spack/repos/builtin/packages/recordproto/package.py +++ b/var/spack/repos/builtin/packages/recordproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/redis/package.py b/var/spack/repos/builtin/packages/redis/package.py index 50928fc4f6..fa863bb4b3 100644 --- a/var/spack/repos/builtin/packages/redis/package.py +++ b/var/spack/repos/builtin/packages/redis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/redset/package.py b/var/spack/repos/builtin/packages/redset/package.py index d875c1ddfc..d06eaca108 100644 --- a/var/spack/repos/builtin/packages/redset/package.py +++ b/var/spack/repos/builtin/packages/redset/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class Redset(CMakePackage): """Create MPI communicators for disparate redundancy sets""" homepage = "https://github.com/ECP-VeloC/redset" - url = "https://github.com/ECP-VeloC/redset/archive/v0.0.2.zip" + url = "https://github.com/ECP-VeloC/redset/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/redset.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/redundans/package.py b/var/spack/repos/builtin/packages/redundans/package.py index 88cfdbc510..d5ad3cf722 100644 --- a/var/spack/repos/builtin/packages/redundans/package.py +++ b/var/spack/repos/builtin/packages/redundans/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/regcm/package.py b/var/spack/repos/builtin/packages/regcm/package.py index fc80deb4d0..05625de77b 100644 --- a/var/spack/repos/builtin/packages/regcm/package.py +++ b/var/spack/repos/builtin/packages/regcm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -45,11 +45,11 @@ class Regcm(AutotoolsPackage): description='Build NetCDF using the high performance parallel ' 'NetCDF implementation.') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-fortran') depends_on('hdf5') depends_on('mpi') - depends_on('netcdf +parallel-netcdf', when='+pnetcdf') + depends_on('netcdf-c +parallel-netcdf', when='+pnetcdf') intel_msg = ('Intel compiler not working with this specific version of ' 'RegCM (generates a bug at runtime): please install a newer ' diff --git a/var/spack/repos/builtin/packages/relax/package.py b/var/spack/repos/builtin/packages/relax/package.py index 7b8488fe43..d2ac4aa1c8 100644 --- a/var/spack/repos/builtin/packages/relax/package.py +++ b/var/spack/repos/builtin/packages/relax/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/relion/package.py b/var/spack/repos/builtin/packages/relion/package.py index a9ab80b849..c1966af792 100644 --- a/var/spack/repos/builtin/packages/relion/package.py +++ b/var/spack/repos/builtin/packages/relion/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,10 +15,18 @@ class Relion(CMakePackage, CudaPackage): homepage = "http://http://www2.mrc-lmb.cam.ac.uk/relion" git = "https://github.com/3dem/relion.git" + # 3.1 is beta but referenced in published papers + # prefer stable 3.0 until no longer beta + version('3.1_beta', branch='ver3.1') + + # 3.0.8 latest release in 3.0 branch + # prefer for now + version('3.0.8', tag='3.0.8', preferred=True) version('3.0.7', tag='3.0.7') - # relion has no develop branch though pulling from master - # should be considered the same as develop - version('develop', branch='master') + + # relion master contains development code + # contains 3.0 branch code + version('master') variant('gui', default=True, description="build the gui") variant('cuda', default=True, description="enable compute on gpu") @@ -34,9 +42,7 @@ class Relion(CMakePackage, CudaPackage): 'Profiling', 'Benchmarking')) depends_on('mpi') - # relion will not build with newer versions of cmake - # per https://github.com/3dem/relion/issues/380 - depends_on('cmake@3:3.9.4', type='build') + depends_on('cmake@3:', type='build') depends_on('fftw precision=float,double') depends_on('fltk', when='+gui') depends_on('libtiff') diff --git a/var/spack/repos/builtin/packages/rempi/package.py b/var/spack/repos/builtin/packages/rempi/package.py index 4668b3aaae..a7c394f1ab 100644 --- a/var/spack/repos/builtin/packages/rempi/package.py +++ b/var/spack/repos/builtin/packages/rempi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rename/package.py b/var/spack/repos/builtin/packages/rename/package.py index 2b777a4288..6cf3c49278 100644 --- a/var/spack/repos/builtin/packages/rename/package.py +++ b/var/spack/repos/builtin/packages/rename/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rendercheck/package.py b/var/spack/repos/builtin/packages/rendercheck/package.py index bf3de64fef..03961b1dba 100644 --- a/var/spack/repos/builtin/packages/rendercheck/package.py +++ b/var/spack/repos/builtin/packages/rendercheck/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/renderproto/package.py b/var/spack/repos/builtin/packages/renderproto/package.py index e189368b0b..2bd9fa30ea 100644 --- a/var/spack/repos/builtin/packages/renderproto/package.py +++ b/var/spack/repos/builtin/packages/renderproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py index f5b2e69f42..15aa062b35 100644 --- a/var/spack/repos/builtin/packages/repeatmasker/package.py +++ b/var/spack/repos/builtin/packages/repeatmasker/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -29,6 +29,8 @@ class Repeatmasker(Package): depends_on('phrap-crossmatch-swat', type=('build', 'run'), when='+crossmatch') + patch('utf8.patch') + def url_for_version(self, version): url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz' return url.format(version.dashed) diff --git a/var/spack/repos/builtin/packages/repeatmasker/utf8.patch b/var/spack/repos/builtin/packages/repeatmasker/utf8.patch new file mode 100644 index 0000000000..529b8809d5 --- /dev/null +++ b/var/spack/repos/builtin/packages/repeatmasker/utf8.patch @@ -0,0 +1,198 @@ +diff -ru a/RepeatMasker b/RepeatMasker +--- a/RepeatMasker 2020-01-01 16:16:26.201675025 -0600 ++++ b/RepeatMasker 2020-01-01 16:18:02.059526821 -0600 +@@ -1347,7 +1347,7 @@ + ## + ## Globals Used: None + ## +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub adjustFragmentPositions { + my $batcher = shift; + my $catfile = shift; +@@ -1456,7 +1456,7 @@ + ## to decypher this subroutine. + ## + ## Globals Used: none +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub locateISElements { + my %options = %{ shift() }; + my $batcher = shift; +@@ -2951,7 +2951,7 @@ + ## + ## Globals Used: None + ## Globals Modified: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub runLowComplexTests { + my %options = %{ shift() }; # The RepeatMasker option hashtable + my $DIRECTORY = shift; +@@ -3988,7 +3988,7 @@ + ## + ## Globals Used: None + ## Globals Modified: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub runSearchStages { + my %options = %{ shift() }; # The RepeatMasker option hashtable + my $DIRECTORY = shift; +@@ -4707,7 +4707,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub chooseMatrices { + my $GC_frac = shift; + +@@ -4910,7 +4910,7 @@ + ## + ## Globals Used: None + ## +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub preMaskLevelFilter { + my $searchResults = shift; + +@@ -4999,7 +4999,7 @@ + ## + ## Globals Used: None + ## +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub filterResults { + my %options = %{ shift() }; + my $chooseClass = shift; +@@ -5860,7 +5860,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub calcSimpleRepeatComplexityFromName { + my %num = ( "A", 0, "C", 0, "G", 0, "T", 0 ); + my %log = ( "A", 0, "C", 0, "G", 0, "T", 0 ); +@@ -5902,7 +5902,7 @@ + ## revamped to use a SearchResultCollection. + ## + ## NO Globals Used +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub getSegments { + my $resultsCollection = shift; + +@@ -6661,7 +6661,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub saveOldFiles { + my $fijl = shift; + my $fileend = shift; +@@ -6708,7 +6708,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub SkipFile { + my $file = shift; + +@@ -6734,7 +6734,7 @@ + ## about how files are passed to repeatmasker etc.. + ## + ## Globals Used: ARGV[0] +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub createTempDir { + my %options = %{ shift() }; + my $date = shift; +@@ -6792,7 +6792,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + ### Interrupt handler used by systemint() ### + sub handler { + my ( $sig ) = @_; +@@ -6808,7 +6808,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + ### systemint -- Interruptible system call routine. ### + sub systemint { + my ( $cmd ) = @_; +@@ -6869,7 +6869,7 @@ + ## Expects $options{'dir'} ( if set ) to already exist. + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub cleanUp { + my %options = %{ shift() }; + my $runnumber = shift; +@@ -6987,7 +6987,7 @@ + ## matching sequences. + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub createLib { + my $options = %{ shift() }; + my $db = shift; +@@ -7322,7 +7322,7 @@ + ## will create the frozen databases for WUBlast. + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub processCustomLib { + my $options = %{ shift() }; + my $tempdir = shift; +@@ -7416,7 +7416,7 @@ + ## refined. + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub buildRefineableHash { + my $db = shift; + +@@ -7447,7 +7447,7 @@ + ## Returns + ## + ## Globals Used: None +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub initLibraries { + my %options = %{ shift() }; + my $rmLibDir = shift; +diff -ru a/SimpleBatcher.pm b/SimpleBatcher.pm +--- a/SimpleBatcher.pm 2020-01-01 16:16:26.203675022 -0600 ++++ b/SimpleBatcher.pm 2020-01-01 16:17:24.464585016 -0600 +@@ -559,7 +559,7 @@ + ## } + ## }; + ## +-##------------------------------------------------------------------------##· ++##------------------------------------------------------------------------##· + sub _packBatches { + my $this = shift; + my $seqDBObj = shift; +diff -ru a/util/wublastToCrossmatch.pl b/util/wublastToCrossmatch.pl +--- a/util/wublastToCrossmatch.pl 2020-01-01 16:16:26.202675024 -0600 ++++ b/util/wublastToCrossmatch.pl 2020-01-01 16:17:38.181563793 -0600 +@@ -244,7 +244,7 @@ + + =cut + +-##-------------------------------------------------------------------------##· ++##-------------------------------------------------------------------------##· + sub publicMethod { + my %parameters = @_; + diff --git a/var/spack/repos/builtin/packages/repeatmodeler/package.py b/var/spack/repos/builtin/packages/repeatmodeler/package.py index fa395f4109..3231dd18e8 100644 --- a/var/spack/repos/builtin/packages/repeatmodeler/package.py +++ b/var/spack/repos/builtin/packages/repeatmodeler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,7 +18,7 @@ class Repeatmodeler(Package): depends_on('perl', type=('build', 'run')) depends_on('perl-json', type=('build', 'run')) depends_on('perl-uri', type=('build', 'run')) - depends_on('perl-lwp', type=('build', 'run')) + depends_on('perl-libwww-perl', type=('build', 'run')) depends_on('repeatmasker', type='run') depends_on('recon+repeatmasker', type='run') diff --git a/var/spack/repos/builtin/packages/repeatscout/package.py b/var/spack/repos/builtin/packages/repeatscout/package.py index 005650ab0d..78a7a54093 100644 --- a/var/spack/repos/builtin/packages/repeatscout/package.py +++ b/var/spack/repos/builtin/packages/repeatscout/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/resourceproto/package.py b/var/spack/repos/builtin/packages/resourceproto/package.py index d7b0fb5b0d..103ebc3927 100644 --- a/var/spack/repos/builtin/packages/resourceproto/package.py +++ b/var/spack/repos/builtin/packages/resourceproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/revbayes/package.py b/var/spack/repos/builtin/packages/revbayes/package.py index 50176857bf..7cf707a72e 100644 --- a/var/spack/repos/builtin/packages/revbayes/package.py +++ b/var/spack/repos/builtin/packages/revbayes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,7 +12,11 @@ class Revbayes(CMakePackage): homepage = "https://revbayes.github.io" url = "https://github.com/revbayes/revbayes/archive/v1.0.11.tar.gz" + git = "https://github.com/revbayes/revbayes.git" + version('develop', branch='development') + version('1.0.13', sha256='472b4ccc44d813c1ff1b8d27e8ccf3d96388de79aa1688b3714f683ba65038fa') + version('1.0.12', sha256='d79f3a9bc72305cab35009d11e1f027fcaacde7329a4c49b5b8285588a8d3588') version('1.0.11', sha256='7e81b1952e3a63cb84617fa632f4ccdf246b4d79e7d537a423540de047dadf50') version('1.0.10', sha256='95e9affe8ca8d62880cf46778b6ec9dd8726e62a185670ebcbadf2eb2bb79f93') @@ -21,9 +25,14 @@ class Revbayes(CMakePackage): depends_on('boost') depends_on('mpi', when='+mpi') - conflicts('%gcc@7.1.0:') + conflicts('%gcc@7.1.0:', when='@:1.0.12') - root_cmakelists_dir = 'projects/cmake/build' + @property + def root_cmakelists_dir(self): + if self.spec.version > Version('1.0.13') and '+mpi' in self.spec: + return 'projects/cmake/build-mpi' + else: + return 'projects/cmake/build' @run_before('cmake') def regenerate(self): @@ -44,3 +53,9 @@ class Revbayes(CMakePackage): else: install_path = join_path(self.build_directory, '..', 'rb') install(install_path, prefix.bin) + + @when('@1.0.12:1.0.13') + def install(self, spec, prefix): + mkdirp(prefix.bin) + install_path = join_path(self.build_directory, '..', 'rb') + install(install_path, prefix.bin) diff --git a/var/spack/repos/builtin/packages/rgb/package.py b/var/spack/repos/builtin/packages/rgb/package.py index 4d316373f1..2e4f56342b 100644 --- a/var/spack/repos/builtin/packages/rgb/package.py +++ b/var/spack/repos/builtin/packages/rgb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rhash/package.py b/var/spack/repos/builtin/packages/rhash/package.py index a5d63c204f..975a37b6ba 100644 --- a/var/spack/repos/builtin/packages/rhash/package.py +++ b/var/spack/repos/builtin/packages/rhash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rlwrap/package.py b/var/spack/repos/builtin/packages/rlwrap/package.py index 04e2cf7df8..a3d0e4c41a 100644 --- a/var/spack/repos/builtin/packages/rlwrap/package.py +++ b/var/spack/repos/builtin/packages/rlwrap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rmats/package.py b/var/spack/repos/builtin/packages/rmats/package.py index 52539d9c78..0563c5ddfd 100644 --- a/var/spack/repos/builtin/packages/rmats/package.py +++ b/var/spack/repos/builtin/packages/rmats/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rmlab/package.py b/var/spack/repos/builtin/packages/rmlab/package.py index 5e819bc1dc..21e96c51c4 100644 --- a/var/spack/repos/builtin/packages/rmlab/package.py +++ b/var/spack/repos/builtin/packages/rmlab/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rna-seqc/package.py b/var/spack/repos/builtin/packages/rna-seqc/package.py index a33762a9b6..0f357ae0c0 100644 --- a/var/spack/repos/builtin/packages/rna-seqc/package.py +++ b/var/spack/repos/builtin/packages/rna-seqc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rnaz/package.py b/var/spack/repos/builtin/packages/rnaz/package.py new file mode 100644 index 0000000000..89679aa4ef --- /dev/null +++ b/var/spack/repos/builtin/packages/rnaz/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Rnaz(AutotoolsPackage): + """RNAz - predicting structural noncoding RNAs.""" + + homepage = "https://www.tbi.univie.ac.at/software/RNAz" + url = "https://www.tbi.univie.ac.at/software/RNAz/RNAz-2.1.tar.gz" + + version('2.1', sha256='b32ec0361889319f2058f224d6c456c853dbc30dff4dba90c53a8f9fd7b83be5') diff --git a/var/spack/repos/builtin/packages/rngstreams/package.py b/var/spack/repos/builtin/packages/rngstreams/package.py index 3fdaff3b04..4c6483d30e 100644 --- a/var/spack/repos/builtin/packages/rngstreams/package.py +++ b/var/spack/repos/builtin/packages/rngstreams/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rocketmq/package.py b/var/spack/repos/builtin/packages/rocketmq/package.py new file mode 100644 index 0000000000..b3630b06ea --- /dev/null +++ b/var/spack/repos/builtin/packages/rocketmq/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Rocketmq(Package): + """ + Apache RocketMQ is a distributed messaging and streaming platform + with low latency, high performance and reliability, trillion-level + capacity and flexible scalability. + """ + + homepage = "https://rocketmq.apache.org/" + url = "https://archive.apache.org/dist/rocketmq/4.5.2/rocketmq-all-4.5.2-bin-release.zip" + + version('4.6.0', sha256='584910d50639297808dd0b86fcdfaf431efd9607009a44c6258d9a0e227748fe') + version('4.5.2', sha256='f7711ef9c203d7133e70e0e1e887025d7dd80d29f6d5283ca6022b12576b8aba') + version('4.5.1', sha256='0c46e4b652b007d07e9c456eb2e275126b9210c27cd56bee518809f33c8ed437') + version('4.5.0', sha256='d75dc26291b47413f7c565bc65499501e3499f01beb713246586f72844e31042') + version('4.4.0', sha256='8a948e240e8d2ebbf4c40c180105d088a937f82a594cd1f2ae527b20349f1d34') + version('4.3.2', sha256='e31210a86266ee218eb6ff4f8ca6e211439895459c3bdad162067b573d9e3415') + + depends_on('java@8:', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/rocksdb/package.py b/var/spack/repos/builtin/packages/rocksdb/package.py index e002c5b14e..67b9ddea44 100644 --- a/var/spack/repos/builtin/packages/rocksdb/package.py +++ b/var/spack/repos/builtin/packages/rocksdb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,10 +10,12 @@ class Rocksdb(MakefilePackage): """RocksDB: A Persistent Key-Value Store for Flash and RAM Storage""" homepage = "https://github.com/facebook/rocksdb" - url = 'https://github.com/facebook/rocksdb/archive/v5.17.2.tar.gz' + url = 'https://github.com/facebook/rocksdb/archive/v6.5.3.tar.gz' git = 'https://github.com/facebook/rocksdb.git' version('develop', git=git, branch='master', submodules=True) + version('6.5.3', sha256='6dc023a11d61d00c8391bd44f26ba7db06c44be228c10b552edc84e02d7fbde2') + version('5.18.3', sha256='7fb6738263d3f2b360d7468cf2ebe333f3109f3ba1ff80115abd145d75287254') version('5.17.2', sha256='101f05858650a810c90e4872338222a1a3bf3b24de7b7d74466814e6a95c2d28') version('5.16.6', sha256='f0739edce1707568bdfb36a77638fd5bae287ca21763ce3e56cf0bfae8fff033') version('5.15.10', sha256='26d5d4259fa352ae1604b5b4d275f947cacc006f4f7d2ef0b815056601b807c0') @@ -24,6 +26,7 @@ class Rocksdb(MakefilePackage): variant('static', default=True, description='Build static library') variant('zlib', default=True, description='Enable zlib compression support') variant('zstd', default=False, description='Enable zstandard compression support') + variant('tbb', default=False, description='Enable Intel TBB support') depends_on('bzip2', when='+bzip2') depends_on('gflags') @@ -31,6 +34,7 @@ class Rocksdb(MakefilePackage): depends_on('snappy', when='+snappy') depends_on('zlib', when='+zlib') depends_on('zstd', when='+zstd') + depends_on('tbb', when='+tbb') phases = ['install'] @@ -44,17 +48,35 @@ class Rocksdb(MakefilePackage): cflags = [] ldflags = [] + if spec.satisfies('%gcc@9:'): + cflags.append('-Wno-error=deprecated-copy') + cflags.append('-Wno-error=pessimizing-move') + cflags.append('-Wno-error=redundant-move') + if '+zlib' in self.spec: cflags.append('-I' + self.spec['zlib'].prefix.include) ldflags.append(self.spec['zlib'].libs.ld_flags) + else: + env['ROCKSDB_DISABLE_ZLIB'] = 'YES' + if '+bz2' in self.spec: cflags.append('-I' + self.spec['bz2'].prefix.include) ldflags.append(self.spec['bz2'].libs.ld_flags) + else: + env['ROCKSDB_DISABLE_BZIP'] = 'YES' + + if '+tbb' in self.spec: + cflags.append(spec['tbb'].headers.cpp_flags) + ldflags.append('-L' + spec['tbb'].prefix.lib) + else: + env['ROCKSDB_DISABLE_TBB'] = 'YES' for pkg in ['lz4', 'snappy', 'zstd']: if '+' + pkg in self.spec: cflags.append(self.spec[pkg].headers.cpp_flags) ldflags.append(self.spec[pkg].libs.ld_flags) + else: + env['ROCKSDB_DISABLE_' + pkg.upper()] = 'YES' cflags.append(self.spec['gflags'].headers.cpp_flags) ldflags.append(self.spec['gflags'].libs.ld_flags) diff --git a/var/spack/repos/builtin/packages/rockstar/package.py b/var/spack/repos/builtin/packages/rockstar/package.py index ebf47ab45d..80d9138f5f 100644 --- a/var/spack/repos/builtin/packages/rockstar/package.py +++ b/var/spack/repos/builtin/packages/rockstar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rodinia/package.py b/var/spack/repos/builtin/packages/rodinia/package.py index 49aeaee3a5..6310dc5444 100644 --- a/var/spack/repos/builtin/packages/rodinia/package.py +++ b/var/spack/repos/builtin/packages/rodinia/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/root/README.md b/var/spack/repos/builtin/packages/root/README.md new file mode 100644 index 0000000000..d808498b34 --- /dev/null +++ b/var/spack/repos/builtin/packages/root/README.md @@ -0,0 +1,170 @@ +# ROOT Recipe Notes + +ROOT has a significant number of build options. Not all of them are supported by this package recipe at this time. Relevant notes on support (or lack thereof) for various options is below. + +## Fixed and unsupported options + +### Missing dependencies + +The following configuration options are unsupported (set to `OFF`) due to missing dependencies: + +#### `alien` + +Requires `libgapiUI` from ALICE. + +#### `dcache` + +DCache support depends on `libdcap` from DESY. + +#### `gfal` + +#### `http` + +ROOT looks for and uses the FastCGI package on the system if found, creating a possible non-portable dependency. There is currently no `fastcgi` recipe, nor any way to unconditionally disable the search for the package. + +#### `monalisa` + +Monitoring with Monalisa depends on `libapmoncpp`. + +#### `odbc` + +#### `oracle` + +#### `pythia8` + +#### `tcmalloc` + +#### `veccore` + +#### `xinetd` + +### Discontinued options + +Support for several options was discontinued in ROOT without prior support in the recipe: + +#### `afdsmgrd` + +#### `afs` + +#### `bonjour` + +#### `castor` + +#### `chirp` + +#### `geocad` + +#### `glite` + +#### `globus` + +#### `hdfs` + +#### `ios` + +#### `krb5` + +#### `ldap` + +#### `rfio` + +#### `ruby` + +#### `sapdb` + +#### `srp` + +### Other fixed or unsupported options + +### `arrow=OFF` + +#### `asimage=ON`, `astiff=ON`, `builtin_afterimage=ON` + +Full control of `asimage` and `astiff` would require a package recipe for libAfterImage or Afterstep. In their absence, we use the provided and internally built version of libAfterImage. + +#### `ccache=OFF` + +Only useful for repeated builds. + +#### `cling=OFF` + +The use of Cling is assumed. + +#### `cxxmodules` + +This option should not be confused with `runtime_cxxmodules`. `cxxmodules` is an optimization that affects only the efficiency of building ROOT. + +#### `exceptions=ON` + +Support for C++ exceptions is assumed. + +#### `explicitlink=ON` + +Use of explicit linking when making shared libraries is assumed. + +#### `fail-on-missing=ON` + +Failure on missing dependencies is assumed (_vs_ automatically setting `builtin_XXX`). + +#### `gnuinstall=OFF` + +GNU-compliant install layout. + +#### `libcxx` + +This option controls use of the libC++ standard C++ library via compiler options. It is set automatically by ROOT's configuration on macOS >=10.7 when a Clang compiler is configured. Due to complexities related to compiler options and the way a compiler might have been configured, configurable support is disabled until (at least) Spack supports the standard library as a virtual dependency. + +#### `pch=ON` + +The use of pre-compiled headers when building is assumed. + +#### `roottest=OFF` + +`roottest` requires access to the network. + +#### `runtime_cxxmodules=OFF` + +This option tells ROOT to generate and use PCMs for its own libraries. This functionality is experimental for ROOT < 6.20, and is currently not supported by the recipe. + +#### `shared=ON` + +The use of shared libraries is assumed. + +#### `soversion=ON` + +The use of versioning for shared libraries is assumed. + +#### `testing` + +The building of ROOT's test suite and its availability for use by CTest is pegged to Spack's determination of whether testing is required for the current installation procedure. + +## Variants and version dependent support for options + +Some configuration options are version dependent---unavailable before or after a specific version. The current accounting for such options in the recipe is far from exhaustive, and a survey of the various options and the versions that support them would be useful. However, accounting for them is somewhat clumsy absent a `when` clause for variants, or similar. + +### Conflicting variants since 6.18 + +#### `memstat` + +#### `qt4` + +Representing the obsolete `qt` and `qtgsi` ROOT build options. + +#### `table` + +### Temporarily conflicting variants + +The `http` variant is currently an unconditional conflict due to the non-portable dependency mentioned above. + +## Permanently removed variants + +The following variants have been removed from the recipe as they have always been ineffective: + +* `avahi` +* `kerberos` +* `ldap` +* `libcxx` +* `odbc` +* `tiff` + +In addition, the `test` variant has been removed as its actions are irrelevant to the installed source---the corresponding `testing` ROOT option is enabled if and only if `self.run_tests` is set. diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py index 7087572191..a3c9202833 100644 --- a/var/spack/repos/builtin/packages/root/package.py +++ b/var/spack/repos/builtin/packages/root/package.py @@ -1,10 +1,11 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +from spack.util.environment import is_system_path import sys @@ -14,6 +15,8 @@ class Root(CMakePackage): homepage = "https://root.cern.ch" url = "https://root.cern/download/root_v6.16.00.source.tar.gz" + maintainers = ['chissg', 'HadrienG2'] + # ###################### Versions ########################## # Master branch @@ -23,9 +26,13 @@ class Root(CMakePackage): # Development version (when more recent than production). # Production version - version('6.16.00', sha256='2a45055c6091adaa72b977c512f84da8ef92723c30837c7e2643eecc9c5ce4d8', preferred=True) + version('6.18.04', sha256='315a85fc8363f8eb1bffa0decbf126121258f79bd273513ed64795675485cfa4', + preferred=True) # Old versions + version('6.18.02', sha256='50ffffdbf2585a536c77a03f54aa631926138275ffeee02e5a16dde87e978c1d') + version('6.18.00', sha256='e6698d6cfe585f186490b667163db65e7d1b92a2447658d77fa831096383ea71') + version('6.16.00', sha256='2a45055c6091adaa72b977c512f84da8ef92723c30837c7e2643eecc9c5ce4d8') version('6.14.08', sha256='1b63b51cfb4dc20f1f5749faac6bbd1098eccab777f8b49911257d77186c73c4') version('6.14.06', sha256='0fb943b61396f282b289e35c455a9ab60126229be1bd3f04a8f00b37c13ab432') version('6.14.04', sha256='463ec20692332a422cfb5f38c78bedab1c40ab4d81be18e99b50cf9f53f596cf') @@ -38,7 +45,6 @@ class Root(CMakePackage): version('6.06.06', sha256='0a7d702a130a260c72cb6ea754359eaee49a8c4531b31f23de0bfcafe3ce466b') version('6.06.04', sha256='ab86dcc80cbd8e704099af0789e23f49469932ac4936d2291602301a7aa8795b') version('6.06.02', sha256='18a4ce42ee19e1a810d5351f74ec9550e6e422b13b5c58e0c3db740cdbc569d1') - version('5.34.38', sha256='2c3bda69601d94836bdd88283a6585b4774eafc813deb6aa348df0af2922c4d2') # ###################### Patches ########################## @@ -52,7 +58,7 @@ class Root(CMakePackage): # Some ROOT versions did not honor the option to avoid building an # internal version of unuran, _cf_ # https://github.com/root-project/ROOT/commit/3e60764f133218b6938e5aa4986de760e8f058d9. - patch('honor-unuran-switch.patch', level=1, when='@:6.13.99') + patch('honor-unuran-switch.patch', level=1, when='@6.08.06:6.13.99') # 6.16.00 fails to handle particular build option combinations, _cf_ # https://github.com/root-project/ROOT/commit/e0ae0483985d90a71a6cabd10d3622dfd1c15611. patch('root7-webgui.patch', level=1, when='@6.16.00') @@ -66,15 +72,11 @@ class Root(CMakePackage): patch('root6-60606-mathmore.patch', when='@6.06.06') # ###################### Variants ########################## + # See README.md for specific notes about what ROOT configuration + # options are or are not supported, and why. - variant('avahi', default=False, - description='Compile with avahi') variant('aqua', default=False, description='Enable Aqua interface') - # No need for a specific variant: libafterimage is not provided by spack - # By default always true, we get the builtin included in the source - # variant('asimage', default=True, - # description='Enable image processing support') variant('davix', default=True, description='Compile with external Davix') variant('emacs', default=False, @@ -100,12 +102,6 @@ class Root(CMakePackage): description='Enable HTTP server support') variant('jemalloc', default=False, description='Enable using the jemalloc allocator') - variant('kerberos', default=False, - description='Enable Kerberos support') - variant('ldap', default=False, - description='Enable LDAP support') - variant('libcxx', default=False, - description='Build using libc++') variant('math', default=True, description='Build the new libMathMore extended math library') variant('memstat', default=False, @@ -115,17 +111,12 @@ class Root(CMakePackage): variant('minuit', default=True, description='Automatically search for support libraries') variant('mysql', default=False) - variant('odbc', default=False, - description='Enable ODBC support') variant('opengl', default=True, description='Enable OpenGL support') - # variant('oracle', default=False) - not supported by spack variant('postgres', default=False, description='Enable postgres support') variant('pythia6', default=False, description='Enable pythia6 support') - # variant('pythia8', default=False, - not suported by spack - # description='Enable pythia8 support') variant('python', default=True, description='Enable Python ROOT bindings') variant('qt4', default=False, @@ -148,12 +139,8 @@ class Root(CMakePackage): description='Build libTable contrib library') variant('tbb', default=True, description='TBB multi-threading support') - variant('test', default=False, - description='Enable test suit of ROOT with CTest') variant('threads', default=True, description='Enable using thread library') - variant('tiff', default=True, - description='Include Tiff support in image processing') variant('tmva', default=True, description='Build TMVA multi variate analysis library') variant('unuran', default=True, @@ -162,10 +149,10 @@ class Root(CMakePackage): description='Enable Vc for adding new types for SIMD programming') variant('vdt', default=True, description='Enable set of fast and vectorisable math functions') + variant('vmc', default=False, + description='Enable the Virtual Monte Carlo interface') variant('x', default=True, description='Enable set of graphical options') - # variant('xinetd', default=False, - not supported by spack - # description='Enable a daemon process manager') variant('xml', default=True, description='Enable XML parser interface') variant('xrootd', default=False, @@ -181,7 +168,8 @@ class Root(CMakePackage): # ###################### Dependencies ###################### - depends_on('cmake@3.4.3:', type='build') + depends_on('cmake@3.4.3:', type='build', when='@:6.16.99') + depends_on('cmake@3.9:', type='build', when='@6.18.00:') depends_on('pkgconfig', type='build') depends_on('blas') @@ -204,7 +192,7 @@ class Root(CMakePackage): depends_on('libsm', when="+x") # OpenGL - depends_on('ftgl@2.1.3-rc5', when="+x+opengl") + depends_on('ftgl@2.4.0:', when="+x+opengl") depends_on('glew', when="+x+opengl") depends_on('gl', when="+x+opengl") depends_on('glu', when="+x+opengl") @@ -216,57 +204,30 @@ class Root(CMakePackage): # TMVA depends_on('py-numpy', when='+tmva') - # Asimage variant would need one of these two - # For the moment, we use the libafterimage provided by the root sources - # depends_on('libafterimage', when='+asimage') - not supported - # depends_on('afterstep@2.2.11', when='+asimage') - not supported - # Optional dependencies - depends_on('avahi', when='+avahi') depends_on('davix', when='+davix') depends_on('cfitsio', when='+fits') depends_on('fftw', when='+fftw') depends_on('graphviz', when='+graphviz') depends_on('gsl', when='+gsl') - depends_on('http', when='+http') depends_on('jemalloc', when='+jemalloc') - depends_on('kerberos', when='+kerberos') - depends_on('ldap', when='+ldap') - depends_on('libcxx', when='+libcxx') depends_on('mysql-client', when='+mysql') - depends_on('odbc', when='+odbc') - # depends_on('oracle', when='+oracle') depends_on('openssl', when='+ssl') - depends_on('openssl', when='+davix') # Also with davix + depends_on('openssl', when='+davix') # Also with davix depends_on('postgresql', when='+postgres') - depends_on('pythia6+root', when='+pythia6') - # depends_on('pythia@8:8.999', when='+pythia8') - not supported on Spack - depends_on('python@2.7:', when='+python', type=('build', 'run')) + depends_on('pythia6+root', when='+pythia6') + depends_on('python@2.7:', when='+python', type=('build', 'run')) depends_on('r', when='+r', type=('build', 'run')) - depends_on('r-cpp', when='+r', type=('build', 'run')) - depends_on('r-inside', when='+r', type=('build', 'run')) + depends_on('r-rcpp', when='+r', type=('build', 'run')) + depends_on('r-rinside', when='+r', type=('build', 'run')) depends_on('shadow', when='+shadow') depends_on('sqlite', when='+sqlite') depends_on('tbb', when='+tbb') depends_on('unuran', when='+unuran') depends_on('vc', when='+vc') - depends_on('veccore', when='+veccore') depends_on('vdt', when='+vdt') - depends_on('libxml2+python', when='+xml+python') - depends_on('libxml2~python', when='+xml~python') + depends_on('libxml2', when='+xml') depends_on('xrootd', when='+xrootd') - # depends_on('hdfs') - supported (TODO) - - # Not supported - # depends_on('monalisa') - - # Grid packages - not supported yet by Spack - # depends_on('castor') - # depends_on('chirp') - # depends_on('dcap') - # depends_on('gfal') - # depends_on('ldap') - # depends_on('rfio') # ###################### Conflicts ###################### @@ -274,210 +235,163 @@ class Root(CMakePackage): # See https://sft.its.cern.ch/jira/browse/ROOT-7517 conflicts('%intel') + # ROOT <6.08 was incompatible with the GCC 5+ ABI + conflicts('%gcc@5.0.0:', when='@:6.07.99') + + # The version of Clang featured in ROOT <6.12 fails to build with + # GCC 9.2.1, which we can safely extrapolate to the GCC 9 series. + conflicts('%gcc@9.0.0:', when='@:6.11.99') + + # ROOT <6.14 was incompatible with Python 3.7+ + conflicts('python@3.7:', when='@:6.13.99 +python') + + # See README.md + conflicts('+http', + msg='HTTP server currently unsupported due to dependency issues') + # Incompatible variants - conflicts('+tmva', when='~gsl', msg="TVMA requires GSL") - conflicts('cxxstd=11', when='+root7', msg="root7 requires at least C++14") + conflicts('+opengl', when='~x', msg='OpenGL requires X') + conflicts('+tmva', when='~gsl', msg='TVMA requires GSL') + conflicts('cxxstd=11', when='+root7', msg='root7 requires at least C++14') - # Feature removed: - conflicts('+memstat', when='@6.18.00:', - msg="Obsolete option +memstat selected.") - conflicts('+memstat', when='@master', - msg="Obsolete option +memstat selected.") + # Feature removed in 6.18: + [(conflicts('+{0}'.format(pkg), when='@6.18.00:', + msg='Obsolete option +{0} selected.'.format(pkg))) for pkg in + ('memstat', 'qt4', 'table')] def cmake_args(self): spec = self.spec - options = [] - - # #################### Base Settings ####################### - - # ROOT should not download its own dependencies - options = [ - '-Dexplicitlink=ON', - '-Dexceptions=ON', - '-Dfail-on-missing=ON', - '-Dshared=ON', - '-Dsoversion=ON', - '-Dbuiltin_llvm=ON', - '-Dbuiltin_afterimage=ON', - '-Dasimage:BOOL=ON', # if afterimage is taken from builtin - '-Dastiff:BOOL=ON', # asimage and astiff must be ON too - '-Dbuiltin_cfitsio:BOOL=OFF', - '-Dbuiltin_davix:BOOL=OFF', - '-Dbuiltin_fftw3:BOOL=OFF', - '-Dbuiltin_freetype:BOOL=OFF', - '-Dbuiltin_ftgl:BOOL=OFF', - '-Dbuiltin_gl2ps:BOOL=OFF', - '-Dbuiltin_glew:BOOL=OFF', - '-Dbuiltin_gsl:BOOL=OFF', - '-Dbuiltin_lzma:BOOL=OFF', - '-Dbuiltin_openssl:BOOL=OFF', - '-Dbuiltin_pcre:BOOL=OFF', - '-Dbuiltin_tbb:BOOL=OFF', - '-Dbuiltin_unuran:BOOL=OFF', - '-Dbuiltin_vc:BOOL=OFF', - '-Dbuiltin_vdt:BOOL=OFF', - '-Dbuiltin_veccore:BOOL=OFF', - '-Dbuiltin_xrootd:BOOL=OFF', - '-Dbuiltin_zlib:BOOL=OFF' - ] - - # LZ4 and xxhash do not work as external deps for older versions - options.extend([ - '-Dbuiltin_lz4:BOOL=%s' % ( - 'ON' if self.spec.satisfies('@6.12.02:6.12.99') else 'OFF'), - '-Dbuiltin_xxhash:BOOL=%s' % ( - 'ON' if self.spec.satisfies('@6.12.02:6.12.99') else 'OFF'), - ]) - - # #################### ROOT options ####################### - - options.extend([ - '-Dx11:BOOL=%s' % ( - 'ON' if '+x' in spec else 'OFF'), - '-Dxft:BOOL=%s' % ( - 'ON' if '+x' in spec else 'OFF'), - '-Dbonjour:BOOL=%s' % ( - 'ON' if '+avahi' in spec else 'OFF'), - '-Dcocoa:BOOL=%s' % ( - 'ON' if '+aqua' in spec else 'OFF'), - # -Dcxxmodules=OFF # use clang C++ modules - '-Ddavix:BOOL=%s' % ( - 'ON' if '+davix' in spec else 'OFF'), - '-Dfftw3:BOOL=%s' % ( - 'ON' if '+fftw' in spec else 'OFF'), - '-Dfitsio:BOOL=%s' % ( - 'ON' if '+fits' in spec else 'OFF'), - '-Dfortran:BOOL=%s' % ( - 'ON' if '+fortran' in spec else 'OFF'), - '-Dftgl:BOOL=%s' % ( - 'ON' if '+opengl' in spec else 'OFF'), - '-Dgdml:BOOL=%s' % ( - 'ON' if '+gdml' in spec else 'OFF'), - '-Dgl2ps:BOOL=%s' % ( - 'ON' if '+opengl' in spec else 'OFF'), - '-Dgenvector:BOOL=%s' % ( - 'ON' if '+math' in spec else 'OFF'), # default ON - '-Dgminimal:BOOL=%s' % ( # Reduce unwanted surprises - 'ON' if '+gminimal' in spec else 'OFF'), # Default ON - '-Dgsl_shared:BOOL=%s' % ( - 'ON' if '+gsl' in spec else 'OFF'), - '-Dgviz:BOOL=%s' % ( - 'ON' if '+graphviz' in spec else 'OFF'), - '-Dhttp:BOOL=%s' % ( - 'ON' if '+http' in spec else 'OFF'), - '-Dimt:BOOL=%s' % ( - 'ON' if '+tbb' in spec else 'OFF'), - '-Djemalloc:BOOL=%s' % ( - 'ON' if '+jemalloc' in spec else 'OFF'), - '-Dkrb5:BOOL=%s' % ( - 'ON' if '+kerberos' in spec else 'OFF'), - '-Dldap:BOOL=%s' % ( - 'ON' if '+ldap' in spec else 'OFF'), - '-Dlibcxx:BOOL=%s' % ( - 'ON' if '+libcxx' in spec else 'OFF'), - '-Dmathmore:BOOL=%s' % ( - 'ON' if '+math' in spec else 'OFF'), - '-Dmemstat:BOOL=%s' % ( - 'ON' if '+memstat' in spec else 'OFF'), - '-Dminimal:BOOL=%s' % ( - 'ON' if '+minimal' in spec else 'OFF'), - '-Dminuit:BOOL=%s' % ( - 'ON' if '+minuit' in spec else 'OFF'), - '-Dminuit2:BOOL=%s' % ( - 'ON' if '+minuit' in spec else 'OFF'), - '-Dmysql:BOOL=%s' % ( - 'ON' if '+mysql' in spec else 'OFF'), - '-Dodbc:BOOL=%s' % ( - 'ON' if '+odbc' in spec else 'OFF'), - '-Dopengl:BOOL=%s' % ( - 'ON' if '+opengl' in spec else 'OFF'), - '-Doracle:BOOL=%s' % ( - 'ON' if '+oracle' in spec else 'OFF'), # not supported - '-Dpch:BOOL=%s' % ( - 'ON' if '+pch' in spec else 'OFF'), # needs cling - '-Dpgsql:BOOL=%s' % ( - 'ON' if '+postgres' in spec else 'OFF'), - '-Dpythia6:BOOL=%s' % ( - 'ON' if '+pythia6' in spec else 'OFF'), - # Force not to build pythia8 (not supported yet by spack), to avoid - # wrong defaults from ROOT at build time - '-Dpythia8:BOOL=%s' % ( - 'ON' if '+pythia8' in spec else 'OFF'), - '-Dpython:BOOL=%s' % ( - 'ON' if self.spec.satisfies('+python ^python@2.7:2.99.99') - else 'OFF'), - '-Dpython3:BOOL=%s' % ( - 'ON' if self.spec.satisfies('+python ^python@3.0:') - else 'OFF'), - '-Dqt:BOOL=%s' % ( - 'ON' if '+qt4' in spec else 'OFF'), - '-Dqtgsi:BOOL=%s' % ( - 'ON' if '+qt4' in spec else 'OFF'), - '-Dr:BOOL=%s' % ( - 'ON' if '+R' in spec else 'OFF'), - '-Droofit:BOOL=%s' % ( - 'ON' if '+roofit' in spec else 'OFF'), - '-Droot7:BOOL=%s' % ( - 'ON' if '+root7' in spec else 'OFF'), # requires C++14 - '-Dwebui:BOOL=%s' % ( - 'ON' if '+root7' in spec else 'OFF'), # requires root7 - '-Drpath:BOOL=%s' % ( - 'ON' if '+rpath' in spec else 'OFF'), - '-Dshadowpw:BOOL=%s' % ( - 'ON' if '+shadow' in spec else 'OFF'), - '-Dsqlite:BOOL=%s' % ( - 'ON' if '+sqlite' in spec else 'OFF'), - '-Dssl:BOOL=%s' % ( - 'ON' if '+ssl' in spec else 'OFF'), - '-Dtable:BOOL=%s' % ( - 'ON' if '+table' in spec else 'OFF'), - '-Dtbb:BOOL=%s' % ( - 'ON' if '+tbb' in spec else 'OFF'), - '-Dtesting:BOOL=%s' % ( - 'ON' if '+test' in spec else 'OFF'), - '-Dthread:BOOL=%s' % ( - 'ON' if '+threads' in spec else 'OFF'), - '-Dtmva:BOOL=%s' % ( - 'ON' if '+tmva' in spec else 'OFF'), - '-Dunuran:BOOL=%s' % ( - 'ON' if '+unuran' in spec else 'OFF'), - '-Dvc:BOOL=%s' % ( - 'ON' if '+vc' in spec else 'OFF'), - '-Dveccore:BOOL=%s' % ( - 'ON' if '+veccore' in spec else 'OFF'), # not supported - '-Dvdt:BOOL=%s' % ( - 'ON' if '+vdt' in spec else 'OFF'), - '-Dxml:BOOL=%s' % ( - 'ON' if '+xml' in spec else 'OFF'), # default ON - '-Dxrootd:BOOL=%s' % ( - 'ON' if '+xrootd' in spec else 'OFF'), # default ON - - # Fixed options - '-Dafdsmrgd:BOOL=OFF', # not supported - '-Dafs:BOOL=OFF', # not supported - '-Dalien:BOOL=OFF', - '-Dcastor:BOOL=OFF', # not supported - '-Dccache:BOOL=OFF', # not supported - '-Dchirp:BOOL=OFF', - '-Dcling:BOOL=ON', - '-Ddcache:BOOL=OFF', # not supported - '-Dgeocad:BOOL=OFF', # not supported - '-Dgfal:BOOL=OFF', # not supported - '-Dglite:BOOL=OFF', # not supported - '-Dglobus:BOOL=OFF', - '-Dgnuinstall:BOOL=OFF', - '-Dhdfs:BOOL=OFF', # TODO pending to add - '-Dmonalisa:BOOL=OFF', # not supported - '-Drfio:BOOL=OFF', # not supported - '-Droottest:BOOL=OFF', # requires network - '-Druby:BOOL=OFF', # unmantained upstream - # Use clang C++ modules, experimental - '-Druntime_cxxmodules:BOOL=OFF', - '-Dsapdb:BOOL=OFF', # option not implemented - '-Dsrp:BOOL=OFF', # option not implemented - '-Dtcmalloc:BOOL=OFF' - - ]) + + # ###################### Boolean Options ###################### + # For option list format see _process_opts(), below. + + # Options controlling gross build / config behavior. + control_opts\ + = [ + ['cxxmodules', False], + ['exceptions', True], + ['explicitlink', True], + ['fail-on-missing', True], + ['fortran'], + ['gminimal'], + ['gnuinstall', False], + ['libcxx', False], + ['pch', True], + ['roottest', False], + ['rpath'], + ['runtime_cxxmodules', False], + ['shared', True], + ['soversion', True], + ['testing', self.run_tests], + ['thread', 'threads'] + ] + + # Options related to ROOT's ability to download and build its own + # dependencies. Per Spack convention, this should generally be avoided. + builtin_opts\ + = [ + ['builtin_afterimage', True], + ['builtin_cfitsio', False], + ['builtin_davix', False], + ['builtin_fftw3', False], + ['builtin_freetype', False], + ['builtin_ftgl', False], + ['builtin_gl2ps', False], + ['builtin_glew', False], + ['builtin_gsl', False], + ['builtin_llvm', True], + ['builtin_lz4', self.spec.satisfies('@6.12.02:6.12.99')], + ['builtin_lzma', False], + ['builtin_openssl', False], + ['builtin_pcre', False], + ['builtin_tbb', False], + ['builtin_unuran', False], + ['builtin_vc', False], + ['builtin_vdt', False], + ['builtin_veccore', False], + ['builtin_xrootd', False], + ['builtin_xxhash', self.spec.satisfies('@6.12.02:6.12.99')], + ['builtin_zlib', False] + ] + + # Features + feature_opts\ + = [ + ['afdsmrgd', False], + ['afs', False], + ['alien', False], + ['arrow', False], + ['asimage', True], + ['astiff', True], + ['bonjour', False], + ['castor', False], + ['ccache', False], + ['chirp', False], + ['cling', True], + ['cocoa', 'aqua'], + ['davix'], + ['dcache', False], + ['fftw3', 'fftw'], + ['fitsio', 'fits'], + ['ftgl', 'opengl'], + ['gdml'], + ['genvector', 'math'], + ['geocad', False], + ['gfal', False], + ['gl2ps', 'opengl'], + ['glite', False], + ['globus', False], + ['gsl_shared', 'gsl'], + ['gviz', 'graphviz'], + ['hdfs', False], + ['http'], # See conflicts + ['imt', 'tbb'], + ['jemalloc'], + ['krb5', False], + ['ldap', False], + ['mathmore', 'math'], + ['memstat'], # See conflicts + ['minimal'], + ['minuit'], + ['minuit2', 'minuit'], + ['monalisa', False], + ['mysql'], + ['odbc'], + ['opengl'], + ['oracle', False], + ['pgsql', 'postgres'], + ['pythia6'], + ['pythia8', False], + ['python', self.spec.satisfies('+python')], + ['qt', 'qt4'], # See conflicts + ['qtgsi', 'qt4'], # See conflicts + ['r', 'R'], + ['rfio', False], + ['roofit'], + ['root7'], # See conflicts + ['ruby', False], + ['sapdb', False], + ['shadowpw', 'shadow'], + ['sqlite'], + ['srp', False], + ['ssl'], + ['table'], + ['tbb'], + ['tcmalloc', False], + ['tmva'], + ['unuran'], + ['vc'], + ['vdt'], + ['veccore'], + ['vmc'], + ['webui', 'root7'], # requires root7 + ['x11', 'x'], + ['xft', 'x'], + ['xml'], + ['xrootd'] + ] + + options = self._process_opts(control_opts, builtin_opts, feature_opts) # #################### Compiler options #################### @@ -488,9 +402,11 @@ class Root(CMakePackage): '-DCMAKE_CXX_FLAGS=-D__builtin_unreachable=__builtin_trap', ]) - options.append( - '-Dcxx{0}=ON'.format(self.spec.variants['cxxstd'].value) - ) + # Method for selecting C++ standard depends on ROOT version + options.append(('-DCMAKE_CXX_STANDARD={0}' if + self.spec.satisfies('@6.18.00:') else + '-Dcxx{0}:BOOL=ON').format + (self.spec.variants['cxxstd'].value)) if 'mysql-client' in self.spec: options.append('-DCMAKE_PROGRAM_PATH={0}'.format( @@ -505,25 +421,79 @@ class Root(CMakePackage): if '+python' in self.spec: options.append('-DPYTHON_EXECUTABLE=%s' % spec['python'].command.path) + return options - def setup_environment(self, spack_env, run_env): - run_env.set('ROOTSYS', self.prefix) - run_env.set('ROOT_VERSION', 'v{0}'.format(self.version.up_to(1))) - run_env.prepend_path('PYTHONPATH', self.prefix.lib) + def setup_build_environment(self, env): if 'lz4' in self.spec: - spack_env.append_path('CMAKE_PREFIX_PATH', - self.spec['lz4'].prefix) - spack_env.set('SPACK_INCLUDE_DIRS', '', force=True) - - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('ROOTSYS', self.prefix) - spack_env.set('ROOT_VERSION', 'v{0}'.format(self.version.up_to(1))) - spack_env.prepend_path('PYTHONPATH', self.prefix.lib) - spack_env.prepend_path('PATH', self.prefix.bin) - spack_env.append_path('CMAKE_MODULE_PATH', '{0}/cmake' - .format(self.prefix)) - run_env.set('ROOTSYS', self.prefix) - run_env.set('ROOT_VERSION', 'v{0}'.format(self.version.up_to(1))) - run_env.prepend_path('PYTHONPATH', self.prefix.lib) - run_env.prepend_path('PATH', self.prefix.bin) + env.append_path('CMAKE_PREFIX_PATH', + self.spec['lz4'].prefix) + + # This hack is made necessary by a header name collision between + # asimage's "import.h" and Python's "import.h" headers... + env.set('SPACK_INCLUDE_DIRS', '', force=True) + + # ...but it breaks header search for any ROOT dependency which does not + # use CMake. To resolve this, we must bring back those dependencies's + # include paths into SPACK_INCLUDE_DIRS. + # + # But in doing so, we must be careful not to inject system header paths + # into SPACK_INCLUDE_DIRS, even in a deprioritized form, because some + # system/compiler combinations don't like having -I/usr/include around. + def add_include_path(dep_name): + include_path = self.spec[dep_name].prefix.include + if not is_system_path(include_path): + env.append_path('SPACK_INCLUDE_DIRS', include_path) + + # With that done, let's go fixing those deps + if self.spec.satisfies('+x @:6.08.99'): + add_include_path('xextproto') + if self.spec.satisfies('@:6.12.99'): + add_include_path('zlib') + if '+x' in self.spec: + add_include_path('fontconfig') + add_include_path('libx11') + add_include_path('xproto') + if '+opengl' in self.spec: + add_include_path('glew') + add_include_path('mesa-glu') + + def setup_run_environment(self, env): + env.set('ROOTSYS', self.prefix) + env.set('ROOT_VERSION', 'v{0}'.format(self.version.up_to(1))) + env.prepend_path('PYTHONPATH', self.prefix.lib) + + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('ROOTSYS', self.prefix) + env.set('ROOT_VERSION', 'v{0}'.format(self.version.up_to(1))) + env.prepend_path('PYTHONPATH', self.prefix.lib) + env.prepend_path('PATH', self.prefix.bin) + env.append_path('CMAKE_MODULE_PATH', '{0}/cmake' + .format(self.prefix)) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.set('ROOTSYS', self.prefix) + env.set('ROOT_VERSION', 'v{0}'.format(self.version.up_to(1))) + env.prepend_path('PYTHONPATH', self.prefix.lib) + env.prepend_path('PATH', self.prefix.bin) + + def _process_opts(self, *opt_lists): + """Process all provided boolean option lists into CMake arguments. + + Args: + opt_list (list): list of elements, each of which is a list: + <cmake-option>[, <bool-or-controlling-variant-name>] + The optional element in each sub-list defaults to + <cmake-option> if ommited. + """ + + def _process_opt(opt_name, cond_or_variant=None): + val = cond_or_variant if \ + isinstance(cond_or_variant, bool) else \ + ('+{variant}'.format(variant=cond_or_variant or opt_name) + in self.spec) + return '-D{opt}:BOOL={val}'.format(opt=opt_name, val='ON' if + val else 'OFF') + + return [_process_opt(*opt_info) for opt_list in opt_lists for + opt_info in opt_list] diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py index 23b497a2e7..326da4854b 100644 --- a/var/spack/repos/builtin/packages/rose/package.py +++ b/var/spack/repos/builtin/packages/rose/package.py @@ -1,12 +1,8 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -# ----------------------------------------------------------------------------- -# Author: Justin Too -# ----------------------------------------------------------------------------- - from spack import * @@ -16,18 +12,49 @@ class Rose(AutotoolsPackage): (Developed at Lawrence Livermore National Lab)""" homepage = "http://rosecompiler.org/" - # url = "https://github.com/rose-compiler/rose-develop/archive/v0.9.7.0.tar.gz" - url = "https://github.com/rose-compiler/rose-develop/archive/v0.9.9.104.zip" - git = "https://github.com/rose-compiler/rose-develop.git" + url = "https://github.com/rose-compiler/rose/archive/v0.9.13.0.zip" + git = "https://github.com/rose-compiler/rose.git" + + maintainers = ['pinnown'] # -------------------------------------------------------------------------- # ROSE Versions # -------------------------------------------------------------------------- - version("0.9.10.0", sha256="7b53b6913fd6ca0c5050b630dae380f3e6b0897cde6148172ba01095f71cbaca") - # git versions - version("0.9.9.52", commit="bd4fc0cc332ce62d9fa54db19879507d9e4f239b") - version("develop", branch="master") + version("0.9.13.0", sha256="64092793dfd38d476152696721e29a410bb31dc3eeb6064c7520087aa8c904a6") + + # Version for edg binary is found in src/frontend/CxxFrontend/EDG_VERSION + # EDG_VERSION may be different from ROSE_VERSION + resource(name="roseBinaryEDG-5-0-x86_64-pc-linux-gnu-gnu-4.9-5.0.9.12.52.tar.gz", + expand=False, + placement="rose-build/src/frontend/CxxFrontend/", + when="@0.9.13.0 %gcc@4.9.0:4.9.99", + url="http://edg-binaries.rosecompiler.org/roseBinaryEDG-5-0-x86_64-pc-linux-gnu-gnu-4.9-5.0.9.12.52.tar.gz", + sha256="fb4b50606bdc681b864bbece46d344d7775780ffe7883aa96305d732c9c04a1c") + + resource(name="roseBinaryEDG-5-0-x86_64-pc-linux-gnu-gnu-5-5.0.9.12.52.tar.gz", + expand=False, + placement="rose-build/src/frontend/CxxFrontend/", + when="@0.9.13.0 %gcc@5.0:5.99", + url="http://edg-binaries.rosecompiler.org/roseBinaryEDG-5-0-x86_64-pc-linux-gnu-gnu-5-5.0.9.12.52.tar.gz", + sha256="584f8f721274f0f2d5c9a0c7701c045af99580ea7cd1d50999e20c2a897298fb") + + resource(name="roseBinaryEDG-5-0-x86_64-pc-linux-gnu-gnu-6-5.0.9.12.52.tar.gz", + expand=False, + placement="rose-build/src/frontend/CxxFrontend/", + when="@0.9.13.0 %gcc@6.0:6.99", + url="http://edg-binaries.rosecompiler.org/roseBinaryEDG-5-0-x86_64-pc-linux-gnu-gnu-6-5.0.9.12.52.tar.gz", + sha256="561cd5a944d0dd01689aa0bea8eccf30fc994cd20c4c05da7943c6f36cec25b5") + + resource(name="roseBinaryEDG-5-0-x86_64-pc-linux-gnu-gnu-7-5.0.9.12.52.tar.gz", + expand=False, + placement="rose-build/src/frontend/CxxFrontend/", + when="@0.9.13.0 %gcc@7.0:7.99", + url="http://edg-binaries.rosecompiler.org/roseBinaryEDG-5-0-x86_64-pc-linux-gnu-gnu-7-5.0.9.12.52.tar.gz", + sha256="800a178804e8b5e936942b4eb036cc61e5d5ad43551cb4fd901ec42ba7e7a176") + + # git versions depends on internet connection at build time + version("develop", branch="develop") # -------------------------------------------------------------------------- # Dependencies @@ -35,15 +62,10 @@ class Rose(AutotoolsPackage): depends_on("autoconf@2.69:", type="build") depends_on("automake@1.14:", type="build") depends_on("libtool@2.4:", type="build") - depends_on("boost@1.56.0:", when="~cxx11") # C++11 compatible boost and gcc versions required for +cxx11 variant: - # https://github.com/spack/spack/wiki/Telcon%3A-2015-05-14 - depends_on("boost@1.60.0: cxxstd=11", when="+cxx11") - - # TODO: Doesn't seem to be a way to require a specific compiler: https://github.com/spack/spack/issues/896 - # https://www.gnu.org/software/gcc/projects/cxx-status.html#cxx11 - # depends_on("%gcc@4.8.1:", when="^boost@1.60.0: cxxstd=11") + depends_on("boost@1.60.0:1.64.0,1.65.1,1.66.0:1.67.0 cxxstd=11", when="+cxx11") + depends_on("boost@1.60.0:1.64.0,1.65.1,1.66.0:1.67.0", when="~cxx11") # -------------------------------------------------------------------------- # Variants @@ -54,6 +76,8 @@ class Rose(AutotoolsPackage): variant("tests", default=False, description="Build the tests directory") variant("tutorial", default=False, description="Build the tutorial directory") + variant("tools", default=False, description="Build a selection of ROSE based tools") + variant( "mvapich2_backend", default=False, @@ -69,12 +93,10 @@ class Rose(AutotoolsPackage): variant("cxx", default=True, description="Enable c++ language support") # Use spack install cxxflags=-std=c++11 - variant("cxx11", default=False, description="Enable c++11 language support") + variant("cxx11", default=True, description="Enable c++11 language support") variant("fortran", default=False, description="Enable fortran language support") - - variant("java", default=False, description="Enable java language support") - depends_on("jdk", when="+java") + depends_on("java@8", when="+fortran") variant("z3", default=False, description="Enable z3 theorem prover") depends_on("z3", when="+z3") @@ -99,34 +121,7 @@ class Rose(AutotoolsPackage): build_directory = "rose-build" - def patch(self): - spec = self.spec - - # ROSE needs its to compute its EDG - # binary compatibility signature for C/C++ and for its - # --version information. - # - # git rev-parse HEAD - # git log -1 --format="%at" - # - with open("VERSION", "w") as f: - if "@0.9.9.104:" in spec: - # EDG: 27acd506c6b0e4b1c5f7573c642e3e407237eddd - f.write("66c87e9395126a7ab8663d81f0e0b99d6e09131e 1504924600") - elif "@0.9.9.0:" in spec: - # EDG: 46306e9f73d3ccd690be300aefdaf766a9ba3f70 - f.write("14d3ebdd7f83cbcc295e6ed45b45d2e9ed32b5ff 1492716108") - elif "@0.9.7.0:" in spec: - # EDG: 8e63f421f9107ef6c7882b57f9c83e3878623ffa - f.write("992c21ad06893bc1e9e7688afe0562eee0fda021 1460595442") - elif "@0.9.10.0:" in spec: - # EDG: f4624773cb93dfcc67a00efb5e9e8affeb57fb73 - f.write("277fea7e1e5305e5b3c86b550a0c1354e8285b96 1523991417") - else: - raise InstallError("Unknown ROSE version!") - def autoreconf(self, spec, prefix): - # if not spec.satisfies('@develop'): with working_dir(self.stage.source_path): bash = which("bash") bash("build") @@ -146,7 +141,6 @@ class Rose(AutotoolsPackage): "binaries" if "+binanalysis" in spec else "", "c" if "+c" in spec else "", "c++" if "+cxx" in spec else "", - "java" if "+java" in spec else "", "fortran" if "+fortran" in spec else "", ] return list(filter(None, langs)) @@ -161,14 +155,8 @@ class Rose(AutotoolsPackage): cc = spack_cc cxx = spack_cxx - if spec.satisfies("@0.9.8:"): - edg = "4.12" - else: - edg = "4.9" - args = [ "--disable-boost-version-check", - "--enable-edg_version={0}".format(edg), "--with-alternate_backend_C_compiler={0}".format(cc), "--with-alternate_backend_Cxx_compiler={0}".format(cxx), "--with-boost={0}".format(spec["boost"].prefix), @@ -190,7 +178,7 @@ class Rose(AutotoolsPackage): else: args.append("--disable-tutorial-directory") - if "+java" in spec: + if "+fortran" in spec: args.append("--with-java={0}".format(spec["java"].prefix)) else: args.append("--without-java") @@ -212,9 +200,9 @@ class Rose(AutotoolsPackage): return args - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if "+codethorn" in self.spec: - spack_env.set("CXXFLAGS", "-std=c++11") + env.set("CXXFLAGS", "-std=c++11") def build(self, spec, prefix): # Spack will automatically pass ncpus as the number of make jobs. @@ -224,45 +212,23 @@ class Rose(AutotoolsPackage): # $ srun -n1 spack install rose # with working_dir(self.build_directory): - # ROSE needs the EDG version for C/C++ - with open("src/frontend/CxxFrontend/EDG-submodule-sha1", "w") as f: - if "@0.9.9.104" in spec: - f.write("27acd506c6b0e4b1c5f7573c642e3e407237eddd") - elif "@0.9.9.52" in spec: - f.write("56a826126289414db5436e6c49879b99d046d26d") - elif "@0.9.9.0" in spec: - f.write("46306e9f73d3ccd690be300aefdaf766a9ba3f70") - elif "@0.9.7.0" in spec: - f.write("8e63f421f9107ef6c7882b57f9c83e3878623ffa") - elif "@0.9.10.0" in spec: - f.write("f4624773cb93dfcc67a00efb5e9e8affeb57fb73") - else: - raise InstallError("Unknown ROSE version for EDG!") # Compile librose - with working_dir("src"): - make() - - # Install librose - with working_dir("src"): - make("install") + make("core") - # Install "official" ROSE-based tools - make("install-core") - - with working_dir("tools"): - make("install") + if "+tools" in spec: + make("tools") # ----------------------------------------------------------------- # ROSE-based Projects # ----------------------------------------------------------------- if "+codethorn" in spec: with working_dir("projects/CodeThorn"): - make("install") + make() if "+autopar" in spec: with working_dir("projects/autoParallelization"): - make("install") + make() if "+polyopt" in spec: mkdir = which("mkdir") @@ -278,3 +244,23 @@ class Rose(AutotoolsPackage): "projects/PolyOpt2/install.sh" ) ) + + def install(self, spec, prefix): + with working_dir(self.build_directory): + + # Compile and Install librose + make("install-core") + + if "+tools" in spec: + make("install-tools") + + # ----------------------------------------------------------------- + # ROSE-based Projects + # ----------------------------------------------------------------- + if "+codethorn" in spec: + with working_dir("projects/CodeThorn"): + make("install") + + if "+autopar" in spec: + with working_dir("projects/autoParallelization"): + make("install") diff --git a/var/spack/repos/builtin/packages/ross/package.py b/var/spack/repos/builtin/packages/ross/package.py index 62d65cc095..cfdca27161 100644 --- a/var/spack/repos/builtin/packages/ross/package.py +++ b/var/spack/repos/builtin/packages/ross/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/routino/package.py b/var/spack/repos/builtin/packages/routino/package.py index 4b46d47d4d..b1b7fafccc 100644 --- a/var/spack/repos/builtin/packages/routino/package.py +++ b/var/spack/repos/builtin/packages/routino/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rpcsvc-proto/package.py b/var/spack/repos/builtin/packages/rpcsvc-proto/package.py index 44d2be710a..fd89714027 100644 --- a/var/spack/repos/builtin/packages/rpcsvc-proto/package.py +++ b/var/spack/repos/builtin/packages/rpcsvc-proto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rr/package.py b/var/spack/repos/builtin/packages/rr/package.py index 5fa46341af..6b3bb93a51 100644 --- a/var/spack/repos/builtin/packages/rr/package.py +++ b/var/spack/repos/builtin/packages/rr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rsbench/package.py b/var/spack/repos/builtin/packages/rsbench/package.py index cb71349e21..08ca35a20f 100644 --- a/var/spack/repos/builtin/packages/rsbench/package.py +++ b/var/spack/repos/builtin/packages/rsbench/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rsem/package.py b/var/spack/repos/builtin/packages/rsem/package.py index eb8b6cb314..8e24f7bfcd 100644 --- a/var/spack/repos/builtin/packages/rsem/package.py +++ b/var/spack/repos/builtin/packages/rsem/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rstart/package.py b/var/spack/repos/builtin/packages/rstart/package.py index 50e3838efd..777706c67b 100644 --- a/var/spack/repos/builtin/packages/rstart/package.py +++ b/var/spack/repos/builtin/packages/rstart/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rsync/package.py b/var/spack/repos/builtin/packages/rsync/package.py index 919100cb03..d89467c13d 100644 --- a/var/spack/repos/builtin/packages/rsync/package.py +++ b/var/spack/repos/builtin/packages/rsync/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rt-tests/package.py b/var/spack/repos/builtin/packages/rt-tests/package.py new file mode 100644 index 0000000000..4310ae5718 --- /dev/null +++ b/var/spack/repos/builtin/packages/rt-tests/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RtTests(Package): + """ + Suite of real-time tests - cyclictest, hwlatdetect, pip_stress, + pi_stress, pmqtest, ptsematest, rt-migrate-test, sendme, signaltest, + sigwaittest, svsematest. + """ + + homepage = "https://git.kernel.org" + url = "https://git.kernel.org/pub/scm/utils/rt-tests/rt-tests.git/snapshot/rt-tests-1.2.tar.gz" + + version('1.2', sha256='7ccde036059c87681a4b00e7138678d9551b1232113441f6edda31ea45452426') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/rtags/package.py b/var/spack/repos/builtin/packages/rtags/package.py index 4ee2464b4e..6ae39013aa 100644 --- a/var/spack/repos/builtin/packages/rtags/package.py +++ b/var/spack/repos/builtin/packages/rtags/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rtax/package.py b/var/spack/repos/builtin/packages/rtax/package.py index df47eac7f4..830e9b8073 100644 --- a/var/spack/repos/builtin/packages/rtax/package.py +++ b/var/spack/repos/builtin/packages/rtax/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ruby-gnuplot/package.py b/var/spack/repos/builtin/packages/ruby-gnuplot/package.py index 1ba329e482..20bef687bc 100644 --- a/var/spack/repos/builtin/packages/ruby-gnuplot/package.py +++ b/var/spack/repos/builtin/packages/ruby-gnuplot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ruby-narray/package.py b/var/spack/repos/builtin/packages/ruby-narray/package.py index 5e8c7d23f5..7c05259f1b 100644 --- a/var/spack/repos/builtin/packages/ruby-narray/package.py +++ b/var/spack/repos/builtin/packages/ruby-narray/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ruby-ronn/package.py b/var/spack/repos/builtin/packages/ruby-ronn/package.py index d11957a3d9..de2a8e6da4 100644 --- a/var/spack/repos/builtin/packages/ruby-ronn/package.py +++ b/var/spack/repos/builtin/packages/ruby-ronn/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ruby-rubyinline/package.py b/var/spack/repos/builtin/packages/ruby-rubyinline/package.py index 55bbe3be34..39f53e8c2e 100644 --- a/var/spack/repos/builtin/packages/ruby-rubyinline/package.py +++ b/var/spack/repos/builtin/packages/ruby-rubyinline/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ruby-svn2git/package.py b/var/spack/repos/builtin/packages/ruby-svn2git/package.py index 32e7120173..a183267c8f 100644 --- a/var/spack/repos/builtin/packages/ruby-svn2git/package.py +++ b/var/spack/repos/builtin/packages/ruby-svn2git/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ruby-terminal-table/package.py b/var/spack/repos/builtin/packages/ruby-terminal-table/package.py index cea27b4de2..ba6790b3d4 100644 --- a/var/spack/repos/builtin/packages/ruby-terminal-table/package.py +++ b/var/spack/repos/builtin/packages/ruby-terminal-table/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 2fbbc0c537..b2e2c6f6fa 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -63,7 +63,7 @@ class Ruby(AutotoolsPackage): args.append('--with-tk=%s' % self.spec['tk'].prefix) return args - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): # TODO: do this only for actual extensions. # Set GEM_PATH to include dependent gem directories ruby_paths = [] @@ -71,10 +71,10 @@ class Ruby(AutotoolsPackage): if d.package.extends(self.spec): ruby_paths.append(d.prefix) - spack_env.set_path('GEM_PATH', ruby_paths) + env.set_path('GEM_PATH', ruby_paths) # The actual installation path for this gem - spack_env.set('GEM_HOME', dependent_spec.prefix) + env.set('GEM_HOME', dependent_spec.prefix) def setup_dependent_package(self, module, dependent_spec): """Called before ruby modules' install() methods. Sets GEM_HOME diff --git a/var/spack/repos/builtin/packages/rust-bindgen/package.py b/var/spack/repos/builtin/packages/rust-bindgen/package.py index fb5d7ca7be..47563a9064 100644 --- a/var/spack/repos/builtin/packages/rust-bindgen/package.py +++ b/var/spack/repos/builtin/packages/rust-bindgen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py index b494870301..2ae30b5c03 100644 --- a/var/spack/repos/builtin/packages/rust/package.py +++ b/var/spack/repos/builtin/packages/rust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ class Rust(Package): git = "https://github.com/rust-lang/rust.git" version('develop', branch='master') + version('1.41.0', tag='1.41.0') version('1.34.0', tag='1.34.0') version('1.32.0', tag='1.32.0') version('1.31.1', tag='1.31.1') diff --git a/var/spack/repos/builtin/packages/sabre/package.py b/var/spack/repos/builtin/packages/sabre/package.py index 165a6b2e51..6f7a647154 100644 --- a/var/spack/repos/builtin/packages/sabre/package.py +++ b/var/spack/repos/builtin/packages/sabre/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/saga-gis/package.py b/var/spack/repos/builtin/packages/saga-gis/package.py index 04ba7f6b92..49d070daf5 100644 --- a/var/spack/repos/builtin/packages/saga-gis/package.py +++ b/var/spack/repos/builtin/packages/saga-gis/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,7 @@ class SagaGis(AutotoolsPackage): git = "git://git.code.sf.net/p/saga-gis/code" version('develop', branch='master') + version('7.4.0', branch='release-7.4.0') version('7.3.0', branch='release-7.3.0') version('7.1.1', branch='release-7.1.1') version('7.1.0', branch='release-7.1.0') @@ -38,31 +39,52 @@ class SagaGis(AutotoolsPackage): variant('gui', default=True, description='Build GUI and interactive SAGA tools') variant('odbc', default=True, description='Build with ODBC support') + # FIXME Saga-gis configure file disables triangle even if # --enable-triangle flag is used # variant('triangle', default=True, description='Build with triangle.c + # non free for commercial use otherwise use qhull') - variant('libfire', default=True, description='Build with libfire (non free for commercial usage)') - variant('openmp', default=True, description='Build with OpenMP enabled') - variant('python', default=False, description='Build Python extension') + variant('libfire', default=True, description='Build with libfire (non free for commercial usage)') + variant('openmp', default=True, description='Build with OpenMP enabled') + variant('python', default=False, description='Build Python extension') + + variant('postgresql', default=False, description='Build with PostgreSQL library') + variant('opencv', default=False, description='Build with libraries using OpenCV') depends_on('autoconf', type='build') depends_on('automake', type='build') depends_on('libtool', type='build') depends_on('m4', type='build') - # FIXME unnecessary dependency on python3 because of implicit python3 - # dependency through meson by a dependency of wx/gtkplus - depends_on('python@3:') - + depends_on('libharu') depends_on('wxwidgets') - depends_on('gdal') - depends_on('proj@:5') - + depends_on('postgresql', when='+postgresql') depends_on('unixodbc', when='+odbc') + + # SAGA-GIS requires projects.h from proj + depends_on('proj') + # https://sourceforge.net/p/saga-gis/bugs/271/ + depends_on('proj@:5', when='@:7.2.999') + + # Saga-Gis depends on legacy opencv API removed in opencv 4.x + depends_on('opencv@:3', when='+opencv') + # Set jpeg provider (similar to #8133) + depends_on('libjpeg', when='+opencv') + # Set hl variant due to similar issue #7145 + depends_on('hdf5+hl') + + # write support for grib2 is available since 2.3.0 (https://gdal.org/drivers/raster/grib.html) + depends_on('gdal@2.3:+grib+hdf5+netcdf') + + depends_on('gdal@2.3:2.4+grib+hdf5+netcdf', when='@:7.2.999') + depends_on('libgeotiff@:1.4', when='@:7.2.999') + # FIXME Saga-Gis uses a wrong include path # depends_on('qhull', when='~triangle') + depends_on('swig', type='build', when='+python') + extends('python', when='+python') configure_directory = "saga-gis" @@ -79,5 +101,11 @@ class SagaGis(AutotoolsPackage): args += self.enable_or_disable('libfire') args += self.enable_or_disable('openmp') args += self.enable_or_disable('python') + args += self.with_or_without('postgresql') return args + + def setup_run_environment(self, env): + # Point saga to its tool set, will be loaded during runtime + env.set("SAGA_MLB", self.prefix.lib.saga) + env.set("SAGA_TLB", self.prefix.lib.saga) diff --git a/var/spack/repos/builtin/packages/sailfish/package.py b/var/spack/repos/builtin/packages/sailfish/package.py index 2a87a2c4ed..ea202bb58f 100644 --- a/var/spack/repos/builtin/packages/sailfish/package.py +++ b/var/spack/repos/builtin/packages/sailfish/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/salmon/package.py b/var/spack/repos/builtin/packages/salmon/package.py index bc24483e01..c75450eb4a 100644 --- a/var/spack/repos/builtin/packages/salmon/package.py +++ b/var/spack/repos/builtin/packages/salmon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sambamba/package.py b/var/spack/repos/builtin/packages/sambamba/package.py index 094b18ce5f..72e318baf6 100644 --- a/var/spack/repos/builtin/packages/sambamba/package.py +++ b/var/spack/repos/builtin/packages/sambamba/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/samblaster/package.py b/var/spack/repos/builtin/packages/samblaster/package.py index bc69c0b78f..9c87c4b7b9 100644 --- a/var/spack/repos/builtin/packages/samblaster/package.py +++ b/var/spack/repos/builtin/packages/samblaster/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/samrai/package.py b/var/spack/repos/builtin/packages/samrai/package.py index 9843f2a0e4..358aa884f0 100644 --- a/var/spack/repos/builtin/packages/samrai/package.py +++ b/var/spack/repos/builtin/packages/samrai/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -95,6 +95,6 @@ class Samrai(AutotoolsPackage): return options - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): if self.spec.satisfies('@3.12:'): - spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag) + env.append_flags('CXXFLAGS', self.compiler.cxx11_flag) diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py index e4624d46e4..ad1eb5e38d 100644 --- a/var/spack/repos/builtin/packages/samtools/package.py +++ b/var/spack/repos/builtin/packages/samtools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,6 +14,7 @@ class Samtools(Package): homepage = "www.htslib.org" url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" + version('1.10', sha256='7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585') version('1.9', sha256='083f688d7070082411c72c27372104ed472ed7a620591d06f928e653ebc23482') version('1.8', sha256='c942bc1d9b85fd1b05ea79c5afd2805d489cd36b2c2d8517462682a4d779be16') version('1.7', sha256='e7b09673176aa32937abd80f95f432809e722f141b5342186dfef6a53df64ca1') @@ -23,27 +24,39 @@ class Samtools(Package): version('1.3.1', sha256='6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e') version('1.2', sha256='420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa') + depends_on('zlib') depends_on('ncurses') + depends_on('perl', type='run') + depends_on('python', type='run') + # htslib became standalone @1.3.1, must use corresponding version - depends_on('htslib@1.9', when='@1.9') - depends_on('htslib@1.8', when='@1.8') - depends_on('htslib@1.7', when='@1.7') - depends_on('htslib@1.6', when='@1.6') - depends_on('htslib@1.5', when='@1.5') - depends_on('htslib@1.4', when='@1.4') + depends_on('htslib@1.10.2', when='@1.10') + depends_on('htslib@1.9', when='@1.9') + depends_on('htslib@1.8', when='@1.8') + depends_on('htslib@1.7', when='@1.7') + depends_on('htslib@1.6', when='@1.6') + depends_on('htslib@1.5', when='@1.5') + depends_on('htslib@1.4', when='@1.4') depends_on('htslib@1.3.1', when='@1.3.1') - depends_on('zlib') - depends_on('bzip2') def install(self, spec, prefix): + if '+termlib' in spec['ncurses']: + curses_lib = '-lncursesw -ltinfow' + else: + curses_lib = '-lncursesw' + if self.spec.version >= Version('1.3.1'): - configure('--prefix={0}'.format(prefix), '--with-ncurses', - 'CURSES_LIB=-lncursesw') + configure('--prefix={0}'.format(prefix), + '--with-htslib={0}'.format(self.spec['htslib'].prefix), + '--with-ncurses', + 'CURSES_LIB={0}'.format(curses_lib)) make() make('install') else: - make("prefix=%s" % prefix) - make("prefix=%s" % prefix, "install") + make('prefix={0}'.format(prefix), + 'LIBCURSES={0}'.format(curses_lib)) + make('prefix={0}'.format(prefix), 'install') + # Install dev headers and libs for legacy apps depending on them mkdir(prefix.include) mkdir(prefix.lib) diff --git a/var/spack/repos/builtin/packages/sandbox/package.py b/var/spack/repos/builtin/packages/sandbox/package.py index 37f48f2080..b512e9fae9 100644 --- a/var/spack/repos/builtin/packages/sandbox/package.py +++ b/var/spack/repos/builtin/packages/sandbox/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sas/package.py b/var/spack/repos/builtin/packages/sas/package.py index 39e25b97ae..8b09cf4d79 100644 --- a/var/spack/repos/builtin/packages/sas/package.py +++ b/var/spack/repos/builtin/packages/sas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/satsuma2/package.py b/var/spack/repos/builtin/packages/satsuma2/package.py index f6db1542e0..8d1e0eea29 100644 --- a/var/spack/repos/builtin/packages/satsuma2/package.py +++ b/var/spack/repos/builtin/packages/satsuma2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/savanna/package.py b/var/spack/repos/builtin/packages/savanna/package.py index 127c4966d3..37da8bd766 100644 --- a/var/spack/repos/builtin/packages/savanna/package.py +++ b/var/spack/repos/builtin/packages/savanna/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/saws/package.py b/var/spack/repos/builtin/packages/saws/package.py index 2ad6670a8c..8a55cc896a 100644 --- a/var/spack/repos/builtin/packages/saws/package.py +++ b/var/spack/repos/builtin/packages/saws/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sbt/package.py b/var/spack/repos/builtin/packages/sbt/package.py index 4af58b0ceb..63484249da 100644 --- a/var/spack/repos/builtin/packages/sbt/package.py +++ b/var/spack/repos/builtin/packages/sbt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/scala/package.py b/var/spack/repos/builtin/packages/scala/package.py index 9d990009cb..a5226af1cf 100644 --- a/var/spack/repos/builtin/packages/scala/package.py +++ b/var/spack/repos/builtin/packages/scala/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,8 @@ class Scala(Package): homepage = "https://www.scala-lang.org/" url = "https://downloads.lightbend.com/scala/2.12.1/scala-2.12.1.tgz" + version('2.13.1', sha256='6918ccc494e34810a7254ad2c4e6f0e1183784c22e7b4801b7dbc8d1994a04db') + version('2.12.10', sha256='3b12bda3300fedd91f64fc7f9165fd45c58328b1b760af24ca6ffe92e3b0656a') version('2.12.5', sha256='b261ffe9a495b12e9dda2ed37331e579547e4d1b8b5810161b6c3b39ac806aa1') version('2.12.1', sha256='4db068884532a3e27010df17befaca0f06ea50f69433d58e06a5e63c7a3cc359') version('2.11.11', sha256='12037ca64c68468e717e950f47fc77d5ceae5e74e3bdca56f6d02fd5bfd6900b') diff --git a/var/spack/repos/builtin/packages/scalasca/package.py b/var/spack/repos/builtin/packages/scalasca/package.py index ec6d0d9bb7..fed9cb30dc 100644 --- a/var/spack/repos/builtin/packages/scalasca/package.py +++ b/var/spack/repos/builtin/packages/scalasca/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/scallop/package.py b/var/spack/repos/builtin/packages/scallop/package.py index 7199c179de..a05aa44a5d 100644 --- a/var/spack/repos/builtin/packages/scallop/package.py +++ b/var/spack/repos/builtin/packages/scallop/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/scalpel/package.py b/var/spack/repos/builtin/packages/scalpel/package.py index db1861e5aa..6ce6d23c8b 100644 --- a/var/spack/repos/builtin/packages/scalpel/package.py +++ b/var/spack/repos/builtin/packages/scalpel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,8 +13,9 @@ class Scalpel(MakefilePackage): """ homepage = "http://scalpel.sourceforge.net/index.html" - url = "https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz" + url = "https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.4.tar.gz" + version('0.5.4', sha256='506f731b3886def158c15fd8b74fa98390f304a507d2040972e6b09ddefac8f0') version('0.5.3', sha256='d45b569fe3aa5934883bc7216c243d53168351c23e020d96a46fa77a1563b65e') depends_on('perl@5.10.0:') diff --git a/var/spack/repos/builtin/packages/scan-for-matches/package.py b/var/spack/repos/builtin/packages/scan-for-matches/package.py index 10cb9b7179..c4abe6d7d0 100644 --- a/var/spack/repos/builtin/packages/scan-for-matches/package.py +++ b/var/spack/repos/builtin/packages/scan-for-matches/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py index 3dead9eabb..328fa558ab 100644 --- a/var/spack/repos/builtin/packages/scons/package.py +++ b/var/spack/repos/builtin/packages/scons/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,7 @@ class Scons(PythonPackage): homepage = "http://scons.org" url = "https://pypi.io/packages/source/s/scons/scons-3.1.1.tar.gz" + version('3.1.2', sha256='8aaa483c303efeb678e6f7c776c8444a482f8ddc3ad891f8b6cdd35264da9a1f') version('3.1.1', sha256='fd44f8f2a4562e7e5bc8c63c82b01e469e8115805a3e9c2923ee54cdcd6678b3') version('3.1.0', sha256='94e0d0684772d3e6d9368785296716e0ed6ce757270b3ed814e5aa72d3163890') version('3.0.5', sha256='e95eaae17d9e490cf12cd37f091a6cbee8a628b5c8dbd3cab1f348f602f46462') diff --git a/var/spack/repos/builtin/packages/scorec-core/package.py b/var/spack/repos/builtin/packages/scorec-core/package.py index b78f46fbfe..adb88f2aae 100644 --- a/var/spack/repos/builtin/packages/scorec-core/package.py +++ b/var/spack/repos/builtin/packages/scorec-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/scorep/package.py b/var/spack/repos/builtin/packages/scorep/package.py index df44111cb7..96c3eae2e4 100644 --- a/var/spack/repos/builtin/packages/scorep/package.py +++ b/var/spack/repos/builtin/packages/scorep/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py index 935de81075..0a96559763 100644 --- a/var/spack/repos/builtin/packages/scotch/package.py +++ b/var/spack/repos/builtin/packages/scotch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,6 +14,7 @@ class Scotch(Package): url = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.4.tar.gz" list_url = "http://gforge.inria.fr/frs/?group_id=248" + version('6.0.8', sha256='0ba3f145026174304f910c8770a3cbb034f213c91d939573751cfbb4fd46d45e') version('6.0.6', sha256='686f0cad88d033fe71c8b781735ff742b73a1d82a65b8b1586526d69729ac4cf') version('6.0.5a', sha256='5b21b95e33acd5409d682fa7253cefbdffa8db82875549476c006d8cbe7c556f') version('6.0.4', sha256='f53f4d71a8345ba15e2dd4e102a35fd83915abf50ea73e1bf6efe1bc2b4220c7') diff --git a/var/spack/repos/builtin/packages/scr/package.py b/var/spack/repos/builtin/packages/scr/package.py index 133c89eff3..63d0af34eb 100644 --- a/var/spack/repos/builtin/packages/scr/package.py +++ b/var/spack/repos/builtin/packages/scr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/screen/package.py b/var/spack/repos/builtin/packages/screen/package.py index 100f5479ac..d68164b4d4 100644 --- a/var/spack/repos/builtin/packages/screen/package.py +++ b/var/spack/repos/builtin/packages/screen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,13 +6,13 @@ from spack import * -class Screen(AutotoolsPackage): +class Screen(AutotoolsPackage, GNUMirrorPackage): """Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells. """ homepage = "https://www.gnu.org/software/screen/" - url = "https://ftpmirror.gnu.org/screen/screen-4.3.1.tar.gz" + gnu_mirror_path = "screen/screen-4.3.1.tar.gz" version('4.6.2', sha256='1b6922520e6a0ce5e28768d620b0f640a6631397f95ccb043b70b91bb503fa3a') version('4.3.1', sha256='fa4049f8aee283de62e283d427f2cfd35d6c369b40f7f45f947dbfd915699d63') diff --git a/var/spack/repos/builtin/packages/scripts/package.py b/var/spack/repos/builtin/packages/scripts/package.py index 93387b06c4..b31da8db92 100644 --- a/var/spack/repos/builtin/packages/scripts/package.py +++ b/var/spack/repos/builtin/packages/scripts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/scrnsaverproto/package.py b/var/spack/repos/builtin/packages/scrnsaverproto/package.py index d337db7b89..8ddb8377e9 100644 --- a/var/spack/repos/builtin/packages/scrnsaverproto/package.py +++ b/var/spack/repos/builtin/packages/scrnsaverproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/scs/make_gpu.patch b/var/spack/repos/builtin/packages/scs/make_gpu.patch new file mode 100644 index 0000000000..3e38d832cc --- /dev/null +++ b/var/spack/repos/builtin/packages/scs/make_gpu.patch @@ -0,0 +1,14 @@ +diff --git a/Makefile.orig b/Makefile +index b4f2bc9..8a28fc4 100644 +--- a/Makefile.orig ++++ b/Makefile +@@ -129,7 +129,8 @@ install: $(INSTALL_INC_FILES) $(INSTALL_TARGETS) + $(INSTALL) -d $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR) + $(INSTALL) -m 644 $(INSTALL_INC_FILES) $(INSTALL_INC_DIR) + $(INSTALL) -m 644 $(INSTALL_TARGETS) $(INSTALL_LIB_DIR) +-install_gpu: $(INSTALL_INC_FILES) $(INSTALL_GPU_TARGETS) ++install_gpu: $(INSTALL_INC_FILES) $(INSTALL_GPU_TARGETS) $(INSTALL_TARGETS) + $(INSTALL) -d $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR) + $(INSTALL) -m 644 $(INSTALL_INC_FILES) $(INSTALL_INC_DIR) + $(INSTALL) -m 644 $(INSTALL_GPU_TARGETS) $(INSTALL_LIB_DIR) ++ $(INSTALL) -m 644 $(INSTALL_TARGETS) $(INSTALL_LIB_DIR) diff --git a/var/spack/repos/builtin/packages/scs/package.py b/var/spack/repos/builtin/packages/scs/package.py new file mode 100644 index 0000000000..5d783d0dc4 --- /dev/null +++ b/var/spack/repos/builtin/packages/scs/package.py @@ -0,0 +1,41 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Scs(MakefilePackage): + """A C package that solves convex cone problems via operator splitting""" + + homepage = "https://github.com/cvxgrp/scs" + url = "https://github.com/cvxgrp/scs/archive/2.1.1.tar.gz" + + version('2.1.1', sha256='0e20b91e8caf744b84aa985ba4e98cc7235ee33612b2bad2bf31ea5ad4e07d93') + + variant('cuda', default=False, description='Build with Cuda support') + + depends_on('blas') + depends_on('lapack') + depends_on('cuda', when='+cuda') + + # make sure install_gpu target installs all libs not only the gpu ones + patch('make_gpu.patch') + + def edit(self, spec, prefix): + filter_file(r'-lblas', spec['blas'].libs.ld_flags, 'scs.mk') + filter_file(r'-llapack', spec['lapack'].libs.ld_flags, 'scs.mk') + + def build(self, spec, prefix): + if '+cuda' in spec: + make('default', 'gpu') + else: + make() + + def install(self, spec, prefix): + if '+cuda' in spec: + make('PREFIX=' + prefix, 'install_gpu') + else: + make('PREFIX=' + prefix, 'install') diff --git a/var/spack/repos/builtin/packages/sctk/package.py b/var/spack/repos/builtin/packages/sctk/package.py index c530a1fe96..c81dda0e3c 100644 --- a/var/spack/repos/builtin/packages/sctk/package.py +++ b/var/spack/repos/builtin/packages/sctk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sdl2-image/package.py b/var/spack/repos/builtin/packages/sdl2-image/package.py index 76356d708e..83541f234d 100644 --- a/var/spack/repos/builtin/packages/sdl2-image/package.py +++ b/var/spack/repos/builtin/packages/sdl2-image/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sdl2/package.py b/var/spack/repos/builtin/packages/sdl2/package.py index 06a083a73a..0ea1b2441c 100644 --- a/var/spack/repos/builtin/packages/sdl2/package.py +++ b/var/spack/repos/builtin/packages/sdl2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sdsl-lite/package.py b/var/spack/repos/builtin/packages/sdsl-lite/package.py index 5023ddf05b..d5d2a251c0 100644 --- a/var/spack/repos/builtin/packages/sdsl-lite/package.py +++ b/var/spack/repos/builtin/packages/sdsl-lite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/seacas/package.py b/var/spack/repos/builtin/packages/seacas/package.py index f02cb9b09e..0e5ac9b72a 100644 --- a/var/spack/repos/builtin/packages/seacas/package.py +++ b/var/spack/repos/builtin/packages/seacas/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -26,6 +26,8 @@ class Seacas(CMakePackage): # ###################### Versions ########################## version('master', branch='master') + version('2019-12-18', sha256='f82cfa276ebc5fe6054852383da16eba7a51c81e6640c73b5f01fc3109487c6f') + version('2019-10-14', sha256='ca4cf585cdbc15c25f302140fe1f61ee1a30d72921e032b9a854492b6c61fb91') version('2019-08-20', sha256='a82c1910c2b37427616dc3716ca0b3c1c77410db6723aefb5bea9f47429666e5') version('2019-07-26', sha256='651dac832b0cfee0f63527f563415c8a65b8e4d79242735c1e2aec606f6b2e17') @@ -71,8 +73,8 @@ class Seacas(CMakePackage): # Everything should be compiled position independent (-fpic) - depends_on('netcdf@4.6.2:+mpi+parallel-netcdf', when='+mpi') - depends_on('netcdf@4.6.2:~mpi', when='~mpi') + depends_on('netcdf-c@4.6.2:+mpi+parallel-netcdf', when='+mpi') + depends_on('netcdf-c@4.6.2:~mpi', when='~mpi') depends_on('cgns@develop+mpi+scoping', when='+cgns +mpi') depends_on('cgns@develop~mpi+scoping', when='+cgns ~mpi') depends_on('adios2@develop~mpi', when='+adios2 ~mpi') @@ -198,10 +200,10 @@ class Seacas(CMakePackage): ]) # ##################### Dependencies ########################## - # Always need NetCDF + # Always need NetCDF-C options.extend([ '-DTPL_ENABLE_Netcdf:BOOL=ON', - '-DNetCDF_ROOT:PATH=%s' % spec['netcdf'].prefix, + '-DNetCDF_ROOT:PATH=%s' % spec['netcdf-c'].prefix, ]) if '+metis' in spec: diff --git a/var/spack/repos/builtin/packages/sed/package.py b/var/spack/repos/builtin/packages/sed/package.py index b9af55888f..3565c3c9ef 100644 --- a/var/spack/repos/builtin/packages/sed/package.py +++ b/var/spack/repos/builtin/packages/sed/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,9 +6,9 @@ from spack import * -class Sed(AutotoolsPackage): +class Sed(AutotoolsPackage, GNUMirrorPackage): """GNU implementation of the famous stream editor.""" homepage = "http://www.gnu.org/software/sed/" - url = "https://ftpmirror.gnu.org/sed/sed-4.2.2.tar.bz2" + gnu_mirror_path = "sed/sed-4.2.2.tar.bz2" version('4.2.2', sha256='f048d1838da284c8bc9753e4506b85a1e0cc1ea8999d36f6995bcb9460cddbd7') diff --git a/var/spack/repos/builtin/packages/sensei/package.py b/var/spack/repos/builtin/packages/sensei/package.py new file mode 100644 index 0000000000..fa2e534166 --- /dev/null +++ b/var/spack/repos/builtin/packages/sensei/package.py @@ -0,0 +1,134 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Sensei(CMakePackage): + """SENSEI is a platform for scalable in-situ analysis and visualization. + Its design motto is 'Write once, run everywhere', this means that once + the application is instrumented with SENSEI it can use existing and + future analysis backends. Existing backends include: Paraview/Catalyst, + Visit/Libsim, ADIOS, Python scripts, and so on.""" + + homepage = "https://sensei-insitu.org" + url = "https://gitlab.kitware.com/sensei/sensei/-/archive/v3.1.0/sensei-v3.1.0.tar.gz" + git = "https://gitlab.kitware.com/sensei/sensei.git" + maintainers = ['sshudler'] + + version('master', branch='master') + version('3.1.0', sha256='9a3e6d0d5bb6170ee666586435434da1708b3876fd448b9d41142571ed9da939') + version('3.0.0', sha256='0aabbea03ade9947c88fc0aa6d3cbaf3c8267e8504e384a041445678a95e58eb') + version('2.1.1', sha256='8a27ebf133fef00a59e4b29433762e6560bf20214072de7808836eb668bb5687') + version('2.1.0', sha256='b7af21a25523cf6cd8934d797471b75ca32881166625d71f24b5c8b6d727ca99') + version('2.0.0', sha256='df48eab035e1acdd8edf5159955c05306f9ca48117effacc4a6b77c3fb24f62b') + version('1.1.0', sha256='e5a4ba691573ff6c7b0d4793665e218ee5868ebcc0198915d1f16a4b7b92a368') + version('1.0.0', sha256='bdcb03c56b51f2795ec5a7e85a5abb01d473d192fac50f2a8bf2608cc3564ff8') + + variant('sencore', default=True, description='Enables the SENSEI core library') + variant('catalyst', default=True, description='Build with ParaView-Catalyst support') + variant('libsim', default=False, description='Build with VisIt-Libsim support') + variant('vtkio', default=True, description='Enable adaptors to write to VTK XML format') + variant('adios', default=False, description='Enable ADIOS adaptors and endpoints') + variant('hdf5', default=False, description='Enables HDF5 adaptors and endpoints') + variant('python', default=False, description='Enable Python bindings') + variant('miniapps', default=True, description='Enable the parallel 3D and oscillators miniapps') + variant('cxxstd', default='11', values=('11', '14', '17'), multi=False, description='Use the specified C++ standard when building.') + + # All SENSEI versions up to 2.1.1 support only Python 2, so in this case + # Paraview 6 cannot be used since it requires Python 3. Starting from + # version 3, SENSEI supports Python 3. + depends_on("paraview@5.5.0:5.5.2+python+mpi+hdf5", when="@:2.1.1 +catalyst") + depends_on("paraview@5.6:+python3+mpi+hdf5", when="@3: +catalyst") + depends_on("visit", when="+libsim") + depends_on("vtk", when="+libsim") + depends_on("vtk", when="~libsim ~catalyst") + depends_on("adios", when="+adios") + depends_on("hdf5", when="+hdf5") + # SENSEI 3 supports Python 3, earlier versions upport only Python 2 + depends_on("python@:2.7.16", when="@:2.1.1 +python", type=('build', 'run')) + depends_on("python@3:", when="@3: +python", type=('build', 'run')) + depends_on("py-numpy", when="+python", type=('build', 'run')) + depends_on("py-mpi4py", when="+python", type=('build', 'run')) + depends_on("swig", when="+python", type='build') + depends_on('cmake@3.6:', when="@3:", type='build') + + # Can have either LibSim or Catalyst, but not both + conflicts('+libsim', when='+catalyst') + # hdf5 variant is available only for SENSEI 3 + conflicts('+hdf5', when='@:2.1.1') + + def cmake_args(self): + spec = self.spec + + # -Ox flags are set by default in CMake based on the build type + args = [ + '-DCMAKE_CXX_STANDARD={0}'.format(spec.variants['cxxstd'].value), + '-DCMAKE_C_STANDARD=11', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON', + '-DENABLE_SENSEI:BOOL={0}'.format( + 'ON' if '+sencore' in spec else 'OFF') + ] + + vtk_dir_needed = True + + if '+catalyst' in spec: + args.extend([ + '-DENABLE_CATALYST:BOOL=ON', + '-DENABLE_CATALYST_PYTHON:BOOL=ON', + '-DParaView_DIR:PATH={0}'.format(spec['paraview'].prefix) + ]) + vtk_dir_needed = False + else: + args.append('-DENABLE_CATALYST:BOOL=OFF') + + if '+libsim' in spec: + args.extend([ + '-DENABLE_LIBSIM:BOOL=ON', + '-DVISIT_DIR:PATH={0}'.format(spec['visit'].prefix), + '-DVTK_DIR:PATH={0}'.format(spec['vtk'].prefix) + ]) + vtk_dir_needed = False + else: + args.append('-DENABLE_LIBSIM:BOOL=OFF') + + vtkio_switch = 'ON' if '+vtkio' in spec else 'OFF' + args.append('-DENABLE_VTK_IO:BOOL={0}'.format(vtkio_switch)) + + python_switch = 'OFF' + if '+python' in spec: + python_switch = 'ON' + python_path = spec['python'].command.path + args.append('-DPYTHON_EXECUTABLE:FILEPATH={0}'.format(python_path)) + if spec.satisfies('@3:'): + args.append('-DSENSEI_PYTHON_VERSION=3') + args.append('-DENABLE_PYTHON:BOOL={0}'.format(python_switch)) + + if '+adios' in spec: + if spec.satisfies('@3:'): + args.append('-DENABLE_ADIOS1:BOOL=ON') + else: + args.append('-DENABLE_ADIOS:BOOL=ON') + args.append('-DADIOS_DIR:PATH={0}'.format(spec['adios'].prefix)) + else: + args.append('-DENABLE_ADIOS:BOOL=OFF') + + if '+hdf5' in spec: + args.extend([ + '-DENABLE_HDF5:BOOL=ON', + '-DHDF5_DIR:PATH={0}'.format(spec['hdf5'].prefix) + ]) + + if vtk_dir_needed: + args.append('-DVTK_DIR:PATH={0}'.format(spec['vtk'].prefix)) + + args.extend([ + '-DENABLE_PARALLEL3D:BOOL={0}'.format( + 'ON' if '+miniapps' in spec else 'OFF'), + '-DENABLE_OSCILLATORS:BOOL={0}'.format( + 'ON' if '+miniapps' in spec else 'OFF') + ]) + + return args diff --git a/var/spack/repos/builtin/packages/sentieon-genomics/package.py b/var/spack/repos/builtin/packages/sentieon-genomics/package.py index e53b191198..e58877abbc 100644 --- a/var/spack/repos/builtin/packages/sentieon-genomics/package.py +++ b/var/spack/repos/builtin/packages/sentieon-genomics/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,6 +24,7 @@ class SentieonGenomics(Package): homepage = "https://www.sentieon.com/" url = "file://{0}/sentieon-genomics-201808.01.tar.gz".format(os.getcwd()) + version('201808.07', sha256='fb66b18a7b99e44968eb2c3a6a5b761d6b1e70fba9f7dfc4e5db3a74ab3d3dd9') version('201808.01', sha256='6d77bcd5a35539549b28eccae07b19a3b353d027720536e68f46dcf4b980d5f7') # Licensing. diff --git a/var/spack/repos/builtin/packages/seqan/package.py b/var/spack/repos/builtin/packages/seqan/package.py index 96b4799efb..f70a6a7d52 100644 --- a/var/spack/repos/builtin/packages/seqan/package.py +++ b/var/spack/repos/builtin/packages/seqan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/seqkit/package.py b/var/spack/repos/builtin/packages/seqkit/package.py index 2a58be05b6..7ac7e979d9 100644 --- a/var/spack/repos/builtin/packages/seqkit/package.py +++ b/var/spack/repos/builtin/packages/seqkit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/seqprep/package.py b/var/spack/repos/builtin/packages/seqprep/package.py index cdb4b1fcb2..06ce717785 100644 --- a/var/spack/repos/builtin/packages/seqprep/package.py +++ b/var/spack/repos/builtin/packages/seqprep/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/seqtk/package.py b/var/spack/repos/builtin/packages/seqtk/package.py index 1e32dc6911..eab48389bb 100644 --- a/var/spack/repos/builtin/packages/seqtk/package.py +++ b/var/spack/repos/builtin/packages/seqtk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py index 7f2c10b084..4c762bf9a5 100644 --- a/var/spack/repos/builtin/packages/serf/package.py +++ b/var/spack/repos/builtin/packages/serf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sessreg/package.py b/var/spack/repos/builtin/packages/sessreg/package.py index bcdaf36000..8b0d762b05 100644 --- a/var/spack/repos/builtin/packages/sessreg/package.py +++ b/var/spack/repos/builtin/packages/sessreg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/setxkbmap/package.py b/var/spack/repos/builtin/packages/setxkbmap/package.py index 5ab188da5c..8f5093cbcf 100644 --- a/var/spack/repos/builtin/packages/setxkbmap/package.py +++ b/var/spack/repos/builtin/packages/setxkbmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sfcgal/package.py b/var/spack/repos/builtin/packages/sfcgal/package.py new file mode 100644 index 0000000000..021ba1bb97 --- /dev/null +++ b/var/spack/repos/builtin/packages/sfcgal/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Sfcgal(CMakePackage): + """ + SFCGAL is a C++ wrapper library around CGAL with the aim of supporting + ISO 19107:2013 and OGC Simple Features Access 1.2 for 3D operations. SFCGAL + provides standard compliant geometry types and operations, that can be + accessed from its C or C++ APIs. + """ + + homepage = "http://www.sfcgal.org/" + url = "https://github.com/Oslandia/SFCGAL/archive/v1.3.7.tar.gz" + + version('1.3.7', sha256='30ea1af26cb2f572c628aae08dd1953d80a69d15e1cac225390904d91fce031b') + + # Ref: http://oslandia.github.io/SFCGAL/installation.html + depends_on('cgal@4.3 +core') + depends_on('boost@1.54.0:1.69.0') + depends_on('mpfr@2.2.1:') + depends_on('gmp@4.2:') + + def cmake_args(self): + # It seems viewer is discontinued as of v1.3.0 + # https://github.com/Oslandia/SFCGAL/releases/tag/v1.3.0 + # Also, see https://github.com/Oslandia/SFCGAL-viewer + return ['-DSFCGAL_BUILD_VIEWER=OFF'] diff --git a/var/spack/repos/builtin/packages/sga/package.py b/var/spack/repos/builtin/packages/sga/package.py index 1a6eb2886b..5114f38cf4 100644 --- a/var/spack/repos/builtin/packages/sga/package.py +++ b/var/spack/repos/builtin/packages/sga/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/shadow/package.py b/var/spack/repos/builtin/packages/shadow/package.py index 052a21d521..99cef1fa47 100644 --- a/var/spack/repos/builtin/packages/shadow/package.py +++ b/var/spack/repos/builtin/packages/shadow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/shapeit/package.py b/var/spack/repos/builtin/packages/shapeit/package.py index 9eb398aa74..d0fa2e6d02 100644 --- a/var/spack/repos/builtin/packages/shapeit/package.py +++ b/var/spack/repos/builtin/packages/shapeit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/shared-mime-info/package.py b/var/spack/repos/builtin/packages/shared-mime-info/package.py index c6cabe1d48..25cfe11182 100644 --- a/var/spack/repos/builtin/packages/shared-mime-info/package.py +++ b/var/spack/repos/builtin/packages/shared-mime-info/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,8 +24,8 @@ class SharedMimeInfo(AutotoolsPackage): depends_on('gettext', type='build') depends_on('pkgconfig', type='build') - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path("XDG_DATA_DIRS", - self.prefix.share) - run_env.prepend_path("XDG_DATA_DIRS", - self.prefix.share) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path('XDG_DATA_DIRS', self.prefix.share) diff --git a/var/spack/repos/builtin/packages/shiny-server/package.py b/var/spack/repos/builtin/packages/shiny-server/package.py index d26ece50b1..87cefed936 100644 --- a/var/spack/repos/builtin/packages/shiny-server/package.py +++ b/var/spack/repos/builtin/packages/shiny-server/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -47,10 +47,8 @@ class ShinyServer(CMakePackage): bash('-c', 'bin/npm --python="$PYTHON" install') bash('-c', 'bin/node ./ext/node/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js --python="$PYTHON" rebuild') # noqa: E501 - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', - join_path(self.prefix, 'shiny-server', 'bin')) + def setup_run_environment(self, env): + env.prepend_path('PATH', join_path(self.prefix, 'shiny-server', 'bin')) # shiny comes with its own pandoc; hook it up... - run_env.prepend_path('PATH', - join_path(self.prefix, 'shiny-server', - 'ext', 'pandoc', 'static')) + env.prepend_path('PATH', join_path( + self.prefix, 'shiny-server', 'ext', 'pandoc', 'static')) diff --git a/var/spack/repos/builtin/packages/shocklibs/package.py b/var/spack/repos/builtin/packages/shocklibs/package.py index 55395897f5..49e9b76828 100644 --- a/var/spack/repos/builtin/packages/shocklibs/package.py +++ b/var/spack/repos/builtin/packages/shocklibs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/shoremap/package.py b/var/spack/repos/builtin/packages/shoremap/package.py index d7b51dafff..c03aa6e186 100644 --- a/var/spack/repos/builtin/packages/shoremap/package.py +++ b/var/spack/repos/builtin/packages/shoremap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/shortbred/package.py b/var/spack/repos/builtin/packages/shortbred/package.py index d94bf8c36c..e64fb340e9 100644 --- a/var/spack/repos/builtin/packages/shortbred/package.py +++ b/var/spack/repos/builtin/packages/shortbred/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,5 +28,5 @@ class Shortbred(Package): install('shortbred_quantify.py', prefix.bin) install_tree('src', prefix.src) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PYTHONPATH', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('PYTHONPATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/shortstack/package.py b/var/spack/repos/builtin/packages/shortstack/package.py index 315b1fb5a1..22de260298 100644 --- a/var/spack/repos/builtin/packages/shortstack/package.py +++ b/var/spack/repos/builtin/packages/shortstack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/showfont/package.py b/var/spack/repos/builtin/packages/showfont/package.py index ff3c7b8ae8..fa7bad6765 100644 --- a/var/spack/repos/builtin/packages/showfont/package.py +++ b/var/spack/repos/builtin/packages/showfont/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/shuffile/package.py b/var/spack/repos/builtin/packages/shuffile/package.py index 13ba8b96b4..1dc23f1a2c 100644 --- a/var/spack/repos/builtin/packages/shuffile/package.py +++ b/var/spack/repos/builtin/packages/shuffile/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,7 @@ class Shuffile(CMakePackage): """Shuffle files between MPI ranks""" homepage = "https://github.com/ECP-VeloC/shuffile" - url = "https://github.com/ECP-VeloC/shuffile/archive/v0.0.2.zip" + url = "https://github.com/ECP-VeloC/shuffile/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/shuffile.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/sickle/package.py b/var/spack/repos/builtin/packages/sickle/package.py index 2ccb2d54cf..5b61aea14e 100644 --- a/var/spack/repos/builtin/packages/sickle/package.py +++ b/var/spack/repos/builtin/packages/sickle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/siesta/package.py b/var/spack/repos/builtin/packages/siesta/package.py index 70d52a2607..17b8e5ec74 100644 --- a/var/spack/repos/builtin/packages/siesta/package.py +++ b/var/spack/repos/builtin/packages/siesta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,7 +23,7 @@ class Siesta(Package): depends_on('blas') depends_on('lapack') depends_on('scalapack') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-fortran') phases = ['configure', 'build', 'install'] @@ -40,7 +40,7 @@ class Siesta(Package): spec['blas'].libs), '--with-scalapack=%s' % spec['scalapack'].libs, '--with-netcdf=%s' % (spec['netcdf-fortran'].libs + - spec['netcdf'].libs), + spec['netcdf-c'].libs), # need to specify MPIFC explicitly below, otherwise # Intel's mpiifort is not found 'MPIFC=%s' % spec['mpi'].mpifc diff --git a/var/spack/repos/builtin/packages/signalp/package.py b/var/spack/repos/builtin/packages/signalp/package.py index fbaaff574e..4ed3336763 100644 --- a/var/spack/repos/builtin/packages/signalp/package.py +++ b/var/spack/repos/builtin/packages/signalp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -39,5 +39,5 @@ class Signalp(Package): install_tree('lib', prefix.lib) install_tree('syn', prefix.syn) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/signify/package.py b/var/spack/repos/builtin/packages/signify/package.py index 4c44ec8391..519556aa32 100644 --- a/var/spack/repos/builtin/packages/signify/package.py +++ b/var/spack/repos/builtin/packages/signify/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,5 +16,5 @@ class Signify(MakefilePackage): depends_on('libbsd@0.8:') - def setup_environment(self, spack_env, run_env): - spack_env.set('PREFIX', self.prefix) + def setup_build_environment(self, env): + env.set('PREFIX', self.prefix) diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py index a8588acc2e..420e8fe59e 100644 --- a/var/spack/repos/builtin/packages/silo/package.py +++ b/var/spack/repos/builtin/packages/silo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/simgrid/package.py b/var/spack/repos/builtin/packages/simgrid/package.py index 70869c7922..b62ed1923c 100644 --- a/var/spack/repos/builtin/packages/simgrid/package.py +++ b/var/spack/repos/builtin/packages/simgrid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/simmetrix-simmodsuite/package.py b/var/spack/repos/builtin/packages/simmetrix-simmodsuite/package.py new file mode 100644 index 0000000000..75ec47b39b --- /dev/null +++ b/var/spack/repos/builtin/packages/simmetrix-simmodsuite/package.py @@ -0,0 +1,242 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +def simmodsuite_releases(): + releases = [ + { + 'version': '14.0-191122', + 'components': { + 'gmadv': ['01cea5f7aff5e442ea544df054969740ad33e2ff4097cf02de31874d16a0c7c2', 'advmodel'], + 'msadapt': ['69839698f24969f97963869fd212bdcff0b5d52dd40ec3fdc710d878e43b527a', 'base'], + 'gmvoxel': ['bfea15e1fc5d258ed9db69132042a848ca81995e92bf265215e4b88d08a308a8', 'voxel'], + 'gmabstract': ['dccdcd4b71758e4110cd69b0befa7875e5c1f3871f87478410c6676da3f39092', 'abstract'], + 'fdcore': ['6981b2eb0c0143e6abc3ec29918fc3552f81018755770bf922d2491275984e1a', 'base'], + 'msparallelmesh': ['1e1a431ec9dd85354ff42c6a2a41df7fbe3dfe5d296f40105c4d3aa372639dc3', 'parallelmesh'], + 'mscore': ['bca80fcb2c86e7b6dc0259681ccd73197ce85c47f00f1910bd6b518fa0b3a092', 'base'], + 'discrete': ['430e5f2270864b1ab9c8dff75d2510147a0c5cde8af0828975d9e38661be3a35', 'discrete'], + 'gmimport': ['e83b3c43b7c695fa96ed42253a4b317a2882bcb8987fd3225c09492e353e49aa', 'import'], + 'pskrnl': ['31455cfce746b2339b3644f3890d4444014fb839654a9f576ec747d28ff6c1c4', 'parasolid'], + 'gmcore': ['af5d89b9ce266cac5b45f2bf96e1324e87e54c6e2f568bd5b6a85c41122d39e4', 'base'], + 'aciskrnl': ['764e5633e6d502951788accfb8c34ed59430a4779a44d1775fd67f9aab8a654a', 'acis'], + 'msparalleladapt': ['8ae607112958f6b9d319736c71a6597cf99a8a59ceed733f2a939cb9cfa6dd67', 'paralleladapt'], + 'psint': ['f6c90b2fe87e690b2cba20f357d03c5962fed91541d6b79e01dc25cb8f01d1e0', 'parasolid'], + 'msadv': ['f18a8285d539cb07b00fde06fe970d958eceabf2a10182bcca6c8ad1c074c395', 'adv'], + }, + 'docs': { + 'MeshSim': ['f3c475072f270ff49ac2f6639ca1cddb0642889648cbea7df1a3f1b85f7cac36', 'base'], + 'GeomSimVoxel': ['9f4ee5a8204fee1d899cb912e0379f8be7a826e81ca0a0d8a670a4b804ca1276', 'voxel'], + 'MeshSimAdvanced': ['8c8bc3709238e600e8938c7c345588f8947d89eae98a228b0d0e3d46f5f4c0d9', 'adv'], + 'GeomSimDiscreteModeling': ['4e8e26a88e8a5ad396a637597a52f5973d8f77abc0a5b99fa737caf37226d6cc', 'discrete'], + 'GeomSimAdvanced': ['5efb38317d6be7862ce34024922ca372b30691a30af820474e2e26e4c3055278', 'advmodel'], + 'GeomSimParasolid': ['6851bdaf6d96e7b2335fce3394825e9876800f0aba0a42644758dc1bd06f60fe', 'parasolid'], + 'GeomSimImport': ['d931ecfc332460c825b473c0950c7ae8ff9f845e0d1565f85bfd7698da5e6d26', 'import'], + 'ParallelMeshSim': ['0f0d235b25a660271e401488e412220f574b341dadb827f7b82f0e93172b5cdb', 'parallelmesh'], + 'ParallelMeshSimAdapt': ['7964ebbd7e8d971ea85fc5260e44f7e876da5ad474dc67d8d6fc939bfa5ba454', 'paralleladapt'], + 'GeomSimAcis': ['dea82efbc4e3043ecda163be792ef295057e08be17654a7783ce7ca5e786f950', 'acis'], + 'MeshSimAdapt': ['ee4d5595572c1fe1a0d78bd9b85c774a55e994c48170450d6c5f34b05fcf2411', 'base'], + 'FieldSim': ['6b09b4ab278911d3e9229fd4cd8dc92ba188f151d42d9d7b96d542aad2af1fac', 'base'], + 'GeomSim': ['0673823d649998367c0e427055911eae971bb6e8c76625882e7a7901f4d18c44', 'base'], + 'GeomSimDiscrete': ['58dfd33fc5cdd2ab24e9084377943f28d5ba68b8c017b11b71cde64c5e4f2113', 'discrete'], + 'GeomSimAbstract': ['16248cd2a0d133029eb4b79d61397da008e4d5b5c3eaf0161a0a44148b0bc519', 'abstract'], + } + }, + { + 'version': '12.0-191027', + 'components': { + 'gmadv': ['1a133523062974c4d9acb1d52baa3893dc891482aebaaeb79a7dc907461d5dbc', 'advmodel'], + 'fdcore': ['c3a89093f811cb489698d203dbe68ca910e6c67ea75c0a7aba73dd369508b9ec', 'base'], + 'mscore': ['a2f043278d45d8729020b663c66c57960fcec33dafd3d90db55f0a9e32723bce', 'base'], + 'msparallelmesh': ['2f6fd47d3c5c2f1ece4634985a522ac599d3cee20ad8a4623f252cc75aa32c4c', 'parallelmesh'], + 'msparalleladapt': ['8d288730b1300215a32f3b21624bd2e0e2d8a684fe928459757fcec7e0aeb7d3', 'paralleladapt'], + 'gmabstract': ['3b608f21e6c11db5bb48e49f9cd7e9d88aeec4feadebd778529a5c9d506d08c6', 'abstract'], + 'gmimport': ['fc1626c7b1522b90eaa3926e1253b84d28440c7df8634decdedb79b5229be800', 'import'], + 'discrete': ['a15ead08138f0c59c7ee46cd0d348d4f26e1b021d2580a134cf2b84a7337bcf9', 'discrete'], + 'aciskrnl': ['8773f00e08d237052c877e79d1a869214f59891e812d70df938b2a5e5423a96f', 'acis'], + 'msadv': ['41bdb9555ab9feb0891f0832a49fc29777d40957473f315e1c33e1c0077cba7d', 'adv'], + 'psint': ['b040ab48833eb2a748f757e2de6929f3002aa98db459ba92bd9a88e443e5cb07', 'parasolid'], + 'gmvoxel': ['19fba83c9c7eac20d9613236530fbae652dc8edef35233214f0f92b81c91a877', 'voxel'], + 'msadapt': ['1a752adb6724c3328fffb26f1aebed007d3c2a5df725cd29aa0cf0fdfda1f39a', 'base'], + 'gmcore': ['ec95bae84b36644e6e04cf0a6b4e813a51990d0a30519176ebb8a05f681af7f2', 'base'], + 'pskrnl': ['7b7b4952513e06c8c23aa8f7c1748f5c199d9af70ea06c4a359412237ed8ac1d', 'parasolid'], + }, + 'docs': { + 'FieldSim': ['5109d91fe61ccdaf0af5aa869aea9c38ec98760746ec3983d100f870cbb1cb63', 'base'], + 'ParallelMeshSim': ['a1e6618a77022a9580beac4c698dd4b9aa70f617a27db9ce13ab1f2388475290', 'parallelmesh'], + 'GeomSimAcis': ['f0319b32eb417fa9b237575d9b2dc1c061848888c36fd4da97d97cdbb3cf19c3', 'acis'], + 'GeomSimAbstract': ['c44023e6944522057c47925db49089031c7de9b67938ca6a987e04fadfeda9b7', 'abstract'], + 'GeomSimDiscrete': ['ad648752fa7d2dc1ce234a612e28ce84eb1f064a1decadf17b42e9fe56967350', 'discrete'], + 'MeshSimAdapt': ['dcb7d6ec74c910b41b5ae707d9fd4664fcb3a0fdb2c876caaa28a6f1cf701024', 'base'], + 'MeshSim': ['e5a8cb300b1e13b9f2733bf8b738872ffb37d9df15836a6ab264483c10000696', 'base'], + 'GeomSimParasolid': ['2bf33cc5b3879716437d45fde0a02caaa165e37d248d05b4b00708e76573a15e', 'parasolid'], + 'GeomSimImport': ['5309433dcdce660e062412f070719eefcc6299764e9b0169533ff343c9c9c406', 'import'], + 'ParallelMeshSimAdapt': ['2e8e0ceede3107b85dba9536f3bbf5e6959793073a5147548cfb01ca568c8da2', 'paralleladapt'], + 'GeomSimDiscreteModeling': ['ff88ec234b890315cc36539e3f73f4f977dab94160860950e7b7ee0303c9b55e', 'discrete'], + 'GeomSim': ['62ae33372f999d5e62a1b7b161ddd7de04c055adc85cfd258e088c95b76d5fef', 'base'], + 'GeomSimVoxel': ['7a624ddaebd833077511acac3efd4b4c1dab09bd9feff40aba0813182eeb262f', 'voxel'], + 'GeomSimAdvanced': ['f0ab801ddf3d701a4ac3f8c47900cc858a4488eb0fe2f663504ba260cd270d20', 'advmodel'], + 'MeshSimAdvanced': ['bb532027e4fcc311a7c376383da010aed5ee133a9122b186a4e5c7d0cf1d976b', 'adv'], + } + } + ] + return releases + + +def simmetrix_makecomponenturl(name): + """only supporting the linux libraries""" + prefix = "file://{0}/".format(os.getcwd()) + suffix = "-" + "linux64.tgz" + return prefix + name + suffix + + +def simmetrix_makedocurl(name): + """doc zip files are not os/arch specific""" + prefix = "file://{0}/".format(os.getcwd()) + suffix = '.zip' + return prefix + name + suffix + + +def simmetrix_setkernelcmakeprefixpath(spec, path, env): + if '+acis' in spec: + env.append_path('CMAKE_PREFIX_PATH', join_path(path, 'acisKrnl')) + env.append_path('LD_LIBRARY_PATH', join_path(path, 'acisKrnl')) + if '+parasolid' in spec: + env.append_path('CMAKE_PREFIX_PATH', join_path(path, 'psKrnl')) + env.append_path('LD_LIBRARY_PATH', join_path(path, 'psKrnl')) + + +def simmetrix_resource(name, url, sha256, condition): + # The tarballs/zips each have the same directory structure. Because of + # this, and the bug in spack described here: + # https://github.com/spack/spack/pull/3553#issuecomment-391424244 + # , they cannot be expanded into the source root directory. + # Once this is fixed the 'destination=name' argument can be removed. + resource( + name=name, + url=url, + sha256=sha256, + destination=name, + when=condition + ) + + +class SimmetrixSimmodsuite(Package): + """Simmetrix' Simulation Modeling Suite is a set of component software + toolkits that allow developers to easily implement geometry-based + simulation applications. + Each component of the Simulation Modeling Suite is designed to address + specific capabilities: + | MeshSim - automatic mesh generation + | FieldSim - simulation data management + | GeomSim - direct, untranslated access to geometry from a wide variety + of sources + """ + + homepage = "http://www.simmetrix.com/products/SimulationModelingSuite/main.html" + + license_required = True + license_vars = ['SIM_LICENSE_FILE'] + + variant('base', default=True, description='enable the base components') + variant('advmodel', default=False, description='enable advaced modeling') + variant('abstract', default=False, description='enable abstract modeling') + variant('voxel', default=False, description='enable voxel modeling') + variant('discrete', default=False, description='enable discrete modeling') + variant('acis', default=False, description='enable acis modeling') + variant('parasolid', default=False, description='enable parasolid modeling') + variant('granite', default=False, description='enable granite modeling') + variant('import', default=False, description='enable import modeling') + variant('adv', default=False, description='enable advanced meshing') + variant('parallelmesh', default=False, description='enable parallel meshing') + variant('paralleladapt', default=False, description='enable parallel adaptation') + + depends_on('mpi') + + oslib = 'x64_rhel7_gcc48' + + releases = simmodsuite_releases() + for release in releases: + # define the version using the mscore tarball + sim_version = release['version'] + main_pkg_name = 'mscore' + url = simmetrix_makecomponenturl(main_pkg_name) + sha256 = release['components'][main_pkg_name][0] + version(sim_version, sha256=sha256, url=url) + # define resources for the other tarballs + for name, atts in release['components'].items(): + # skip the tarball used for the version(...) call + if name == 'mscore': + continue + sha256 = atts[0] + feature = atts[1] + url = simmetrix_makecomponenturl(name) + condition = "@{0}+{1}".format(sim_version, feature) + simmetrix_resource(name, url, sha256, condition) + # define resources for the document zip files + for name, atts in release['docs'].items(): + sha256 = atts[0] + feature = atts[1] + url = simmetrix_makedocurl(name) + condition = "@{0}+{1}".format(sim_version, feature) + simmetrix_resource(name, url, sha256, condition) + + def setup_dependent_build_environment(self, env, dependent_spec): + archlib = join_path(prefix.lib, self.oslib) + env.append_path('CMAKE_PREFIX_PATH', archlib) + simmetrix_setkernelcmakeprefixpath(self.spec, archlib, env) + + def setup_run_environment(self, env): + archlib = join_path(prefix.lib, self.oslib) + env.append_path('CMAKE_PREFIX_PATH', archlib) + simmetrix_setkernelcmakeprefixpath(self.spec, archlib, env) + + def install(self, spec, prefix): + if not spec.satisfies('platform=linux'): + raise InstallError('Only the linux platform is supported') + source_path = self.stage.source_path + for release in simmodsuite_releases(): + simversion = release['version'] + if simversion != spec.version.string: + continue + for name, atts in release['components'].items(): + feature = atts[1] + if '+' + feature in spec: + if name == 'mscore': + install_tree(join_path(source_path, 'lib'), prefix.lib) + install_tree( + join_path(source_path, 'include'), + prefix.include) + else: + path = join_path( + source_path, + name, + self.version.string) + install_tree(path, prefix) + for name, atts in release['docs'].items(): + feature = atts[1] + if '+' + feature in spec: + path = join_path( + source_path, + name, + self.version.string) + install_tree(path, prefix) + + workdir = prefix.code.PartitionWrapper + if '+parallelmesh' in spec: + with working_dir(workdir): + mpi_id = spec['mpi'].name + spec['mpi'].version.string + # build the wrapper lib + make("-f", "Makefile.custom", + "CC=%s" % spec['mpi'].mpicc, + "CXX=%s" % spec['mpi'].mpicxx, + "PARALLEL=%s" % mpi_id, + "PQUAL=-%s" % mpi_id, + "OPTFLAGS=-O2 -DNDEBUG " + self.compiler.pic_flag) + libname = 'libSimPartitionWrapper-' + mpi_id + '.a' + wrapperlibpath = join_path(workdir, 'lib', libname) + install(wrapperlibpath, join_path(prefix.lib, self.oslib)) diff --git a/var/spack/repos/builtin/packages/simplemoc/package.py b/var/spack/repos/builtin/packages/simplemoc/package.py index 4735eed7c7..0745910d9c 100644 --- a/var/spack/repos/builtin/packages/simplemoc/package.py +++ b/var/spack/repos/builtin/packages/simplemoc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/simul/package.py b/var/spack/repos/builtin/packages/simul/package.py index 5d99fd021e..90f5922403 100644 --- a/var/spack/repos/builtin/packages/simul/package.py +++ b/var/spack/repos/builtin/packages/simul/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/simulationio/package.py b/var/spack/repos/builtin/packages/simulationio/package.py index 51b43719d8..352d06e19c 100644 --- a/var/spack/repos/builtin/packages/simulationio/package.py +++ b/var/spack/repos/builtin/packages/simulationio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class Simulationio(CMakePackage): """SimulationIO: Efficient and convenient I/O for large PDE simulations""" homepage = "https://github.com/eschnett/SimulationIO" - url = "https://github.com/eschnett/SimulationIO/archive/version/0.1.0.tar.gz" + url = "https://github.com/eschnett/SimulationIO/archive/version/9.0.1.tar.gz" git = "https://github.com/eschnett/SimulationIO.git" version('develop', branch='master') @@ -23,7 +23,7 @@ class Simulationio(CMakePackage): variant('pic', default=True, description="Produce position-independent code") - depends_on('hdf5 +cxx @:1.10.0-patch1') + depends_on('hdf5 +cxx @1.10.1:') depends_on('julia', when='+julia', type=('build', 'run')) depends_on('py-h5py', when='+python', type=('build', 'run')) depends_on('py-numpy', when='+python', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/singularity-legacy/package.py b/var/spack/repos/builtin/packages/singularity-legacy/package.py index c8f40f46ce..d70eff6b10 100644 --- a/var/spack/repos/builtin/packages/singularity-legacy/package.py +++ b/var/spack/repos/builtin/packages/singularity-legacy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/singularity/package.py b/var/spack/repos/builtin/packages/singularity/package.py index 43e40ac039..e97f18ce83 100644 --- a/var/spack/repos/builtin/packages/singularity/package.py +++ b/var/spack/repos/builtin/packages/singularity/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -27,6 +27,7 @@ class Singularity(MakefilePackage): maintainers = ['ArangoGutierrez', 'alalazo'] version('master', branch='master') + version('3.5.2', sha256='f9c21e289377a4c40ed7a78a0c95e1ff416dec202ed49a6c616dd2c37700eab8') version('3.4.1', sha256='638fd7cc5ab2a20e779b8768f73baf21909148339d6c4edf6ff61349c53a70c2') version('3.4.0', sha256='eafb27f1ffbed427922ebe2b5b95d1c9c09bfeb897518867444fe230e3e35e41') version('3.3.0', sha256='070530a472e7e78492f1f142c8d4b77c64de4626c4973b0589f0d18e1fcf5b4f') @@ -87,10 +88,9 @@ class Singularity(MakefilePackage): build_targets = ['-C', 'builddir', 'parallel=False'] install_targets = ['install', '-C', 'builddir', 'parallel=False'] - def setup_environment(self, spack_env, run_env): - # Point GOPATH at the top of the staging dir for the build - # step. - spack_env.prepend_path('GOPATH', self.gopath) + def setup_build_environment(self, env): + # Point GOPATH at the top of the staging dir for the build step. + env.prepend_path('GOPATH', self.gopath) # `singularity` has a fixed path where it will look for # mksquashfs. If it lives somewhere else you need to specify the diff --git a/var/spack/repos/builtin/packages/sirius/package.py b/var/spack/repos/builtin/packages/sirius/package.py index 900077c9ac..5ac903e263 100644 --- a/var/spack/repos/builtin/packages/sirius/package.py +++ b/var/spack/repos/builtin/packages/sirius/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,9 +14,19 @@ class Sirius(CMakePackage, CudaPackage): homepage = "https://github.com/electronic-structure/SIRIUS" url = "https://github.com/electronic-structure/SIRIUS/archive/v6.1.5.tar.gz" list_url = "https://github.com/electronic-structure/SIRIUS/releases" + git = "https://github.com/electronic-structure/SIRIUS.git" - version('6.1.5', sha256='379f0a2e5208fd6d91c2bd4939c3a5c40002975fb97652946fa1bfe4a3ef97cb') + version('develop', branch='develop') + version('master', branch='master') + + version('6.4.3', sha256='4d1effeadb84b3e1efd7d9ac88018ef567aa2e0aa72e1112f0abf2e493e2a189') + version('6.4.2', sha256='40b9b66deebb6538fc0f4cd802554d0d763ea6426b9b2f0e8db8dc617e494479') + version('6.4.1', sha256='86f25c71517952a63e92e0a9bcf66d27e4afb2b0d67cf84af480f116b8e7f53c') + version('6.4.0', sha256='bc61758b71dd2996e2ff515b8c3560b2c69c00931cb2811a163a31bcfea4436e') + version('6.3.4', sha256='8839e988b4bb6ef99b6180f7fba03a5537e31fce51bb3e4c2298b513d6a07e0a') + version('6.3.3', sha256='7ba30a4e5c9a545433251211454ec0d59b74ba8941346057bc7de11e7f6886f7') version('6.3.2', sha256='1723e5ad338dad9a816369a6957101b2cae7214425406b12e8712c82447a7ee5') + version('6.1.5', sha256='379f0a2e5208fd6d91c2bd4939c3a5c40002975fb97652946fa1bfe4a3ef97cb') variant('shared', default=False, description="Build shared libraries") variant('openmp', default=True, description="Build with OpenMP support") @@ -25,8 +35,12 @@ class Sirius(CMakePackage, CudaPackage): variant('elpa', default=False, description="Use ELPA") variant('vdwxc', default=False, description="Enable libvdwxc support") variant('scalapack', default=False, description="Enable scalapack support") + variant('magma', default=False, description="Enable MAGMA support") + variant('build_type', default='Release', + description='CMake build type', + values=('Debug', 'Release', 'RelWithDebInfo')) - depends_on('python') + depends_on('python', type=('build', 'run')) depends_on('mpi') depends_on('gsl') depends_on('lapack') @@ -35,19 +49,29 @@ class Sirius(CMakePackage, CudaPackage): depends_on('spglib') depends_on('hdf5+hl') depends_on('pkgconfig', type='build') - depends_on('py-mpi4py', when='+python') - depends_on('py-pybind11', when='+python') - + depends_on('py-numpy', when='+python', type=('build', 'run')) + depends_on('py-scipy', when='+python', type=('build', 'run')) + depends_on('py-h5py', when='+python', type=('build', 'run')) + depends_on('py-mpi4py', when='+python', type=('build', 'run')) + depends_on('py-pyyaml', when='+python', type=('build', 'run')) + depends_on('py-mpi4py', when='+python', type=('build', 'run')) + depends_on('py-voluptuous', when='+python', type=('build', 'run')) + depends_on('py-pybind11', when='+python', type=('build', 'run')) + depends_on('magma', when='+magma') + + depends_on('spfft', when='@6.4.0:~cuda') + depends_on('spfft+cuda', when='@6.4.0:+cuda') depends_on('elpa+openmp', when='+elpa+openmp') depends_on('elpa~openmp', when='+elpa~openmp') depends_on('libvdwxc+mpi', when='+vdwxc') depends_on('scalapack', when='+scalapack') depends_on('cuda', when='+cuda') + extends('python', when='+python') conflicts('+shared', when='@6.3.0:') # option to build shared libraries has been removed # TODO: - # add support for MAGMA, CRAY_LIBSCI, ROCm, testing + # add support for CRAY_LIBSCI, ROCm, testing patch("strip-spglib-include-subfolder.patch", when='@6.1.5') patch("link-libraries-fortran.patch", when='@6.1.5') @@ -96,6 +120,7 @@ class Sirius(CMakePackage, CudaPackage): args = [ _def('+openmp'), _def('+elpa'), + _def('+magma'), _def('+vdwxc'), _def('+scalapack'), _def('+fortran', 'CREATE_FORTRAN_BINDINGS'), @@ -137,7 +162,7 @@ class Sirius(CMakePackage, CudaPackage): if '+cuda' in spec: cuda_arch = spec.variants['cuda_arch'].value - if cuda_arch: + if cuda_arch[0] != 'none': args += [ '-DCMAKE_CUDA_FLAGS=-arch=sm_{0}'.format(cuda_arch[0]) ] diff --git a/var/spack/repos/builtin/packages/skilion-onedrive/package.py b/var/spack/repos/builtin/packages/skilion-onedrive/package.py index 7c948df36e..5349544227 100644 --- a/var/spack/repos/builtin/packages/skilion-onedrive/package.py +++ b/var/spack/repos/builtin/packages/skilion-onedrive/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/skopeo/package.py b/var/spack/repos/builtin/packages/skopeo/package.py index 475bfff26a..4f0372639c 100644 --- a/var/spack/repos/builtin/packages/skopeo/package.py +++ b/var/spack/repos/builtin/packages/skopeo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,6 +14,7 @@ class Skopeo(MakefilePackage): homepage = "https://github.com/containers/skopeo" url = "https://github.com/containers/skopeo/archive/v0.1.39.tar.gz" + version('0.1.40', sha256='ee1e33245938fcb622f5864fac860e2d8bfa2fa907af4b5ffc3704ed0db46bbf') version('0.1.39', sha256='e9d70f7f7b891675a816f06a22df0490285ad20eefbd91f5da69ca12f56c29f2') version('0.1.38', sha256='104ceb9c582dc5c3a49dd1752c4c326bba03f2f801596f089372e831f48ed705') version('0.1.37', sha256='49c0c1b2c2f32422d3230f827ae405fc554fb34af41a54e59b2121ac1500505d') diff --git a/var/spack/repos/builtin/packages/sl/package.py b/var/spack/repos/builtin/packages/sl/package.py index a3c858d245..2b3e9bb16a 100644 --- a/var/spack/repos/builtin/packages/sl/package.py +++ b/var/spack/repos/builtin/packages/sl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/slate/package.py b/var/spack/repos/builtin/packages/slate/package.py index 85f31667c5..f8b33d7372 100644 --- a/var/spack/repos/builtin/packages/slate/package.py +++ b/var/spack/repos/builtin/packages/slate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,11 +31,10 @@ class Slate(Package): conflicts('%gcc@:5') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if('+cuda' in self.spec): - spack_env.prepend_path('CPATH', self.spec['cuda'].prefix.include) - spack_env.prepend_path('CPATH', self.spec['intel-mkl'].prefix - + '/mkl/include') + env.prepend_path('CPATH', self.spec['cuda'].prefix.include) + env.prepend_path('CPATH', self.spec['intel-mkl'].prefix.mkl.include) def install(self, spec, prefix): f_cuda = "1" if spec.variants['cuda'].value else "0" diff --git a/var/spack/repos/builtin/packages/sleef/package.py b/var/spack/repos/builtin/packages/sleef/package.py index 8718026346..4573e8f196 100644 --- a/var/spack/repos/builtin/packages/sleef/package.py +++ b/var/spack/repos/builtin/packages/sleef/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py index 8313705cbf..2c72af0342 100644 --- a/var/spack/repos/builtin/packages/slepc/package.py +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,7 @@ class Slepc(Package): homepage = "http://slepc.upv.es" url = "http://slepc.upv.es/download/distrib/slepc-3.6.2.tar.gz" - git = "https://bitbucket.org/slepc/slepc.git" + git = "https://gitlab.com/slepc/slepc.git" maintainers = ['joseeroman', 'balay'] @@ -101,6 +101,6 @@ class Slepc(Package): make('install', parallel=False) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): # set up SLEPC_DIR for everyone using SLEPc package - spack_env.set('SLEPC_DIR', self.prefix) + env.set('SLEPC_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/slurm/package.py b/var/spack/repos/builtin/packages/slurm/package.py index 94a1c90a80..bfa6621f07 100644 --- a/var/spack/repos/builtin/packages/slurm/package.py +++ b/var/spack/repos/builtin/packages/slurm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/smalt/package.py b/var/spack/repos/builtin/packages/smalt/package.py index 54d968db71..1e6e11f365 100644 --- a/var/spack/repos/builtin/packages/smalt/package.py +++ b/var/spack/repos/builtin/packages/smalt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/smof/package.py b/var/spack/repos/builtin/packages/smof/package.py index d2a2409f59..41d41aeac0 100644 --- a/var/spack/repos/builtin/packages/smof/package.py +++ b/var/spack/repos/builtin/packages/smof/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/smproxy/package.py b/var/spack/repos/builtin/packages/smproxy/package.py index 24652e99c6..e76e32e6c9 100644 --- a/var/spack/repos/builtin/packages/smproxy/package.py +++ b/var/spack/repos/builtin/packages/smproxy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/snakemake/package.py b/var/spack/repos/builtin/packages/snakemake/package.py index 5ccca9bbc3..08fa3b36aa 100644 --- a/var/spack/repos/builtin/packages/snakemake/package.py +++ b/var/spack/repos/builtin/packages/snakemake/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/snap-berkeley/package.py b/var/spack/repos/builtin/packages/snap-berkeley/package.py index 51694c94b3..90d970e277 100644 --- a/var/spack/repos/builtin/packages/snap-berkeley/package.py +++ b/var/spack/repos/builtin/packages/snap-berkeley/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/snap-korf/package.py b/var/spack/repos/builtin/packages/snap-korf/package.py index 930d8c28e7..c028c69796 100644 --- a/var/spack/repos/builtin/packages/snap-korf/package.py +++ b/var/spack/repos/builtin/packages/snap-korf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -38,6 +38,6 @@ class SnapKorf(MakefilePackage): install_tree('HMM', prefix.HMM) install_tree('DNA', prefix.DNA) - def setup_environment(self, spack_env, run_env): - run_env.set('ZOE', self.prefix) - run_env.prepend_path('PATH', self.prefix) + def setup_run_environment(self, env): + env.set('ZOE', self.prefix) + env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/snap/package.py b/var/spack/repos/builtin/packages/snap/package.py index 26239d5ffe..3815d3ac64 100644 --- a/var/spack/repos/builtin/packages/snap/package.py +++ b/var/spack/repos/builtin/packages/snap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/snappy/package.py b/var/spack/repos/builtin/packages/snappy/package.py index 460cc21963..3516c53d1d 100644 --- a/var/spack/repos/builtin/packages/snappy/package.py +++ b/var/spack/repos/builtin/packages/snappy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/snbone/package.py b/var/spack/repos/builtin/packages/snbone/package.py index ab556517eb..a349593b5a 100644 --- a/var/spack/repos/builtin/packages/snbone/package.py +++ b/var/spack/repos/builtin/packages/snbone/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sniffles/package.py b/var/spack/repos/builtin/packages/sniffles/package.py index b6dca88203..fafa8a1f9d 100644 --- a/var/spack/repos/builtin/packages/sniffles/package.py +++ b/var/spack/repos/builtin/packages/sniffles/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/snpeff/package.py b/var/spack/repos/builtin/packages/snpeff/package.py index d0c60c586e..d2e4d1cede 100644 --- a/var/spack/repos/builtin/packages/snpeff/package.py +++ b/var/spack/repos/builtin/packages/snpeff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/snphylo/package.py b/var/spack/repos/builtin/packages/snphylo/package.py index ae40685066..04eaf44d0e 100644 --- a/var/spack/repos/builtin/packages/snphylo/package.py +++ b/var/spack/repos/builtin/packages/snphylo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -33,5 +33,5 @@ class Snphylo(Package): bash('./setup.sh', input=f) install_tree('.', prefix) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.spec.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/snptest/package.py b/var/spack/repos/builtin/packages/snptest/package.py index ae41ac24ce..eb47242a29 100644 --- a/var/spack/repos/builtin/packages/snptest/package.py +++ b/var/spack/repos/builtin/packages/snptest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/soapdenovo-trans/package.py b/var/spack/repos/builtin/packages/soapdenovo-trans/package.py index f21b371a44..12497e05cc 100644 --- a/var/spack/repos/builtin/packages/soapdenovo-trans/package.py +++ b/var/spack/repos/builtin/packages/soapdenovo-trans/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/soapdenovo2/package.py b/var/spack/repos/builtin/packages/soapdenovo2/package.py index 65a8210ddf..e14f3545cc 100644 --- a/var/spack/repos/builtin/packages/soapdenovo2/package.py +++ b/var/spack/repos/builtin/packages/soapdenovo2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sofa-c/package.py b/var/spack/repos/builtin/packages/sofa-c/package.py index 5b926c33ef..f953033781 100644 --- a/var/spack/repos/builtin/packages/sofa-c/package.py +++ b/var/spack/repos/builtin/packages/sofa-c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sollve/package.py b/var/spack/repos/builtin/packages/sollve/package.py new file mode 100644 index 0000000000..3b605580be --- /dev/null +++ b/var/spack/repos/builtin/packages/sollve/package.py @@ -0,0 +1,309 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Sollve(CMakePackage): + """The SOLLVE Project aims at scaling OpenMP by leveraging LLVM for exascale + performance and portability of applications. This package provides a + collection of Clang/LLVM compilers and an OpenMP runtime library. + """ + + homepage = 'https://www.bnl.gov/compsci/projects/SOLLVE/' + git = "https://github.com/SOLLVE/llvm.git" + + family = 'compiler' # Used by lmod + + # NOTE: The debug version of LLVM is an order of magnitude larger than + # the release version, and may take up 20-30 GB of space. If you want + # to save space, build with `build_type=Release`. + + variant('clang', default=True, + description="Build the LLVM C/C++/Objective-C compiler frontend") + variant('lldb', default=True, description="Build the LLVM debugger") + variant('lld', default=True, description="Build the LLVM linker") + variant('internal_unwind', default=True, + description="Build the libcxxabi libunwind") + variant('polly', default=True, + description="Build the LLVM polyhedral optimization plugin") + variant('libcxx', default=True, + description="Build the LLVM C++ standard library") + variant('compiler-rt', default=True, + description="Build LLVM compiler runtime, including sanitizers") + variant('gold', default=True, + description="Add support for LTO with the gold linker plugin") + variant('shared_libs', default=False, + description="Build all components as shared libraries, faster, " + "less memory to build, less stable") + variant('link_dylib', default=False, + description="Build and link the libLLVM shared library rather " + "than static") + variant('all_targets', default=False, + description="Build all supported targets, default targets " + "<current arch>,NVPTX,AMDGPU,CppBackend") + variant('build_type', default='Release', + description='CMake build type', + values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel')) + variant('omp_tsan', default=False, + description="Build with OpenMP capable thread sanitizer") + variant('python', default=False, description="Install python bindings") + variant('argobots', default=True, description="Use Argobots in BOLT") + extends('python', when='+python') + + # Build dependency + depends_on('cmake@3.4.3:', type='build') + depends_on('python', type='build') + + # openmp dependencies + depends_on('perl-data-dumper', type=('build')) + depends_on('argobots', when='+argobots') + + # lldb dependencies + depends_on('ncurses', when='+lldb') + depends_on('swig', when='+lldb') + depends_on('libedit', when='+lldb') + depends_on('py-six', when='+lldb +python', type=('build', 'run')) + + # gold support + depends_on('binutils+gold', when='+gold') + + # develop version. + version("develop") + resource(name='compiler-rt', + svn='http://llvm.org/svn/llvm-project/compiler-rt/trunk', + destination='projects', when='@develop+compiler-rt', + placement='compiler-rt') + resource(name='openmp', git='https://github.com/pmodels/bolt.git', + destination='projects', when='@develop+clang', placement='openmp') + resource(name='polly', git='https://github.com/SOLLVE/polly.git', + destination='tools', when='@develop+polly', placement='polly') + resource(name='libcxx', git='https://github.com/SOLLVE/libcxx.git', + destination='projects', when='@develop+libcxx', + placement='libcxx') + resource(name='libcxxabi', git='https://github.com/SOLLVE/libcxxabi.git', + destination='projects', when='@develop+libcxx', + placement='libcxxabi') + resource(name='cfe', git='https://github.com/SOLLVE/clang.git', + destination='tools', when='@develop+clang', placement='clang') + resource(name='lldb', svn='http://llvm.org/svn/llvm-project/lldb/trunk', + destination='tools', when='@develop+lldb', placement='lldb') + resource(name='lld', svn='http://llvm.org/svn/llvm-project/lld/trunk', + destination='tools', when='@develop+lld', placement='lld') + resource(name='libunwind', + svn='http://llvm.org/svn/llvm-project/libunwind/trunk', + destination='projects', when='@develop+internal_unwind', + placement='libunwind') + + # 1.0a2 based on LLVM 9.0+ + version("1.0a2", commit="cb4343bda9e57076a74dee23236ac9737e07594f") + resource(name='compiler-rt', + svn='https://llvm.org/svn/llvm-project/compiler-rt/trunk', + revision=373130, destination='projects', + when='@1.0a2+compiler-rt', placement='compiler-rt') + resource(name='openmp', git='https://github.com/pmodels/bolt.git', + commit="0a0033b09cfb672c119cf41eeb54eda7664681bc", + destination='projects', when='@1.0a2+clang', placement='openmp') + resource(name='polly', git='https://github.com/SOLLVE/polly.git', + commit="96168ae6fb436e95cd756950855a57b895070047", + destination='tools', when='@1.0a2+polly', placement='polly') + resource(name='libcxx', git='https://github.com/SOLLVE/libcxx.git', + commit="9637883af0357acf02c87fae5efb71661d21f516", + destination='projects', when='@1.0a2+libcxx', placement='libcxx') + resource(name='libcxxabi', git='https://github.com/SOLLVE/libcxxabi.git', + commit="3ed912b3b014a3af862c3b2cd0795ad43afadf31", + destination='projects', when='@1.0a2+libcxx', + placement='libcxxabi') + resource(name='cfe', git='https://github.com/SOLLVE/clang.git', + commit="774bc67094a1baa2dbdab705b0cac061048a062e", + destination='tools', when='@1.0a2+clang', placement='clang') + resource(name='lldb', + svn='http://llvm.org/svn/llvm-project/lldb/trunk', + revision=373127, destination='tools', when='@1.0a2+lldb', + placement='lldb') + resource(name='lld', svn='http://llvm.org/svn/llvm-project/lld/trunk/', + revision=373077, destination='tools', when='@1.0a2+lld', + placement='lld') + resource(name='libunwind', + svn='http://llvm.org/svn/llvm-project/libunwind/trunk', + revision=372427, destination='projects', + when='@1.0a2+internal_unwind', placement='libunwind') + + conflicts('+clang_extra', when='~clang') + conflicts('+lldb', when='~clang') + + conflicts('%gcc@:5.0.999') + conflicts('+omp_tsan') + + @run_before('cmake') + def check_darwin_lldb_codesign_requirement(self): + if not self.spec.satisfies('+lldb platform=darwin'): + return + codesign = which('codesign') + mkdir('tmp') + llvm_check_file = join_path('tmp', 'llvm_check') + copy('/usr/bin/false', llvm_check_file) + + try: + codesign('-f', '-s', 'lldb_codesign', '--dryrun', + llvm_check_file) + + except ProcessError: + explanation = ('The "lldb_codesign" identity must be available' + ' to build LLVM with LLDB. See https://llvm.org/' + 'svn/llvm-project/lldb/trunk/docs/code-signing' + '.txt for details on how to create this identity.') + raise RuntimeError(explanation) + + def setup_build_environment(self, env): + env.append_flags('CXXFLAGS', self.compiler.cxx11_flag) + + def setup_run_environment(self, env): + if '+clang' in self.spec: + env.set('CC', join_path(self.spec.prefix.bin, 'clang')) + env.set('CXX', join_path(self.spec.prefix.bin, 'clang++')) + + def cmake_args(self): + spec = self.spec + cmake_args = [ + '-DLLVM_REQUIRES_RTTI:BOOL=ON', + '-DLLVM_ENABLE_RTTI:BOOL=ON', + '-DLLVM_ENABLE_EH:BOOL=ON', + '-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp', + '-DPYTHON_EXECUTABLE:PATH={0}'.format(spec['python'].command.path), + ] + + # TODO: Instead of unconditionally disabling CUDA, add a "cuda" variant + # (see TODO above), and set the paths if enabled. + cmake_args.extend([ + '-DCUDA_TOOLKIT_ROOT_DIR:PATH=IGNORE', + '-DCUDA_SDK_ROOT_DIR:PATH=IGNORE', + '-DCUDA_NVCC_EXECUTABLE:FILEPATH=IGNORE', + '-DLIBOMPTARGET_DEP_CUDA_DRIVER_LIBRARIES:STRING=IGNORE']) + + if '+gold' in spec: + cmake_args.append('-DLLVM_BINUTILS_INCDIR=' + + spec['binutils'].prefix.include) + + if '+polly' in spec: + cmake_args.append('-DLINK_POLLY_INTO_TOOLS:Bool=ON') + else: + cmake_args.extend(['-DLLVM_EXTERNAL_POLLY_BUILD:Bool=OFF', + '-DLLVM_TOOL_POLLY_BUILD:Bool=OFF', + '-DLLVM_POLLY_BUILD:Bool=OFF', + '-DLLVM_POLLY_LINK_INTO_TOOLS:Bool=OFF']) + + if '+python' in spec and '+lldb' in spec: + cmake_args.append('-DLLDB_USE_SYSTEM_SIX:Bool=TRUE') + else: + cmake_args.append('-DLLDB_USE_SYSTEM_SIX:Bool=FALSE') + + if '+clang' in spec: + cmake_args.append('-DLLVM_EXTERNAL_CLANG_BUILD:Bool=ON') + else: + cmake_args.append('-DLLVM_EXTERNAL_CLANG_BUILD:Bool=OFF') + + if '+lldb' in spec: + cmake_args.extend(['-DLLVM_EXTERNAL_LLDB_BUILD:Bool=ON', + '-DLLVM_TOOL_LLDB_BUILD:Bool=ON']) + else: + cmake_args.extend(['-DLLVM_EXTERNAL_LLDB_BUILD:Bool=OFF', + '-DLLVM_TOOL_LLDB_BUILD:Bool=OFF']) + + if '+lld' in spec: + cmake_args.append('-DLLVM_TOOL_LLD_BUILD:Bool=ON') + else: + cmake_args.append('-DLLVM_TOOL_LLD_BUILD:Bool=OFF') + + if '+internal_unwind' in spec: + cmake_args.append('-DLLVM_EXTERNAL_LIBUNWIND_BUILD:Bool=ON') + else: + cmake_args.append('-DLLVM_EXTERNAL_LIBUNWIND_BUILD:Bool=OFF') + + if '+libcxx' in spec: + cmake_args.append('-DCLANG_DEFAULT_CXX_STDLIB=libc++') + cmake_args.append('-DLLVM_EXTERNAL_LIBCXX_BUILD:Bool=ON') + cmake_args.append('-DLLVM_EXTERNAL_LIBCXXABI_BUILD:Bool=ON') + else: + cmake_args.append('-DLLVM_EXTERNAL_LIBCXX_BUILD:Bool=OFF') + cmake_args.append('-DLLVM_EXTERNAL_LIBCXXABI_BUILD:Bool=OFF') + + if '+compiler-rt' in spec: + cmake_args.append('-DLLVM_EXTERNAL_COMPILER_RT_BUILD:Bool=ON') + else: + cmake_args.append('-DLLVM_EXTERNAL_COMPILER_RT_BUILD:Bool=OFF') + + if '+shared_libs' in spec: + cmake_args.append('-DBUILD_SHARED_LIBS:Bool=ON') + else: + cmake_args.append('-DBUILD_SHARED_LIBS:Bool=OFF') + + if '+link_dylib' in spec: + cmake_args.append('-DLLVM_LINK_LLVM_DYLIB:Bool=ON') + else: + cmake_args.append('-DLLVM_LINK_LLVM_DYLIB:Bool=OFF') + + if '+all_targets' not in spec: # all is default on cmake + targets = [] + if spec.target.family == 'x86' or spec.target.family == 'x86_64': + targets.append('X86') + elif spec.target.family == 'arm': + targets.append('ARM') + elif spec.target.family == 'aarch64': + targets.append('AArch64') + elif (spec.target.family == 'sparc' or + spec.target.family == 'sparc64'): + targets.append('Sparc') + elif (spec.target.family == 'ppc64' or + spec.target.family == 'ppc64le' or + spec.target.family == 'ppc' or + spec.target.family == 'ppcle'): + targets.append('PowerPC') + + cmake_args.append( + '-DLLVM_TARGETS_TO_BUILD:STRING=' + ';'.join(targets)) + + if '+omp_tsan' in spec: + cmake_args.append('-DLIBOMP_TSAN_SUPPORT=ON') + else: + cmake_args.append('-DLIBOMP_TSAN_SUPPORT=OFF') + + if '+argobots' in spec: + cmake_args.extend([ + '-DLIBOMP_USE_ITT_NOTIFY=OFF', + '-DLIBOMP_USE_ARGOBOTS=ON', + '-DLIBOMP_ARGOBOTS_INSTALL_DIR=' + spec['argobots'].prefix]) + else: + # LIBOMP_USE_ITT_NOTIFY should be set to a default value. + cmake_args.append('-DLIBOMP_USE_ARGOBOTS=OFF') + + if self.compiler.name == 'gcc': + gcc_prefix = ancestor(self.compiler.cc, 2) + cmake_args.append('-DGCC_INSTALL_PREFIX=' + gcc_prefix) + + if spec.satisfies('platform=linux'): + cmake_args.append('-DCMAKE_BUILD_WITH_INSTALL_RPATH=1') + + return cmake_args + + @run_before('build') + def pre_install(self): + with working_dir(self.build_directory): + # When building shared libraries these need to be installed first + make('install-LLVMTableGen') + if self.spec.version >= Version('4.0.0'): + # LLVMDemangle target was added in 4.0.0 + make('install-LLVMDemangle') + make('install-LLVMSupport') + + @run_after('install') + def post_install(self): + if '+clang' in self.spec and '+python' in self.spec: + install_tree( + 'tools/clang/bindings/python/clang', + join_path(site_packages_dir, 'clang')) + + with working_dir(self.build_directory): + install_tree('bin', self.prefix.libexec.llvm) diff --git a/var/spack/repos/builtin/packages/somatic-sniper/package.py b/var/spack/repos/builtin/packages/somatic-sniper/package.py index a148459687..792c8551cb 100644 --- a/var/spack/repos/builtin/packages/somatic-sniper/package.py +++ b/var/spack/repos/builtin/packages/somatic-sniper/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sortmerna/package.py b/var/spack/repos/builtin/packages/sortmerna/package.py index afdd5b8167..3369f9b3a8 100644 --- a/var/spack/repos/builtin/packages/sortmerna/package.py +++ b/var/spack/repos/builtin/packages/sortmerna/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sosflow/package.py b/var/spack/repos/builtin/packages/sosflow/package.py index f1eaf23b9b..161eed24dc 100644 --- a/var/spack/repos/builtin/packages/sosflow/package.py +++ b/var/spack/repos/builtin/packages/sosflow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,14 +21,15 @@ class Sosflow(CMakePackage): depends_on('pkgconfig') depends_on('mpi') - def setup_environment(self, spack_env, run_env): - spack_env.set('SOS_HOST_KNOWN_AS', 'SPACK-SOS-BUILD') - spack_env.set('SOS_HOST_NODE_NAME', 'SPACK-SOS-NODE') - spack_env.set('SOS_HOST_DETAILED', 'SPACK-SOS-DETAILED') - - run_env.set('SOS_ROOT', self.spec.prefix) - run_env.set('SOS_BUILD_DIR', self.spec.prefix) - run_env.set('SOS_CMD_PORT', '22500') - run_env.set('SOS_WORK', env['HOME']) - run_env.set('SOS_EVPATH_MEETUP', env['HOME']) - run_env.set('SOS_ENV_SET', 'true') + def setup_build_environment(self, env): + env.set('SOS_HOST_KNOWN_AS', 'SPACK-SOS-BUILD') + env.set('SOS_HOST_NODE_NAME', 'SPACK-SOS-NODE') + env.set('SOS_HOST_DETAILED', 'SPACK-SOS-DETAILED') + + def setup_run_environment(self, env): + env.set('SOS_ROOT', self.spec.prefix) + env.set('SOS_BUILD_DIR', self.spec.prefix) + env.set('SOS_CMD_PORT', '22500') + env.set('SOS_WORK', env['HOME']) + env.set('SOS_EVPATH_MEETUP', env['HOME']) + env.set('SOS_ENV_SET', 'true') diff --git a/var/spack/repos/builtin/packages/sowing/package.py b/var/spack/repos/builtin/packages/sowing/package.py index 7721c03475..e32ff6d605 100644 --- a/var/spack/repos/builtin/packages/sowing/package.py +++ b/var/spack/repos/builtin/packages/sowing/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sox/package.py b/var/spack/repos/builtin/packages/sox/package.py index 98e4ade490..db936cf60f 100644 --- a/var/spack/repos/builtin/packages/sox/package.py +++ b/var/spack/repos/builtin/packages/sox/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/spades/package.py b/var/spack/repos/builtin/packages/spades/package.py index b032d1f210..266d1cbcde 100644 --- a/var/spack/repos/builtin/packages/spades/package.py +++ b/var/spack/repos/builtin/packages/spades/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/span-lite/package.py b/var/spack/repos/builtin/packages/span-lite/package.py index 213fb3fa03..ea22806822 100644 --- a/var/spack/repos/builtin/packages/span-lite/package.py +++ b/var/spack/repos/builtin/packages/span-lite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/spark/package.py b/var/spack/repos/builtin/packages/spark/package.py index 9b05e3b4bf..7458a82068 100644 --- a/var/spack/repos/builtin/packages/spark/package.py +++ b/var/spack/repos/builtin/packages/spark/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -47,7 +47,7 @@ class Spark(Package): install('RELEASE', prefix) @when('+hadoop') - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): hadoop = self.spec['hadoop'].command hadoop.add_default_env('JAVA_HOME', self.spec['java'].home) hadoop_classpath = hadoop('classpath', output=str) @@ -56,4 +56,4 @@ class Spark(Package): # module files hadoop_classpath = re.sub(r'[\s+]', '', hadoop_classpath) - run_env.set('SPARK_DIST_CLASSPATH', hadoop_classpath) + env.set('SPARK_DIST_CLASSPATH', hadoop_classpath) diff --git a/var/spack/repos/builtin/packages/sparsehash/package.py b/var/spack/repos/builtin/packages/sparsehash/package.py index 4a1d3d706b..0591029f36 100644 --- a/var/spack/repos/builtin/packages/sparsehash/package.py +++ b/var/spack/repos/builtin/packages/sparsehash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sparta/package.py b/var/spack/repos/builtin/packages/sparta/package.py index e72eb9a850..ab1460aae4 100644 --- a/var/spack/repos/builtin/packages/sparta/package.py +++ b/var/spack/repos/builtin/packages/sparta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/spdlog/package.py b/var/spack/repos/builtin/packages/spdlog/package.py index 962131ff28..e4aad3bf42 100644 --- a/var/spack/repos/builtin/packages/spdlog/package.py +++ b/var/spack/repos/builtin/packages/spdlog/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/spectrum-mpi/package.py b/var/spack/repos/builtin/packages/spectrum-mpi/package.py index cdbd94260a..8cdd82e2ae 100644 --- a/var/spack/repos/builtin/packages/spectrum-mpi/package.py +++ b/var/spack/repos/builtin/packages/spectrum-mpi/package.py @@ -1,9 +1,8 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * +import os.path class SpectrumMpi(Package): @@ -19,41 +18,41 @@ class SpectrumMpi(Package): def setup_dependent_package(self, module, dependent_spec): # get the compiler names if '%xl' in dependent_spec or '%xl_r' in dependent_spec: - self.spec.mpicc = join_path(self.prefix.bin, 'mpixlc') - self.spec.mpicxx = join_path(self.prefix.bin, 'mpixlC') - self.spec.mpif77 = join_path(self.prefix.bin, 'mpixlf') - self.spec.mpifc = join_path(self.prefix.bin, 'mpixlf') + self.spec.mpicc = os.path.join(self.prefix.bin, 'mpixlc') + self.spec.mpicxx = os.path.join(self.prefix.bin, 'mpixlC') + self.spec.mpif77 = os.path.join(self.prefix.bin, 'mpixlf') + self.spec.mpifc = os.path.join(self.prefix.bin, 'mpixlf') elif '%pgi' in dependent_spec: - self.spec.mpicc = join_path(self.prefix.bin, 'mpipgicc') - self.spec.mpicxx = join_path(self.prefix.bin, 'mpipgic++') - self.spec.mpif77 = join_path(self.prefix.bin, 'mpipgifort') - self.spec.mpifc = join_path(self.prefix.bin, 'mpipgifort') + self.spec.mpicc = os.path.join(self.prefix.bin, 'mpipgicc') + self.spec.mpicxx = os.path.join(self.prefix.bin, 'mpipgic++') + self.spec.mpif77 = os.path.join(self.prefix.bin, 'mpipgifort') + self.spec.mpifc = os.path.join(self.prefix.bin, 'mpipgifort') else: - self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') - self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx') - self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') - self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpicc = os.path.join(self.prefix.bin, 'mpicc') + self.spec.mpicxx = os.path.join(self.prefix.bin, 'mpicxx') + self.spec.mpif77 = os.path.join(self.prefix.bin, 'mpif77') + self.spec.mpifc = os.path.join(self.prefix.bin, 'mpif90') - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): if '%xl' in dependent_spec or '%xl_r' in dependent_spec: - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpixlc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpixlC')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpixlf')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpixlf')) + env.set('MPICC', os.path.join(self.prefix.bin, 'mpixlc')) + env.set('MPICXX', os.path.join(self.prefix.bin, 'mpixlC')) + env.set('MPIF77', os.path.join(self.prefix.bin, 'mpixlf')) + env.set('MPIF90', os.path.join(self.prefix.bin, 'mpixlf')) elif '%pgi' in dependent_spec: - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpipgicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpipgic++')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpipgifort')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpipgifort')) + env.set('MPICC', os.path.join(self.prefix.bin, 'mpipgicc')) + env.set('MPICXX', os.path.join(self.prefix.bin, 'mpipgic++')) + env.set('MPIF77', os.path.join(self.prefix.bin, 'mpipgifort')) + env.set('MPIF90', os.path.join(self.prefix.bin, 'mpipgifort')) else: - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + env.set('MPICC', os.path.join(self.prefix.bin, 'mpicc')) + env.set('MPICXX', os.path.join(self.prefix.bin, 'mpic++')) + env.set('MPIF77', os.path.join(self.prefix.bin, 'mpif77')) + env.set('MPIF90', os.path.join(self.prefix.bin, 'mpif90')) - spack_env.set('OMPI_CC', spack_cc) - spack_env.set('OMPI_CXX', spack_cxx) - spack_env.set('OMPI_FC', spack_fc) - spack_env.set('OMPI_F77', spack_f77) + env.set('OMPI_CC', spack_cc) + env.set('OMPI_CXX', spack_cxx) + env.set('OMPI_FC', spack_fc) + env.set('OMPI_F77', spack_f77) - spack_env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib) + env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/speex/package.py b/var/spack/repos/builtin/packages/speex/package.py index ae9cfd02c9..734d811f7f 100644 --- a/var/spack/repos/builtin/packages/speex/package.py +++ b/var/spack/repos/builtin/packages/speex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/spfft/package.py b/var/spack/repos/builtin/packages/spfft/package.py new file mode 100644 index 0000000000..0f680564a8 --- /dev/null +++ b/var/spack/repos/builtin/packages/spfft/package.py @@ -0,0 +1,50 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Spfft(CMakePackage): + """Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support.""" + + homepage = "https://github.com/eth-cscs/SpFFT" + url = "https://github.com/eth-cscs/SpFFT/archive/v0.9.8.zip" + + version('0.9.10', sha256='9cbbb7ba5e53e17eeb45e809841d8272e5333f739c2442a99c3e255c1ddec3e9') + version('0.9.9', sha256='a8fd7a2d767716bb73185ca03bf4c106c6981b79130f3e456e5d2e744a2b3ba0') + version('0.9.8', sha256='f49fa51316bbfa68309e951d2375e1f6904120c93868cbe13bc2974c0b801a3f') + + variant('openmp', default=True, description="Build with OpenMP support") + variant('mpi', default=True, description="enable MPI") + variant('single_precision', default=False, description="Sinlge precision") + variant('gpu_direct', default=False, description="GPU aware MPI") + variant('static', default=False, description="build static library") + variant('cuda', default=False, description="CUDA") + variant('fortran', default=False, description="enable fortran") + variant('build_type', default='Release', description='CMake build type', + values=('Debug', 'Release', 'RelWithDebInfo')) + depends_on('fftw') + depends_on('mpi', when='+mpi') + depends_on('cuda', when='+cuda') + + def cmake_args(self): + args = [] + if self.spec.satisfies('+openmp'): + args += ["-DSPFFT_OMP=On"] + if self.spec.satisfies('+mpi'): + args += ["-DSPFFT_MPI=On"] + if self.spec.satisfies('+single_precision'): + args += ["-DSPFFT_SINGLE_PRECISION=On"] + if self.spec.satisfies('+gpu_direct'): + args += ["-DSPFFT_GPU_DIRECT=On"] + if self.spec.satisfies('+cuda'): + args += ["-DSPFFT_GPU_BACKEND=CUDA"] + if self.spec.satisfies('+fortran'): + args += ["-DSPFFT_FORTAN=On"] + if self.spec.satisfies('+static'): + args += ["-DSPFFT_STATIC=On"] + + return args diff --git a/var/spack/repos/builtin/packages/spglib/package.py b/var/spack/repos/builtin/packages/spglib/package.py index 981d30fb83..e832b85eab 100644 --- a/var/spack/repos/builtin/packages/spglib/package.py +++ b/var/spack/repos/builtin/packages/spglib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sph2pipe/package.py b/var/spack/repos/builtin/packages/sph2pipe/package.py index 2581312641..c6b2f7a1f1 100644 --- a/var/spack/repos/builtin/packages/sph2pipe/package.py +++ b/var/spack/repos/builtin/packages/sph2pipe/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/spherepack/package.py b/var/spack/repos/builtin/packages/spherepack/package.py index f638ea91d4..8ef671f0a7 100644 --- a/var/spack/repos/builtin/packages/spherepack/package.py +++ b/var/spack/repos/builtin/packages/spherepack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/spindle/package.py b/var/spack/repos/builtin/packages/spindle/package.py index 8106bc9206..2b7296e6d3 100644 --- a/var/spack/repos/builtin/packages/spindle/package.py +++ b/var/spack/repos/builtin/packages/spindle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/spm/package.py b/var/spack/repos/builtin/packages/spm/package.py index 0d39675dc0..1545c3d2dd 100644 --- a/var/spack/repos/builtin/packages/spm/package.py +++ b/var/spack/repos/builtin/packages/spm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/spot/package.py b/var/spack/repos/builtin/packages/spot/package.py index fe0def9622..6ada8fe0ce 100644 --- a/var/spack/repos/builtin/packages/spot/package.py +++ b/var/spack/repos/builtin/packages/spot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sqlite/package.py b/var/spack/repos/builtin/packages/sqlite/package.py index 2621678b1b..f8dd0e4948 100644 --- a/var/spack/repos/builtin/packages/sqlite/package.py +++ b/var/spack/repos/builtin/packages/sqlite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sqlitebrowser/package.py b/var/spack/repos/builtin/packages/sqlitebrowser/package.py index 2b89b4d6f8..6cd8eeb9b8 100644 --- a/var/spack/repos/builtin/packages/sqlitebrowser/package.py +++ b/var/spack/repos/builtin/packages/sqlitebrowser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/squashfs/package.py b/var/spack/repos/builtin/packages/squashfs/package.py index 1e148da95c..62cd3c690a 100644 --- a/var/spack/repos/builtin/packages/squashfs/package.py +++ b/var/spack/repos/builtin/packages/squashfs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,6 +13,7 @@ class Squashfs(MakefilePackage): url = 'https://downloads.sourceforge.net/project/squashfs/squashfs/squashfs4.3/squashfs4.3.tar.gz' # version sha1 + version('4.4', sha256='a981b3f3f2054b5a2e658851a3c06a2460ad04a9a8a645e0afe063a63fdbb07e') version('4.3', sha256='0d605512437b1eb800b4736791559295ee5f60177e102e4d4ccd0ee241a5f3f6') version('4.2', sha256='d9e0195aa922dbb665ed322b9aaa96e04a476ee650f39bbeadb0d00b24022e96') version('4.1', sha256='3a870d065a25b3f5467bc6d9ed34340befab51a3f9e4b7e3792ea0ff4e06046a') diff --git a/var/spack/repos/builtin/packages/squid/package.py b/var/spack/repos/builtin/packages/squid/package.py index a039bbedc5..dd944edbad 100644 --- a/var/spack/repos/builtin/packages/squid/package.py +++ b/var/spack/repos/builtin/packages/squid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,5 +10,6 @@ class Squid(AutotoolsPackage): """C function library for sequence analysis.""" homepage = "http://eddylab.org/software.html" + url = "http://eddylab.org/software/squid/squid-1.9g.tar.gz" - version('1.9g', sha256='302f42e8794aa4dbcfa0996c14fb7a70a7c4397fc45c2bbd2748055460d8dca7', url='http://eddylab.org/software/squid/squid.tar.gz') + version('1.9g', sha256='302f42e8794aa4dbcfa0996c14fb7a70a7c4397fc45c2bbd2748055460d8dca7') diff --git a/var/spack/repos/builtin/packages/sra-toolkit/package.py b/var/spack/repos/builtin/packages/sratoolkit/package.py index 972f4d8a70..c399d1b617 100644 --- a/var/spack/repos/builtin/packages/sra-toolkit/package.py +++ b/var/spack/repos/builtin/packages/sratoolkit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class SraToolkit(Package): +class Sratoolkit(Package): """The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.""" @@ -18,10 +18,6 @@ class SraToolkit(Package): version('2.9.2', sha256='17dbe13aa1ed7955d31e1e76e8b62786e80a77e9ed9d396631162dc3ad8b716d') version('2.8.2-1', sha256='b053061aae7c6d00162fe0f514be4128a60365b4b2b5b36e7f4798b348b55cf5') - def url_for_version(self, version): - url = 'https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/{0}/sratoolkit.{0}-centos_linux64.tar.gz' - return url.format(version) - def install(self, spec, prefix): install_tree('bin', prefix.bin, symlinks=True) install_tree('example', prefix.example) diff --git a/var/spack/repos/builtin/packages/ssht/package.py b/var/spack/repos/builtin/packages/ssht/package.py index 41cefac4f0..293ab0eedd 100644 --- a/var/spack/repos/builtin/packages/ssht/package.py +++ b/var/spack/repos/builtin/packages/ssht/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sspace-longread/package.py b/var/spack/repos/builtin/packages/sspace-longread/package.py index 48f4df8e16..d96f6faded 100644 --- a/var/spack/repos/builtin/packages/sspace-longread/package.py +++ b/var/spack/repos/builtin/packages/sspace-longread/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sspace-standard/package.py b/var/spack/repos/builtin/packages/sspace-standard/package.py index 768bd3afb1..5ce8febf46 100644 --- a/var/spack/repos/builtin/packages/sspace-standard/package.py +++ b/var/spack/repos/builtin/packages/sspace-standard/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -48,6 +48,6 @@ class SspaceStandard(Package): install_tree('tools', prefix.tools) install(rootscript, prefix) - def setup_environment(self, spack_env, run_env): - run_env.set('SSPACE_HOME', prefix) - run_env.prepend_path('PATH', prefix) + def setup_run_environment(self, env): + env.set('SSPACE_HOME', self.prefix) + env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/sst-core/package.py b/var/spack/repos/builtin/packages/sst-core/package.py index df8e9690b9..b28ae4cea0 100644 --- a/var/spack/repos/builtin/packages/sst-core/package.py +++ b/var/spack/repos/builtin/packages/sst-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sst-dumpi/package.py b/var/spack/repos/builtin/packages/sst-dumpi/package.py index 1acd67b6fb..0710c5607e 100644 --- a/var/spack/repos/builtin/packages/sst-dumpi/package.py +++ b/var/spack/repos/builtin/packages/sst-dumpi/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sst-macro/package.py b/var/spack/repos/builtin/packages/sst-macro/package.py index 1c591eb9c4..e7333c9a5b 100644 --- a/var/spack/repos/builtin/packages/sst-macro/package.py +++ b/var/spack/repos/builtin/packages/sst-macro/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/stacks/package.py b/var/spack/repos/builtin/packages/stacks/package.py index 0245fb1d8c..c7d6803227 100644 --- a/var/spack/repos/builtin/packages/stacks/package.py +++ b/var/spack/repos/builtin/packages/stacks/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/staden-io-lib/package.py b/var/spack/repos/builtin/packages/staden-io-lib/package.py index 4b5c56be28..21c0fee40f 100644 --- a/var/spack/repos/builtin/packages/staden-io-lib/package.py +++ b/var/spack/repos/builtin/packages/staden-io-lib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/star-ccm-plus/package.py b/var/spack/repos/builtin/packages/star-ccm-plus/package.py index c673623d98..ec7d503fcd 100644 --- a/var/spack/repos/builtin/packages/star-ccm-plus/package.py +++ b/var/spack/repos/builtin/packages/star-ccm-plus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/star/package.py b/var/spack/repos/builtin/packages/star/package.py index f63132951c..b12bb6f9bb 100644 --- a/var/spack/repos/builtin/packages/star/package.py +++ b/var/spack/repos/builtin/packages/star/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/startup-notification/package.py b/var/spack/repos/builtin/packages/startup-notification/package.py index 1d1fdc6446..448fe1e05a 100644 --- a/var/spack/repos/builtin/packages/startup-notification/package.py +++ b/var/spack/repos/builtin/packages/startup-notification/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py index f8d9dd2bab..86338a2b9d 100644 --- a/var/spack/repos/builtin/packages/stat/package.py +++ b/var/spack/repos/builtin/packages/stat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -49,6 +49,7 @@ class Stat(AutotoolsPackage): depends_on('py-xdot', when='@4.0.1:') depends_on('swig') depends_on('mpi', when='+examples') + depends_on('boost') patch('configure_mpicxx.patch', when='@2.1.0') @@ -60,6 +61,7 @@ class Stat(AutotoolsPackage): "--with-graphlib=%s" % spec['graphlib'].prefix, "--with-stackwalker=%s" % spec['dyninst'].prefix, "--with-python=%s" % spec['python'].command.path, + "--with-boost=%s" % spec['boost'].prefix, ] if '+fgfs' in spec: args.append('--with-fgfs=%s' diff --git a/var/spack/repos/builtin/packages/stata/package.py b/var/spack/repos/builtin/packages/stata/package.py index 6f19adda53..59dee6cf13 100644 --- a/var/spack/repos/builtin/packages/stata/package.py +++ b/var/spack/repos/builtin/packages/stata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -37,9 +37,9 @@ class Stata(Package): return "file://{0}/Stata{1}Linux64.tar.gz".format(os.getcwd(), version) # STATA is simple and needs really just the PATH set. - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', prefix) - run_env.prepend_path('LD_LIBRARY_PATH', self.spec['libpng'].prefix.lib) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix) + env.prepend_path('LD_LIBRARY_PATH', self.spec['libpng'].prefix.lib) # Extracting the file provides the following: # ./unix/ diff --git a/var/spack/repos/builtin/packages/stc/package.py b/var/spack/repos/builtin/packages/stc/package.py index ce52a418f2..790f1b66c3 100644 --- a/var/spack/repos/builtin/packages/stc/package.py +++ b/var/spack/repos/builtin/packages/stc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,7 +11,7 @@ class Stc(AutotoolsPackage): """STC: The Swift-Turbine Compiler""" homepage = 'http://swift-lang.org/Swift-T' - url = 'http://swift-lang.github.io/swift-t-downloads/spack/stc-0.0.0.tar.gz' + url = 'http://swift-lang.github.io/swift-t-downloads/spack/stc-0.8.3.tar.gz' git = "https://github.com/swift-lang/swift-t.git" version('master', branch='master') diff --git a/var/spack/repos/builtin/packages/steps/package.py b/var/spack/repos/builtin/packages/steps/package.py index 41ef74c681..4489e34539 100644 --- a/var/spack/repos/builtin/packages/steps/package.py +++ b/var/spack/repos/builtin/packages/steps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -55,7 +55,7 @@ class Steps(CMakePackage): args.append('-DBLAS_LIBRARIES=' + spec['blas'].libs.joined(";")) return args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # This recipe exposes a Python package from a C++ CMake project. # This hook is required to reproduce what Spack PythonPackage does. - run_env.prepend_path('PYTHONPATH', self.prefix) + env.prepend_path('PYTHONPATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/storm/package.py b/var/spack/repos/builtin/packages/storm/package.py new file mode 100644 index 0000000000..a4da7325cd --- /dev/null +++ b/var/spack/repos/builtin/packages/storm/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Storm(Package): + """ + Storm is a distributed realtime computation system. Similar to how + Hadoop provides a set of general primitives for doing batch processing, + Storm provides a set of general primitives for doing realtime computation. + """ + + homepage = "https://www-eu.apache.org/dist/storm" + url = "https://www-eu.apache.org/dist/storm/apache-storm-2.1.0/apache-storm-2.1.0.tar.gz" + url_list = homepage + list_depth = 2 + + version('2.1.0', sha256='e279a495dda42af7d9051543989f74a1435a5bda53e795a1de4a1def32027fc4') + version('2.0.0', sha256='0a4a6f985242a99f899a01bd01dacf9365f381e2acc473caa84073fbe84f6703') + version('1.2.3', sha256='d45322253db06353a521284f31b30bd964dab859f3a279a305bd79112803425a') + + depends_on('java', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/stow/package.py b/var/spack/repos/builtin/packages/stow/package.py index 508b30d715..bc3515407d 100644 --- a/var/spack/repos/builtin/packages/stow/package.py +++ b/var/spack/repos/builtin/packages/stow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Stow(AutotoolsPackage): +class Stow(AutotoolsPackage, GNUMirrorPackage): """GNU Stow: a symlink farm manager GNU Stow is a symlink farm manager which takes distinct @@ -15,7 +15,7 @@ class Stow(AutotoolsPackage): installed in the same place.""" homepage = "https://www.gnu.org/software/stow/" - url = "https://ftpmirror.gnu.org/stow/stow-2.2.2.tar.bz2" + gnu_mirror_path = "stow/stow-2.2.2.tar.bz2" version('2.2.2', sha256='a0022034960e47a8d23dffb822689f061f7a2d9101c9835cf11bf251597aa6fd') version('2.2.0', sha256='86bc30fe1d322a5c80ff3bd7580c2758149aad7c3bbfa18b48a9d95c25d66b05') diff --git a/var/spack/repos/builtin/packages/strace/package.py b/var/spack/repos/builtin/packages/strace/package.py index f3573480b4..f1b282e530 100644 --- a/var/spack/repos/builtin/packages/strace/package.py +++ b/var/spack/repos/builtin/packages/strace/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/stream/package.py b/var/spack/repos/builtin/packages/stream/package.py index 507cb4114a..e7c937ce26 100644 --- a/var/spack/repos/builtin/packages/stream/package.py +++ b/var/spack/repos/builtin/packages/stream/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/strelka/package.py b/var/spack/repos/builtin/packages/strelka/package.py index 3481643fb5..a86a19cf21 100644 --- a/var/spack/repos/builtin/packages/strelka/package.py +++ b/var/spack/repos/builtin/packages/strelka/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/stress/package.py b/var/spack/repos/builtin/packages/stress/package.py index 93cb340220..b407eede15 100644 --- a/var/spack/repos/builtin/packages/stress/package.py +++ b/var/spack/repos/builtin/packages/stress/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/string-view-lite/package.py b/var/spack/repos/builtin/packages/string-view-lite/package.py index 98e00d7bdf..d2dbd7ad39 100644 --- a/var/spack/repos/builtin/packages/string-view-lite/package.py +++ b/var/spack/repos/builtin/packages/string-view-lite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/stringtie/package.py b/var/spack/repos/builtin/packages/stringtie/package.py index 6e92476e6d..afbca1b813 100644 --- a/var/spack/repos/builtin/packages/stringtie/package.py +++ b/var/spack/repos/builtin/packages/stringtie/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/structure/package.py b/var/spack/repos/builtin/packages/structure/package.py index 0ab0bfad58..646530bc3a 100644 --- a/var/spack/repos/builtin/packages/structure/package.py +++ b/var/spack/repos/builtin/packages/structure/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/strumpack/package.py b/var/spack/repos/builtin/packages/strumpack/package.py index d2dfc424f5..29a5893acf 100644 --- a/var/spack/repos/builtin/packages/strumpack/package.py +++ b/var/spack/repos/builtin/packages/strumpack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,12 +18,14 @@ class Strumpack(CMakePackage): iterative solvers.""" homepage = "http://portal.nersc.gov/project/sparse/strumpack" - url = "https://github.com/pghysels/STRUMPACK/archive/v3.0.3.tar.gz" + url = "https://github.com/pghysels/STRUMPACK/archive/v3.3.0.tar.gz" git = "https://github.com/pghysels/STRUMPACK.git" maintainers = ['pghysels'] version('master', branch='master') + version('3.3.0', sha256='499fd3b58656b4b6495496920e5372895861ebf15328be8a7a9354e06c734bc7') + version('3.2.0', sha256='34d93e1b2a3b8908ef89804b7e08c5a884cbbc0b2c9f139061627c0d2de282c1') version('3.1.1', sha256='c1c3446ee023f7b24baa97b24907735e89ce4ae9f5ef516645dfe390165d1778') version('3.1.0', sha256='b4f91b7d433955518b04538be1c726afc5de4bffb163e982ef8844d391b26fa7') version('3.0.3', sha256='2bd2a40d9585b769ae4ba461de02c6e36433bf2b21827f824a50f2fdf73389f7') @@ -32,6 +34,7 @@ class Strumpack(CMakePackage): version('3.0.0', sha256='7acd9b4653b8b11380de733c80b164348ca00f9226904f5dc166a8e3db88cd20') version('2.2.0', sha256='8fe73875cbbb29ed1faf714e3bf13ad538eb062e39d7d5e73cb9c4aafb571e24') + variant('shared', default=False, description='Build shared libraries') variant('mpi', default=True, description='Use MPI') variant('openmp', default=True, description='Enable thread parallellism via tasking with OpenMP') @@ -39,6 +42,8 @@ class Strumpack(CMakePackage): description='Enable use of ParMetis') variant('scotch', default=False, description='Enable use of Scotch') + variant('butterflypack', default=True, + description='Enable use of ButterflyPACK') variant('c_interface', default=True, description='Enable C interface') variant('count_flops', default=False, @@ -59,8 +64,11 @@ class Strumpack(CMakePackage): depends_on('parmetis', when='+parmetis') depends_on('scotch~metis', when='+scotch') depends_on('scotch~metis+mpi', when='+scotch+mpi') + depends_on('butterflypack@1.1.0:', when='+butterflypack+mpi') conflicts('+parmetis', when='~mpi') + conflicts('+butterflypack', when='~mpi') + conflicts('+butterflypack', when='strumpack@:3.2.0') patch('intel-19-compile.patch', when='@3.1.1') @@ -90,11 +98,17 @@ class Strumpack(CMakePackage): if spec.satisfies('@3.0.4:'): args.extend([ '-DTPL_ENABLE_PARMETIS=%s' % on_off('+parmetis'), - '-DTPL_ENABLE_SCOTCH=%s' % on_off('+scotch') + '-DTPL_ENABLE_SCOTCH=%s' % on_off('+scotch'), + '-DTPL_ENABLE_BPACK=%s' % on_off('+butterflypack') ]) else: args.extend([ '-DSTRUMPACK_USE_PARMETIS=%s' % on_off('+parmetis'), '-DSTRUMPACK_USE_SCOTCH=%s' % on_off('+scotch') ]) + + args.extend([ + '-DBUILD_SHARED_LIBS=%s' % on_off('+shared') + ]) + return args diff --git a/var/spack/repos/builtin/packages/sublime-text/package.py b/var/spack/repos/builtin/packages/sublime-text/package.py index 3f22f4fdda..942e62d311 100644 --- a/var/spack/repos/builtin/packages/sublime-text/package.py +++ b/var/spack/repos/builtin/packages/sublime-text/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/subread/package.py b/var/spack/repos/builtin/packages/subread/package.py index 5124d75d89..32d8e9abf1 100644 --- a/var/spack/repos/builtin/packages/subread/package.py +++ b/var/spack/repos/builtin/packages/subread/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,7 +12,7 @@ class Subread(MakefilePackage): sequencing data.""" homepage = "http://subread.sourceforge.net/" - url = "https://downloads.sourceforge.net/project/subread/subread-1.5.2/subread-1.5.2-source.tar.gz" + url = "https://iweb.dl.sourceforge.net/project/subread/subread-1.5.2/subread-1.5.2-source.tar.gz" version('2.0.0', sha256='bd7b45f7d8872b0f5db5d23a385059f21d18b49e432bcb6e3e4a879fe51b41a8') version('1.6.4', sha256='b7bd0ee3b0942d791aecce6454d2f3271c95a010beeeff2daf1ff71162e43969') diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py index de26e0dece..4e3f774037 100644 --- a/var/spack/repos/builtin/packages/subversion/package.py +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -34,7 +34,7 @@ class Subversion(AutotoolsPackage): extends('perl', when='+perl') depends_on('swig@1.3.24:3.0.0', when='+perl') - depends_on('perl-term-readkey', when='+perl') + depends_on('perl-termreadkey', when='+perl') # Installation has race cases. parallel = False diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index 6c0896b5b1..10f99dfbb6 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,15 +11,20 @@ class SuiteSparse(Package): SuiteSparse is a suite of sparse matrix algorithms """ homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' - url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.2.0.tar.gz' - - version('5.3.0', sha256='90e69713d8c454da5a95a839aea5d97d8d03d00cc1f667c4bdfca03f640f963d') - version('5.2.0', sha256='3c46c035ea8217649958a0f73360e825b0c9dcca4e32a9349d2c7678c0d48813') - version('5.1.0', sha256='1b1371074224c6844697f3a55024d185b7ff6ffa49ac141d433fbb1aadf426f5') - version('4.5.5', sha256='b9a98de0ddafe7659adffad8a58ca3911c1afa8b509355e7aa58b02feb35d9b6') - version('4.5.4', sha256='698b5c455645bb1ad29a185f0d52025f3bd7cb7261e182c8878b0eb60567a714') - version('4.5.3', sha256='6199a3a35fbce82b155fd2349cf81d2b7cddaf0dac218c08cb172f9bc143f37a') - version('4.5.1', sha256='ac4524b9f69c4f8c2652d720b146c92a414c1943f86d46df49b4ff8377ae8752') + url = 'https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v4.5.3.tar.gz' + git = 'https://github.com/DrTimothyAldenDavis/SuiteSparse.git' + + version('5.6.0', sha256='76d34d9f6dafc592b69af14f58c1dc59e24853dcd7c2e8f4c98ffa223f6a1adb') + version('5.5.0', sha256='63c73451734e2bab19d1915796c6776565ea6aea5da4063a9797ecec60da2e3d') + version('5.4.0', sha256='d9d62d539410d66550d0b795503a556830831f50087723cb191a030525eda770') + version('5.3.0', sha256='d8ef4bee4394d2f07299d4688b83bbd98e9d3a2ebbe1c1632144b6f7095ce165') + version('5.2.0', sha256='68c431aef3d9a0b02e97803eb61671c5ecb9d36fd292a807db87067dadb36e53') + version('5.1.2', sha256='97dc5fdc7f78ff5018e6a1fcc841e17a9af4e5a35cebd62df6922349bf12959e') + version('5.1.0', sha256='0b0e03c63e67b04529bb6248808d2a8c82259d40b30fc5a7599f4b6f7bdd4dc6') + version('5.0.0', sha256='2f8694d9978033659f10ceb8bdb19147d3c519a0251b8de84be6ba8824d30517') + version('4.5.6', sha256='1c7b7a265a1d6c606095eb8aa3cb8e27821f1b7f5bc04f28df6d62906e02f4e4') + version('4.5.5', sha256='80d1d9960a6ec70031fecfe9adfe5b1ccd8001a7420efb50d6fa7326ef14af91') + version('4.5.3', sha256='b6965f9198446a502cde48fb0e02236e75fa5700b94c7306fc36599d57b563f4') variant('tbb', default=False, description='Build with Intel TBB') variant('pic', default=True, description='Build position independent code (required to link with shared libraries)') @@ -122,6 +127,13 @@ class SuiteSparse(Package): 'CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX=%s' % prefix + ' -DCMAKE_LIBRARY_PATH=%s' % prefix.lib] + # In those SuiteSparse versions calling "make install" in one go is + # not possible, mainly because of GraphBLAS. Thus compile first and + # install in a second run. + if (self.spec.version >= Version('5.4.0') and + self.spec.version <= Version('5.6.0')): + make('default', *make_args) + make('install', *make_args) @property diff --git a/var/spack/repos/builtin/packages/sumaclust/package.py b/var/spack/repos/builtin/packages/sumaclust/package.py index 9c90fe1564..fe23e8ecfe 100644 --- a/var/spack/repos/builtin/packages/sumaclust/package.py +++ b/var/spack/repos/builtin/packages/sumaclust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sundials/FindPackageMultipass.cmake.patch b/var/spack/repos/builtin/packages/sundials/FindPackageMultipass.cmake.patch new file mode 100644 index 0000000000..623c94a3c5 --- /dev/null +++ b/var/spack/repos/builtin/packages/sundials/FindPackageMultipass.cmake.patch @@ -0,0 +1,69 @@ +diff --git a/config/FindPackageMultipass.cmake b/config/FindPackageMultipass.cmake +index 128eee9..847c246 100644 +--- a/config/FindPackageMultipass.cmake ++++ b/config/FindPackageMultipass.cmake +@@ -138,7 +138,10 @@ macro (MULTIPASS_SOURCE_RUNS includes libraries source runs language) + math (EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1") # Why can't I add to a cache variable? + set (MULTIPASS_TEST_COUNT ${_tmp} CACHE INTERNAL "Unique test ID") + set (testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs}) +- set (testdir ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp) ++ set (testdir ${PROJECT_BINARY_DIR}/PETSC_test) ++ if (NOT EXISTS ${testdir}) ++ file(MAKE_DIRECTORY ${testdir}) ++ endif () + set (CMAKE_REQUIRED_INCLUDES ${includes}) + set (CMAKE_REQUIRED_LIBRARIES ${libraries}) + # if MPI is available, use it for the test +@@ -148,24 +151,38 @@ macro (MULTIPASS_SOURCE_RUNS includes libraries source runs language) + set (REQUIRED_COMPILER ${CMAKE_${language}_COMPILER}) + endif () + if(${language} STREQUAL "C") +- file(WRITE ${testdir}/src.c "${source}") +- try_run(${testname} _compiles ${testdir} ${testdir}/src.c +- CMAKE_FLAGS -DCMAKE_C_COMPILER=${REQUIRED_COMPILER} -DINCLUDE_DIRECTORIES=${CMAKE_REQUIRED_INCLUDES} +- LINK_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES}) +- elseif(${language} STREQUAL "CXX") +- file(WRITE ${testdir}/src.cxx "${source}") +- try_run(${testname} _compiles ${testdir} ${testdir}/src.cxx +- CMAKE_FLAGS -DCMAKE_CXX_COMPILER=${REQUIRED_COMPILER} -DINCLUDE_DIRECTORIES=${CMAKE_REQUIRED_INCLUDES} +- LINK_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES}) +- endif() +- # ${testname} is the exit code returned by try_run, +- # so 0 is success and anything else is a failure. +- if (${testname}) +- set (${runs} FALSE) ++ set (extension c) + else () ++ set (extension cxx) ++ endif () ++ # Create simple test code ++ file(WRITE ${testdir}/src.${extension} "${source}") ++ # Create a CMakeLists.txt file for the test code ++ file(WRITE ${testdir}/CMakeLists.txt ++ "cmake_minimum_required(VERSION 3.5)\n" ++ "project(ctest ${language})\n" ++ "set(CMAKE_VERBOSE_MAKEFILE ON)\n" ++ "set(CMAKE_${language}_COMPILER \"${REQUIRED_COMPILER}\")\n" ++ "set(CMAKE_${language}_FLAGS \"${CMAKE_${language}_FLAGS}\")\n" ++ "include_directories(${CMAKE_REQUIRED_INCLUDES})\n" ++ "add_executable(ctest src.${extension})\n" ++ "target_link_libraries(ctest ${CMAKE_REQUIRED_LIBRARIES})\n") ++ # Attempt to compile the test code ++ try_compile(${testname} ${testdir} ${testdir} ctest ++ OUTPUT_VARIABLE _output) ++ # Write output compiling the test code ++ file(WRITE ${testdir}/src.out "${_output}") ++ # To ensure we do not use stuff from the previous attempts, ++ # we must remove the CMakeFiles directory. ++ file(REMOVE_RECURSE ${testdir}/CMakeFiles) ++ # Process test result ++ if (${testname}) + set (${runs} TRUE) ++ else () ++ set (${runs} FALSE) + endif () + unset (_compiles) ++ unset (_output) + endmacro (MULTIPASS_SOURCE_RUNS) + + diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py index 632bde8634..db1dd42753 100644 --- a/var/spack/repos/builtin/packages/sundials/package.py +++ b/var/spack/repos/builtin/packages/sundials/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -194,6 +194,7 @@ class Sundials(CMakePackage): # remove OpenMP header file and function from hypre vector test code patch('test_nvector_parhyp.patch', when='@2.7.0:3.0.0') + patch('FindPackageMultipass.cmake.patch', when='@5.0.0') # ========================================================================== # SUNDIALS Settings diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index c49a624b17..989158356d 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -40,6 +40,9 @@ class SuperluDist(CMakePackage): depends_on('parmetis') depends_on('metis@5:') + patch('xl-611.patch', when='@:6.1.1 %xl') + patch('xl-611.patch', when='@:6.1.1 %xl_r') + def cmake_args(self): spec = self.spec args = [ @@ -51,9 +54,15 @@ class SuperluDist(CMakePackage): '-DUSE_XSDK_DEFAULTS=YES', '-DTPL_PARMETIS_LIBRARIES=%s' % spec['parmetis'].libs.ld_flags + ';' + spec['metis'].libs.ld_flags, - '-DTPL_PARMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include + '-DTPL_PARMETIS_INCLUDE_DIRS=%s' % + spec['parmetis'].prefix.include + + ';' + spec['metis'].prefix.include ] + if (spec.satisfies('%xl') or spec.satisfies('%xl_r')) and \ + spec.satisfies('@:6.1.1'): + args.append('-DCMAKE_C_FLAGS=-DNoChange') + if '+int64' in spec: args.append('-DXSDK_INDEX_SIZE=64') else: @@ -63,6 +72,7 @@ class SuperluDist(CMakePackage): args.append('-Denable_openmp=ON') else: args.append('-Denable_openmp=OFF') + args.append('-DCMAKE_DISABLE_FIND_PACKAGE_OpenMP=ON') if '+shared' in spec: args.append('-DBUILD_SHARED_LIBS:BOOL=ON') diff --git a/var/spack/repos/builtin/packages/superlu-dist/xl-611.patch b/var/spack/repos/builtin/packages/superlu-dist/xl-611.patch new file mode 100644 index 0000000000..92b6a3c730 --- /dev/null +++ b/var/spack/repos/builtin/packages/superlu-dist/xl-611.patch @@ -0,0 +1,26 @@ +commit e51132dbd022139933678b3a751a9b3148fafd19 +Author: Satish Balay <balay@mcs.anl.gov> +Date: Tue Nov 12 16:07:08 2019 -0600 + + add ztrtri_ mapping for xlf + +diff --git a/SRC/Cnames.h b/SRC/Cnames.h +index 792f514..ebef619 100644 +--- a/SRC/Cnames.h ++++ b/SRC/Cnames.h +@@ -179,6 +179,7 @@ at the top-level directory. + #define zher2_ ZHER2 + #define zgeru_ ZGERU + ++#define ztrtri_ ZTRTRI + /* + #define mc64id_dist MC64ID_DIST + #define mc64ad_dist MC64AD_DIST +@@ -307,6 +308,7 @@ at the top-level directory. + #define zher2_ zher2 + #define zgeru_ zgeru + ++#define ztrtri_ ztrtri + /* + #define mc64id_dist mc64id_dist + #define mc64ad_dist mc64ad_dist diff --git a/var/spack/repos/builtin/packages/superlu-mt/package.py b/var/spack/repos/builtin/packages/superlu-mt/package.py index 74bf6e9c0f..889e95f5bb 100644 --- a/var/spack/repos/builtin/packages/superlu-mt/package.py +++ b/var/spack/repos/builtin/packages/superlu-mt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py index dfc81f662b..14f9483945 100644 --- a/var/spack/repos/builtin/packages/superlu/package.py +++ b/var/spack/repos/builtin/packages/superlu/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/supernova/package.py b/var/spack/repos/builtin/packages/supernova/package.py index 43ccbe50c6..a83a14dfab 100644 --- a/var/spack/repos/builtin/packages/supernova/package.py +++ b/var/spack/repos/builtin/packages/supernova/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -36,8 +36,8 @@ class Supernova(Package): def url_for_version(self, version): return "file://{0}/supernova-{1}.tar.gz".format(os.getcwd(), version) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix) def install(self, spec, prefix): rm = which('rm') diff --git a/var/spack/repos/builtin/packages/sw4lite/package.py b/var/spack/repos/builtin/packages/sw4lite/package.py index a6378dd569..1ada4f1889 100644 --- a/var/spack/repos/builtin/packages/sw4lite/package.py +++ b/var/spack/repos/builtin/packages/sw4lite/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/swap-assembler/package.py b/var/spack/repos/builtin/packages/swap-assembler/package.py index f8cca4ca62..04a6a63f9c 100644 --- a/var/spack/repos/builtin/packages/swap-assembler/package.py +++ b/var/spack/repos/builtin/packages/swap-assembler/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/swarm/package.py b/var/spack/repos/builtin/packages/swarm/package.py index 9bb73e805b..4f38c7522e 100644 --- a/var/spack/repos/builtin/packages/swarm/package.py +++ b/var/spack/repos/builtin/packages/swarm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/swfft/package.py b/var/spack/repos/builtin/packages/swfft/package.py index ea23a67038..f6bfae90ec 100644 --- a/var/spack/repos/builtin/packages/swfft/package.py +++ b/var/spack/repos/builtin/packages/swfft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/swftools/package.py b/var/spack/repos/builtin/packages/swftools/package.py index 779358df74..02a658599d 100644 --- a/var/spack/repos/builtin/packages/swftools/package.py +++ b/var/spack/repos/builtin/packages/swftools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py index cf538d24c0..c3c594f07e 100644 --- a/var/spack/repos/builtin/packages/swiftsim/package.py +++ b/var/spack/repos/builtin/packages/swiftsim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -33,14 +33,15 @@ class Swiftsim(AutotoolsPackage): depends_on('hdf5~mpi', when='~mpi') depends_on('hdf5+mpi', when='+mpi') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # Needed to be able to download from the Durham gitlab repository tty.warn('Setting "GIT_SSL_NO_VERIFY=1"') tty.warn('This is needed to clone SWIFT repository') - spack_env.set('GIT_SSL_NO_VERIFY', 1) + env.set('GIT_SSL_NO_VERIFY', 1) def configure_args(self): - return ['--prefix=%s' % self.prefix, - '--enable-mpi' if '+mpi' in self.spec else '--disable-mpi', - '--with-metis={0}'.format(self.spec['metis'].prefix), - '--enable-optimization'] + return [ + '--enable-mpi' if '+mpi' in self.spec else '--disable-mpi', + '--with-metis={0}'.format(self.spec['metis'].prefix), + '--enable-optimization' + ] diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py index a716916865..ac48fb1246 100644 --- a/var/spack/repos/builtin/packages/swig/package.py +++ b/var/spack/repos/builtin/packages/swig/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/swipl/package.py b/var/spack/repos/builtin/packages/swipl/package.py new file mode 100644 index 0000000000..6cba487a7d --- /dev/null +++ b/var/spack/repos/builtin/packages/swipl/package.py @@ -0,0 +1,71 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Swipl(CMakePackage): + """ SWI-Prolog is a versatile implementation of the Prolog language. + Although SWI-Prolog gained its popularity primarily in education, + its development is mostly driven by the needs for application development. + This is facilitated by a rich interface to other IT components by + supporting many document types and (network) protocols as well as a + comprehensive low-level interface to C that is the basis for high-level + interfaces to C++, Java (bundled), C#, Python, etc (externally available). + + Data type extensions such as dicts and strings as well as full support + for Unicode and unbounded integers simplify smooth exchange of data + with other components.""" + + homepage = "https://www.swi-prolog.org" + url = "https://www.swi-prolog.org/download/stable/src/swipl-8.0.3.tar.gz" + + maintainers = ['alexrobomind'] + + version('8.0.3', sha256='cee59c0a477c8166d722703f6e52f962028f3ac43a5f41240ecb45dbdbe2d6ae') + + variant('gmp', default=True, description='bignum and rational number support') + variant('xpce', default=True, description='GUI support') + variant('ssl', default=True, description='SSL support') + variant('zlib', default=True, description='Compressed streams support') + variant('odbc', default=True, description='ODBC database access') + variant('unwind', default=True, description='Build with stack traces in crash reports') + + depends_on('uuid') + depends_on('readline') + + depends_on('gmp', when='+gmp') + depends_on('unwind', when='+unwind') + depends_on('unixodbc', when='+odbc') + depends_on('openssl', when='+ssl') + depends_on('zlib', when='+zlib') + + depends_on('libxt', when='+xpce') + depends_on('libx11', when='+xpce') + depends_on('libjpeg', when='+xpce') + depends_on('libxpm', when='+xpce') + + depends_on('libxft', when='+xpce') + depends_on('fontconfig', when='+xpce') + depends_on('pkgconfig', when='+xpce', type='build') + + conflicts('%intel', msg='Test builds with ICC failed when creating startup image') + + def cmake_args(self): + args = [] + + def append_switch(variant, cmake_flag): + val = 'ON' if variant in self.spec else 'OFF' + + flagdef = '-D' + cmake_flag + ':BOOL=' + val + args.append(flagdef) + + append_switch('+gmp', 'USE_GMP') + append_switch('+xpce', 'SWIPL_PACKAGES_X') + append_switch('+odbc', 'SWIPL_PACKAGES_ODBC') + + # The variants ssl and zlib are implicitly set up by CMake + + return args diff --git a/var/spack/repos/builtin/packages/symengine/package.py b/var/spack/repos/builtin/packages/symengine/package.py index e2cc2cef7f..ceb1b9a5ed 100644 --- a/var/spack/repos/builtin/packages/symengine/package.py +++ b/var/spack/repos/builtin/packages/symengine/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,6 +15,7 @@ class Symengine(CMakePackage): git = "https://github.com/symengine/symengine.git" version('develop', branch='master') + version('0.5.0', sha256='5d02002f00d16a0928d1056e6ecb8f34fd59f3bfd8ed0009a55700334dbae29b') version('0.4.0', sha256='dd755901a9e2a49e53ba3bbe3f565f94265af05299e57a7b592186dd35916a1b') version('0.3.0', sha256='591463cb9e741d59f6dfd39a7943e3865d3afe9eac47d1a9cbf5ca74b9c49476') version('0.2.0', sha256='64d050b0b9decd12bf4ea3b7d18d3904dd7cb8baaae9fbac1b8068e3c59709be') diff --git a/var/spack/repos/builtin/packages/sympol/package.py b/var/spack/repos/builtin/packages/sympol/package.py index ed9623c74c..70e860953a 100644 --- a/var/spack/repos/builtin/packages/sympol/package.py +++ b/var/spack/repos/builtin/packages/sympol/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/sysstat/package.py b/var/spack/repos/builtin/packages/sysstat/package.py new file mode 100644 index 0000000000..4d6ec48bc2 --- /dev/null +++ b/var/spack/repos/builtin/packages/sysstat/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Sysstat(AutotoolsPackage): + """The sysstat package contains various utilities, common to many + commercial Unixes, to monitor system performance and usage activity + Sysstat also contains tools you can schedule via cron or systemd to + collect and historize performance and activity data.""" + + homepage = "https://github.com/sysstat" + url = "https://github.com/sysstat/sysstat/archive/v12.1.6.tar.gz" + + version('12.2.0', sha256='614ab9fe8e7937a3edb7b2b6760792a3764ea3a7310ac540292dd0e3dfac86a6') + version('12.1.7', sha256='293b31ca414915896c639a459f4d03a742b3a472953975394bef907b245b3a9f') + version('12.1.6', sha256='50f4cbf023f8b933ed6f1fee0e6d33e508d9dc20355a47f6927e0c6046c6acf6') + version('12.1.5', sha256='d0ea36f278fe10c7978be2a383cb8055c1277d60687ac9030ba694a08a80f6ff') diff --git a/var/spack/repos/builtin/packages/sz/fix_optimization.patch b/var/spack/repos/builtin/packages/sz/fix_optimization.patch new file mode 100644 index 0000000000..208a7791ee --- /dev/null +++ b/var/spack/repos/builtin/packages/sz/fix_optimization.patch @@ -0,0 +1,11 @@ +--- spack-src/configure.org 2019-12-05 10:58:07.408584611 +0900 ++++ spack-src/configure 2019-12-05 10:58:29.670909716 +0900 +@@ -3019,7 +3019,7 @@ + + + # Checks for programs. +-: ${CFLAGS=-O3 -std=c99 -Wall} ++: ${CFLAGS=-O2 -std=c99 -Wall} + ac_ext=c + ac_cpp='$CPP $CPPFLAGS' + ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' diff --git a/var/spack/repos/builtin/packages/sz/package.py b/var/spack/repos/builtin/packages/sz/package.py index 955503bfbf..3453a5675e 100644 --- a/var/spack/repos/builtin/packages/sz/package.py +++ b/var/spack/repos/builtin/packages/sz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -11,11 +11,14 @@ class Sz(AutotoolsPackage): """Error-bounded Lossy Compressor for HPC Data.""" homepage = "https://collab.cels.anl.gov/display/ESR/SZ" - url = "https://github.com/disheng222/SZ/archive/v2.0.2.0.tar.gz" + url = "https://github.com/disheng222/SZ/archive/v2.1.8.0.tar.gz" + maintainers = ['disheng222'] + parallel = False git = "https://github.com/disheng222/SZ.git" version('develop', branch='master') + version('2.1.8.0', sha256='8d6bceb59a03d52e601e29d9b35c21b146c248abae352f9a4828e91d8d26aa24') version('2.0.2.0', sha256='176c65b421bdec8e91010ffbc9c7bf7852c799972101d6b66d2a30d9702e59b0') version('1.4.13.5', sha256='b5e37bf3c377833eed0a7ca0471333c96cd2a82863abfc73893561aaba5f18b9') version('1.4.13.4', sha256='c99b95793c48469cac60e6cf82f921babf732ca8c50545a719e794886289432b') @@ -32,6 +35,10 @@ class Sz(AutotoolsPackage): variant('fortran', default=False, description='Enable fortran compilation') + # Part of latest sources don't support -O3 optimization + # with Fujitsu compiler. + patch('fix_optimization.patch', when='@2.0.2.0:%fj') + def configure_args(self): args = [] if '+fortran' in self.spec: diff --git a/var/spack/repos/builtin/packages/tabix/package.py b/var/spack/repos/builtin/packages/tabix/package.py index 47208e6e7a..2e358da82d 100644 --- a/var/spack/repos/builtin/packages/tabix/package.py +++ b/var/spack/repos/builtin/packages/tabix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tajo/package.py b/var/spack/repos/builtin/packages/tajo/package.py new file mode 100644 index 0000000000..5fb12d6bd3 --- /dev/null +++ b/var/spack/repos/builtin/packages/tajo/package.py @@ -0,0 +1,36 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Tajo(Package): + """ + Tajo is a relational and distributed data warehouse system for Hadoop + Tajo is designed for low-latency and scalable ad-hoc queries, online + aggregation and ETL on large-data sets by leveraging advanced database + techniques. It supports SQL standards. It has its own query engine which + allows direct control of distributed execution and data flow. As a result, + Tajo has a variety of query evaluation strategies and more optimization + opportunities. In addition, Tajo will have a native columnar execution + and and its optimizer. + """ + + homepage = "http://tajo.apache.org/" + url = "https://www-eu.apache.org/dist/tajo/tajo-0.11.3/tajo-0.11.3.tar.gz" + list_url = "https://www-eu.apache.org/dist/tajo/" + list_depth = 1 + + version('0.11.3', sha256='9be736f13575aefc68f94eff376ef284ca3af8b0bdceb6d9d825980bb10a44e8') + version('0.11.2', sha256='8a7a5b63b799cd3db275f3a3e265063594c60ec6b8ca394bf2c88b1d1867779f') + version('0.11.1', sha256='723a2bf02c1109652aabc5786b087634dcca014083569d368a9d4ce118d87b91') + version('0.11.0', sha256='0714b4c49afdd40010f9d1af9443a2a38453157f6352abd908da6ebfafa8abca') + version('0.10.1', sha256='754bd6d34fd4ed1b142d50b9025747167c3fbf819ee04711aca8d8842a53a625') + version('0.10.0', sha256='66e56ac5948e01779d9bf14f9a3f8145dec9ed3273b84dd66d9f08d581dad433') + + depends_on('java', type='run') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/talass/package.py b/var/spack/repos/builtin/packages/talass/package.py index 42406fa464..4633eb9cf5 100644 --- a/var/spack/repos/builtin/packages/talass/package.py +++ b/var/spack/repos/builtin/packages/talass/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/talloc/package.py b/var/spack/repos/builtin/packages/talloc/package.py index b7c81bdc60..0172ef46dc 100644 --- a/var/spack/repos/builtin/packages/talloc/package.py +++ b/var/spack/repos/builtin/packages/talloc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tantan/package.py b/var/spack/repos/builtin/packages/tantan/package.py index f4dc72643a..d9a8847635 100644 --- a/var/spack/repos/builtin/packages/tantan/package.py +++ b/var/spack/repos/builtin/packages/tantan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tar/package.py b/var/spack/repos/builtin/packages/tar/package.py index 3ef16bbfcd..de12fd2344 100644 --- a/var/spack/repos/builtin/packages/tar/package.py +++ b/var/spack/repos/builtin/packages/tar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,12 +6,12 @@ from spack import * -class Tar(AutotoolsPackage): +class Tar(AutotoolsPackage, GNUMirrorPackage): """GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation.""" homepage = "https://www.gnu.org/software/tar/" - url = "https://ftpmirror.gnu.org/tar/tar-1.32.tar.gz" + gnu_mirror_path = "tar/tar-1.32.tar.gz" version('1.32', sha256='b59549594d91d84ee00c99cf2541a3330fed3a42c440503326dab767f2fbb96c') version('1.31', sha256='b471be6cb68fd13c4878297d856aebd50551646f4e3074906b1a74549c40d5a2') diff --git a/var/spack/repos/builtin/packages/targetp/package.py b/var/spack/repos/builtin/packages/targetp/package.py index 98dd560103..7d691f2fc7 100644 --- a/var/spack/repos/builtin/packages/targetp/package.py +++ b/var/spack/repos/builtin/packages/targetp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -44,6 +44,6 @@ class Targetp(Package): install_tree('tmp', prefix.tmp) install('targetp', prefix.targetp) - def setup_environment(self, spack_env, run_env): - run_env.set('TARGETP', self.prefix) - run_env.prepend_path('PATH', self.prefix) + def setup_run_environment(self, env): + env.set('TARGETP', self.prefix) + env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/task/package.py b/var/spack/repos/builtin/packages/task/package.py index 3aa1722eef..4d1d54565c 100644 --- a/var/spack/repos/builtin/packages/task/package.py +++ b/var/spack/repos/builtin/packages/task/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/taskd/package.py b/var/spack/repos/builtin/packages/taskd/package.py index 4d038cd18b..1456d4cabb 100644 --- a/var/spack/repos/builtin/packages/taskd/package.py +++ b/var/spack/repos/builtin/packages/taskd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tasmanian/package.py b/var/spack/repos/builtin/packages/tasmanian/package.py index 3b4a7682d3..87ddc99db4 100644 --- a/var/spack/repos/builtin/packages/tasmanian/package.py +++ b/var/spack/repos/builtin/packages/tasmanian/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tassel/package.py b/var/spack/repos/builtin/packages/tassel/package.py index f78e9e19a0..7de1648af4 100644 --- a/var/spack/repos/builtin/packages/tassel/package.py +++ b/var/spack/repos/builtin/packages/tassel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,5 +21,5 @@ class Tassel(Package): def install(self, spec, prefix): install_tree('.', prefix.bin) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('CLASSPATH', prefix.bin.lib) + def setup_run_environment(self, env): + env.prepend_path('CLASSPATH', self.prefix.bin.lib) diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py index 50c826b610..2aadb64590 100644 --- a/var/spack/repos/builtin/packages/tau/package.py +++ b/var/spack/repos/builtin/packages/tau/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -262,7 +262,7 @@ class Tau(Package): if os.path.isdir(src) and not os.path.exists(dest): os.symlink(join_path(subdir, d), dest) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): pattern = join_path(self.prefix.lib, 'Makefile.*') files = glob.glob(pattern) @@ -272,4 +272,4 @@ class Tau(Package): # directory to inspect. The conditional below will set `TAU_MAKEFILE` # in the latter case. if files: - run_env.set('TAU_MAKEFILE', files[0]) + env.set('TAU_MAKEFILE', files[0]) diff --git a/var/spack/repos/builtin/packages/tcl-itcl/package.py b/var/spack/repos/builtin/packages/tcl-itcl/package.py index ec6457e69d..370f37872b 100644 --- a/var/spack/repos/builtin/packages/tcl-itcl/package.py +++ b/var/spack/repos/builtin/packages/tcl-itcl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tcl-tcllib/package.py b/var/spack/repos/builtin/packages/tcl-tcllib/package.py index ea985d3b9d..4f372e7aa3 100644 --- a/var/spack/repos/builtin/packages/tcl-tcllib/package.py +++ b/var/spack/repos/builtin/packages/tcl-tcllib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tcl-tclxml/package.py b/var/spack/repos/builtin/packages/tcl-tclxml/package.py index a11268bfb3..086edbf9bc 100644 --- a/var/spack/repos/builtin/packages/tcl-tclxml/package.py +++ b/var/spack/repos/builtin/packages/tcl-tclxml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py index a76c748262..28ee2bd2a4 100644 --- a/var/spack/repos/builtin/packages/tcl/package.py +++ b/var/spack/repos/builtin/packages/tcl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -97,17 +97,17 @@ class Tcl(AutotoolsPackage): return join_path(self.tcl_lib_dir, 'tcl{0}'.format(self.version.up_to(2))) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # When using Tkinter from within spack provided python+tkinter, python # will not be able to find Tcl/Tk unless TCL_LIBRARY is set. - run_env.set('TCL_LIBRARY', join_path(self.prefix, self.tcl_lib_dir)) + env.set('TCL_LIBRARY', join_path(self.prefix, self.tcl_lib_dir)) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Set TCLLIBPATH to include the tcl-shipped directory for extensions and any other tcl extension it depends on. For further info see: https://wiki.tcl.tk/1787""" - spack_env.set('TCL_LIBRARY', join_path(self.prefix, self.tcl_lib_dir)) + env.set('TCL_LIBRARY', join_path(self.prefix, self.tcl_lib_dir)) # If we set TCLLIBPATH, we must also ensure that the corresponding # tcl is found in the build environment. This to prevent cases @@ -116,7 +116,7 @@ class Tcl(AutotoolsPackage): # it boils down to the same situation we have here. path = os.path.dirname(self.command.path) if not is_system_path(path): - spack_env.prepend_path('PATH', path) + env.prepend_path('PATH', path) tcl_paths = [join_path(self.prefix, self.tcl_builtin_lib_dir)] @@ -130,12 +130,16 @@ class Tcl(AutotoolsPackage): # "TCLLIBPATH is a Tcl list, not some platform-specific # colon-separated or semi-colon separated format" tcllibpath = ' '.join(tcl_paths) - spack_env.set('TCLLIBPATH', tcllibpath) + env.set('TCLLIBPATH', tcllibpath) + + def setup_dependent_run_environment(self, env, dependent_spec): + """Set TCLLIBPATH to include the tcl-shipped directory for + extensions and any other tcl extension it depends on. + For further info see: https://wiki.tcl.tk/1787""" # For run time environment set only the path for # dependent_spec and prepend it to TCLLIBPATH if dependent_spec.package.extends(self.spec): dependent_tcllibpath = join_path(dependent_spec.prefix, self.tcl_lib_dir) - run_env.prepend_path('TCLLIBPATH', dependent_tcllibpath, - separator=' ') + env.prepend_path('TCLLIBPATH', dependent_tcllibpath, separator=' ') diff --git a/var/spack/repos/builtin/packages/tclap/package.py b/var/spack/repos/builtin/packages/tclap/package.py index 39e4386f31..6097dfbcde 100644 --- a/var/spack/repos/builtin/packages/tclap/package.py +++ b/var/spack/repos/builtin/packages/tclap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tcoffee/package.py b/var/spack/repos/builtin/packages/tcoffee/package.py index 4742cc2fe8..36cf8a6389 100644 --- a/var/spack/repos/builtin/packages/tcoffee/package.py +++ b/var/spack/repos/builtin/packages/tcoffee/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tcptrace/package.py b/var/spack/repos/builtin/packages/tcptrace/package.py index 97d5321b70..b2e41e8d26 100644 --- a/var/spack/repos/builtin/packages/tcptrace/package.py +++ b/var/spack/repos/builtin/packages/tcptrace/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tcsh/package.py b/var/spack/repos/builtin/packages/tcsh/package.py index 505ae92ce3..19bdde1503 100644 --- a/var/spack/repos/builtin/packages/tcsh/package.py +++ b/var/spack/repos/builtin/packages/tcsh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tealeaf/package.py b/var/spack/repos/builtin/packages/tealeaf/package.py index 834f99db38..53c4c7c090 100644 --- a/var/spack/repos/builtin/packages/tealeaf/package.py +++ b/var/spack/repos/builtin/packages/tealeaf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ class Tealeaf(MakefilePackage): """ homepage = "http://uk-mac.github.io/TeaLeaf/" - url = "http://mantevo.org/downloads/releaseTarballs/miniapps/TeaLeaf/TeaLeaf-1.0.tar.gz" + url = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/TeaLeaf-1.0.tar.gz" tags = ['proxy-app'] diff --git a/var/spack/repos/builtin/packages/teckit/package.py b/var/spack/repos/builtin/packages/teckit/package.py new file mode 100644 index 0000000000..f8ac04816a --- /dev/null +++ b/var/spack/repos/builtin/packages/teckit/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Teckit(AutotoolsPackage): + """TECkit is a low-level toolkit intended to be used by applications for + conversions between text encodings. For example, it can be used when + importing legacy text into a Unicode-based application. + + The primary component of TECkit is a library: the TECkit engine. The engine + relies on mapping tables in a specific, documented binary format. The + TECkit compiler creates these tables from plain-text, human-readable + descriptions.""" + + homepage = "https://scripts.sil.org/cms/scripts/page.php?cat_id=TECkit" + url = "https://github.com/silnrsi/teckit/releases/download/v2.5.9/teckit-2.5.9.tar.gz" + + version('2.5.9', sha256='6823fb3142efa34e5d74de35d37cdf4724efbf577f5ff15a8e2b364e6ef47d3d') + + depends_on('expat') + depends_on('zlib') + + def configure_args(self): + args = ['--with-system-zlib'] + return args diff --git a/var/spack/repos/builtin/packages/tecplot/package.py b/var/spack/repos/builtin/packages/tecplot/package.py index 6501c78ce7..d741cb7df7 100644 --- a/var/spack/repos/builtin/packages/tecplot/package.py +++ b/var/spack/repos/builtin/packages/tecplot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/templight-tools/package.py b/var/spack/repos/builtin/packages/templight-tools/package.py index 1c558cdc7e..debc9e82ce 100644 --- a/var/spack/repos/builtin/packages/templight-tools/package.py +++ b/var/spack/repos/builtin/packages/templight-tools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/templight/package.py b/var/spack/repos/builtin/packages/templight/package.py index 34f75964e1..371999266d 100644 --- a/var/spack/repos/builtin/packages/templight/package.py +++ b/var/spack/repos/builtin/packages/templight/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -101,10 +101,12 @@ class Templight(CMakePackage): with open("tools/clang/tools/CMakeLists.txt", "a") as cmake_lists: cmake_lists.write("add_clang_subdirectory(templight)") - def setup_environment(self, spack_env, run_env): - spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag) - run_env.set('CC', join_path(self.spec.prefix.bin, 'templight')) - run_env.set('CXX', join_path(self.spec.prefix.bin, 'templight++')) + def setup_build_environment(self, env): + env.append_flags('CXXFLAGS', self.compiler.cxx11_flag) + + def setup_run_environment(self, env): + env.set('CC', join_path(self.spec.prefix.bin, 'templight')) + env.set('CXX', join_path(self.spec.prefix.bin, 'templight++')) def cmake_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/tensorflow-serving-client/package.py b/var/spack/repos/builtin/packages/tensorflow-serving-client/package.py new file mode 100644 index 0000000000..6b2b74649f --- /dev/null +++ b/var/spack/repos/builtin/packages/tensorflow-serving-client/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class TensorflowServingClient(CMakePackage): + """A prebuilt tensorflow serving client from the tensorflow serving + proto files""" + + homepage = "https://github.com/figroc/tensorflow-serving-client" + url = "https://github.com/figroc/tensorflow-serving-client/archive/v2.1.0.tar.gz" + + version('2.1.0', sha256='7a31d8cfa1d861f73953d4728665dd6d74e205d1fa01062a6c2b1aeee4674f73') + version('2.0.0', sha256='55310ad484f257173ad5194df7f7116b2049260c3d29049ef8d789d1d8bd9948') + + depends_on('protobuf') + depends_on('grpc') diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py index 34926fabac..6d434c6e14 100644 --- a/var/spack/repos/builtin/packages/tetgen/package.py +++ b/var/spack/repos/builtin/packages/tetgen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tethex/package.py b/var/spack/repos/builtin/packages/tethex/package.py index 3b78e89d7d..88c3412b66 100644 --- a/var/spack/repos/builtin/packages/tethex/package.py +++ b/var/spack/repos/builtin/packages/tethex/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/texinfo/fix_unescaped_braces.patch b/var/spack/repos/builtin/packages/texinfo/fix_unescaped_braces.patch new file mode 100644 index 0000000000..d473151116 --- /dev/null +++ b/var/spack/repos/builtin/packages/texinfo/fix_unescaped_braces.patch @@ -0,0 +1,16 @@ +--- spack-src/tp/Texinfo/Parser.pm.org 2019-11-18 15:02:20.184202910 +0900 ++++ spack-src/tp/Texinfo/Parser.pm 2019-11-18 15:02:46.927022528 +0900 +@@ -5478,11 +5478,11 @@ + } + } elsif ($command eq 'clickstyle') { + # REMACRO +- if ($line =~ /^\s+@([[:alnum:]][[:alnum:]\-]*)({})?\s*/) { ++ if ($line =~ /^\s+@([[:alnum:]][[:alnum:]\-]*)(\{\})?\s*/) { + $args = ['@'.$1]; + $self->{'clickstyle'} = $1; + $remaining = $line; +- $remaining =~ s/^\s+@([[:alnum:]][[:alnum:]\-]*)({})?\s*(\@(c|comment)((\@|\s+).*)?)?//; ++ $remaining =~ s/^\s+@([[:alnum:]][[:alnum:]\-]*)(\{\})?\s*(\@(c|comment)((\@|\s+).*)?)?//; + $has_comment = 1 if (defined($4)); + } else { + $self->line_error (sprintf($self->__( diff --git a/var/spack/repos/builtin/packages/texinfo/fix_unescaped_braces_2.patch b/var/spack/repos/builtin/packages/texinfo/fix_unescaped_braces_2.patch new file mode 100644 index 0000000000..0b9d9762b2 --- /dev/null +++ b/var/spack/repos/builtin/packages/texinfo/fix_unescaped_braces_2.patch @@ -0,0 +1,17 @@ +--- texinfo-6.0/tp/Texinfo/Parser.pm.org 2019-11-20 15:51:15.193575181 +0900 ++++ texinfo-6.0/tp/Texinfo/Parser.pm 2019-11-20 15:51:59.648252047 +0900 +@@ -5650,12 +5650,12 @@ + } + } elsif ($command eq 'clickstyle') { + # REMACRO +- if ($line =~ /^\s+@([[:alnum:]][[:alnum:]\-]*)({})?\s*/) { ++ if ($line =~ /^\s+@([[:alnum:]][[:alnum:]\-]*)(\{\})?\s*/) { + $args = ['@'.$1]; + $self->{'clickstyle'} = $1 + unless(_ignore_global_commands($self)); + $remaining = $line; +- $remaining =~ s/^\s+@([[:alnum:]][[:alnum:]\-]*)({})?\s*(\@(c|comment)((\@|\s+).*)?)?//; ++ $remaining =~ s/^\s+@([[:alnum:]][[:alnum:]\-]*)(\{\})?\s*(\@(c|comment)((\@|\s+).*)?)?//; + $has_comment = 1 if (defined($4)); + } else { + $self->line_error (sprintf($self->__( diff --git a/var/spack/repos/builtin/packages/texinfo/fix_unescaped_braces_3.patch b/var/spack/repos/builtin/packages/texinfo/fix_unescaped_braces_3.patch new file mode 100644 index 0000000000..1df58784a1 --- /dev/null +++ b/var/spack/repos/builtin/packages/texinfo/fix_unescaped_braces_3.patch @@ -0,0 +1,17 @@ +--- texinfo-5.0/tp/Texinfo/Parser.pm.org 2019-11-20 15:53:10.625719249 +0900 ++++ texinfo-5.0/tp/Texinfo/Parser.pm 2019-11-20 15:53:42.949119841 +0900 +@@ -5299,12 +5299,12 @@ + } + } elsif ($command eq 'clickstyle') { + # REMACRO +- if ($line =~ /^\s+@([[:alnum:]][[:alnum:]\-]*)({})?\s*/) { ++ if ($line =~ /^\s+@([[:alnum:]][[:alnum:]\-]*)(\{\})?\s*/) { + $args = ['@'.$1]; + $self->{'clickstyle'} = $1 + unless(_ignore_global_commands($self)); + my $remaining = $line; +- $remaining =~ s/^\s+@([[:alnum:]][[:alnum:]\-]*)({})?\s*//; ++ $remaining =~ s/^\s+@([[:alnum:]][[:alnum:]\-]*)(\{\})?\s*//; + $self->line_warn(sprintf($self->__( + "remaining argument on \@%s line: %s"), + $command, $remaining), $line_nr) if ($remaining); diff --git a/var/spack/repos/builtin/packages/texinfo/package.py b/var/spack/repos/builtin/packages/texinfo/package.py index 155c138b45..77af84703f 100644 --- a/var/spack/repos/builtin/packages/texinfo/package.py +++ b/var/spack/repos/builtin/packages/texinfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,7 +7,7 @@ from spack import * -class Texinfo(AutotoolsPackage): +class Texinfo(AutotoolsPackage, GNUMirrorPackage): """Texinfo is the official documentation format of the GNU project. It was invented by Richard Stallman and Bob Chassell many years ago, @@ -15,7 +15,7 @@ class Texinfo(AutotoolsPackage): of the time. It is used by many non-GNU projects as well.""" homepage = "https://www.gnu.org/software/texinfo/" - url = "https://ftpmirror.gnu.org/texinfo/texinfo-6.0.tar.gz" + gnu_mirror_path = "texinfo/texinfo-6.0.tar.gz" version('6.5', sha256='d34272e4042c46186ddcd66bd5d980c0ca14ff734444686ccf8131f6ec8b1427') version('6.3', sha256='300a6ba4958c2dd4a6d5ce60f0a335daf7e379f5374f276f6ba31a221f02f606') @@ -25,3 +25,14 @@ class Texinfo(AutotoolsPackage): version('5.0', sha256='2c579345a39a2a0bb4b8c28533f0b61356504a202da6a25d17d4d866af7f5803') depends_on('perl') + + # Fix unescaped braces in regexps. + # Ref: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=898994 + patch('fix_unescaped_braces.patch', when='@6.3:') + patch('fix_unescaped_braces_2.patch', when='@5.1:6.0') + patch('fix_unescaped_braces_3.patch', when='@5.0') + + # Apply this fix to perform thread-safe processing in code + # that uses the global locale. + # Ref: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=902771 + patch('update_locale_handling.patch', when='@6.3:') diff --git a/var/spack/repos/builtin/packages/texinfo/update_locale_handling.patch b/var/spack/repos/builtin/packages/texinfo/update_locale_handling.patch new file mode 100644 index 0000000000..12c2024ada --- /dev/null +++ b/var/spack/repos/builtin/packages/texinfo/update_locale_handling.patch @@ -0,0 +1,25 @@ +--- spack-src/tp/Texinfo/Convert/XSParagraph/xspara.c.org 2019-11-18 17:33:07.717005871 +0900 ++++ spack-src/tp/Texinfo/Convert/XSParagraph/xspara.c 2019-11-18 17:34:56.318436594 +0900 +@@ -248,6 +248,11 @@ + + dTHX; + ++#if PERL_VERSION > 27 || (PERL_VERSION == 27 && PERL_SUBVERSION > 8) ++ /* needed due to thread-safe locale handling in newer perls */ ++ switch_to_global_locale(); ++#endif ++ + if (setlocale (LC_CTYPE, "en_US.UTF-8") + || setlocale (LC_CTYPE, "en_US.utf8")) + goto success; +@@ -319,6 +324,10 @@ + else + { + success: ; ++#if PERL_VERSION > 27 || (PERL_VERSION == 27 && PERL_SUBVERSION > 8) ++ /* needed due to thread-safe locale handling in newer perls */ ++ sync_locale(); ++#endif + free (utf8_locale); + /* + fprintf (stderr, "tried to set LC_CTYPE to UTF-8.\n"); diff --git a/var/spack/repos/builtin/packages/texlive/package.py b/var/spack/repos/builtin/packages/texlive/package.py index cd8e685bbc..42969052c8 100644 --- a/var/spack/repos/builtin/packages/texlive/package.py +++ b/var/spack/repos/builtin/packages/texlive/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,29 +6,67 @@ from spack import * import os import platform +import glob -class Texlive(Package): - """TeX Live is a free software distribution for the TeX typesetting - system. Heads up, it's is not a reproducible installation.""" +class Texlive(AutotoolsPackage): + """TeX Live is an easy (we hope) way to get up and running with the TeX + document production system. It provides a comprehensive TeX system with + binaries for most flavors of Unix, including GNU/Linux, macOS, and also + Windows. It includes all the major TeX-related programs, macro packages, + and fonts that are free software, including support for many languages + around the world.""" homepage = "http://www.tug.org/texlive" + url = 'http://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2019/texlive-20190410-source.tar.xz' + base_url = 'http://ftp.math.utah.edu/pub/tex/historic/systems/texlive/{year}/texlive-{version}-{dist}.tar.xz' + list_url = 'http://ftp.math.utah.edu/pub/tex/historic/systems/texlive' + list_depth = 1 - # Install from specific site because the texlive mirrors do not - # all update in synchrony. - # - # BEWARE: TexLive updates their installs frequently (probably why - # they call it *Live*...). There is no good way to provide a - # repeatable install of the package. - # - # We're now pulling the installation bits from tug.org's repo of - # historic bits. This means that the checksum for the installer - # itself is stable. Don't let that fool you though, it's still - # installing TeX **LIVE** from e.g. ctan.math.... below, which is - # not reproducible. + # Below is the url for a binary distribution. This was originally how this + # was distributed in Spack, but should be considered deprecated. Note that + # the "live" version will pull down the packages so it requires an Internet + # connection at install time and the package versions could change over + # time. It is better to use a version built from tarballs, as defined with + # the "releases" below. version('live', sha256='44aa41b5783e345b7021387f19ac9637ff1ce5406a59754230c666642dfe7750', url='ftp://tug.org/historic/systems/texlive/2019/install-tl-unx.tar.gz') + # Add information for new versions below. + releases = [ + { + 'version': '20190410', + 'year': '2019', + 'sha256_source': 'd2a29fef04e34dc3d2d2296c18995fc357aa7625e7a6bbf40fb92d83d3d0d7b5', + 'sha256_texmf': 'c2ec974abc98b91995969e7871a0b56dbc80dd8508113ffcff6923e912c4c402', + }, + ] + + for release in releases: + version( + release['version'], + sha256=release['sha256_source'], + url=base_url.format( + year=release['year'], + version=release['version'], + dist='source' + ) + ) + + resource( + name='texmf', + url=base_url.format( + year=release['year'], + version=release['version'], + dist='texmf' + ), + sha256=release['sha256_texmf'], + when='@{0}'.format( + release['version'] + ) + ) + + # The following variant is only for the "live" binary installation. # There does not seem to be a complete list of schemes. # Examples include: # full scheme (everything) @@ -42,15 +80,111 @@ class Texlive(Package): 'scheme', default='small', values=('minimal', 'basic', 'small', 'medium', 'full'), - description='Package subset to install' + description='Package subset to install, only meaningful for "live" ' + 'version' ) - depends_on('perl', type='build') + depends_on('perl', type='build', when='@live') + depends_on('pkgconfig', when='@2019:', type='build') + + depends_on('cairo+X', when='@2019:') + depends_on('freetype', when='@2019:') + depends_on('ghostscript', when='@2019:') + depends_on('gmp', when='@2019:') + depends_on('harfbuzz+graphite2', when='@2019:') + depends_on('icu4c', when='@2019:') + depends_on('libgd', when='@2019:') + depends_on('libpaper', when='@2019:') + depends_on('libpng', when='@2019:') + depends_on('libxaw', when='@2019:') + depends_on('libxt', when='@2019:') + depends_on('mpfr', when='@2019:') + depends_on('perl', when='@2019:') + depends_on('pixman', when='@2019:') + depends_on('poppler', when='@2019:') + depends_on('teckit', when='@2019:') + depends_on('zlib', when='@2019:') + depends_on('zziplib', when='@2019:') + + build_directory = 'spack-build' + + def tex_arch(self): + tex_arch = '{0}-{1}'.format(platform.machine(), + platform.system().lower()) + return tex_arch + + @when('@2019:') + def configure_args(self): + args = [ + '--bindir={0}'.format(join_path(self.prefix.bin, self.tex_arch())), + '--disable-dvisvgm', + '--disable-native-texlive-build', + '--disable-static', + '--enable-shared', + '--with-banner-add= - Spack', + '--dataroot={0}'.format(self.prefix), + '--with-system-cairo', + '--with-system-freetype2', + '--with-system-gd', + '--with-system-gmp', + '--with-system-graphite2', + '--with-system-harfbuzz', + '--with-system-icu', + '--with-system-libpaper', + '--with-system-libpng', + '--with-system-mpfr', + '--with-system-pixman', + '--with-system-poppler', + '--with-system-teckit', + '--with-system-zlib', + '--with-system-zziplib', + ] + + return args + + @run_after('install') + def setup_texlive(self): + if not self.spec.satisfies('@live'): + mkdirp(self.prefix.tlpkg.TeXLive) + for files in glob.glob('texk/tests/TeXLive/*'): + install(files, self.prefix.tlpkg.TeXLive) + + with working_dir('spack-build'): + make('texlinks') + + copy_tree('texlive-{0}-texmf'.format(self.version.string), + self.prefix) + + # Create and run setup utilities + fmtutil_sys = Executable(join_path(self.prefix.bin, + self.tex_arch(), 'fmtutil-sys')) + mktexlsr = Executable(join_path(self.prefix.bin, self.tex_arch(), + 'mktexlsr')) + mtxrun = Executable(join_path(self.prefix.bin, self.tex_arch(), + 'mtxrun')) + mktexlsr() + fmtutil_sys('--all') + mtxrun('--generate') + + else: + pass + + def setup_run_environment(self, env): + env.prepend_path('PATH', join_path(self.prefix.bin, self.tex_arch())) + + @when('@live') + def autoreconf(self, spec, prefix): + touch('configure') + + @when('@live') + def configure(self, spec, prefix): + pass - def setup_environment(self, spack_env, run_env): - suffix = "%s-%s" % (platform.machine(), platform.system().lower()) - run_env.prepend_path('PATH', join_path(self.prefix.bin, suffix)) + @when('@live') + def build(self, spec, prefix): + pass + @when('@live') def install(self, spec, prefix): # Using texlive's mirror system leads to mysterious problems, # in lieu of being able to specify a repository as a variant, hardwire diff --git a/var/spack/repos/builtin/packages/texstudio/package.py b/var/spack/repos/builtin/packages/texstudio/package.py index 4c59d2a482..888a8679a8 100644 --- a/var/spack/repos/builtin/packages/texstudio/package.py +++ b/var/spack/repos/builtin/packages/texstudio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/textparser/package.py b/var/spack/repos/builtin/packages/textparser/package.py index 3f38d21f85..85252633a0 100644 --- a/var/spack/repos/builtin/packages/textparser/package.py +++ b/var/spack/repos/builtin/packages/textparser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tfel/package.py b/var/spack/repos/builtin/packages/tfel/package.py index 910508be6d..86305d69f8 100644 --- a/var/spack/repos/builtin/packages/tfel/package.py +++ b/var/spack/repos/builtin/packages/tfel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -29,12 +29,13 @@ class Tfel(CMakePackage): """ homepage = "http://tfel.sourceforge.net" - url = "https://github.com/thelfer/tfel/archive/TFEL-3.2.0.tar.gz" + url = "https://github.com/thelfer/tfel/archive/TFEL-3.3.0.tar.gz" git = "https://github.com/thelfer/tfel.git" maintainers = ['thelfer'] # development branches version("master", branch="master") + version("rliv-3.3", branch="rliv-3.3") version("rliv-3.2", branch="rliv-3.2") version("rliv-3.1", branch="rliv-3.1") version("rliv-3.0", branch="rliv-3.0") @@ -42,13 +43,17 @@ class Tfel(CMakePackage): version("rliv-1.2", branch="rliv-1.2") # released version + version('3.3.0', sha256='884ad68b0fbbededc3a602d559433c24114ae4534dc9f0a759d31ca3589dace0') + version('3.2.2', sha256='69b01ae0d1f9140b619aaa9135948284ff40d4654672c335e55ab4934c02eb43') version('3.2.1', sha256='12786480524a7fe86889120fb334fa00211dfd44ad5ec71e2279e7adf1ddc807') version('3.2.0', sha256='089d79745e9f267a2bd03dcd8841d484e668bd27f5cc2ff7453634cb39016848') + version('3.1.5', sha256='e22cf2110f19666f004b8acda32e87beae74721f82e7f83fd0c4fafb86812763') version('3.1.4', sha256='8dc2904fc930636976baaf7e91ac89c0377afb1629c336343dfad8ab651cf87d') version('3.1.3', sha256='2022fa183d2c2902ada982ec6550ebe15befafcb748fd988fc9accdde7976a42') version('3.1.2', sha256='2eaa191f0699031786d8845ac769320a42c7e035991d82b3738289886006bfba') version('3.1.1', sha256='a4c0c21c6c22752cc90c82295a6bafe637b3395736c66fcdfcfe4aeccb5be7af') version('3.1.0', sha256='dd67b400b5f157aef503aa3615b9bf6b52333876a29e75966f94ee3f79ab37ad') + version('3.0.5', sha256='abf58f87962cf98b6129e873a841819a2a751f2ebd4e08490eb89fb933cd7887') version('3.0.4', sha256='e832d421a0dc9f315c60c5ea23f958dcaa299913c50a4eb73bde0e053067a3cc') version('3.0.3', sha256='3ff1c14bcc27e9b615aab5748eaf3afac349050b27b55a2b57648aba28b801ac') version('3.0.2', sha256='edd54ac652e99621410137ea2f7f90f133067615a17840440690365e2c3906f5') @@ -81,6 +86,12 @@ class Tfel(CMakePackage): variant('java', default=False, description='Enables java interface') + # only since TFEL-3.3, no effect on version below + variant('comsol', default=True, + description='Enables comsol interface') + variant('diana-fea', default=True, + description='Enables DIANA-FEA interface') + variant('build_type', default='Release', description='The build type to build', values=('Debug', 'Release')) @@ -99,7 +110,8 @@ class Tfel(CMakePackage): args = [] for i in ['fortran', 'java', 'aster', 'abaqus', 'calculix', - 'ansys', 'europlexus', 'cyrano', 'lsdyna', 'python']: + 'ansys', 'europlexus', 'cyrano', 'lsdyna', 'python', + 'comsol', 'diana-fea']: if '+' + i in self.spec: args.append("-Denable-{0}=ON".format(i)) else: @@ -128,5 +140,7 @@ class Tfel(CMakePackage): if '+python_bindings' in self.spec: args.append('-DBOOST_ROOT={0}'. format(self.spec['boost'].prefix)) + args.append('-DBoost_NO_SYSTEM_PATHS=ON') + args.append('-DBoost_NO_BOOST_CMAKE=ON') return args diff --git a/var/spack/repos/builtin/packages/the-platinum-searcher/package.py b/var/spack/repos/builtin/packages/the-platinum-searcher/package.py index 25ede7c527..9c7c6a68a0 100644 --- a/var/spack/repos/builtin/packages/the-platinum-searcher/package.py +++ b/var/spack/repos/builtin/packages/the-platinum-searcher/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/the-silver-searcher/package.py b/var/spack/repos/builtin/packages/the-silver-searcher/package.py index 72fb8ded9d..905fdabba2 100644 --- a/var/spack/repos/builtin/packages/the-silver-searcher/package.py +++ b/var/spack/repos/builtin/packages/the-silver-searcher/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/thornado-mini/package.py b/var/spack/repos/builtin/packages/thornado-mini/package.py index a676848f62..34e40e8233 100644 --- a/var/spack/repos/builtin/packages/thornado-mini/package.py +++ b/var/spack/repos/builtin/packages/thornado-mini/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py index 0644ed1fea..92f77e0331 100644 --- a/var/spack/repos/builtin/packages/thrift/package.py +++ b/var/spack/repos/builtin/packages/thrift/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,8 +17,10 @@ class Thrift(Package): """ homepage = "http://thrift.apache.org" - url = "http://apache.mirrors.ionfish.org/thrift/0.9.2/thrift-0.9.2.tar.gz" + url = "http://apache.mirrors.ionfish.org/thrift/0.11.0/thrift-0.11.0.tar.gz" + version('0.13.0', sha256='7ad348b88033af46ce49148097afe354d513c1fca7c607b59c33ebb6064b5179') + version('0.12.0', sha256='c336099532b765a6815173f62df0ed897528a9d551837d627c1f87fadad90428') version('0.11.0', sha256='c4ad38b6cb4a3498310d405a91fef37b9a8e79a50cd0968148ee2524d2fa60c2') version('0.10.0', sha256='2289d02de6e8db04cbbabb921aeb62bfe3098c4c83f36eec6c31194301efa10b') version('0.9.3', sha256='b0740a070ac09adde04d43e852ce4c320564a292f26521c46b78e0641564969e') @@ -47,10 +49,10 @@ class Thrift(Package): depends_on('zlib', when='+c') depends_on('libevent', when='+c') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if '+pic' in self.spec: - spack_env.append_flags('CFLAGS', self.compiler.pic_flag) - spack_env.append_flags('CXXFLAGS', self.compiler.pic_flag) + env.append_flags('CFLAGS', self.compiler.pic_flag) + env.append_flags('CXXFLAGS', self.compiler.pic_flag) def install(self, spec, prefix): env['PY_PREFIX'] = prefix diff --git a/var/spack/repos/builtin/packages/thrust/package.py b/var/spack/repos/builtin/packages/thrust/package.py index 59152487c0..fb6942afc4 100644 --- a/var/spack/repos/builtin/packages/thrust/package.py +++ b/var/spack/repos/builtin/packages/thrust/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tig/package.py b/var/spack/repos/builtin/packages/tig/package.py index dd78e87561..68e54bc05d 100644 --- a/var/spack/repos/builtin/packages/tig/package.py +++ b/var/spack/repos/builtin/packages/tig/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/time/package.py b/var/spack/repos/builtin/packages/time/package.py index 4f15a7513b..0744b22509 100644 --- a/var/spack/repos/builtin/packages/time/package.py +++ b/var/spack/repos/builtin/packages/time/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -7,12 +7,12 @@ from spack import * -class Time(AutotoolsPackage): +class Time(AutotoolsPackage, GNUMirrorPackage): """The time command runs another program, then displays information about the resources used by that program.""" homepage = "https://www.gnu.org/software/time/" - url = "https://ftpmirror.gnu.org/time/time-1.9.tar.gz" + gnu_mirror_path = "time/time-1.9.tar.gz" version('1.9', sha256='fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e') diff --git a/var/spack/repos/builtin/packages/timemory/package.py b/var/spack/repos/builtin/packages/timemory/package.py new file mode 100644 index 0000000000..53dada7f34 --- /dev/null +++ b/var/spack/repos/builtin/packages/timemory/package.py @@ -0,0 +1,124 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +# +# ---------------------------------------------------------------------------- + +from spack import * + + +class Timemory(CMakePackage): + """Timing + Memory + Hardware Counter Utilities for C/C++/CUDA/Python""" + + homepage = 'https://timemory.readthedocs.io/en/latest/' + git = 'https://github.com/NERSC/timemory.git' + maintainers = ['jrmadsen'] + + version('master', branch='master', submodules=True) + version('develop', branch='develop', submodules=True) + version('3.0.1', commit='ef638e1cde90275ce7c0e12fc4902c27bcbdeefd', + submodules=True) + version('3.0.0', commit='b36b1673b2c6b7ff3126d8261bef0f8f176c7beb', + submodules=True) + + variant('python', default=True, description='Enable Python support') + variant('mpi', default=False, description='Enable MPI support') + variant('tau', default=True, description='Enable TAU support') + variant('papi', default=True, description='Enable PAPI support') + variant('cuda', default=True, description='Enable CUDA support') + variant('cupti', default=True, description='Enable CUPTI support') + variant('upcxx', default=False, description='Enable UPC++ support') + variant('gotcha', default=True, description='Enable GOTCHA support') + variant('likwid', default=True, description='Enable LIKWID support') + variant('caliper', default=True, description='Enable Caliper support') + variant('gperftools', default=True, + description='Enable gperftools support') + + depends_on('cmake@3.11:', type='build') + + extends('python', when='+python') + depends_on('python@3:', when='+python', type=('build', 'run')) + depends_on('py-numpy', when='+python', type=('run')) + depends_on('py-pillow', when='+python', type=('run')) + depends_on('py-matplotlib', when='+python', type=('run')) + depends_on('mpi', when='+mpi') + depends_on('tau', when='+tau') + depends_on('papi', when='+papi') + depends_on('cuda', when='+cuda') + depends_on('cuda', when='+cupti') + depends_on('upcxx', when='+upcxx') + depends_on('gotcha', when='+gotcha') + depends_on('likwid', when='+likwid') + depends_on('caliper', when='+caliper') + depends_on('gperftools', when='+gperftools') + + conflicts('+cupti', when='~cuda', msg='CUPTI requires CUDA') + + def cmake_args(self): + spec = self.spec + + # Use spack install of Caliper and/or GOTCHA + # instead of internal submodule build + args = [ + '-DTIMEMORY_BUILD_GOTCHA=OFF', + '-DTIMEMORY_BUILD_CALIPER=OFF', + '-DTIMEMORY_BUILD_TOOLS=ON', + '-DTIMEMORY_BUILD_TESTING=OFF', + '-DTIMEMORY_BUILD_EXTRA_OPTIMIZATIONS=ON', + '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON', + ] + + if '+python' in spec: + args.append('-DPYTHON_EXECUTABLE={0}'.format( + spec['python'].command.path)) + args.append('-DTIMEMORY_USE_PYTHON=ON') + args.append('-DTIMEMORY_BUILD_PYTHON=ON') + args.append('-DTIMEMORY_TLS_MODEL=global-dynamic') + else: + args.append('-DTIMEMORY_USE_PYTHON=OFF') + args.append('-DTIMEMORY_BUILD_PYTHON=OFF') + + if '+caliper' in spec: + args.append('-DTIMEMORY_USE_CALIPER=ON') + else: + args.append('-DTIMEMORY_USE_CALIPER=OFF') + + if '+tau' in spec: + args.append('-DTIMEMORY_USE_TAU=ON') + else: + args.append('-DTIMEMORY_USE_TAU=OFF') + + if '+likwid' in spec: + args.append('-DTIMEMORY_USE_LIKWID=ON') + else: + args.append('-DTIMEMORY_USE_LIKWID=OFF') + + if '+papi' in spec: + args.append('-DTIMEMORY_USE_PAPI=ON') + args.append('-DPAPI_ROOT_DIR={0}'.format(spec['papi'].prefix)) + else: + args.append('-DTIMEMORY_USE_PAPI=OFF') + + if '+mpi' in spec: + args.append('-DMPI_C_COMPILER={0}'.format(spec['mpi'].mpicc)) + args.append('-DMPI_CXX_COMPILER={0}'.format(spec['mpi'].mpicxx)) + else: + args.append('-DTIMEMORY_USE_MPI=OFF') + + if '+gotcha' in spec: + args.append('-DTIMEMORY_USE_GOTCHA=ON') + else: + args.append('-DTIMEMORY_USE_GOTCHA=OFF') + + if '+cuda' in spec: + args.append('-DTIMEMORY_USE_CUDA=ON') + else: + args.append('-DTIMEMORY_USE_CUDA=OFF') + + if '+cupti' in spec: + args.append('-DTIMEMORY_USE_CUPTI=ON') + else: + args.append('-DTIMEMORY_USE_CUPTI=OFF') + + return args diff --git a/var/spack/repos/builtin/packages/tinker/package.py b/var/spack/repos/builtin/packages/tinker/package.py new file mode 100644 index 0000000000..7a15b81107 --- /dev/null +++ b/var/spack/repos/builtin/packages/tinker/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Tinker(CMakePackage): + """The Tinker molecular modeling software is a complete and general + package for molecular mechanics and dynamics, with some special + features for biopolymers. + """ + + homepage = "https://dasher.wustl.edu/tinker/" + url = "https://dasher.wustl.edu/tinker/downloads/tinker-8.7.1.tar.gz" + + version('8.7.1', sha256='0d6eff8bbc9be0b37d62b6fd3da35bb5499958eafe67aa9c014c4648c8b46d0f') + patch('tinker-8.7.1-cmake.patch') + + depends_on('fftw') + + root_cmakelists_dir = 'source' diff --git a/var/spack/repos/builtin/packages/tinker/tinker-8.7.1-cmake.patch b/var/spack/repos/builtin/packages/tinker/tinker-8.7.1-cmake.patch new file mode 100644 index 0000000000..e07d05a7dc --- /dev/null +++ b/var/spack/repos/builtin/packages/tinker/tinker-8.7.1-cmake.patch @@ -0,0 +1,113 @@ +From c31e54353cf587c83c823544849226840fdb26da Mon Sep 17 00:00:00 2001 +From: Christoph Junghans <junghans@votca.org> +Date: Sat, 23 Nov 2019 19:40:58 -0700 +Subject: [PATCH] add initial version of CMake build system + +--- + source/CMakeLists.txt | 94 +++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 94 insertions(+) + create mode 100644 source/CMakeLists.txt + +diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt +new file mode 100644 +index 0000000..c1f9831 +--- /dev/null ++++ b/source/CMakeLists.txt +@@ -0,0 +1,94 @@ ++cmake_minimum_required(VERSION 3.10) ++ ++project(tinker VERSION 8.7.1 LANGUAGES Fortran) ++ ++include(GNUInstallDirs) ++find_package(PkgConfig REQUIRED) ++pkg_check_modules(FFTW3 REQUIRED IMPORTED_TARGET fftw3) ++ ++add_library(tinker ++ action.f active.f align.f analysis.f analyz.f angang.f angbnd.f ++ angles.f angpot.f angtor.f argue.f ascii.f atmlst.f atomid.f atoms.f ++ attach.f baoab.f basefile.f bath.f beeman.f bicubic.f bitor.f bitors.f ++ bndpot.f bndstr.f bonds.f born.f bound.f bounds.f boxes.f bussi.f ++ calendar.f cell.f center.f charge.f chgpen.f chgpot.f chgtrn.f ++ chkpole.f chkring.f chkxyz.f cholesky.f chrono.f chunks.f clock.f ++ cluster.f column.f command.f connect.f connolly.f control.f couple.f ++ cspline.f ctrpot.f cutoffs.f damping.f deflate.f delete.f deriv.f ++ diagq.f diffeq.f dipole.f disgeo.f disp.f dma.f domega.f dsppot.f ++ eangang.f eangang1.f eangang2.f eangang3.f eangle.f eangle1.f ++ eangle2.f eangle3.f eangtor.f eangtor1.f eangtor2.f eangtor3.f ebond.f ++ ebond1.f ebond2.f ebond3.f ebuck.f ebuck1.f ebuck2.f ebuck3.f ++ echarge.f echarge1.f echarge2.f echarge3.f echgdpl.f echgdpl1.f ++ echgdpl2.f echgdpl3.f echgtrn.f echgtrn1.f echgtrn2.f echgtrn3.f ++ edipole.f edipole1.f edipole2.f edipole3.f edisp.f edisp1.f edisp2.f ++ edisp3.f egauss.f egauss1.f egauss2.f egauss3.f egeom.f egeom1.f ++ egeom2.f egeom3.f ehal.f ehal1.f ehal2.f ehal3.f eimprop.f eimprop1.f ++ eimprop2.f eimprop3.f eimptor.f eimptor1.f eimptor2.f eimptor3.f elj.f ++ elj1.f elj2.f elj3.f embed.f emetal.f emetal1.f emetal2.f emetal3.f ++ emm3hb.f emm3hb1.f emm3hb2.f emm3hb3.f empole.f empole1.f empole2.f ++ empole3.f energi.f energy.f eopbend.f eopbend1.f eopbend2.f eopbend3.f ++ eopdist.f eopdist1.f eopdist2.f eopdist3.f epitors.f epitors1.f ++ epitors2.f epitors3.f epolar.f epolar1.f epolar2.f epolar3.f erepel.f ++ erepel1.f erepel2.f erepel3.f erf.f erxnfld.f erxnfld1.f erxnfld2.f ++ erxnfld3.f esolv.f esolv1.f esolv2.f esolv3.f estrbnd.f estrbnd1.f ++ estrbnd2.f estrbnd3.f estrtor.f estrtor1.f estrtor2.f estrtor3.f ++ etors.f etors1.f etors2.f etors3.f etortor.f etortor1.f etortor2.f ++ etortor3.f eurey.f eurey1.f eurey2.f eurey3.f evcorr.f ewald.f extra.f ++ extra1.f extra2.f extra3.f faces.f fatal.f fft.f fft3d.f fftpack.f ++ field.f fields.f files.f final.f flatten.f fracs.f freeunit.f freeze.f ++ geometry.f getarc.f getint.f getkey.f getmol.f getmol2.f getnumb.f ++ getpdb.f getprm.f getref.f getstring.f gettext.f getword.f getxyz.f ++ ghmcstep.f gkstuf.f gradient.f gradrgd.f gradrot.f group.f groups.f ++ grpline.f gyrate.f hescut.f hessian.f hessn.f hessrgd.f hessrot.f ++ hpmf.f hybrid.f ielscf.f image.f impose.f improp.f imptor.f induce.f ++ inertia.f inform.f initatom.f initial.f initprm.f initres.f initrot.f ++ insert.f inter.f invbeta.f invert.f iounit.f jacobi.f kanang.f ++ kangang.f kangle.f kangs.f kangtor.f kantor.f katom.f katoms.f kbond.f ++ kbonds.f kcharge.f kchgtrn.f kchrge.f kcpen.f kctrn.f kdipol.f ++ kdipole.f kdisp.f kdsp.f kewald.f kextra.f keys.f kgeom.f khbond.f ++ kimprop.f kimptor.f kinetic.f kiprop.f kitors.f kmetal.f kmpole.f ++ kmulti.f kopbend.f kopbnd.f kopdist.f kopdst.f korbit.f korbs.f ++ kpitor.f kpitors.f kpolar.f kpolr.f krepel.f krepl.f ksolv.f kstbnd.f ++ kstrbnd.f kstrtor.f ksttor.f ktors.f ktorsn.f ktortor.f ktrtor.f ++ kurey.f kurybr.f kvdw.f kvdwpr.f kvdws.f lattice.f lbfgs.f light.f ++ lights.f limits.f linmin.f makeint.f makeref.f makexyz.f math.f ++ maxwell.f mdinit.f mdrest.f mdsave.f mdstat.f mdstuf.f mechanic.f ++ merck.f merge.f minima.f molcul.f moldyn.f molecule.f moment.f ++ moments.f mplpot.f mpole.f mrecip.f mutant.f mutate.f nblist.f neigh.f ++ nextarg.f nexttext.f nonpol.f nose.f nspline.f nucleo.f number.f ++ numeral.f numgrad.f ocvm.f omega.f opbend.f opdist.f openend.f ++ openmp.f optinit.f optsave.f orbital.f orbits.f orient.f orthog.f ++ output.f overlap.f params.f paths.f pbstuf.f pdb.f phipsi.f picalc.f ++ piorbs.f pistuf.f pitors.f pme.f pmestuf.f pmpb.f polar.f polgrp.f ++ polopt.f polpcg.f polpot.f poltcg.f polymer.f potent.f potfit.f ++ pressure.f prmkey.f promo.f prtdyn.f prterr.f prtint.f prtmol2.f ++ prtpdb.f prtprm.f prtseq.f prtxyz.f ptable.f qmstuf.f qrfact.f ++ quatfit.f random.f rattle.f readdyn.f readgau.f readgdma.f readint.f ++ readmol.f readmol2.f readpdb.f readprm.f readseq.f readxyz.f refer.f ++ repel.f replica.f reppot.f resdue.f respa.f restrn.f rgddyn.f ++ rgdstep.f rigid.f ring.f rings.f rmsfit.f rotbnd.f rotlist.f rotpole.f ++ rxnfld.f rxnpot.f scales.f sdstep.f search.f sequen.f server.f ++ shakeup.f shunt.f sigmoid.f simplex.f sizes.f sktstuf.f socket.f ++ solute.f sort.f square.f stodyn.f strbnd.f strtor.f suffix.f surface.f ++ surfatom.f switch.f syntrn.f tarray.f tcgstuf.f temper.f titles.f ++ tncg.f torphase.f torpot.f torque.f tors.f torsions.f tortor.f tree.f ++ trimtext.f unitcell.f units.f uprior.f urey.f urypot.f usage.f ++ valfit.f vdw.f vdwpot.f verlet.f version.f vibs.f virial.f volume.f ++ warp.f xtals.f xyzatm.f zatom.f zclose.f zcoord.f) ++install(TARGETS tinker LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE ++ DESTINATION ${CMAKE_INSTALL_LIBDIR}) ++ ++foreach(_BIN ++ alchemy analyze anneal archive bar correlate crystal diffuse ++ distgeom document dynamic gda intedit intxyz minimize minirot ++ minrigid mol2xyz molxyz monte newton newtrot nucleic optimize ++ optirot optrigid path pdbxyz polarize poledit potential ++ prmedit protein pss pssrigid pssrot radial saddle scan sniffer ++ spacefill spectrum superpose testgrad testhess testpair ++ testpol testrot testvir timer timerot torsfit valence vibbig ++ vibrate vibrot xtalfit xtalmin xyzedit xyzint xyzmol2 xyzpdb) ++ add_executable(${_BIN}.x ${_BIN}.f) ++ target_link_libraries(${_BIN}.x tinker PkgConfig::FFTW3) ++ install(TARGETS ${_BIN}.x DESTINATION ${CMAKE_INSTALL_BINDIR}) ++endforeach() +-- +2.23.0 + diff --git a/var/spack/repos/builtin/packages/tinyxml/package.py b/var/spack/repos/builtin/packages/tinyxml/package.py index 22bc9bba8c..3e924e3a9f 100644 --- a/var/spack/repos/builtin/packages/tinyxml/package.py +++ b/var/spack/repos/builtin/packages/tinyxml/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tinyxml2/package.py b/var/spack/repos/builtin/packages/tinyxml2/package.py index a17634158d..1cca1b4c30 100644 --- a/var/spack/repos/builtin/packages/tinyxml2/package.py +++ b/var/spack/repos/builtin/packages/tinyxml2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tioga/package.py b/var/spack/repos/builtin/packages/tioga/package.py index b5d3a5e598..602e5823ef 100644 --- a/var/spack/repos/builtin/packages/tioga/package.py +++ b/var/spack/repos/builtin/packages/tioga/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tippecanoe/package.py b/var/spack/repos/builtin/packages/tippecanoe/package.py index c9f2dc6ad8..4bf4b70125 100644 --- a/var/spack/repos/builtin/packages/tippecanoe/package.py +++ b/var/spack/repos/builtin/packages/tippecanoe/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tix/package.py b/var/spack/repos/builtin/packages/tix/package.py index 47dfc425fa..810ccbe4c5 100644 --- a/var/spack/repos/builtin/packages/tix/package.py +++ b/var/spack/repos/builtin/packages/tix/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py index 0533e54e05..0e1cb3f2c4 100644 --- a/var/spack/repos/builtin/packages/tk/package.py +++ b/var/spack/repos/builtin/packages/tk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -60,14 +60,14 @@ class Tk(AutotoolsPackage): return find_libraries(['libtk{0}'.format(self.version.up_to(2))], root=self.prefix, recursive=True) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): # When using Tkinter from within spack provided python+tkinter, python # will not be able to find Tcl/Tk unless TK_LIBRARY is set. - run_env.set('TK_LIBRARY', join_path(self.prefix.lib, 'tk{0}'.format( + env.set('TK_LIBRARY', join_path(self.prefix.lib, 'tk{0}'.format( self.spec.version.up_to(2)))) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('TK_LIBRARY', join_path(self.prefix.lib, 'tk{0}'.format( + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('TK_LIBRARY', join_path(self.prefix.lib, 'tk{0}'.format( self.spec.version.up_to(2)))) def configure_args(self): diff --git a/var/spack/repos/builtin/packages/tldd/package.py b/var/spack/repos/builtin/packages/tldd/package.py index 9da94a0310..bd3d0f4f2a 100644 --- a/var/spack/repos/builtin/packages/tldd/package.py +++ b/var/spack/repos/builtin/packages/tldd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tmalign/package.py b/var/spack/repos/builtin/packages/tmalign/package.py index d2137f3419..5ee2493c60 100644 --- a/var/spack/repos/builtin/packages/tmalign/package.py +++ b/var/spack/repos/builtin/packages/tmalign/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tmhmm/package.py b/var/spack/repos/builtin/packages/tmhmm/package.py index 50141fc897..9758f58510 100644 --- a/var/spack/repos/builtin/packages/tmhmm/package.py +++ b/var/spack/repos/builtin/packages/tmhmm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py index 39884d2956..6ee165a7b1 100644 --- a/var/spack/repos/builtin/packages/tmux/package.py +++ b/var/spack/repos/builtin/packages/tmux/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,8 @@ class Tmux(AutotoolsPackage): homepage = "http://tmux.github.io" url = "https://github.com/tmux/tmux/releases/download/2.6/tmux-2.6.tar.gz" + version('3.0a', sha256='4ad1df28b4afa969e59c08061b45082fdc49ff512f30fc8e43217d7b0e5f8db9') + version('2.9', sha256='34901232f486fd99f3a39e864575e658b5d49f43289ccc6ee57c365f2e2c2980') version('2.8', sha256='7f6bf335634fafecff878d78de389562ea7f73a7367f268b66d37ea13617a2ba') version('2.7', sha256='9ded7d100313f6bc5a87404a4048b3745d61f2332f99ec1400a7c4ed9485d452') version('2.6', sha256='b17cd170a94d7b58c0698752e1f4f263ab6dc47425230df7e53a6435cc7cd7e8') diff --git a/var/spack/repos/builtin/packages/tmuxinator/package.py b/var/spack/repos/builtin/packages/tmuxinator/package.py index 070e6e895b..1f82efd976 100644 --- a/var/spack/repos/builtin/packages/tmuxinator/package.py +++ b/var/spack/repos/builtin/packages/tmuxinator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tomcat/package.py b/var/spack/repos/builtin/packages/tomcat/package.py new file mode 100644 index 0000000000..8821f482f6 --- /dev/null +++ b/var/spack/repos/builtin/packages/tomcat/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Tomcat(Package): + """ + The Apache Tomcat software is an open source implementation of the + Java Servlet, JavaServer Pages, Java Expression Language and Java + WebSocket technologies. + """ + + homepage = "https://tomcat.apache.org/" + url = "https://archive.apache.org/dist/tomcat/tomcat-9/v9.0.30/bin/apache-tomcat-9.0.30.tar.gz" + + version('9.0.30', sha256='43a9b268671bbd3aace427637fbf577e742b521901e111342321ae901478100b') + version('9.0.29', sha256='1bf634413326ec96972fc1c3ac6666e8e4cab49ad3fc9f5e3228b85208d9c4b0') + version('9.0.27', sha256='6616a150e1593ef1a622298aaef9b889db70c8ee5122d35ad52adfcda1084d10') + version('9.0.26', sha256='b5430890d3b986d6b7ec6a6ef611f9451cbfa933b0a1a3dd48e2cd1f46a63381') + version('9.0.24', sha256='22064138e25f7ab899802804775259a156c06770535b8ce93856beba13dfcf6d') + + def url_for_version(self, version): + url = "https://archive.apache.org/dist/tomcat/tomcat-9/v{0}/bin/apache-tomcat-{0}.tar.gz" + return url.format(version) + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/tophat/package.py b/var/spack/repos/builtin/packages/tophat/package.py index a3d602e3ae..f54df7eca4 100644 --- a/var/spack/repos/builtin/packages/tophat/package.py +++ b/var/spack/repos/builtin/packages/tophat/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tppred/package.py b/var/spack/repos/builtin/packages/tppred/package.py index a4ae099733..d672f9e776 100644 --- a/var/spack/repos/builtin/packages/tppred/package.py +++ b/var/spack/repos/builtin/packages/tppred/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,5 +31,5 @@ class Tppred(Package): install_tree('example', prefix.example) install_tree('tppred2modules', prefix.modules) - def setup_environment(self, spack_env, run_env): - run_env.set('TPPRED_ROOT', prefix) + def setup_run_environment(self, env): + env.set('TPPRED_ROOT', self.prefix) diff --git a/var/spack/repos/builtin/packages/tracer/package.py b/var/spack/repos/builtin/packages/tracer/package.py index 6b77746c7d..400078f1ff 100644 --- a/var/spack/repos/builtin/packages/tracer/package.py +++ b/var/spack/repos/builtin/packages/tracer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/transabyss/package.py b/var/spack/repos/builtin/packages/transabyss/package.py index 85cf56bd85..3ae4936857 100644 --- a/var/spack/repos/builtin/packages/transabyss/package.py +++ b/var/spack/repos/builtin/packages/transabyss/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,7 +16,7 @@ class Transabyss(Package): depends_on('abyss@1.5.2') depends_on('python@2.7.6:', type=('build', 'run')) - depends_on('py-igraph@0.7.0:', type=('build', 'run')) + depends_on('py-python-igraph@0.7.0:', type=('build', 'run')) depends_on('blat') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/transdecoder/package.py b/var/spack/repos/builtin/packages/transdecoder/package.py index b49b67ae9b..9e621a2152 100644 --- a/var/spack/repos/builtin/packages/transdecoder/package.py +++ b/var/spack/repos/builtin/packages/transdecoder/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -29,6 +29,6 @@ class Transdecoder(MakefilePackage): install_tree('PerlLib', prefix.PerlLib) install_tree('util', prefix.util) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', prefix) - run_env.prepend_path('PATH', prefix.util) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix) + env.prepend_path('PATH', self.prefix.util) diff --git a/var/spack/repos/builtin/packages/transposome/package.py b/var/spack/repos/builtin/packages/transposome/package.py index 48bd94ff0a..434e1307d4 100644 --- a/var/spack/repos/builtin/packages/transposome/package.py +++ b/var/spack/repos/builtin/packages/transposome/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/transset/package.py b/var/spack/repos/builtin/packages/transset/package.py index 725d13e198..9b79b092ef 100644 --- a/var/spack/repos/builtin/packages/transset/package.py +++ b/var/spack/repos/builtin/packages/transset/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/trapproto/package.py b/var/spack/repos/builtin/packages/trapproto/package.py index 27c5e46e5e..a2c6f20d32 100644 --- a/var/spack/repos/builtin/packages/trapproto/package.py +++ b/var/spack/repos/builtin/packages/trapproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tree/package.py b/var/spack/repos/builtin/packages/tree/package.py index d4cf705bfd..c3823d313c 100644 --- a/var/spack/repos/builtin/packages/tree/package.py +++ b/var/spack/repos/builtin/packages/tree/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/treesub/package.py b/var/spack/repos/builtin/packages/treesub/package.py index a53884f87a..0a4dad25d6 100644 --- a/var/spack/repos/builtin/packages/treesub/package.py +++ b/var/spack/repos/builtin/packages/treesub/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/trf/package.py b/var/spack/repos/builtin/packages/trf/package.py index 5ba92e6ae9..635b7e2830 100644 --- a/var/spack/repos/builtin/packages/trf/package.py +++ b/var/spack/repos/builtin/packages/trf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/triangle/package.py b/var/spack/repos/builtin/packages/triangle/package.py index ba0ce5a3ef..882b8b472b 100644 --- a/var/spack/repos/builtin/packages/triangle/package.py +++ b/var/spack/repos/builtin/packages/triangle/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py b/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py index f1bc186dcf..f0393510e1 100644 --- a/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py +++ b/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -10,7 +10,6 @@ class TrilinosCatalystIossAdapter(CMakePackage): """Adapter for Trilinos Seacas Ioss and Paraview Catalyst""" homepage = "https://trilinos.org/" - url = "https://github.com/trilinos/Trilinos/archive/trilinos-release-12-12-1.tar.gz" git = "https://github.com/trilinos/Trilinos.git" version('develop', branch='develop') @@ -20,17 +19,17 @@ class TrilinosCatalystIossAdapter(CMakePackage): depends_on('flex', type='build') depends_on('paraview+mpi+python+osmesa') depends_on('py-numpy', type=('build', 'run')) - # Here we avoid paraview trying to use netcdf~parallel-netcdf - # which is netcdf's default, even though paraview depends on 'netcdf' + # Here we avoid paraview trying to use netcdf-c~parallel-netcdf + # which is netcdf-c's default, even though paraview depends on 'netcdf-c' # without any variants. Concretizer bug? - depends_on('netcdf+parallel-netcdf') + depends_on('netcdf-c+parallel-netcdf') root_cmakelists_dir = join_path('packages', 'seacas', 'libraries', 'ioss', 'src', 'visualization', 'ParaViewCatalystIossAdapter') - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PYTHONPATH', self.prefix.python) + def setup_run_environment(self, env): + env.prepend_path('PYTHONPATH', self.prefix.python) def cmake_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 3a456ee093..74e6b7f85e 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -35,6 +35,7 @@ class Trilinos(CMakePackage): version('xsdk-0.2.0', tag='xsdk-0.2.0') version('develop', branch='develop') version('master', branch='master') + version('12.18.1', commit='55a75997332636a28afc9db1aee4ae46fe8d93e7') # tag trilinos-release-12-8-1 version('12.14.1', sha256='52a4406cca2241f5eea8e166c2950471dd9478ad6741cbb2a7fc8225814616f0') version('12.12.1', sha256='5474c5329c6309224a7e1726cf6f0d855025b2042959e4e2be2748bd6bb49e18') version('12.10.1', sha256='ab81d917196ffbc21c4927d42df079dd94c83c1a08bda43fef2dd34d0c1a5512') @@ -192,6 +193,12 @@ class Trilinos(CMakePackage): when='+dtk @12.14.0:12.14.99') resource(name='dtk', git='https://github.com/ornl-cees/DataTransferKit.git', + commit='edfa050cd46e2274ab0a0b7558caca0079c2e4ca', # tag 3.1-rc1 + placement='DataTransferKit', + submodules=True, + when='+dtk @12.18:12.18.99') + resource(name='dtk', + git='https://github.com/ornl-cees/DataTransferKit.git', branch='master', placement='DataTransferKit', submodules=True, @@ -255,7 +262,7 @@ class Trilinos(CMakePackage): conflicts('+dtk', when='~teuchos') conflicts('+dtk', when='~tpetra') # Only allow DTK with Trilinos 12.14 and develop - conflicts('+dtk', when='@0:12.12.99,12.16.0:99,master') + conflicts('+dtk', when='@0:12.12.99,master') conflicts('+fortrilinos', when='~fortran') conflicts('+fortrilinos', when='@:99') conflicts('+fortrilinos', when='@master') @@ -297,8 +304,8 @@ class Trilinos(CMakePackage): # MPI related dependencies depends_on('mpi') - depends_on('netcdf@:4.7.1+mpi', when="~pnetcdf") - depends_on('netcdf+mpi+parallel-netcdf', when="+pnetcdf@master,12.12.1:") + depends_on('netcdf-c+mpi', when="~pnetcdf") + depends_on('netcdf-c+mpi+parallel-netcdf', when="+pnetcdf@master,12.12.1:") depends_on('parallel-netcdf', when="+pnetcdf@master,12.12.1:") depends_on('parmetis', when='+metis') depends_on('cgns', when='+cgns') @@ -505,7 +512,7 @@ class Trilinos(CMakePackage): '-DLAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names), '-DLAPACK_LIBRARY_DIRS=%s' % ';'.join(lapack.directories), '-DTPL_ENABLE_Netcdf:BOOL=ON', - '-DNetCDF_ROOT:PATH=%s' % spec['netcdf'].prefix, + '-DNetCDF_ROOT:PATH=%s' % spec['netcdf-c'].prefix, '-DTPL_ENABLE_X11:BOOL=%s' % ( 'ON' if '+x11' in spec else 'OFF'), '-DTrilinos_ENABLE_Gtest:BOOL=%s' % ( diff --git a/var/spack/repos/builtin/packages/trimal/package.py b/var/spack/repos/builtin/packages/trimal/package.py index 998b3f574e..dce8604c50 100644 --- a/var/spack/repos/builtin/packages/trimal/package.py +++ b/var/spack/repos/builtin/packages/trimal/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/trimgalore/package.py b/var/spack/repos/builtin/packages/trimgalore/package.py index fd26b945ed..71632ab647 100644 --- a/var/spack/repos/builtin/packages/trimgalore/package.py +++ b/var/spack/repos/builtin/packages/trimgalore/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,6 +14,9 @@ class Trimgalore(Package): homepage = "https://github.com/FelixKrueger/TrimGalore" url = "https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.tar.gz" + version('0.6.4', sha256='eb57e18203d8a1dce1397b930a348a9969eebaa758b8a7304d04c22f216cea2d') + version('0.6.3', sha256='c85104452dbb5cfa8c9307920e804fb53baaad355ce656b111f5243e5eb92db4') + version('0.6.2', sha256='c50b841bdc294a6cdc6a27fb7bfbed1973541d20a68a4708584b817c58b3f376') version('0.6.1', sha256='658578c29d007fe66f9ab49608442be703a6fcf535db06eb82659c7edccb62b0') version('0.6.0', sha256='f374dfa4c94e2ad50c63276dda0f341fd95b29cb1d5a0e2ad56e8b0168b758ec') version('0.4.5', sha256='a6b97e554944ddc6ecd50e78df486521f17225d415aad84e9911163faafe1f3c') diff --git a/var/spack/repos/builtin/packages/trimmomatic/package.py b/var/spack/repos/builtin/packages/trimmomatic/package.py index b75fcd802f..45ee3a23db 100644 --- a/var/spack/repos/builtin/packages/trimmomatic/package.py +++ b/var/spack/repos/builtin/packages/trimmomatic/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py index 997e36c0ef..8bdc10dd79 100644 --- a/var/spack/repos/builtin/packages/trinity/package.py +++ b/var/spack/repos/builtin/packages/trinity/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -52,7 +52,7 @@ class Trinity(MakefilePackage): depends_on("samtools", type="run") depends_on("py-numpy", type="run") depends_on("express", type="run") - depends_on("perl-dbfile", type="run") + depends_on("perl-db-file", type="run") depends_on("perl-uri", type="run") depends_on("r-fastcluster", type="run") depends_on("r-ctc", type="run") @@ -85,7 +85,9 @@ class Trinity(MakefilePackage): force_remove(join_path(prefix.bin, 'trinity-plugins', 'slclust', 'bin', '.hidden')) - def setup_environment(self, spack_env, run_env): - run_env.set('TRINITY_HOME', self.prefix.bin) - run_env.prepend_path('PATH', self.prefix.bin.util) - spack_env.append_flags('CXXFLAGS', self.compiler.openmp_flag) + def setup_build_environment(self, env): + env.append_flags('CXXFLAGS', self.compiler.openmp_flag) + + def setup_run_environment(self, env): + env.set('TRINITY_HOME', self.prefix.bin) + env.prepend_path('PATH', self.prefix.bin.util) diff --git a/var/spack/repos/builtin/packages/trinotate/package.py b/var/spack/repos/builtin/packages/trinotate/package.py index d0a24d608f..00c0ad3953 100644 --- a/var/spack/repos/builtin/packages/trinotate/package.py +++ b/var/spack/repos/builtin/packages/trinotate/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/trnascan-se/package.py b/var/spack/repos/builtin/packages/trnascan-se/package.py index 1f9509556c..cad1a15e90 100644 --- a/var/spack/repos/builtin/packages/trnascan-se/package.py +++ b/var/spack/repos/builtin/packages/trnascan-se/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,3 +13,10 @@ class TrnascanSe(AutotoolsPackage): url = "http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz" version('2.0.0', sha256='0dde1c07142e4bf77b21d53ddf3eeb1ef8c52248005a42323d13f8d7c798100c') + + depends_on('infernal@1.1.2', type='run', when='@2.0.0') + + def patch(self): + filter_file('infernal_dir: {bin_dir}', + 'infernal_dir: %s' % self.spec['infernal'].prefix.bin, + 'tRNAscan-SE.conf.src', string=True) diff --git a/var/spack/repos/builtin/packages/turbine/package.py b/var/spack/repos/builtin/packages/turbine/package.py index 4788efd070..c180037304 100644 --- a/var/spack/repos/builtin/packages/turbine/package.py +++ b/var/spack/repos/builtin/packages/turbine/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,7 @@ class Turbine(AutotoolsPackage): """Turbine: The Swift/T runtime""" homepage = 'http://swift-lang.org/Swift-T' - url = 'http://swift-lang.github.io/swift-t-downloads/spack/turbine-0.0.0.tar.gz' + url = 'http://swift-lang.github.io/swift-t-downloads/spack/turbine-1.2.3.tar.gz' git = "https://github.com/swift-lang/swift-t.git" configure_directory = 'turbine/code' @@ -44,12 +44,12 @@ class Turbine(AutotoolsPackage): depends_on('libtool', type='build', when='@master') depends_on('m4', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('CC', spec['mpi'].mpicc) - spack_env.set('CXX', spec['mpi'].mpicxx) - spack_env.set('CXXLD', spec['mpi'].mpicxx) + env.set('CC', spec['mpi'].mpicc) + env.set('CXX', spec['mpi'].mpicxx) + env.set('CXXLD', spec['mpi'].mpicxx) @property def configure_directory(self): diff --git a/var/spack/repos/builtin/packages/turbomole/package.py b/var/spack/repos/builtin/packages/turbomole/package.py index fc331a1429..501f06d3ca 100644 --- a/var/spack/repos/builtin/packages/turbomole/package.py +++ b/var/spack/repos/builtin/packages/turbomole/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -52,9 +52,8 @@ class Turbomole(Package): return def install(self, spec, prefix): - if spec.satisfies('@:7.0.2'): - calculate_version = 'calculate_2.4_linux64' - molecontrol_version = 'MoleControl_2.5' + calculate_version = 'calculate_2.4_linux64' + molecontrol_version = 'MoleControl_2.5' tm_arch = self.get_tm_arch() @@ -114,33 +113,25 @@ class Turbomole(Package): install('mpirun_scripts/ricc2', join_path(dst, 'mpirun_scripts')) install('mpirun_scripts/ridft', join_path(dst, 'mpirun_scripts')) - def setup_environment(self, spack_env, run_env): - if self.spec.satisfies('@:7.0.2'): - molecontrol_version = 'MoleControl_2.5' + def setup_run_environment(self, env): + molecontrol_version = 'MoleControl_2.5' tm_arch = self.get_tm_arch() - run_env.set('TURBODIR', join_path(self.prefix, 'TURBOMOLE')) - run_env.set('MOLE_CONTROL', - join_path(self.prefix, 'TURBOMOLE', molecontrol_version)) + env.set('TURBODIR', self.prefix.TURBOMOLE) + env.set('MOLE_CONTROL', + join_path(self.prefix, 'TURBOMOLE', molecontrol_version)) - run_env.prepend_path('PATH', - join_path(self.prefix, 'TURBOMOLE', 'thermocalc')) - run_env.prepend_path('PATH', - join_path(self.prefix, 'TURBOMOLE', 'scripts')) + env.prepend_path('PATH', self.prefix.TURBOMOLE.thermocalc) + env.prepend_path('PATH', self.prefix.TURBOMOLE.scripts) if '+mpi' in self.spec: - run_env.set('PARA_ARCH', 'MPI') - run_env.prepend_path('PATH', - join_path(self.prefix, - 'TURBOMOLE', 'bin', '%s_mpi' - % tm_arch)) + env.set('PARA_ARCH', 'MPI') + env.prepend_path('PATH', join_path( + self.prefix, 'TURBOMOLE', 'bin', '%s_mpi' % tm_arch)) elif '+smp' in self.spec: - run_env.set('PARA_ARCH', 'SMP') - run_env.prepend_path('PATH', - join_path(self.prefix, - 'TURBOMOLE', 'bin', '%s_smp' - % tm_arch)) + env.set('PARA_ARCH', 'SMP') + env.prepend_path('PATH', join_path( + self.prefix, 'TURBOMOLE', 'bin', '%s_smp' % tm_arch)) else: - run_env.prepend_path('PATH', - join_path(self.prefix, - 'TURBOMOLE', 'bin', tm_arch)) + env.prepend_path('PATH', join_path( + self.prefix, 'TURBOMOLE', 'bin', tm_arch)) diff --git a/var/spack/repos/builtin/packages/tut/package.py b/var/spack/repos/builtin/packages/tut/package.py index 41c86909c9..621fd4c072 100644 --- a/var/spack/repos/builtin/packages/tut/package.py +++ b/var/spack/repos/builtin/packages/tut/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/twm/package.py b/var/spack/repos/builtin/packages/twm/package.py index 64c80ec3eb..3f86cb06cf 100644 --- a/var/spack/repos/builtin/packages/twm/package.py +++ b/var/spack/repos/builtin/packages/twm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/tycho2/package.py b/var/spack/repos/builtin/packages/tycho2/package.py index ae5db9c416..a7c22ec56d 100644 --- a/var/spack/repos/builtin/packages/tycho2/package.py +++ b/var/spack/repos/builtin/packages/tycho2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/typhon/package.py b/var/spack/repos/builtin/packages/typhon/package.py index d29fdab8b0..350bd6ded2 100644 --- a/var/spack/repos/builtin/packages/typhon/package.py +++ b/var/spack/repos/builtin/packages/typhon/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/typhonio/package.py b/var/spack/repos/builtin/packages/typhonio/package.py index 92e96acd1f..ac15cf9625 100644 --- a/var/spack/repos/builtin/packages/typhonio/package.py +++ b/var/spack/repos/builtin/packages/typhonio/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ucx/package.py b/var/spack/repos/builtin/packages/ucx/package.py index b5fd8a0590..681fa5b6bf 100644 --- a/var/spack/repos/builtin/packages/ucx/package.py +++ b/var/spack/repos/builtin/packages/ucx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -14,6 +14,7 @@ class Ucx(AutotoolsPackage): url = "https://github.com/openucx/ucx/releases/download/v1.3.1/ucx-1.3.1.tar.gz" # Current + version('1.6.1', sha256='1425648aa03f5fa40e4bc5c4a5a83fe0292e2fe44f6054352fbebbf6d8f342a1') version('1.6.0', sha256='360e885dd7f706a19b673035a3477397d100a02eb618371697c7f3ee4e143e2c') version('1.5.2', sha256='1a333853069860e86ba69b8d071ccc9871209603790e2b673ec61f8086913fad') version('1.5.1', sha256='567119cd80ad2ae6968ecaa4bd1d2a80afadd037ccc988740f668de10d2fdb7e') @@ -25,6 +26,19 @@ class Ucx(AutotoolsPackage): version('1.3.0', sha256='71e69e6d78a4950cc5a1edcbe59bf7a8f8e38d59c9f823109853927c4d442952') version('1.2.2', sha256='914d10fee8f970d4fb286079dd656cf8a260ec7d724d5f751b3109ed32a6da63') version('1.2.1', sha256='fc63760601c03ff60a2531ec3c6637e98f5b743576eb410f245839c84a0ad617') + version('1.2.0', sha256='1e1a62d6d0f89ce59e384b0b5b30b416b8fd8d7cedec4182a5319d0dfddf649c') + + variant('thread_multiple', default=False, + description='Enable thread support in UCP and UCT') depends_on('numactl') depends_on('rdma-core') + + def configure_args(self): + spec = self.spec + config_args = [] + if '+thread_multiple' in spec: + config_args.append('--enable-mt') + else: + config_args.append('--disable-mt') + return config_args diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits/package.py index c5704d6a5e..e20f2b6ccd 100644 --- a/var/spack/repos/builtin/packages/udunits2/package.py +++ b/var/spack/repos/builtin/packages/udunits/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,7 +6,7 @@ from spack import * -class Udunits2(AutotoolsPackage): +class Udunits(AutotoolsPackage): """Automated units conversion""" homepage = "http://www.unidata.ucar.edu/software/udunits" diff --git a/var/spack/repos/builtin/packages/ufo-core/package.py b/var/spack/repos/builtin/packages/ufo-core/package.py index 3dee84e57a..23ce2bf3a2 100644 --- a/var/spack/repos/builtin/packages/ufo-core/package.py +++ b/var/spack/repos/builtin/packages/ufo-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/ufo-filters/package.py b/var/spack/repos/builtin/packages/ufo-filters/package.py index cd199e5945..6b2da72352 100644 --- a/var/spack/repos/builtin/packages/ufo-filters/package.py +++ b/var/spack/repos/builtin/packages/ufo-filters/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/umap/package.py b/var/spack/repos/builtin/packages/umap/package.py index b6077f1c89..e474541c25 100644 --- a/var/spack/repos/builtin/packages/umap/package.py +++ b/var/spack/repos/builtin/packages/umap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/umoci/package.py b/var/spack/repos/builtin/packages/umoci/package.py index 5c501026d4..476e06dd66 100644 --- a/var/spack/repos/builtin/packages/umoci/package.py +++ b/var/spack/repos/builtin/packages/umoci/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/umpire/package.py b/var/spack/repos/builtin/packages/umpire/package.py index 61366135a1..fc33ca7feb 100644 --- a/var/spack/repos/builtin/packages/umpire/package.py +++ b/var/spack/repos/builtin/packages/umpire/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/unblur/package.py b/var/spack/repos/builtin/packages/unblur/package.py index a7c60e24fa..428f44c08e 100644 --- a/var/spack/repos/builtin/packages/unblur/package.py +++ b/var/spack/repos/builtin/packages/unblur/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/uncrustify/package.py b/var/spack/repos/builtin/packages/uncrustify/package.py index c584c4b7b6..99aeaeaab3 100644 --- a/var/spack/repos/builtin/packages/uncrustify/package.py +++ b/var/spack/repos/builtin/packages/uncrustify/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/unibilium/package.py b/var/spack/repos/builtin/packages/unibilium/package.py index a51bb12594..e7570365f3 100644 --- a/var/spack/repos/builtin/packages/unibilium/package.py +++ b/var/spack/repos/builtin/packages/unibilium/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/unifyfs/package.py b/var/spack/repos/builtin/packages/unifyfs/package.py index e3011408c1..98c249d7e6 100644 --- a/var/spack/repos/builtin/packages/unifyfs/package.py +++ b/var/spack/repos/builtin/packages/unifyfs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,11 +16,11 @@ class Unifyfs(AutotoolsPackage): homepage = "https://github.com/LLNL/UnifyFS" git = "https://github.com/LLNL/UnifyFS.git" - url = "https://github.com/LLNL/UnifyFS/releases/download/v0.2.0/unifycr-0.2.0.tar.gz" + url = "https://github.com/LLNL/UnifyFS/releases/download/v0.9.0/unifyfs-0.9.0.tar.gz" maintainers = ['CamStan'] version('develop', branch='dev', preferred=True) - version('0.2.0', sha256='7439b0e885234bc64e8cbb449d8abfadd386692766b6f00647a7b6435efb2066') + version('0.9.0', sha256='e6c73e22ef1c23f3141646aa17058b69c1c4e526886771f8fe982da924265b0f') variant('hdf5', default='False', description='Build with parallel HDF5 (install with `^hdf5~mpi` for serial)') variant('fortran', default='False', description='Build with gfortran support') diff --git a/var/spack/repos/builtin/packages/unison/package.py b/var/spack/repos/builtin/packages/unison/package.py index 3f5744d96f..b0c363667b 100644 --- a/var/spack/repos/builtin/packages/unison/package.py +++ b/var/spack/repos/builtin/packages/unison/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/units/package.py b/var/spack/repos/builtin/packages/units/package.py index 354489d54a..7ee1ecd2e1 100644 --- a/var/spack/repos/builtin/packages/units/package.py +++ b/var/spack/repos/builtin/packages/units/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,11 +6,11 @@ from spack import * -class Units(AutotoolsPackage): +class Units(AutotoolsPackage, GNUMirrorPackage): """GNU units converts between different systems of units""" homepage = "https://www.gnu.org/software/units/" - url = "https://ftpmirror.gnu.org/units/units-2.13.tar.gz" + gnu_mirror_path = "units/units-2.13.tar.gz" version('2.13', sha256='0ba5403111f8e5ea22be7d51ab74c8ccb576dc30ddfbf18a46cb51f9139790ab') diff --git a/var/spack/repos/builtin/packages/unittest-cpp/package.py b/var/spack/repos/builtin/packages/unittest-cpp/package.py index b0b68f2f1e..ffd5b92ec7 100644 --- a/var/spack/repos/builtin/packages/unittest-cpp/package.py +++ b/var/spack/repos/builtin/packages/unittest-cpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/unixodbc/package.py b/var/spack/repos/builtin/packages/unixodbc/package.py index 2a9fac6f33..2802f87aa5 100644 --- a/var/spack/repos/builtin/packages/unixodbc/package.py +++ b/var/spack/repos/builtin/packages/unixodbc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/unrar/package.py b/var/spack/repos/builtin/packages/unrar/package.py index 79bf9d31f7..6972aef3c9 100644 --- a/var/spack/repos/builtin/packages/unrar/package.py +++ b/var/spack/repos/builtin/packages/unrar/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/unuran/package.py b/var/spack/repos/builtin/packages/unuran/package.py index 71f4cc9983..0bd35ee562 100644 --- a/var/spack/repos/builtin/packages/unuran/package.py +++ b/var/spack/repos/builtin/packages/unuran/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/unzip/package.py b/var/spack/repos/builtin/packages/unzip/package.py index e565b64def..224c495a64 100644 --- a/var/spack/repos/builtin/packages/unzip/package.py +++ b/var/spack/repos/builtin/packages/unzip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/upcxx/package.py b/var/spack/repos/builtin/packages/upcxx/package.py index 8afd7286e2..e4806c4c9c 100644 --- a/var/spack/repos/builtin/packages/upcxx/package.py +++ b/var/spack/repos/builtin/packages/upcxx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,6 +23,7 @@ class Upcxx(Package): Access (RMA) and Remote Procedure Call (RPC).""" homepage = "https://upcxx.lbl.gov" + maintainers = ['bonachea'] version('2019.9.0', sha256='7d67ccbeeefb59de9f403acc719f52127a30801a2c2b9774a1df03f850f8f1d4') version('2019.3.2', sha256='dcb0b337c05a0feb2ed5386f5da6c60342412b49cab10f282f461e74411018ad') @@ -37,6 +38,7 @@ class Upcxx(Package): msg='None is unacceptable on Cray.') depends_on('cuda', when='+cuda') + depends_on('python@2.7.5:2.999', type=("build", "run")) def url_for_version(self, version): if version > Version('2019.3.2'): @@ -45,32 +47,33 @@ class Upcxx(Package): url = "https://bitbucket.org/berkeleylab/upcxx/downloads/upcxx-{0}-offline.tar.gz" return url.format(version) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if 'platform=cray' in self.spec: - spack_env.set('GASNET_CONFIGURE_ARGS', '--enable-mpi=probe') + env.set('GASNET_CONFIGURE_ARGS', '--enable-mpi=probe') if 'cross=none' not in self.spec: - spack_env.set('CROSS', self.spec.variants['cross'].value) + env.set('CROSS', self.spec.variants['cross'].value) if '+cuda' in self.spec: - spack_env.set('UPCXX_CUDA', '1') - spack_env.set('UPCXX_CUDA_NVCC', self.spec['cuda'].prefix.bin.nvcc) + env.set('UPCXX_CUDA', '1') + env.set('UPCXX_CUDA_NVCC', self.spec['cuda'].prefix.bin.nvcc) - run_env.set('UPCXX_INSTALL', self.prefix) - run_env.set('UPCXX', self.prefix.bin.upcxx) + def setup_run_environment(self, env): + env.set('UPCXX_INSTALL', self.prefix) + env.set('UPCXX', self.prefix.bin.upcxx) if 'platform=cray' in self.spec: - run_env.set('UPCXX_GASNET_CONDUIT', 'aries') - run_env.set('UPCXX_NETWORK', 'aries') + env.set('UPCXX_GASNET_CONDUIT', 'aries') + env.set('UPCXX_NETWORK', 'aries') def setup_dependent_package(self, module, dep_spec): dep_spec.upcxx = self.prefix.bin.upcxx - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('UPCXX_INSTALL', self.prefix) - spack_env.set('UPCXX', self.prefix.bin.upcxx) + def setup_dependent_build_environment(self, env, dependent_spec): + env.set('UPCXX_INSTALL', self.prefix) + env.set('UPCXX', self.prefix.bin.upcxx) if 'platform=cray' in self.spec: - spack_env.set('UPCXX_GASNET_CONDUIT', 'aries') - spack_env.set('UPCXX_NETWORK', 'aries') + env.set('UPCXX_GASNET_CONDUIT', 'aries') + env.set('UPCXX_NETWORK', 'aries') def install(self, spec, prefix): env['CC'] = self.compiler.cc diff --git a/var/spack/repos/builtin/packages/uriparser/package.py b/var/spack/repos/builtin/packages/uriparser/package.py index 4171d257c9..e2a6536e9f 100644 --- a/var/spack/repos/builtin/packages/uriparser/package.py +++ b/var/spack/repos/builtin/packages/uriparser/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/usearch/package.py b/var/spack/repos/builtin/packages/usearch/package.py index f2bd0ac18e..e9aa3921d8 100644 --- a/var/spack/repos/builtin/packages/usearch/package.py +++ b/var/spack/repos/builtin/packages/usearch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/utf8proc/package.py b/var/spack/repos/builtin/packages/utf8proc/package.py index 2a48842c44..55e7e114c6 100644 --- a/var/spack/repos/builtin/packages/utf8proc/package.py +++ b/var/spack/repos/builtin/packages/utf8proc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/util-linux/package.py b/var/spack/repos/builtin/packages/util-linux/package.py index e9411517bc..49afb16f54 100644 --- a/var/spack/repos/builtin/packages/util-linux/package.py +++ b/var/spack/repos/builtin/packages/util-linux/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/util-macros/package.py b/var/spack/repos/builtin/packages/util-macros/package.py index 26de9b3efd..c30107033f 100644 --- a/var/spack/repos/builtin/packages/util-macros/package.py +++ b/var/spack/repos/builtin/packages/util-macros/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,7 +17,6 @@ class UtilMacros(AutotoolsPackage): version('1.19.1', sha256='18d459400558f4ea99527bc9786c033965a3db45bf4c6a32eefdc07aa9e306a6') version('1.19.0', sha256='2835b11829ee634e19fa56517b4cfc52ef39acea0cd82e15f68096e27cbed0ba') - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): """Adds the ACLOCAL path for autotools.""" - spack_env.append_path('ACLOCAL_PATH', - join_path(self.prefix.share, 'aclocal')) + env.append_path('ACLOCAL_PATH', self.prefix.share.aclocal) diff --git a/var/spack/repos/builtin/packages/uuid/package.py b/var/spack/repos/builtin/packages/uuid/package.py index 76219943e1..3f7a7ec5a8 100644 --- a/var/spack/repos/builtin/packages/uuid/package.py +++ b/var/spack/repos/builtin/packages/uuid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/uvw/package.py b/var/spack/repos/builtin/packages/uvw/package.py index 6e774a0549..cf6a96ee9c 100644 --- a/var/spack/repos/builtin/packages/uvw/package.py +++ b/var/spack/repos/builtin/packages/uvw/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/valgrind/package.py b/var/spack/repos/builtin/packages/valgrind/package.py index 5691af014c..684a5bdfa8 100644 --- a/var/spack/repos/builtin/packages/valgrind/package.py +++ b/var/spack/repos/builtin/packages/valgrind/package.py @@ -1,9 +1,10 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import glob import sys @@ -67,3 +68,10 @@ clang: error: unknown argument: '-static-libubsan' if sys.platform == 'darwin': options.append('--build=amd64-darwin') return options + + # Valgrind the potential for overlong perl shebangs + def patch(self): + for link_tool_in in glob.glob('coregrind/link_tool_exe_*.in'): + filter_file('^#! @PERL@', + '#! /usr/bin/env perl', + link_tool_in) diff --git a/var/spack/repos/builtin/packages/vampirtrace/package.py b/var/spack/repos/builtin/packages/vampirtrace/package.py index 8f5c23ea7d..da22aeb391 100644 --- a/var/spack/repos/builtin/packages/vampirtrace/package.py +++ b/var/spack/repos/builtin/packages/vampirtrace/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vardictjava/package.py b/var/spack/repos/builtin/packages/vardictjava/package.py index a9f0f1b976..7f7fdcf67b 100644 --- a/var/spack/repos/builtin/packages/vardictjava/package.py +++ b/var/spack/repos/builtin/packages/vardictjava/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/variorum/package.py b/var/spack/repos/builtin/packages/variorum/package.py new file mode 100644 index 0000000000..d12efe20cc --- /dev/null +++ b/var/spack/repos/builtin/packages/variorum/package.py @@ -0,0 +1,80 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Variorum(CMakePackage): + """Variorum is a library providing vendor-neutral interfaces for + monitoring and controlling underlying hardware features. + """ + + homepage = "https://variorum.readthedocs.io" + git = "https://github.com/llnl/variorum.git" + url = "https://github.com/llnl/variorum/archive/v0.1.0.tar.gz" + + maintainers = ["slabasan", "rountree"] + + version("0.1.0", tag="v0.1.0") + + ############ + # Variants # + ############ + variant("shared", default=True, description="Build Variorum as shared lib") + variant("docs", default=False, + description="Build Variorum's documentation") + variant("log", default=False, description="Enable Variorum's logs") + variant("build_type", default="Release", + description="CMake build type", + values=("Debug", "Release")) + + ######################## + # Package dependencies # + ######################## + depends_on("cmake@2.8:", type="build") + depends_on("hwloc@1.11.9") + + ######################### + # Documentation related # + ######################### + depends_on("py-sphinx", when="+docs", type="build") + + root_cmakelists_dir = "src" + + def cmake_args(self): + spec = self.spec + cmake_args = [] + + if "+shared" in spec: + cmake_args.append("-DBUILD_SHARED_LIBS=ON") + else: + cmake_args.append("-DBUILD_SHARED_LIBS=OFF") + + if "+docs" in spec: + cmake_args.append("-DBUILD_DOCS=ON") + sphinx_build_exe = join_path( + spec["py-sphinx"].prefix.bin, + "sphinx-build" + ) + cmake_args.append("-DSPHINX_EXECUTABLE=" + sphinx_build_exe) + else: + cmake_args.append("-DBUILD_DOCS=OFF") + + if 'build_type=Debug' in spec: + cmake_args.append("-DVARIORUM_DEBUG=ON") + else: + cmake_args.append("-DVARIORUM_DEBUG=OFF") + + if "+log" in spec: + cmake_args.append("-DVARIORUM_LOG=ON") + else: + cmake_args.append("-DVARIORUM_LOG=OFF") + + if self.run_tests: + cmake_args.append("-DBUILD_TESTS=ON") + else: + cmake_args.append("-DBUILD_TESTS=OFF") + + return cmake_args diff --git a/var/spack/repos/builtin/packages/varscan/package.py b/var/spack/repos/builtin/packages/varscan/package.py index 9b6dc2e36c..ecf83a1e5e 100644 --- a/var/spack/repos/builtin/packages/varscan/package.py +++ b/var/spack/repos/builtin/packages/varscan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -35,6 +35,6 @@ class Varscan(Package): filter_file('varscan.jar', join_path(prefix.jar, jar_file), script, **kwargs) - def setup_environment(self, spack_env, run_env): - run_env.set('VARSCAN_HOME', self.prefix.jar) - run_env.set('CLASSPATH', self.prefix.jar) + def setup_run_environment(self, env): + env.set('VARSCAN_HOME', self.prefix.jar) + env.set('CLASSPATH', self.prefix.jar) diff --git a/var/spack/repos/builtin/packages/vc/package.py b/var/spack/repos/builtin/packages/vc/package.py index 78f084b756..1b06477899 100644 --- a/var/spack/repos/builtin/packages/vc/package.py +++ b/var/spack/repos/builtin/packages/vc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vcftools/package.py b/var/spack/repos/builtin/packages/vcftools/package.py index 5368ddd931..92d49392c5 100644 --- a/var/spack/repos/builtin/packages/vcftools/package.py +++ b/var/spack/repos/builtin/packages/vcftools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,7 +23,7 @@ class Vcftools(AutotoolsPackage): depends_on('perl', type=('build', 'run')) depends_on('zlib') - # this needs to be in sync with what setup_environment adds to + # this needs to be in sync with what setup_run_environment adds to # PERL5LIB below def configure_args(self): return ['--with-pmdir={0}'.format(self.prefix.lib)] @@ -51,5 +51,5 @@ class Vcftools(AutotoolsPackage): kwargs = {'ignore_absent': True, 'backup': False, 'string': False} filter_file(match, substitute, *files, **kwargs) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PERL5LIB', self.prefix.lib) + def setup_run_environment(self, env): + env.prepend_path('PERL5LIB', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/vcsh/package.py b/var/spack/repos/builtin/packages/vcsh/package.py index 8ac126db61..3368c596df 100644 --- a/var/spack/repos/builtin/packages/vcsh/package.py +++ b/var/spack/repos/builtin/packages/vcsh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vdt/package.py b/var/spack/repos/builtin/packages/vdt/package.py index d03dc7dba5..240e39a8e3 100644 --- a/var/spack/repos/builtin/packages/vdt/package.py +++ b/var/spack/repos/builtin/packages/vdt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vecgeom/package.py b/var/spack/repos/builtin/packages/vecgeom/package.py index 599c250ee6..ef2ae4b07b 100644 --- a/var/spack/repos/builtin/packages/vecgeom/package.py +++ b/var/spack/repos/builtin/packages/vecgeom/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/veclibfort/package.py b/var/spack/repos/builtin/packages/veclibfort/package.py index 2a11428999..bfd3fc2d32 100644 --- a/var/spack/repos/builtin/packages/veclibfort/package.py +++ b/var/spack/repos/builtin/packages/veclibfort/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vegas2/package.py b/var/spack/repos/builtin/packages/vegas2/package.py index b61b63a0db..dff83b2adf 100644 --- a/var/spack/repos/builtin/packages/vegas2/package.py +++ b/var/spack/repos/builtin/packages/vegas2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/veloc/package.py b/var/spack/repos/builtin/packages/veloc/package.py index 29c488fbcb..ef1bef0fb5 100644 --- a/var/spack/repos/builtin/packages/veloc/package.py +++ b/var/spack/repos/builtin/packages/veloc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/velvet/package.py b/var/spack/repos/builtin/packages/velvet/package.py index 010be8238a..f205c8034f 100644 --- a/var/spack/repos/builtin/packages/velvet/package.py +++ b/var/spack/repos/builtin/packages/velvet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/verilator/package.py b/var/spack/repos/builtin/packages/verilator/package.py index 89da6e1409..c662ab1b62 100644 --- a/var/spack/repos/builtin/packages/verilator/package.py +++ b/var/spack/repos/builtin/packages/verilator/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -42,8 +42,8 @@ class Verilator(AutotoolsPackage): depends_on('flex') depends_on('perl', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('VERILATOR_ROOT', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('VERILATOR_ROOT', self.prefix) # verilator requires access to its shipped scripts (bin) and include # but the standard make doesn't put it in the correct places diff --git a/var/spack/repos/builtin/packages/verrou/package.py b/var/spack/repos/builtin/packages/verrou/package.py index 79cfd37bc2..265ee2b096 100644 --- a/var/spack/repos/builtin/packages/verrou/package.py +++ b/var/spack/repos/builtin/packages/verrou/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,15 +24,22 @@ class Verrou(AutotoolsPackage): url = "https://github.com/edf-hpc/verrou/archive/v2.0.0.tar.gz" git = "https://github.com/edf-hpc/verrou.git" + maintainers = ['HadrienG2'] + version('develop', branch='master') + version('2.2.0', sha256='d4ea3d19f0c61329723907b5b145d85776bb702643c1605a31f584484d2c5efc') version('2.1.0', sha256='b1ba49f84aebab15b8ab5649946c9c31b53ad1499f6ffb681c98db41ed28566d') version('2.0.0', sha256='798df6e426ec57646a2a626d756b72f0171647ae5b07c982952dae2d71e26045') version('1.1.0', sha256='b5105f61c65680f31551199cd143b2e15f412c34c821537998a7165e315dde2d') + resource(name='valgrind-3.15.0', + url='https://sourceware.org/pub/valgrind/valgrind-3.15.0.tar.bz2', + sha256='417c7a9da8f60dd05698b3a7bc6002e4ef996f14c13f0ff96679a16873e78ab1', + when='@2.2.0:') resource(name='valgrind-3.14.0', url='https://sourceware.org/pub/valgrind/valgrind-3.14.0.tar.bz2', sha256='037c11bfefd477cc6e9ebe8f193bb237fe397f7ce791b4a4ce3fa1c6a520baa5', - when='@2.1.0:') + when='@2.1.0:2.1.99') resource(name='valgrind-3.13.0', url='https://sourceware.org/pub/valgrind/valgrind-3.13.0.tar.bz2', sha256='d76680ef03f00cd5e970bbdcd4e57fb1f6df7d2e2c071635ef2be74790190c3b', diff --git a/var/spack/repos/builtin/packages/vesta/package.py b/var/spack/repos/builtin/packages/vesta/package.py index 918c44b7fb..65a9a0fa12 100644 --- a/var/spack/repos/builtin/packages/vesta/package.py +++ b/var/spack/repos/builtin/packages/vesta/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,9 +21,9 @@ class Vesta(Package): conflicts('%gcc@:5.3') - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PATH', self.prefix) - run_env.prepend_path('LD_LIBRARY_PATH', self.prefix) + def setup_run_environment(self, env): + env.prepend_path('PATH', self.prefix) + env.prepend_path('LD_LIBRARY_PATH', self.prefix) def install(self, spec, prefix): install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/videoproto/package.py b/var/spack/repos/builtin/packages/videoproto/package.py index e50f00e27d..76d04dfc6f 100644 --- a/var/spack/repos/builtin/packages/videoproto/package.py +++ b/var/spack/repos/builtin/packages/videoproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/viennarna/package.py b/var/spack/repos/builtin/packages/viennarna/package.py index 7809750efd..f06629f098 100644 --- a/var/spack/repos/builtin/packages/viennarna/package.py +++ b/var/spack/repos/builtin/packages/viennarna/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/viewres/package.py b/var/spack/repos/builtin/packages/viewres/package.py index 54389960fe..c1e1ccd41e 100644 --- a/var/spack/repos/builtin/packages/viewres/package.py +++ b/var/spack/repos/builtin/packages/viewres/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vigra/package.py b/var/spack/repos/builtin/packages/vigra/package.py index 02686ffb4c..217f55a9bd 100644 --- a/var/spack/repos/builtin/packages/vigra/package.py +++ b/var/spack/repos/builtin/packages/vigra/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py index fe514c97d0..394caaa1ae 100644 --- a/var/spack/repos/builtin/packages/vim/package.py +++ b/var/spack/repos/builtin/packages/vim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -57,6 +57,7 @@ class Vim(AutotoolsPackage): depends_on('libxtst', when="+x") depends_on('ncurses', when="@7.4:") + depends_on('findutils', type='build') def configure_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/virtualgl/package.py b/var/spack/repos/builtin/packages/virtualgl/package.py index aceae5e7e7..15ce52f86b 100644 --- a/var/spack/repos/builtin/packages/virtualgl/package.py +++ b/var/spack/repos/builtin/packages/virtualgl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py index e9bea6592f..2616b689e3 100644 --- a/var/spack/repos/builtin/packages/visit/package.py +++ b/var/spack/repos/builtin/packages/visit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -30,19 +30,21 @@ class Visit(CMakePackage): patch('spack-changes.patch') patch('nonframework-qwt.patch', when='^qt~framework platform=darwin') + patch('parallel-hdf5.patch', when='+hdf5+mpi') depends_on('cmake@3.0:', type='build') depends_on('vtk@8.1.0:+opengl2', when='@3.0:3.0.1') depends_on('vtk@6.1.0~opengl2', when='@:2.999') depends_on('vtk+python', when='+python @3.0:') - depends_on('vtk~mpi') + depends_on('vtk~mpi', when='~mpi') depends_on('vtk+qt', when='+gui') depends_on('qt@4.8.6:4.999', when='+gui @:2.999') depends_on('qt@5.10:', when='+gui @3.0:') depends_on('qwt', when='+gui') depends_on('python@2.6:2.8', when='+python') depends_on('silo+shared', when='+silo') - depends_on('hdf5', when='+hdf5') + depends_on('hdf5~mpi', when='+hdf5~mpi') + depends_on('hdf5+mpi', when='+hdf5+mpi') depends_on('mpi', when='+mpi') depends_on('adios2', when='+adios2') @@ -91,7 +93,7 @@ class Visit(CMakePackage): if '+hdf5' in spec: args.append( '-DVISIT_HDF5_DIR:PATH={0}'.format(spec['hdf5'].prefix)) - if spec.satisfies('^hdf5+mpi', strict=True): + if '+mpi' in spec: args.append('-DVISIT_HDF5_MPI_DIR:PATH={0}'.format( spec['hdf5'].prefix)) diff --git a/var/spack/repos/builtin/packages/visit/parallel-hdf5.patch b/var/spack/repos/builtin/packages/visit/parallel-hdf5.patch new file mode 100644 index 0000000000..f6fca356e8 --- /dev/null +++ b/var/spack/repos/builtin/packages/visit/parallel-hdf5.patch @@ -0,0 +1,19 @@ +--- a/src/CMake/FindHDF5.cmake 2019-02-15 18:31:27.000000000 -0500 ++++ b/src/CMake/FindHDF5.cmake 2019-11-08 07:57:26.000000000 -0500 +@@ -46,7 +46,7 @@ + # + #****************************************************************************/ + +-# Use the HDF5_DIR hint from the config-site .cmake file ++# Use the HDF5_DIR hint from the config-site .cmake file + + INCLUDE(${VISIT_SOURCE_DIR}/CMake/SetUpThirdParty.cmake) + +@@ -73,6 +73,6 @@ + ELSE() + SET_UP_THIRD_PARTY(HDF5 lib include hdf5) + IF(VISIT_PARALLEL) +- SET_UP_THIRD_PARTY(HDF5_MPI lib include hdf5_mpi) ++ SET_UP_THIRD_PARTY(HDF5_MPI lib include hdf5) + ENDIF(VISIT_PARALLEL) + ENDIF() diff --git a/var/spack/repos/builtin/packages/vizglow/package.py b/var/spack/repos/builtin/packages/vizglow/package.py index 9dca69bd10..41118b5f89 100644 --- a/var/spack/repos/builtin/packages/vizglow/package.py +++ b/var/spack/repos/builtin/packages/vizglow/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vmatch/package.py b/var/spack/repos/builtin/packages/vmatch/package.py index 3cedce4ede..60e1bfb66f 100644 --- a/var/spack/repos/builtin/packages/vmatch/package.py +++ b/var/spack/repos/builtin/packages/vmatch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -15,9 +15,5 @@ class Vmatch(Package): version('2.3.0', sha256='5e18d0dddf04e86dad193fcdde6e48f3901365932634125602d8808f35acf979') - def url_for_version(self, version): - url = 'http://www.vmatch.de/distributions/vmatch-{0}-Linux_x86_64-64bit.tar.gz' - return url.format(version) - def install(self, spec, prefix): install_tree(self.stage.source_path, prefix.bin) diff --git a/var/spack/repos/builtin/packages/voropp/package.py b/var/spack/repos/builtin/packages/voropp/package.py index a755e4d704..201c23de24 100644 --- a/var/spack/repos/builtin/packages/voropp/package.py +++ b/var/spack/repos/builtin/packages/voropp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py b/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py new file mode 100644 index 0000000000..6f8636e52a --- /dev/null +++ b/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class VotcaCsgTutorials(CMakePackage): + """Versatile Object-oriented Toolkit for Coarse-graining + Applications (VOTCA) is a package intended to reduce the amount of + routine work when doing systematic coarse-graining of various + systems. The core is written in C++. + + This package contains the VOTCA coarse-graining tutorials. + """ + homepage = "http://www.votca.org" + url = "https://github.com/votca/csg-tutorials/tarball/v1.4" + git = "https://github.com/votca/csg-tutorials.git" + + version('develop', branch='master') + version('1.6_rc1', sha256='87c4d945d2bdcb247e985cd407b0767c441f7810f1237ae65a63617f136e2ac9') + version('1.5.1', sha256='e35cea92df0e7d05ca7b449c1b5d84d887a3a23c7796abe3b84e4d6feec7faca', preferred=True) + version('1.5', sha256='03b841fb94129cf59781a7a5e3b71936c414aa9dfa17a50d7bc856d46274580c') + version('1.4.1', sha256='623724192c3a7d76b603a74a3326f181045f10f38b9f56dce754a90f1a74556e') + version('1.4', sha256='27d50acd68a9d8557fef18ec2b0c62841ae91c22275ab9afbd65c35e4dd5f719') + + for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6_rc1", "develop"]: + depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v)) + depends_on("boost") diff --git a/var/spack/repos/builtin/packages/votca-csg/package.py b/var/spack/repos/builtin/packages/votca-csg/package.py index bf48ceaf21..f4f38e7aa2 100644 --- a/var/spack/repos/builtin/packages/votca-csg/package.py +++ b/var/spack/repos/builtin/packages/votca-csg/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,12 +20,15 @@ class VotcaCsg(CMakePackage): git = "https://github.com/votca/csg.git" version('develop', branch='master') + version('1.6_rc1', sha256='163701a65a34f90e8a850370167a82cbebf2b5c0774b7a8ad07884451fe9e332') + version('1.5.1', sha256='7fca1261bd267bf38d2edd26259730fed3126c0c3fd91fb81940dbe17bb568fd', preferred=True) version('1.5', sha256='160387cdc51f87dd20ff2e2eed97086beee415d48f3c92f4199f6109068c8ff4') version('1.4.1', sha256='41dccaecadd0165c011bec36a113629e27745a5a133d1a042efe4356acdb5450') version('1.4', sha256='c13e7febd792de8c3d426203f089bd4d33b8067f9db5e8840e4579c88b61146e') depends_on("cmake@2.8:", type='build') - for v in ["1.4", "1.4.1", "1.5", "develop"]: - depends_on('votca-tools@%s' % v, when="@%s" % v) + for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6_rc1", "develop"]: + depends_on('votca-tools@%s' % v, when="@%s:%s.0" % (v, v)) + depends_on("boost") depends_on("gromacs~mpi@5.1:") depends_on("hdf5~mpi") diff --git a/var/spack/repos/builtin/packages/votca-csgapps/package.py b/var/spack/repos/builtin/packages/votca-csgapps/package.py new file mode 100644 index 0000000000..40ba51a96f --- /dev/null +++ b/var/spack/repos/builtin/packages/votca-csgapps/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class VotcaCsgapps(CMakePackage): + """Versatile Object-oriented Toolkit for Coarse-graining + Applications (VOTCA) is a package intended to reduce the amount of + routine work when doing systematic coarse-graining of various + systems. The core is written in C++. + + This package contains the VOTCA coarse-graining extra apps. + """ + homepage = "http://www.votca.org" + url = "https://github.com/votca/csgapps/tarball/v1.4" + git = "https://github.com/votca/csgapps.git" + + version('develop', branch='master') + version('1.6_rc1', sha256='069002f93f891e4aeb24920c1b2458bf8ee4842d273481aea5fa32247f815f02') + version('1.5.1', sha256='b4946711e88a1745688b6cce5aad872e6e2ea200fededf38d77a864883e3750e', preferred=True) + version('1.5', sha256='18b40ce6222509bc70aa9d56b8c538cd5903edf7294d6f95530668e555206d5b') + version('1.4.1', sha256='095d9ee4cd49d2fd79c10e0e84e6890b755e54dec6a5cd580a2b4241ba230a2b') + version('1.4', sha256='4ea8348c2f7de3cc488f48fbd8652e69b52515441952766c06ff67ed1aaf69a0') + + for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6_rc1", "develop"]: + depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v)) + depends_on("boost") diff --git a/var/spack/repos/builtin/packages/votca-ctp/package.py b/var/spack/repos/builtin/packages/votca-ctp/package.py index 379f304484..00dccfd4c8 100644 --- a/var/spack/repos/builtin/packages/votca-ctp/package.py +++ b/var/spack/repos/builtin/packages/votca-ctp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,10 +20,10 @@ class VotcaCtp(CMakePackage): git = "https://github.com/votca/ctp.git" version('develop', branch='master') + version('1.5.1', sha256='ef957c2f6b09335d0d27ecb7e1b80b55e76a100247bc0d0b3cfef7718d2a1126') version('1.5', sha256='31eb6bcc9339e575116f0c91fe7a4ce7d4189f31f0640329c993fea911401d65') depends_on("cmake@2.8:", type='build') - for v in ["1.5", "develop"]: - depends_on('votca-tools@%s' % v, when="@%s" % v) - depends_on('votca-csg@%s' % v, when="@%s" % v) + depends_on('votca-tools@1.5.1') + depends_on('votca-csg@1.5.1') depends_on("gsl") diff --git a/var/spack/repos/builtin/packages/votca-tools/package.py b/var/spack/repos/builtin/packages/votca-tools/package.py index 84f90ea9f0..fc276e0a44 100644 --- a/var/spack/repos/builtin/packages/votca-tools/package.py +++ b/var/spack/repos/builtin/packages/votca-tools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,17 +20,22 @@ class VotcaTools(CMakePackage): git = "https://github.com/votca/tools.git" version('develop', branch='master') + version('1.6_rc1', sha256='59b4bb64a93786a693e0cbc743a27c0bc451b9db2b0f63e4d2866f7aba10c268') + version('1.5.1', sha256='4be4fe25a2910e24e1720cd9022d214001d38196033ade8f9d6e618b4f47d5c4', preferred=True) version('1.5', sha256='a82a6596c24ff06e79eab17ca02f4405745ceeeb66369693a59023ad0b62cf22') version('1.4.1', sha256='b6b87f6bec8db641a1d8660422ca44919252a69494b32ba6c8c9ac986bae9a65') version('1.4', sha256='41638122e7e59852af61d391b4ab8c308fd2e16652f768077e13a99d206ec5d3') + # https://github.com/votca/tools/pull/197, fix cmake module + patch("https://github.com/votca/tools/pull/197.patch", sha256="a06cce2a9cee63c8d01e4d1833f9cd2ba817b846c86fdb51ea5c9cd843135e68", when="@1.6_rc1") + depends_on("cmake@2.8:", type='build') depends_on("expat") depends_on("fftw") depends_on("gsl", when="@:1.4.9999") depends_on("eigen@3.3:", when="@1.5:") depends_on("boost") - depends_on("sqlite") + depends_on("sqlite", when="@:1.5.9999") def cmake_args(self): args = [ diff --git a/var/spack/repos/builtin/packages/votca-xtp/package.py b/var/spack/repos/builtin/packages/votca-xtp/package.py index dd4b4233e0..d18611f48b 100644 --- a/var/spack/repos/builtin/packages/votca-xtp/package.py +++ b/var/spack/repos/builtin/packages/votca-xtp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,13 +20,15 @@ class VotcaXtp(CMakePackage): git = "https://github.com/votca/xtp.git" version('develop', branch='master') + version('1.6_rc1', sha256='144e74a6c4d31e490ca2bfaf4a30df12ccdc303efa5a7d1177c9b80035365ad5') + version('1.5.1', sha256='17a7722e5a32d236e4f1f6f88b680da4ba5f52bcf65bca3687c6a1c731d10881', preferred=True) version('1.5', sha256='b40b6d19e13f0650e84b8beebe86ce5c09071624f18d66df826f9d8584b4d3c8') version('1.4.1', sha256='4b53d371d6cf648c9e9e9bd1f104d349cafeaf10a02866e3f1d05c574b595a21') depends_on("cmake@2.8:", type='build') - for v in ["1.4.1", "1.5", "develop"]: - depends_on('votca-tools@%s' % v, when="@%s" % v) - depends_on('votca-csg@%s' % v, when="@%s" % v) - depends_on("votca-ctp@develop", when='@develop') + for v in ["1.4.1", "1.5", "1.5.1", "1.6_rc1", "develop"]: + depends_on('votca-tools@%s' % v, when="@%s:%s.0" % (v, v)) + depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v)) depends_on("libxc", when='@1.5:') - depends_on("ceres-solver", when='@1.5:') + depends_on("ceres-solver", when='@1.5:1.5.9999') + depends_on("hdf5+cxx~mpi") diff --git a/var/spack/repos/builtin/packages/vpfft/package.py b/var/spack/repos/builtin/packages/vpfft/package.py index 112a4a520f..2851288052 100644 --- a/var/spack/repos/builtin/packages/vpfft/package.py +++ b/var/spack/repos/builtin/packages/vpfft/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vpic/package.py b/var/spack/repos/builtin/packages/vpic/package.py index d81474cc5c..846b09650b 100644 --- a/var/spack/repos/builtin/packages/vpic/package.py +++ b/var/spack/repos/builtin/packages/vpic/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vsearch/package.py b/var/spack/repos/builtin/packages/vsearch/package.py index 4598dc4ee4..4448edaf4b 100644 --- a/var/spack/repos/builtin/packages/vsearch/package.py +++ b/var/spack/repos/builtin/packages/vsearch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -12,6 +12,8 @@ class Vsearch(AutotoolsPackage): homepage = "https://github.com/torognes/vsearch" url = "https://github.com/torognes/vsearch/archive/v2.4.3.tar.gz" + version('2.14.1', sha256='388529a39eb0618a09047bf91e0a8ae8c9fd851a05f8d975e299331748f97741') + version('2.13.3', sha256='e5f34ece28b76403d3ba4a673eca41178fe399c35a1023dbc87d0c0da5efaa52') version('2.4.3', sha256='f7ffc2aec5d76bdaf1ffe7fb733102138214cec3e3846eb225455dcc3c088141') depends_on('m4', type='build') diff --git a/var/spack/repos/builtin/packages/vt/package.py b/var/spack/repos/builtin/packages/vt/package.py index 69dfc2ed6b..9fabcaf4bf 100644 --- a/var/spack/repos/builtin/packages/vt/package.py +++ b/var/spack/repos/builtin/packages/vt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/vtkh/package.py b/var/spack/repos/builtin/packages/vtk-h/package.py index 3d60ee9a50..2a934a442a 100644 --- a/var/spack/repos/builtin/packages/vtkh/package.py +++ b/var/spack/repos/builtin/packages/vtk-h/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,62 +28,62 @@ def cmake_cache_entry(name, value, vtype=None): return 'set({0} "{1}" CACHE {2} "")\n\n'.format(name, value, vtype) -class Vtkh(Package): +class VtkH(Package, CudaPackage): """VTK-h is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-h brings together several projects like VTK-m and DIY2 to provide a toolkit with hybrid parallel capabilities.""" homepage = "https://github.com/Alpine-DAV/vtk-h" + url = "https://github.com/Alpine-DAV/vtk-h/releases/download/v0.5.0/vtkh-v0.5.0.tar.gz" git = "https://github.com/Alpine-DAV/vtk-h.git" + maintainers = ['cyrush'] version('develop', branch='develop', submodules=True) - version('0.1.0', branch='develop', tag='v0.1.0', submodules=True) + version('0.5.0', sha256="9014a8a61a8d7ff636866c6e3b1ebb918ff23fa67cf8d4de801c4a2981de8c96") variant("shared", default=True, description="Build vtk-h as shared libs") variant("mpi", default=True, description="build mpi support") - variant("tbb", default=False, description="build tbb support") + variant("serial", default=True, description="build serial (non-mpi) libraries") variant("cuda", default=False, description="build cuda support") variant("openmp", default=(sys.platform != 'darwin'), description="build openmp support") - depends_on("cmake@3.8.2:", type='build') + # use cmake 3.14, newest that provides proper cuda support + # and we have seen errors with cuda in 3.15 + depends_on("cmake@3.14.1:3.14.99", type='build') depends_on("mpi", when="+mpi") - depends_on("intel-tbb", when="@0.1.0+tbb") depends_on("cuda", when="+cuda") - depends_on("vtkm@1.2.0", when="@0.1.0") - depends_on("vtkm@1.2.0+tbb", when="@0.1.0+tbb") - depends_on("vtkm@1.2.0+cuda", when="@0.1.0+cuda") - depends_on("vtkm@1.2.0~shared", when="@0.1.0~shared") - - depends_on("vtkm@master~tbb+openmp", when="@develop+openmp") - depends_on("vtkm@master~tbb~openmp", when="@develop~openmp") - - depends_on("vtkm@master+cuda~tbb+openmp", when="@develop+cuda+openmp") - depends_on("vtkm@master+cuda~tbb~openmp", when="@develop+cuda~openmp") + depends_on("vtk-m@1.5.0~tbb+openmp", when="+openmp") + depends_on("vtk-m@1.5.0~tbb~openmp", when="~openmp") - depends_on("vtkm@master~tbb+openmp~shared", when="@develop+openmp~shared") - depends_on("vtkm@master~tbb~openmp~shared", when="@develop~openmp~shared") + depends_on("vtk-m@1.5.0+cuda~tbb+openmp", when="+cuda+openmp") + depends_on("vtk-m@1.5.0+cuda~tbb~openmp", when="+cuda~openmp") - depends_on("vtkm@master+cuda~tbb+openmp~shared", when="@develop+cuda+openmp~shared") - depends_on("vtkm@master+cuda~tbb~openmp~shared", when="@develop+cuda~openmp~shared") + depends_on("vtk-m@1.5.0~tbb+openmp~shared", when="+openmp~shared") + depends_on("vtk-m@1.5.0~tbb~openmp~shared", when="~openmp~shared") - patch('vtkm_lagrange_cuda_fix.patch') + depends_on("vtk-m@1.5.0+cuda~tbb+openmp~shared", when="+cuda+openmp~shared") + depends_on("vtk-m@1.5.0+cuda~tbb~openmp~shared", when="+cuda~openmp~shared") def install(self, spec, prefix): with working_dir('spack-build', create=True): cmake_args = ["../src", - "-DVTKM_DIR={0}".format(spec["vtkm"].prefix), + "-DVTKM_DIR={0}".format(spec["vtk-m"].prefix), "-DENABLE_TESTS=OFF", "-DBUILD_TESTING=OFF"] - # shared vs static libs - if "+shared" in spec: - cmake_args.append('-DBUILD_SHARED_LIBS=ON') - else: + # shared vs static libs logic + # force static when building with cuda + if "+cuda" in spec: cmake_args.append('-DBUILD_SHARED_LIBS=OFF') + else: + if "+shared" in spec: + cmake_args.append('-DBUILD_SHARED_LIBS=ON') + else: + cmake_args.append('-DBUILD_SHARED_LIBS=OFF') # mpi support if "+mpi" in spec: @@ -94,9 +94,6 @@ class Vtkh(Package): mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec') if os.path.isfile(mpiexe_bin): cmake_args.append("-DMPIEXEC={0}".format(mpiexe_bin)) - # tbb support - if "+tbb" in spec: - cmake_args.append("-DTBB_DIR={0}".format(spec["tbb"].prefix)) # openmp support if "+openmp" in spec: @@ -104,12 +101,13 @@ class Vtkh(Package): # cuda support if "+cuda" in spec: - cmake_args.append("-DENABLE_CUDA=ON") - # this fix is necessary if compiling platform has cuda, but - # no devices (this common for front end nodes on hpc clusters) - # we choose kepler as a lowest common denominator - cmake_args.append("-DVTKm_CUDA_Architecture=kepler") - + cmake_args.append("-DVTKm_ENABLE_CUDA:BOOL=ON") + cmake_args.append("-DENABLE_CUDA:BOOL=ON") + cmake_args.append("-DCMAKE_CUDA_HOST_COMPILER={0}".format( + env["SPACK_CXX"])) + else: + cmake_args.append("-DVTKm_ENABLE_CUDA:BOOL=OFF") + cmake_args.append("-DENABLE_CUDA:BOOL=OFF") # use release, instead of release with debug symbols b/c vtkh libs # can overwhelm compilers with too many symbols for arg in std_cmake_args: @@ -117,15 +115,14 @@ class Vtkh(Package): cmake_args.extend(std_cmake_args) cmake_args.append("-DCMAKE_BUILD_TYPE=Release") cmake(*cmake_args) - if "+cuda" in spec: - # avoid issues with make -j and FindCuda deps - # likely a ordering issue that needs to be resolved - # in vtk-h - make(parallel=False) - else: - make() + make() make("install") + host_cfg_fname = self.create_host_config(spec, + prefix) + + install(host_cfg_fname, prefix) + def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): """ This method creates a 'host-config' file that specifies @@ -203,25 +200,43 @@ class Vtkh(Package): cfg.write(cmake_cache_entry("ENABLE_OPENMP", "ON")) cfg.write("# vtk-m from spack\n") - cfg.write(cmake_cache_entry("VTKM_DIR", spec['vtkm'].prefix)) + cfg.write(cmake_cache_entry("VTKM_DIR", spec['vtk-m'].prefix)) ####################################################################### # Optional Dependencies ####################################################################### ####################### + # Serial + ####################### + + if "+serial" in spec: + cfg.write(cmake_cache_entry("ENABLE_SERIAL", "ON")) + else: + cfg.write(cmake_cache_entry("ENABLE_SERIAL", "OFF")) + + ####################### # MPI ####################### cfg.write("# MPI Support\n") if "+mpi" in spec: + mpicc_path = spec['mpi'].mpicc + mpicxx_path = spec['mpi'].mpicxx + mpifc_path = spec['mpi'].mpifc + # if we are using compiler wrappers on cray systems + # use those for mpi wrappers, b/c spec['mpi'].mpicxx + # etc make return the spack compiler wrappers + # which can trip up mpi detection in CMake 3.14 + if cpp_compiler == "CC": + mpicc_path = "cc" + mpicxx_path = "CC" + mpifc_path = "ftn" cfg.write(cmake_cache_entry("ENABLE_MPI", "ON")) - cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc)) - cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", - spec['mpi'].mpicxx)) - cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", - spec['mpi'].mpifc)) + cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path)) + cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path)) + cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path)) mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec') if os.path.isfile(mpiexe_bin): # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE diff --git a/var/spack/repos/builtin/packages/vtkh/vtkm_lagrange_cuda_fix.patch b/var/spack/repos/builtin/packages/vtk-h/vtkm_lagrange_cuda_fix.patch index 2f90477e76..2f90477e76 100644 --- a/var/spack/repos/builtin/packages/vtkh/vtkm_lagrange_cuda_fix.patch +++ b/var/spack/repos/builtin/packages/vtk-h/vtkm_lagrange_cuda_fix.patch diff --git a/var/spack/repos/builtin/packages/vtkm/package.py b/var/spack/repos/builtin/packages/vtk-m/package.py index eee37bf9af..0a22efb357 100644 --- a/var/spack/repos/builtin/packages/vtkm/package.py +++ b/var/spack/repos/builtin/packages/vtk-m/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -9,7 +9,7 @@ import os import sys -class Vtkm(CMakePackage, CudaPackage): +class VtkM(CMakePackage, CudaPackage): """VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale @@ -18,14 +18,15 @@ class Vtkm(CMakePackage, CudaPackage): architectures.""" homepage = "https://m.vtk.org/" - url = "https://gitlab.kitware.com/api/v4/projects/vtk%2Fvtk-m/repository/archive.tar.gz?sha=v1.3.0" + url = "https://gitlab.kitware.com/vtk/vtk-m/-/archive/v1.5.0/vtk-m-v1.5.0.tar.gz" git = "https://gitlab.kitware.com/vtk/vtk-m.git" version('master', branch='master') - version('1.4.0', sha256="60e1ce73a8c6beda8aed5f2d3ae670b6b0c78c068c6eff4ece769e6d719d5065") - version('1.3.0', sha256="72c2c8525a77a456fe0b6a1af0328dad6b9a688f402a3d3ebfa8942e0b5dba1a") - version('1.2.0', sha256="9103d954284661f6f03e5b18be6d7bc94254603e6abc8fce67f617f4ad325a0e") - version('1.1.0', sha256="a1746b1547d6fb901ea7d7ed50834e8832d6d41ddd497c84d02e1481100d43bc") + version('1.5.0', sha256="b1b13715c7fcc8d17f5c7166ff5b3e9025f6865dc33eb9b06a63471c21349aa8") + version('1.4.0', sha256="8d83cca7cd5e204d10da151ce4f1846c1f7414c7c1e579173d15c5ea0631555a") + version('1.3.0', sha256="f88c1b0a1980f695240eeed9bcccfa420cc089e631dc2917c9728a2eb906df2e") + version('1.2.0', sha256="607272992e05f8398d196f0acdcb4af025a4a96cd4f66614c6341f31d4561763") + version('1.1.0', sha256="78618c81ca741b1fbba0853cb5d7af12c51973b514c268fc96dfb36b853cdb18") # use release, instead of release with debug symbols b/c vtkm libs # can overwhelm compilers with too many symbols @@ -35,7 +36,7 @@ class Vtkm(CMakePackage, CudaPackage): variant("cuda", default=False, description="build cuda support") variant("doubleprecision", default=True, description='enable double precision') - variant("logging", default=True, description="build logging support") + variant("logging", default=False, description="build logging support") variant("mpi", default=False, description="build mpi support") variant("openmp", default=(sys.platform != 'darwin'), description="build openmp support") variant("rendering", default=True, description="build rendering support") @@ -57,22 +58,30 @@ class Vtkm(CMakePackage, CudaPackage): '30': 'kepler', '32': 'kepler', '35': 'kepler', '50': 'maxwell', '52': 'maxwell', '53': 'maxwell', '60': 'pascal', '61': 'pascal', '62': 'pascal', - '70': 'turing', '72': 'turing', '75': 'turing'} + '70': 'volta', '72': 'turing', '75': 'turing'} with working_dir('spack-build', create=True): options = ["-DVTKm_ENABLE_TESTING:BOOL=OFF"] - # shared vs static libs - if "+shared" in spec: - options.append('-DBUILD_SHARED_LIBS=ON') - else: + # shared vs static libs logic + # force building statically with cuda + if "+cuda" in spec: options.append('-DBUILD_SHARED_LIBS=OFF') + else: + if "+shared" in spec: + options.append('-DBUILD_SHARED_LIBS=ON') + else: + options.append('-DBUILD_SHARED_LIBS=OFF') # cuda support if "+cuda" in spec: options.append("-DVTKm_ENABLE_CUDA:BOOL=ON") + options.append("-DCMAKE_CUDA_HOST_COMPILER={0}".format( + env["SPACK_CXX"])) if 'cuda_arch' in spec.variants: cuda_value = spec.variants['cuda_arch'].value - name = gpu_name_table[cuda_value[0]] - options.append( - '-DVTKm_CUDA_Architecture={0}'.format(name)) + cuda_arch = cuda_value[0] + if cuda_arch in gpu_name_table: + vtkm_cuda_arch = gpu_name_table[cuda_arch] + options.append('-DVTKm_CUDA_Architecture={0}'.format( + vtkm_cuda_arch)) else: # this fix is necessary if compiling platform has cuda, but # no devices (this's common for front end nodes on hpc clus @@ -90,8 +99,7 @@ class Vtkm(CMakePackage, CudaPackage): # logging support if "+logging" in spec: - if spec.satisfies('@:1.2.0') and \ - spec['vtkm'].version.string != 'master': + if spec.satisfies('@:1.2.0'): raise InstallError('logging is not supported for\ vtkm version lower than 1.3') options.append("-DVTKm_ENABLE_LOGGING:BOOL=ON") @@ -100,8 +108,7 @@ class Vtkm(CMakePackage, CudaPackage): # mpi support if "+mpi" in spec: - if spec.satisfies('@:1.2.0') and \ - spec['vtkm'].version.string != 'master': + if spec.satisfies('@:1.2.0'): raise InstallError('mpi is not supported for\ vtkm version lower than 1.3') options.append("-DVTKm_ENABLE_MPI:BOOL=ON") @@ -111,8 +118,7 @@ class Vtkm(CMakePackage, CudaPackage): # openmp support if "+openmp" in spec: # openmp is added since version 1.3.0 - if spec.satisfies('@:1.2.0') and \ - spec['vtkm'].version.string != 'master': + if spec.satisfies('@:1.2.0'): raise InstallError('OpenMP is not supported for\ vtkm version lower than 1.3') options.append("-DVTKm_ENABLE_OPENMP:BOOL=ON") diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index 3d9d108ae4..87fce79af2 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,6 +20,7 @@ class Vtk(CMakePackage): maintainers = ['chuckatkins', 'danlipsa'] + version('8.2.0', sha256='34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb') version('8.1.2', sha256='0995fb36857dd76ccfb8bb07350c214d9f9099e80b1e66b4a8909311f24ff0db') version('8.1.1', sha256='71a09b4340f0a9c58559fe946dc745ab68a866cf20636a41d97b6046cb736324') version('8.1.0', sha256='6e269f07b64fb13774f5925161fb4e1f379f4e6a0131c8408c555f6b58ef3cb7') @@ -61,6 +62,7 @@ class Vtk(CMakePackage): if sys.platform != 'darwin': depends_on('glx', when='~osmesa') + depends_on('libxt', when='~osmesa') # Note: it is recommended to use mesa+llvm, if possible. # mesa default is software rendering, llvm makes it faster @@ -69,37 +71,38 @@ class Vtk(CMakePackage): # VTK will need Qt5OpenGL, and qt needs '-opengl' for that depends_on('qt+opengl', when='+qt') - depends_on('mpi', when='+mpi') - depends_on('boost', when='+xdmf') depends_on('boost+mpi', when='+xdmf +mpi') - - depends_on('mpi', when='+mpi') - depends_on('ffmpeg', when='+ffmpeg') + depends_on('mpi', when='+mpi') depends_on('expat') depends_on('freetype') depends_on('glew') - depends_on('hdf5') + # set hl variant explicitly, similar to issue #7145 + depends_on('hdf5+hl') depends_on('jpeg') depends_on('jsoncpp') depends_on('libxml2') depends_on('lz4') - depends_on('netcdf') + depends_on('netcdf-c~mpi', when='~mpi') + depends_on('netcdf-c+mpi', when='+mpi') depends_on('netcdf-cxx') depends_on('libpng') depends_on('libtiff') depends_on('zlib') + depends_on('eigen', when='@8.2.0:') + depends_on('double-conversion', when='@8.2.0:') + depends_on('sqlite', when='@8.2.0:') def url_for_version(self, version): url = "http://www.vtk.org/files/release/{0}/VTK-{1}.tar.gz" return url.format(version.up_to(2), version) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # VTK has some trouble finding freetype unless it is set in # the environment - spack_env.set('FREETYPE_DIR', self.spec['freetype'].prefix) + env.set('FREETYPE_DIR', self.spec['freetype'].prefix) def cmake_args(self): spec = self.spec @@ -117,11 +120,9 @@ class Vtk(CMakePackage): # However, in a few cases we can't do without them yet '-DVTK_USE_SYSTEM_GL2PS:BOOL=OFF', '-DVTK_USE_SYSTEM_LIBHARU=OFF', - '-DVTK_USE_SYSTEM_LIBPROJ4:BOOL=OFF', - '-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=OFF', - '-DNETCDF_DIR={0}'.format(spec['netcdf'].prefix), - '-DNETCDF_C_ROOT={0}'.format(spec['netcdf'].prefix), + '-DNETCDF_DIR={0}'.format(spec['netcdf-c'].prefix), + '-DNETCDF_C_ROOT={0}'.format(spec['netcdf-c'].prefix), '-DNETCDF_CXX_ROOT={0}'.format(spec['netcdf-cxx'].prefix), # Allow downstream codes (e.g. VisIt) to override VTK's classes @@ -132,6 +133,20 @@ class Vtk(CMakePackage): '-DVTK_WRAP_TCL=OFF', ] + # Some variable names have changed + if spec.satisfies('@8.2.0:'): + cmake_args.extend([ + '-DVTK_USE_SYSTEM_OGG:BOOL=OFF', + '-DVTK_USE_SYSTEM_THEORA:BOOL=OFF', + '-DVTK_USE_SYSTEM_LIBPROJ:BOOL=OFF', + '-DVTK_USE_SYSTEM_PUGIXML:BOOL=OFF', + ]) + else: + cmake_args.extend([ + '-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=OFF', + '-DVTK_USE_SYSTEM_LIBPROJ4:BOOL=OFF', + ]) + if '+mpi' in spec: cmake_args.extend([ '-DVTK_Group_MPI:BOOL=ON', diff --git a/var/spack/repos/builtin/packages/wannier90/package.py b/var/spack/repos/builtin/packages/wannier90/package.py index a8e47c96a8..5be0134141 100644 --- a/var/spack/repos/builtin/packages/wannier90/package.py +++ b/var/spack/repos/builtin/packages/wannier90/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/warpx/package.py b/var/spack/repos/builtin/packages/warpx/package.py index 015c38406b..6873bdf9d1 100644 --- a/var/spack/repos/builtin/packages/warpx/package.py +++ b/var/spack/repos/builtin/packages/warpx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -16,10 +16,10 @@ class Warpx(MakefilePackage): """ homepage = "https://ecp-warpx.github.io/index.html" - url = "https://github.com/ECP-WarpX/WarpX" + git = "https://github.com/ECP-WarpX/WarpX.git" - version('master', git='https://github.com/ECP-WarpX/WarpX.git', tag='master') - version('dev', git='https://github.com/ECP-WarpX/WarpX.git', tag='dev') + version('master', tag='master') + version('dev', tag='dev') depends_on('mpi') @@ -94,11 +94,11 @@ class Warpx(MakefilePackage): 'TINY_PROFILE = {0}'.format(torf('+tprof'))) makefile.filter('EBASE .*', 'EBASE = warpx') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # --- Fool the compiler into using the "unknown" configuration. # --- With this, it will use the spack provided mpi. - spack_env.set('HOSTNAME', 'unknown') - spack_env.set('NERSC_HOST', 'unknown') + env.set('HOSTNAME', 'unknown') + env.set('NERSC_HOST', 'unknown') def install(self, spec, prefix): make('WarpxBinDir = {0}'.format(prefix.bin), 'all') diff --git a/var/spack/repos/builtin/packages/watch/package.py b/var/spack/repos/builtin/packages/watch/package.py index 4e805a7bc9..0416cff450 100644 --- a/var/spack/repos/builtin/packages/watch/package.py +++ b/var/spack/repos/builtin/packages/watch/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/wcslib/package.py b/var/spack/repos/builtin/packages/wcslib/package.py index 551306fe8c..147cc9ed72 100644 --- a/var/spack/repos/builtin/packages/wcslib/package.py +++ b/var/spack/repos/builtin/packages/wcslib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/wget/package.py b/var/spack/repos/builtin/packages/wget/package.py index aecb845f11..122b138d10 100644 --- a/var/spack/repos/builtin/packages/wget/package.py +++ b/var/spack/repos/builtin/packages/wget/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -6,14 +6,14 @@ from spack import * -class Wget(AutotoolsPackage): +class Wget(AutotoolsPackage, GNUMirrorPackage): """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" homepage = "http://www.gnu.org/software/wget/" - url = "https://ftpmirror.gnu.org/wget/wget-1.19.1.tar.gz" + gnu_mirror_path = "wget/wget-1.19.1.tar.gz" version('1.20.3', sha256='31cccfc6630528db1c8e3a06f6decf2a370060b982841cfab2b8677400a5092e') version('1.19.1', sha256='9e4f12da38cc6167d0752d934abe27c7b1599a9af294e73829be7ac7b5b4da40') diff --git a/var/spack/repos/builtin/packages/wgsim/package.py b/var/spack/repos/builtin/packages/wgsim/package.py index ecbbab311e..fe6b25ef4a 100644 --- a/var/spack/repos/builtin/packages/wgsim/package.py +++ b/var/spack/repos/builtin/packages/wgsim/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/which/package.py b/var/spack/repos/builtin/packages/which/package.py new file mode 100644 index 0000000000..c95315ee7f --- /dev/null +++ b/var/spack/repos/builtin/packages/which/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +from spack import * + + +class Which(AutotoolsPackage): + """GNU which - is a utility that is used to find which executable (or + alias or shell function) is executed when entered on the shell prompt.""" + + homepage = "https://savannah.gnu.org/projects/which/" + url = "https://ftp.gnu.org/gnu/which/which-2.21.tar.gz" + + version('2.21', sha256='f4a245b94124b377d8b49646bf421f9155d36aa7614b6ebf83705d3ffc76eaad') diff --git a/var/spack/repos/builtin/packages/windowswmproto/package.py b/var/spack/repos/builtin/packages/windowswmproto/package.py index 9213d24557..abdf56436a 100644 --- a/var/spack/repos/builtin/packages/windowswmproto/package.py +++ b/var/spack/repos/builtin/packages/windowswmproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/wireshark/package.py b/var/spack/repos/builtin/packages/wireshark/package.py index 5df47d773b..8939a2adc9 100644 --- a/var/spack/repos/builtin/packages/wireshark/package.py +++ b/var/spack/repos/builtin/packages/wireshark/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,18 +13,19 @@ class Wireshark(CMakePackage): homepage = "https://www.wireshark.org" url = "https://www.wireshark.org/download/src/all-versions/wireshark-2.6.0.tar.xz" + version('3.2.1', sha256='589f640058d6408ebbd695a80ebbd6e7bd99d8db64ecda253d27100dfd27e85b') + version('3.2.0', sha256='4cfd33a19a454ff4002243e9d04d6afd64280a109a21ae652a192f2be2b1b66c') + version('3.1.0', sha256='a7b54f9e35fc69291dcac5104ecbef8260534a75dec5b8105605b6c423fd3de3') + version('3.0.8', sha256='b4bd8189934d82330a053c5b10398f2b625b1e1c8818831ab61739b2d7aa7561') version('2.6.0', sha256='711c7f01d27a8817d58277a5487cef3e3c7bab1c8caaf8f4c92aa21015b9117f') - variant('smi', default=False, description='Build with libsmi') variant('libssh', default=False, description='Build with libssh') variant('nghttp2', default=False, description='Build with nghttp2') variant('qt', default=False, description='Build with qt') - variant('gtk3', default=False, description='Build with gtk3') - variant('gtk', default=False, description='Build with gtk') variant('headers', default=True, description='Install headers') depends_on('bison', type='build') - depends_on('cares') + depends_on('c-ares') depends_on('doxygen', type='build') depends_on('flex', type='build') depends_on('git', type='build') @@ -37,28 +38,28 @@ class Wireshark(CMakePackage): depends_on('lua@5.0.0:5.2.99') depends_on('krb5') depends_on('pkgconfig', type='build') - depends_on('libsmi', when='+smi') depends_on('libssh', when='+libssh') depends_on('nghttp2', when='+nghttp2') - depends_on('portaudio', when='+gtk') - depends_on('portaudio', when='+gtk3') depends_on('qt@4.8:', when='+qt') - depends_on('gtkplus3', when='+gtk3') - depends_on('gtkplus', when='+gtk') - depends_on('adwaita-icon-theme', when='+gtk3') def cmake_args(self): - args = ['-DENEABLE_CARES=ON', - '-DENABLE_GNUTLS=ON', - '-DENABLE_LUA=ON', - '-DENABLE_MAXMINDDB=ON', - '-DYACC_EXECUTABLE=' + self.spec['bison'].prefix.bin.yacc, - '-DGIT_EXECUTABLE=' + self.spec['git'].prefix.bin.git, - '-DPCAP_INCLUDE_DIR=' + self.spec['libpcap'].prefix.include, - '-DPCAP_LIB=' + str(self.spec['libpcap'].libs), - '-DLUA_INCLUDE_DIR=' + self.spec['lua'].prefix.include, - '-DLUA_LIBRARY=' + str(self.spec['lua'].libs) - ] + args = [ + '-DENEABLE_CARES=ON', + '-DENABLE_GNUTLS=ON', + '-DENABLE_LUA=ON', + '-DENABLE_MAXMINDDB=ON', + '-DYACC_EXECUTABLE=' + self.spec['bison'].prefix.bin.yacc, + '-DGIT_EXECUTABLE=' + self.spec['git'].prefix.bin.git, + '-DPCAP_INCLUDE_DIR=' + self.spec['libpcap'].prefix.include, + '-DPCAP_LIB=' + str(self.spec['libpcap'].libs), + '-DLUA_INCLUDE_DIR=' + self.spec['lua'].prefix.include, + '-DLUA_LIBRARY=' + str(self.spec['lua'].libs), + '-DBUILD_wireshark_gtk=OFF', + '-DENABLE_PORTAUDIO=OFF', + '-DENABLE_GTK3=OFF', + '-DBUILD_SMI=OFF', + ] + if self.spec.satisfies('+qt'): args.append('-DBUILD_wireshark=ON') args.append('-DENABLE_APPLICATION_BUNDLE=ON') @@ -71,15 +72,6 @@ class Wireshark(CMakePackage): args.append('-DENABLE_APPLICATION_BUNDLE=OFF') args.append('-DENABLE_QT5=OFF') - if self.spec.satisfies('+gtk3') or self.spec.satisfies('+gtk'): - args.append('-DBUILD_wireshark_gtk=ON') - args.append('-DENABLE_PORTAUDIO=ON') - else: - args.append('-DBUILD_wireshark_gtk=OFF') - args.append('-DENABLE_PORTAUDIO=OFF') - if self.spec.satisfies('+gtk3'): - args.append('-DENABLE_GTK3=ON') - if self.spec.satisfies('+libssh'): args.append('-DBUILD_sshdump=ON') args.append('-DBUILD_ciscodump=ON') @@ -87,11 +79,6 @@ class Wireshark(CMakePackage): args.append('-DBUILD_sshdump=OFF') args.append('-DBUILD_ciscodump=OFF') - if self.spec.satisfies('+smi'): - args.append('-DBUILD_SMI=ON') - else: - args.append('-DBUILD_SMI=OFF') - if self.spec.satisfies('+nghttp2'): args.append('-DBUILD_NGHTTP2=ON') else: diff --git a/var/spack/repos/builtin/packages/wordnet/package.py b/var/spack/repos/builtin/packages/wordnet/package.py index 6bb3ca2dc0..e286b74939 100644 --- a/var/spack/repos/builtin/packages/wordnet/package.py +++ b/var/spack/repos/builtin/packages/wordnet/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -28,6 +28,6 @@ class Wordnet(AutotoolsPackage): return args - def setup_environment(self, spack_env, run_env): - run_env.set('WNHOME', self.prefix) - run_env.set('WNSEARCHDIR', self.prefix.dict) + def setup_run_environment(self, env): + env.set('WNHOME', self.prefix) + env.set('WNSEARCHDIR', self.prefix.dict) diff --git a/var/spack/repos/builtin/packages/workrave/package.py b/var/spack/repos/builtin/packages/workrave/package.py index fa5a597484..85b74f7aff 100644 --- a/var/spack/repos/builtin/packages/workrave/package.py +++ b/var/spack/repos/builtin/packages/workrave/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -67,13 +67,13 @@ class Workrave(AutotoolsPackage): destination='', placement=m4files[1]) - def setup_environment(self, build_env, run_env): + def setup_build_environment(self, env): # unset PYTHONHOME to let system python script with explict # system python sbangs like glib-mkenums work, see #6968 # Without this, we will get # ImportError: No module named site # during build phase when make runs glib-mkenums - build_env.unset('PYTHONHOME') + env.unset('PYTHONHOME') @run_before('autoreconf') def extra_m4(self): diff --git a/var/spack/repos/builtin/packages/wt/package.py b/var/spack/repos/builtin/packages/wt/package.py index 506e445071..dcc08ca12d 100644 --- a/var/spack/repos/builtin/packages/wt/package.py +++ b/var/spack/repos/builtin/packages/wt/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/wtdbg2/package.py b/var/spack/repos/builtin/packages/wtdbg2/package.py index 3c5607dd9a..255ea90560 100644 --- a/var/spack/repos/builtin/packages/wtdbg2/package.py +++ b/var/spack/repos/builtin/packages/wtdbg2/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/wxpropgrid/package.py b/var/spack/repos/builtin/packages/wxpropgrid/package.py index 8e2d0206e4..2055205d30 100644 --- a/var/spack/repos/builtin/packages/wxpropgrid/package.py +++ b/var/spack/repos/builtin/packages/wxpropgrid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/wxwidgets/package.py b/var/spack/repos/builtin/packages/wxwidgets/package.py index c1735f6774..5b31c4e59b 100644 --- a/var/spack/repos/builtin/packages/wxwidgets/package.py +++ b/var/spack/repos/builtin/packages/wxwidgets/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/x11perf/package.py b/var/spack/repos/builtin/packages/x11perf/package.py index c01f894f53..d0cfe0cd92 100644 --- a/var/spack/repos/builtin/packages/x11perf/package.py +++ b/var/spack/repos/builtin/packages/x11perf/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xapian-core/package.py b/var/spack/repos/builtin/packages/xapian-core/package.py index 1ad6471fce..e8a917128a 100644 --- a/var/spack/repos/builtin/packages/xapian-core/package.py +++ b/var/spack/repos/builtin/packages/xapian-core/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xauth/package.py b/var/spack/repos/builtin/packages/xauth/package.py index d178fbd9f6..f3e44bb079 100644 --- a/var/spack/repos/builtin/packages/xauth/package.py +++ b/var/spack/repos/builtin/packages/xauth/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xbacklight/package.py b/var/spack/repos/builtin/packages/xbacklight/package.py index 0fbfe55553..3b8e127c51 100644 --- a/var/spack/repos/builtin/packages/xbacklight/package.py +++ b/var/spack/repos/builtin/packages/xbacklight/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xbiff/package.py b/var/spack/repos/builtin/packages/xbiff/package.py index 1f625dad7c..a21b2b3a27 100644 --- a/var/spack/repos/builtin/packages/xbiff/package.py +++ b/var/spack/repos/builtin/packages/xbiff/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xbitmaps/package.py b/var/spack/repos/builtin/packages/xbitmaps/package.py index c0505646e2..b3bdb90bc1 100644 --- a/var/spack/repos/builtin/packages/xbitmaps/package.py +++ b/var/spack/repos/builtin/packages/xbitmaps/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xbraid/package.py b/var/spack/repos/builtin/packages/xbraid/package.py index 29ccda623a..d3dff7d295 100644 --- a/var/spack/repos/builtin/packages/xbraid/package.py +++ b/var/spack/repos/builtin/packages/xbraid/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcalc/package.py b/var/spack/repos/builtin/packages/xcalc/package.py index 4aadefe775..ba2cdf997a 100644 --- a/var/spack/repos/builtin/packages/xcalc/package.py +++ b/var/spack/repos/builtin/packages/xcalc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcb-demo/package.py b/var/spack/repos/builtin/packages/xcb-demo/package.py index a4d43257e8..83e7eb2666 100644 --- a/var/spack/repos/builtin/packages/xcb-demo/package.py +++ b/var/spack/repos/builtin/packages/xcb-demo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcb-proto/package.py b/var/spack/repos/builtin/packages/xcb-proto/package.py index a9175a950a..7bf70df0e5 100644 --- a/var/spack/repos/builtin/packages/xcb-proto/package.py +++ b/var/spack/repos/builtin/packages/xcb-proto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcb-util-cursor/package.py b/var/spack/repos/builtin/packages/xcb-util-cursor/package.py index 041935cadf..6b241c46c7 100644 --- a/var/spack/repos/builtin/packages/xcb-util-cursor/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-cursor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcb-util-errors/package.py b/var/spack/repos/builtin/packages/xcb-util-errors/package.py index 5db6d332f3..e861511d33 100644 --- a/var/spack/repos/builtin/packages/xcb-util-errors/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-errors/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcb-util-image/package.py b/var/spack/repos/builtin/packages/xcb-util-image/package.py index 5960cd1ae8..e9b341e259 100644 --- a/var/spack/repos/builtin/packages/xcb-util-image/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-image/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py b/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py index 436b3ee2f5..5b51fe0fe5 100644 --- a/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py b/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py index 28b11d1443..864fa51989 100644 --- a/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcb-util-wm/package.py b/var/spack/repos/builtin/packages/xcb-util-wm/package.py index 5decbfbdbd..8e1f8d764f 100644 --- a/var/spack/repos/builtin/packages/xcb-util-wm/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-wm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcb-util-xrm/package.py b/var/spack/repos/builtin/packages/xcb-util-xrm/package.py index 1b590385bc..0c0185f142 100644 --- a/var/spack/repos/builtin/packages/xcb-util-xrm/package.py +++ b/var/spack/repos/builtin/packages/xcb-util-xrm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcb-util/package.py b/var/spack/repos/builtin/packages/xcb-util/package.py index a2549d174b..7b3f1b4a4a 100644 --- a/var/spack/repos/builtin/packages/xcb-util/package.py +++ b/var/spack/repos/builtin/packages/xcb-util/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xclip/package.py b/var/spack/repos/builtin/packages/xclip/package.py index e9eece2cce..167ab66255 100644 --- a/var/spack/repos/builtin/packages/xclip/package.py +++ b/var/spack/repos/builtin/packages/xclip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xclipboard/package.py b/var/spack/repos/builtin/packages/xclipboard/package.py index 7400fac97a..e35d291ec6 100644 --- a/var/spack/repos/builtin/packages/xclipboard/package.py +++ b/var/spack/repos/builtin/packages/xclipboard/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xclock/package.py b/var/spack/repos/builtin/packages/xclock/package.py index 582b3eba84..3c7afeebe5 100644 --- a/var/spack/repos/builtin/packages/xclock/package.py +++ b/var/spack/repos/builtin/packages/xclock/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcmiscproto/package.py b/var/spack/repos/builtin/packages/xcmiscproto/package.py index 37e9501d2e..ec7f589dd0 100644 --- a/var/spack/repos/builtin/packages/xcmiscproto/package.py +++ b/var/spack/repos/builtin/packages/xcmiscproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcmsdb/package.py b/var/spack/repos/builtin/packages/xcmsdb/package.py index a86e15b758..f1b94450b5 100644 --- a/var/spack/repos/builtin/packages/xcmsdb/package.py +++ b/var/spack/repos/builtin/packages/xcmsdb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcompmgr/package.py b/var/spack/repos/builtin/packages/xcompmgr/package.py index aaf8dd39be..769d161dd0 100644 --- a/var/spack/repos/builtin/packages/xcompmgr/package.py +++ b/var/spack/repos/builtin/packages/xcompmgr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xconsole/package.py b/var/spack/repos/builtin/packages/xconsole/package.py index aa8ba6d552..6902995981 100644 --- a/var/spack/repos/builtin/packages/xconsole/package.py +++ b/var/spack/repos/builtin/packages/xconsole/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcursor-themes/package.py b/var/spack/repos/builtin/packages/xcursor-themes/package.py index 98c19d7c77..f25c3934ad 100644 --- a/var/spack/repos/builtin/packages/xcursor-themes/package.py +++ b/var/spack/repos/builtin/packages/xcursor-themes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xcursorgen/package.py b/var/spack/repos/builtin/packages/xcursorgen/package.py index 7344a4b0e3..3300e7f05d 100644 --- a/var/spack/repos/builtin/packages/xcursorgen/package.py +++ b/var/spack/repos/builtin/packages/xcursorgen/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xdbedizzy/package.py b/var/spack/repos/builtin/packages/xdbedizzy/package.py index e19ed50169..109c723eda 100644 --- a/var/spack/repos/builtin/packages/xdbedizzy/package.py +++ b/var/spack/repos/builtin/packages/xdbedizzy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xditview/package.py b/var/spack/repos/builtin/packages/xditview/package.py index d51ef31fc8..0fcd01df59 100644 --- a/var/spack/repos/builtin/packages/xditview/package.py +++ b/var/spack/repos/builtin/packages/xditview/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xdm/package.py b/var/spack/repos/builtin/packages/xdm/package.py index a719d627c0..ce2c89917c 100644 --- a/var/spack/repos/builtin/packages/xdm/package.py +++ b/var/spack/repos/builtin/packages/xdm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xdmf3/package.py b/var/spack/repos/builtin/packages/xdmf3/package.py index 772135846c..33c9e802b9 100644 --- a/var/spack/repos/builtin/packages/xdmf3/package.py +++ b/var/spack/repos/builtin/packages/xdmf3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,7 +13,6 @@ class Xdmf3(CMakePackage): """ homepage = "http://xdmf.org" - url = "https://gitlab.kitware.com/xdmf/xdmf/-/archive/master/xdmf-master.tar.bz2" git = "https://gitlab.kitware.com/xdmf/xdmf.git" # There is no official release of XDMF and development has largely ceased, diff --git a/var/spack/repos/builtin/packages/xdpyinfo/package.py b/var/spack/repos/builtin/packages/xdpyinfo/package.py index 38d6b5ba86..ddf8298d6b 100644 --- a/var/spack/repos/builtin/packages/xdpyinfo/package.py +++ b/var/spack/repos/builtin/packages/xdpyinfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xdriinfo/package.py b/var/spack/repos/builtin/packages/xdriinfo/package.py index a1a3c38065..d7a6ca67ec 100644 --- a/var/spack/repos/builtin/packages/xdriinfo/package.py +++ b/var/spack/repos/builtin/packages/xdriinfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xedit/package.py b/var/spack/repos/builtin/packages/xedit/package.py index 92e8c5d455..83978175ed 100644 --- a/var/spack/repos/builtin/packages/xedit/package.py +++ b/var/spack/repos/builtin/packages/xedit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py index f2448ed478..26d21b342c 100644 --- a/var/spack/repos/builtin/packages/xerces-c/package.py +++ b/var/spack/repos/builtin/packages/xerces-c/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xeus/package.py b/var/spack/repos/builtin/packages/xeus/package.py index d67d32d188..629bbb76a8 100644 --- a/var/spack/repos/builtin/packages/xeus/package.py +++ b/var/spack/repos/builtin/packages/xeus/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -23,7 +23,7 @@ class Xeus(CMakePackage): conflicts('%clang@:3.6') conflicts('%intel@:17') - depends_on('zeromq@4.2.5:-libsodium') + depends_on('libzmq@4.2.5:-libsodium') depends_on('cppzmq@4.3.0:') depends_on('cryptopp@7.0.0:') depends_on('xtl@0.4.0:') diff --git a/var/spack/repos/builtin/packages/xev/package.py b/var/spack/repos/builtin/packages/xev/package.py index 968e47a3a8..58049e456e 100644 --- a/var/spack/repos/builtin/packages/xev/package.py +++ b/var/spack/repos/builtin/packages/xev/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xextproto/package.py b/var/spack/repos/builtin/packages/xextproto/package.py index 88a755eeb9..7837574479 100644 --- a/var/spack/repos/builtin/packages/xextproto/package.py +++ b/var/spack/repos/builtin/packages/xextproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xeyes/package.py b/var/spack/repos/builtin/packages/xeyes/package.py index 0aa1340cbb..e9f3c364db 100644 --- a/var/spack/repos/builtin/packages/xeyes/package.py +++ b/var/spack/repos/builtin/packages/xeyes/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xf86bigfontproto/package.py b/var/spack/repos/builtin/packages/xf86bigfontproto/package.py index d2d97a3c23..93e4bfd780 100644 --- a/var/spack/repos/builtin/packages/xf86bigfontproto/package.py +++ b/var/spack/repos/builtin/packages/xf86bigfontproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xf86dga/package.py b/var/spack/repos/builtin/packages/xf86dga/package.py index 16c3c01cab..9b7921040e 100644 --- a/var/spack/repos/builtin/packages/xf86dga/package.py +++ b/var/spack/repos/builtin/packages/xf86dga/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xf86dgaproto/package.py b/var/spack/repos/builtin/packages/xf86dgaproto/package.py index 25f29f1b66..d51f501f1d 100644 --- a/var/spack/repos/builtin/packages/xf86dgaproto/package.py +++ b/var/spack/repos/builtin/packages/xf86dgaproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xf86driproto/package.py b/var/spack/repos/builtin/packages/xf86driproto/package.py index f299d4c3c6..5b6a401353 100644 --- a/var/spack/repos/builtin/packages/xf86driproto/package.py +++ b/var/spack/repos/builtin/packages/xf86driproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xf86miscproto/package.py b/var/spack/repos/builtin/packages/xf86miscproto/package.py index f0e189899a..6257aeb452 100644 --- a/var/spack/repos/builtin/packages/xf86miscproto/package.py +++ b/var/spack/repos/builtin/packages/xf86miscproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xf86rushproto/package.py b/var/spack/repos/builtin/packages/xf86rushproto/package.py index 3ee53542fd..8e49fb82fc 100644 --- a/var/spack/repos/builtin/packages/xf86rushproto/package.py +++ b/var/spack/repos/builtin/packages/xf86rushproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py b/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py index 1ba37dad8e..a242e58e2b 100644 --- a/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py +++ b/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xfd/package.py b/var/spack/repos/builtin/packages/xfd/package.py index dab0cb18e8..a6483c1d1c 100644 --- a/var/spack/repos/builtin/packages/xfd/package.py +++ b/var/spack/repos/builtin/packages/xfd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xfindproxy/package.py b/var/spack/repos/builtin/packages/xfindproxy/package.py index 04c817f094..9af7f57462 100644 --- a/var/spack/repos/builtin/packages/xfindproxy/package.py +++ b/var/spack/repos/builtin/packages/xfindproxy/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xfontsel/package.py b/var/spack/repos/builtin/packages/xfontsel/package.py index 7eacb5a209..77d363f866 100644 --- a/var/spack/repos/builtin/packages/xfontsel/package.py +++ b/var/spack/repos/builtin/packages/xfontsel/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xfs/package.py b/var/spack/repos/builtin/packages/xfs/package.py index 0821ec4a7f..b51c94b6c5 100644 --- a/var/spack/repos/builtin/packages/xfs/package.py +++ b/var/spack/repos/builtin/packages/xfs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xfsinfo/package.py b/var/spack/repos/builtin/packages/xfsinfo/package.py index 20a3c19da8..28c94fb167 100644 --- a/var/spack/repos/builtin/packages/xfsinfo/package.py +++ b/var/spack/repos/builtin/packages/xfsinfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xfwp/package.py b/var/spack/repos/builtin/packages/xfwp/package.py index 8a8bf4d36e..1cc94e4567 100644 --- a/var/spack/repos/builtin/packages/xfwp/package.py +++ b/var/spack/repos/builtin/packages/xfwp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xgamma/package.py b/var/spack/repos/builtin/packages/xgamma/package.py index 7cdc53f1ac..2f33d45602 100644 --- a/var/spack/repos/builtin/packages/xgamma/package.py +++ b/var/spack/repos/builtin/packages/xgamma/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xgboost/package.py b/var/spack/repos/builtin/packages/xgboost/package.py index 1718567d1c..f65ea1621b 100644 --- a/var/spack/repos/builtin/packages/xgboost/package.py +++ b/var/spack/repos/builtin/packages/xgboost/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xgc/package.py b/var/spack/repos/builtin/packages/xgc/package.py index 708fff1da7..4e5e67bc6a 100644 --- a/var/spack/repos/builtin/packages/xgc/package.py +++ b/var/spack/repos/builtin/packages/xgc/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xhmm/package.py b/var/spack/repos/builtin/packages/xhmm/package.py index a5791fcff5..bff123a68a 100644 --- a/var/spack/repos/builtin/packages/xhmm/package.py +++ b/var/spack/repos/builtin/packages/xhmm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xhost/package.py b/var/spack/repos/builtin/packages/xhost/package.py index b0446d474f..0a001203c2 100644 --- a/var/spack/repos/builtin/packages/xhost/package.py +++ b/var/spack/repos/builtin/packages/xhost/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xineramaproto/package.py b/var/spack/repos/builtin/packages/xineramaproto/package.py index 6226a4ca4f..7ba45673a9 100644 --- a/var/spack/repos/builtin/packages/xineramaproto/package.py +++ b/var/spack/repos/builtin/packages/xineramaproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xinit/package.py b/var/spack/repos/builtin/packages/xinit/package.py index 997b226c09..10b7ff7cb1 100644 --- a/var/spack/repos/builtin/packages/xinit/package.py +++ b/var/spack/repos/builtin/packages/xinit/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xinput/package.py b/var/spack/repos/builtin/packages/xinput/package.py index 5856dd9dc3..e8c9151716 100644 --- a/var/spack/repos/builtin/packages/xinput/package.py +++ b/var/spack/repos/builtin/packages/xinput/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xios/package.py b/var/spack/repos/builtin/packages/xios/package.py index 799bdc03d7..55769026cf 100644 --- a/var/spack/repos/builtin/packages/xios/package.py +++ b/var/spack/repos/builtin/packages/xios/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -21,7 +21,7 @@ class Xios(Package): description='Build for debugging, development or production') # NOTE: oasis coupler could be supported with a variant - # Use spack versions of blitz and netcdf for compatibility + # Use spack versions of blitz and netcdf-c for compatibility # with recent compilers and optimised platform libraries: patch('bld_extern_1.0.patch', when='@:1.0') patch('bld_extern_1.x.patch', when='@1.1:') @@ -30,7 +30,7 @@ class Xios(Package): # followed by a character is broken (e.g. duration '1d'): patch('llvm_bug_17782.patch', when='@1.1: %clang') - depends_on('netcdf+mpi') + depends_on('netcdf-c+mpi') depends_on('netcdf-fortran') depends_on('hdf5+mpi') depends_on('mpi') @@ -60,8 +60,8 @@ class Xios(Package): def xios_path(self): file = join_path('arch', 'arch-SPACK.path') spec = self.spec - paths = {'NETCDF_INC_DIR': spec['netcdf'].prefix.include, - 'NETCDF_LIB_DIR': spec['netcdf'].prefix.lib, + paths = {'NETCDF_INC_DIR': spec['netcdf-c'].prefix.include, + 'NETCDF_LIB_DIR': spec['netcdf-c'].prefix.lib, 'HDF5_INC_DIR': spec['hdf5'].prefix.include, 'HDF5_LIB_DIR': spec['hdf5'].prefix.lib} text = r""" diff --git a/var/spack/repos/builtin/packages/xkbcomp/package.py b/var/spack/repos/builtin/packages/xkbcomp/package.py index 63c0dee249..6cc49d96f9 100644 --- a/var/spack/repos/builtin/packages/xkbcomp/package.py +++ b/var/spack/repos/builtin/packages/xkbcomp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xkbdata/package.py b/var/spack/repos/builtin/packages/xkbdata/package.py index ca1d18599f..54925e455a 100644 --- a/var/spack/repos/builtin/packages/xkbdata/package.py +++ b/var/spack/repos/builtin/packages/xkbdata/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xkbevd/package.py b/var/spack/repos/builtin/packages/xkbevd/package.py index 6bc8da7947..87a9ba0de4 100644 --- a/var/spack/repos/builtin/packages/xkbevd/package.py +++ b/var/spack/repos/builtin/packages/xkbevd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xkbprint/package.py b/var/spack/repos/builtin/packages/xkbprint/package.py index 7b317ea7ad..c86b966b77 100644 --- a/var/spack/repos/builtin/packages/xkbprint/package.py +++ b/var/spack/repos/builtin/packages/xkbprint/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xkbutils/package.py b/var/spack/repos/builtin/packages/xkbutils/package.py index 5bf7e33d7d..1006d875f5 100644 --- a/var/spack/repos/builtin/packages/xkbutils/package.py +++ b/var/spack/repos/builtin/packages/xkbutils/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xkeyboard-config/package.py b/var/spack/repos/builtin/packages/xkeyboard-config/package.py index a3356aaf09..8621af0c46 100644 --- a/var/spack/repos/builtin/packages/xkeyboard-config/package.py +++ b/var/spack/repos/builtin/packages/xkeyboard-config/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -31,6 +31,8 @@ class XkeyboardConfig(AutotoolsPackage): # perl@5.8.1: # perl XML::Parser - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.prepend_path('XKB_CONFIG_ROOT', self.prefix.share.X11.xkb) - run_env.prepend_path('XKB_CONFIG_ROOT', self.prefix.share.X11.xkb) + def setup_dependent_build_environment(self, env, dependent_spec): + env.prepend_path('XKB_CONFIG_ROOT', self.prefix.share.X11.xkb) + + def setup_dependent_run_environment(self, env, dependent_spec): + env.prepend_path('XKB_CONFIG_ROOT', self.prefix.share.X11.xkb) diff --git a/var/spack/repos/builtin/packages/xkill/package.py b/var/spack/repos/builtin/packages/xkill/package.py index 355a7b6cc6..9a9895c13d 100644 --- a/var/spack/repos/builtin/packages/xkill/package.py +++ b/var/spack/repos/builtin/packages/xkill/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xload/package.py b/var/spack/repos/builtin/packages/xload/package.py index 018c3b9f78..77554202e6 100644 --- a/var/spack/repos/builtin/packages/xload/package.py +++ b/var/spack/repos/builtin/packages/xload/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xlogo/package.py b/var/spack/repos/builtin/packages/xlogo/package.py index ce8fc1325c..d367ab76b0 100644 --- a/var/spack/repos/builtin/packages/xlogo/package.py +++ b/var/spack/repos/builtin/packages/xlogo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xlsatoms/package.py b/var/spack/repos/builtin/packages/xlsatoms/package.py index dd8aff90a4..d7e94097e3 100644 --- a/var/spack/repos/builtin/packages/xlsatoms/package.py +++ b/var/spack/repos/builtin/packages/xlsatoms/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xlsclients/package.py b/var/spack/repos/builtin/packages/xlsclients/package.py index cc5e80a889..cd00374204 100644 --- a/var/spack/repos/builtin/packages/xlsclients/package.py +++ b/var/spack/repos/builtin/packages/xlsclients/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xlsfonts/package.py b/var/spack/repos/builtin/packages/xlsfonts/package.py index 4211a5b36a..0cfda1979f 100644 --- a/var/spack/repos/builtin/packages/xlsfonts/package.py +++ b/var/spack/repos/builtin/packages/xlsfonts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xmag/package.py b/var/spack/repos/builtin/packages/xmag/package.py index 9c0183e244..62abefd68c 100644 --- a/var/spack/repos/builtin/packages/xmag/package.py +++ b/var/spack/repos/builtin/packages/xmag/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xman/package.py b/var/spack/repos/builtin/packages/xman/package.py index 813b0cdf85..433a8ee71f 100644 --- a/var/spack/repos/builtin/packages/xman/package.py +++ b/var/spack/repos/builtin/packages/xman/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xmessage/package.py b/var/spack/repos/builtin/packages/xmessage/package.py index d852f54ea4..d1aaee2053 100644 --- a/var/spack/repos/builtin/packages/xmessage/package.py +++ b/var/spack/repos/builtin/packages/xmessage/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xmh/package.py b/var/spack/repos/builtin/packages/xmh/package.py index ae11336b10..68ee0eb8a9 100644 --- a/var/spack/repos/builtin/packages/xmh/package.py +++ b/var/spack/repos/builtin/packages/xmh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xmlf90/package.py b/var/spack/repos/builtin/packages/xmlf90/package.py index d9e51332d9..ff2a2a622b 100644 --- a/var/spack/repos/builtin/packages/xmlf90/package.py +++ b/var/spack/repos/builtin/packages/xmlf90/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xmlto/package.py b/var/spack/repos/builtin/packages/xmlto/package.py index e50a038f99..e7dc54f598 100644 --- a/var/spack/repos/builtin/packages/xmlto/package.py +++ b/var/spack/repos/builtin/packages/xmlto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xmodmap/package.py b/var/spack/repos/builtin/packages/xmodmap/package.py index 3c31297595..8ab2eedc99 100644 --- a/var/spack/repos/builtin/packages/xmodmap/package.py +++ b/var/spack/repos/builtin/packages/xmodmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xmore/package.py b/var/spack/repos/builtin/packages/xmore/package.py index b8b4e68cdc..822dde7848 100644 --- a/var/spack/repos/builtin/packages/xmore/package.py +++ b/var/spack/repos/builtin/packages/xmore/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xorg-cf-files/package.py b/var/spack/repos/builtin/packages/xorg-cf-files/package.py index 36c940682d..0ed5abeb9f 100644 --- a/var/spack/repos/builtin/packages/xorg-cf-files/package.py +++ b/var/spack/repos/builtin/packages/xorg-cf-files/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xorg-docs/package.py b/var/spack/repos/builtin/packages/xorg-docs/package.py index 115186e777..8c653eae30 100644 --- a/var/spack/repos/builtin/packages/xorg-docs/package.py +++ b/var/spack/repos/builtin/packages/xorg-docs/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xorg-gtest/package.py b/var/spack/repos/builtin/packages/xorg-gtest/package.py index 577d4bdb31..87df7ca58d 100644 --- a/var/spack/repos/builtin/packages/xorg-gtest/package.py +++ b/var/spack/repos/builtin/packages/xorg-gtest/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xorg-server/package.py b/var/spack/repos/builtin/packages/xorg-server/package.py index 53260ad16d..f46795ffbf 100644 --- a/var/spack/repos/builtin/packages/xorg-server/package.py +++ b/var/spack/repos/builtin/packages/xorg-server/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py b/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py index 8bf7209c32..3eb8acb129 100644 --- a/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py +++ b/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xphelloworld/package.py b/var/spack/repos/builtin/packages/xphelloworld/package.py index 31c5f00a92..b0bcd86858 100644 --- a/var/spack/repos/builtin/packages/xphelloworld/package.py +++ b/var/spack/repos/builtin/packages/xphelloworld/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xplor-nih/package.py b/var/spack/repos/builtin/packages/xplor-nih/package.py index d190d66fd6..94ad11836a 100644 --- a/var/spack/repos/builtin/packages/xplor-nih/package.py +++ b/var/spack/repos/builtin/packages/xplor-nih/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xplsprinters/package.py b/var/spack/repos/builtin/packages/xplsprinters/package.py index 9214cc6f39..2a7daa8a40 100644 --- a/var/spack/repos/builtin/packages/xplsprinters/package.py +++ b/var/spack/repos/builtin/packages/xplsprinters/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xpr/package.py b/var/spack/repos/builtin/packages/xpr/package.py index 914be1ec8f..56023a0088 100644 --- a/var/spack/repos/builtin/packages/xpr/package.py +++ b/var/spack/repos/builtin/packages/xpr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xprehashprinterlist/package.py b/var/spack/repos/builtin/packages/xprehashprinterlist/package.py index f084e0dbf7..4cd0383461 100644 --- a/var/spack/repos/builtin/packages/xprehashprinterlist/package.py +++ b/var/spack/repos/builtin/packages/xprehashprinterlist/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xprop/package.py b/var/spack/repos/builtin/packages/xprop/package.py index b3c4e79dc4..d5f2c2ea37 100644 --- a/var/spack/repos/builtin/packages/xprop/package.py +++ b/var/spack/repos/builtin/packages/xprop/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xproto/package.py b/var/spack/repos/builtin/packages/xproto/package.py index 915fe00347..ebadd4b2eb 100644 --- a/var/spack/repos/builtin/packages/xproto/package.py +++ b/var/spack/repos/builtin/packages/xproto/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py b/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py index 6a2198e246..f0c082e282 100644 --- a/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py +++ b/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xqilla/package.py b/var/spack/repos/builtin/packages/xqilla/package.py index b1ec632a7d..2235a609e5 100644 --- a/var/spack/repos/builtin/packages/xqilla/package.py +++ b/var/spack/repos/builtin/packages/xqilla/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xrandr/package.py b/var/spack/repos/builtin/packages/xrandr/package.py index 7a246c809e..6f716043b8 100644 --- a/var/spack/repos/builtin/packages/xrandr/package.py +++ b/var/spack/repos/builtin/packages/xrandr/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xrdb/package.py b/var/spack/repos/builtin/packages/xrdb/package.py index 384ea1fd46..d32b966d1a 100644 --- a/var/spack/repos/builtin/packages/xrdb/package.py +++ b/var/spack/repos/builtin/packages/xrdb/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xrefresh/package.py b/var/spack/repos/builtin/packages/xrefresh/package.py index e00067cf6a..fbfbf30886 100644 --- a/var/spack/repos/builtin/packages/xrefresh/package.py +++ b/var/spack/repos/builtin/packages/xrefresh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xrootd/package.py b/var/spack/repos/builtin/packages/xrootd/package.py index b5e67e3131..6b9bf1d14c 100644 --- a/var/spack/repos/builtin/packages/xrootd/package.py +++ b/var/spack/repos/builtin/packages/xrootd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -13,10 +13,8 @@ class Xrootd(CMakePackage): homepage = "http://xrootd.org" url = "http://xrootd.org/download/v4.6.0/xrootd-4.6.0.tar.gz" - version('4.8.5', - sha256='42e4d2cc6f8b442135f09bcc12c7be38b1a0c623a005cb5e69ff3d27997bdf73') - version('4.8.4', - sha256='f148d55b16525567c0f893edf9bb2975f7c09f87f0599463e19e1b456a9d95ba') + version('4.8.5', sha256='42e4d2cc6f8b442135f09bcc12c7be38b1a0c623a005cb5e69ff3d27997bdf73') + version('4.8.4', sha256='f148d55b16525567c0f893edf9bb2975f7c09f87f0599463e19e1b456a9d95ba') version('4.8.3', sha256='9cd30a343758b8f50aea4916fa7bd37de3c37c5b670fe059ae77a8b2bbabf299') version('4.8.2', sha256='8f28ec53e799d4aa55bd0cc4ab278d9762e0e57ac40a4b02af7fc53dcd1bef39') version('4.8.1', sha256='edee2673d941daf7a6e5c963d339d4a69b4db5c4b6f77b4548b3129b42198029') @@ -83,7 +81,7 @@ class Xrootd(CMakePackage): return options - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): cxxstdflag = '' if self.spec.variants['cxxstd'].value == '98': cxxstdflag = self.compiler.cxx98_flag @@ -101,4 +99,4 @@ class Xrootd(CMakePackage): "cxxstd={0}".format(self.spec.variants['cxxstd'].value)) if cxxstdflag: - spack_env.append_flags('CXXFLAGS', cxxstdflag) + env.append_flags('CXXFLAGS', cxxstdflag) diff --git a/var/spack/repos/builtin/packages/xrx/package.py b/var/spack/repos/builtin/packages/xrx/package.py index 3970997b13..580df464dd 100644 --- a/var/spack/repos/builtin/packages/xrx/package.py +++ b/var/spack/repos/builtin/packages/xrx/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xsbench/package.py b/var/spack/repos/builtin/packages/xsbench/package.py index a8b7b42924..3648edc298 100644 --- a/var/spack/repos/builtin/packages/xsbench/package.py +++ b/var/spack/repos/builtin/packages/xsbench/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -18,6 +18,7 @@ class Xsbench(MakefilePackage): tags = ['proxy-app', 'ecp-proxy-app'] + version('19', sha256='57cc44ae3b0a50d33fab6dd48da13368720d2aa1b91cde47d51da78bf656b97e') version('18', sha256='a9a544eeacd1be8d687080d2df4eeb701c04eda31d3806e7c3ea1ff36c26f4b0') version('14', sha256='595afbcba8c1079067d5d17eedcb4ab0c1d115f83fd6f8c3de01d74b23015e2d') version('13', sha256='b503ea468d3720a0369304924477b758b3d128c8074776233fa5d567b7ffcaa2') diff --git a/var/spack/repos/builtin/packages/xscope/package.py b/var/spack/repos/builtin/packages/xscope/package.py index 27e4901e85..3b322267e1 100644 --- a/var/spack/repos/builtin/packages/xscope/package.py +++ b/var/spack/repos/builtin/packages/xscope/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xsd/package.py b/var/spack/repos/builtin/packages/xsd/package.py index 5e9fe14087..17127eb784 100644 --- a/var/spack/repos/builtin/packages/xsd/package.py +++ b/var/spack/repos/builtin/packages/xsd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -24,9 +24,9 @@ class Xsd(MakefilePackage): def install(self, spec, prefix): make('install', 'install_prefix=' + prefix) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): xercesc_lib_flags = self.spec['xerces-c'].libs.search_flags - spack_env.append_flags('LDFLAGS', xercesc_lib_flags) + env.append_flags('LDFLAGS', xercesc_lib_flags) def url_for_version(self, version): url = "https://www.codesynthesis.com/download/xsd/{0}/xsd-{1}+dep.tar.bz2" diff --git a/var/spack/repos/builtin/packages/xsdk/package.py b/var/spack/repos/builtin/packages/xsdk/package.py index 8f1caa0a7c..b2f036a416 100644 --- a/var/spack/repos/builtin/packages/xsdk/package.py +++ b/var/spack/repos/builtin/packages/xsdk/package.py @@ -1,10 +1,11 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import sys class Xsdk(BundlePackage): @@ -18,91 +19,129 @@ class Xsdk(BundlePackage): maintainers = ['balay', 'luszczek'] version('develop') + version('0.5.0') version('0.4.0') version('0.3.0') version('xsdk-0.2.0') variant('debug', default=False, description='Compile in debug mode') variant('cuda', default=False, description='Enable CUDA dependent packages') + variant('trilinos', default=True, description='Enable trilinos package build') variant('omega-h', default=True, description='Enable omega-h package build') + variant('strumpack', default=True, description='Enable strumpack package build') variant('dealii', default=True, description='Enable dealii package build') variant('phist', default=True, description='Enable phist package build') - - depends_on('hypre@develop~internal-superlu+superlu-dist+shared', when='@develop') + variant('ginkgo', default=True, description='Enable ginkgo package build') + variant('libensemble', default=True, description='Enable py-libensemble package build') + variant('precice', default=(sys.platform != 'darwin'), + description='Enable precice package build') + variant('butterflypack', default=True, description='Enable butterflypack package build') + + depends_on('hypre@develop+superlu-dist+shared', when='@develop') + depends_on('hypre@2.18.2+superlu-dist+shared', when='@0.5.0') depends_on('hypre@2.15.1~internal-superlu', when='@0.4.0') depends_on('hypre@2.12.1~internal-superlu', when='@0.3.0') depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0') depends_on('mfem@develop+mpi+hypre+superlu-dist+petsc~sundials+examples+miniapps', when='@develop') + depends_on('mfem@4.0.1-xsdk+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@0.5.0') depends_on('mfem@3.4.0+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@0.4.0') depends_on('mfem@3.3.2+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@0.3.0') depends_on('superlu-dist@develop', when='@develop') + depends_on('superlu-dist@6.1.1', when='@0.5.0') depends_on('superlu-dist@6.1.0', when='@0.4.0') depends_on('superlu-dist@5.2.2', when='@0.3.0') depends_on('superlu-dist@xsdk-0.2.0', when='@xsdk-0.2.0') depends_on('trilinos@develop+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse+tpetra+nox+ifpack2+zoltan2+amesos2~exodus+dtk+intrepid2+shards', - when='@develop') + when='@develop +trilinos') + depends_on('trilinos@12.18.1+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse+tpetra+nox+ifpack2+zoltan2+amesos2~exodus+dtk+intrepid2+shards', + when='@0.5.0 +trilinos') depends_on('trilinos@12.14.1+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse+tpetra+nox+ifpack2+zoltan2+amesos2~exodus+dtk+intrepid2+shards', - when='@0.4.0') + when='@0.4.0 +trilinos') depends_on('trilinos@12.12.1+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse~tpetra~ifpack2~zoltan2~amesos2~exodus', - when='@0.3.0') + when='@0.3.0 +trilinos') depends_on('trilinos@xsdk-0.2.0+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse~tpetra~ifpack2~zoltan2~amesos2~exodus', - when='@xsdk-0.2.0') + when='@xsdk-0.2.0 +trilinos') - depends_on('petsc@develop+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64', + depends_on('petsc +trilinos', when='+trilinos') + depends_on('petsc ~trilinos', when='~trilinos') + depends_on('petsc +batch', when='platform=cray @0.5.0:') + depends_on('petsc@develop+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64', when='@develop') - depends_on('petsc@3.10.3+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64', + depends_on('petsc@3.12.1+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64', + when='@0.5.0') + depends_on('petsc@3.10.3+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64', when='@0.4.0') - depends_on('petsc@3.8.2+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64', + depends_on('petsc@3.8.2+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64', when='@0.3.0') - depends_on('petsc@xsdk-0.2.0+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64', + depends_on('petsc@xsdk-0.2.0+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64', when='@xsdk-0.2.0') - depends_on('dealii@develop~assimp~python~doc~gmsh+petsc+slepc+mpi+trilinos~int64+hdf5~netcdf+metis~sundials~ginkgo~symengine', when='@develop +dealii') - depends_on('dealii@9.0.1~assimp~python~doc~gmsh+petsc~slepc+mpi+trilinos~int64+hdf5~netcdf+metis~ginkgo~symengine', when='@0.4.0 +dealii') + depends_on('dealii +trilinos', when='+trilinos +dealii') + depends_on('dealii ~trilinos', when='~trilinos +dealii') + depends_on('dealii@develop~assimp~python~doc~gmsh+petsc+slepc+mpi~int64+hdf5~netcdf+metis~sundials~ginkgo~symengine', when='@develop +dealii') + depends_on('dealii@9.1.1~assimp~python~doc~gmsh+petsc+slepc+mpi~int64+hdf5~netcdf+metis~sundials~ginkgo~symengine', when='@0.5.0 +dealii') + depends_on('dealii@9.0.1~assimp~python~doc~gmsh+petsc~slepc+mpi~int64+hdf5~netcdf+metis~ginkgo~symengine', when='@0.4.0 +dealii') depends_on('pflotran@develop', when='@develop') + depends_on('pflotran@xsdk-0.5.0', when='@0.5.0') depends_on('pflotran@xsdk-0.4.0', when='@0.4.0') depends_on('pflotran@xsdk-0.3.0', when='@0.3.0') depends_on('pflotran@xsdk-0.2.0', when='@xsdk-0.2.0') depends_on('alquimia@develop', when='@develop') + depends_on('alquimia@xsdk-0.5.0', when='@0.5.0') depends_on('alquimia@xsdk-0.4.0', when='@0.4.0') depends_on('alquimia@xsdk-0.3.0', when='@0.3.0') depends_on('alquimia@xsdk-0.2.0', when='@xsdk-0.2.0') - depends_on('sundials@4.1.0~int64+hypre', when='@develop') + depends_on('sundials+superlu-dist', when='@0.5.0: %gcc@6.1:') + depends_on('sundials@develop~int64+hypre+petsc', when='@develop') + depends_on('sundials@5.0.0~int64+hypre+petsc', when='@0.5.0') depends_on('sundials@3.2.1~int64+hypre', when='@0.4.0') depends_on('sundials@3.1.0~int64+hypre', when='@0.3.0') - depends_on('plasma@18.11.1:', when='@develop %gcc@6.0:') + depends_on('plasma@19.8.1:', when='@develop %gcc@6.0:') + depends_on('plasma@19.8.1:', when='@0.5.0 %gcc@6.0:') depends_on('plasma@18.11.1:', when='@0.4.0 %gcc@6.0:') - depends_on('magma@2.4.0', when='@develop +cuda') + depends_on('magma@2.5.1', when='@develop +cuda') + depends_on('magma@2.5.1', when='@0.5.0 +cuda') depends_on('magma@2.4.0', when='@0.4.0 +cuda') depends_on('magma@2.2.0', when='@0.3.0 +cuda') - depends_on('amrex@develop+sundials', when='@develop %intel') - depends_on('amrex@develop+sundials', when='@develop %gcc') + depends_on('amrex@develop', when='@develop %intel') + depends_on('amrex@develop', when='@develop %gcc') + depends_on('amrex@19.08', when='@0.5.0 %intel') + depends_on('amrex@19.08', when='@0.5.0 %gcc') depends_on('amrex@18.10.1', when='@0.4.0 %intel') depends_on('amrex@18.10.1', when='@0.4.0 %gcc') depends_on('slepc@develop', when='@develop') + depends_on('slepc@3.12.0', when='@0.5.0') depends_on('slepc@3.10.1', when='@0.4.0') + depends_on('omega-h +trilinos', when='+trilinos +omega-h') + depends_on('omega-h ~trilinos', when='~trilinos +omega-h') depends_on('omega-h@develop', when='@develop +omega-h') + depends_on('omega-h@9.29.0', when='@0.5.0 +omega-h') depends_on('omega-h@9.19.1', when='@0.4.0 +omega-h') - depends_on('strumpack@master', when='@develop') - depends_on('strumpack@3.1.1', when='@0.4.0') + depends_on('strumpack@master', when='@develop +strumpack') + depends_on('strumpack@3.3.0', when='@0.5.0 +strumpack') + depends_on('strumpack@3.1.1', when='@0.4.0 +strumpack') depends_on('pumi@develop', when='@develop') + depends_on('pumi@2.2.1', when='@0.5.0') depends_on('pumi@2.2.0', when='@0.4.0') - depends_on('tasmanian@develop+xsdkflags+blas~openmp', when='@develop') - depends_on('tasmanian@develop+xsdkflags+blas+cuda+magma~openmp', when='@develop +cuda') + tasmanian_openmp = '~openmp' if sys.platform == 'darwin' else '+openmp' + depends_on('tasmanian@develop+xsdkflags+blas' + tasmanian_openmp, when='@develop') + depends_on('tasmanian@develop+xsdkflags+blas+cuda+magma' + tasmanian_openmp, when='@develop +cuda') + depends_on('tasmanian@7.0+xsdkflags+mpi+blas' + tasmanian_openmp, when='@0.5.0') + depends_on('tasmanian@7.0+xsdkflags+mpi+blas+cuda+magma' + tasmanian_openmp, when='@0.5.0 +cuda') depends_on('tasmanian@6.0+xsdkflags+blas~openmp', when='@0.4.0') depends_on('tasmanian@6.0+xsdkflags+blas+cuda+magma~openmp', when='@0.4.0 +cuda') @@ -111,8 +150,27 @@ class Xsdk(BundlePackage): # these are type='build' dependencies, but spack reports a conflict anyway. # This will be fixed once the new concretizer becomes available # (says @adamjstewart) - depends_on('phist@develop kernel_lib=tpetra ~fortran ~scamac ~openmp ~host', when='@develop +phist') - depends_on('phist@1.7.5 kernel_lib=tpetra ~fortran ~scamac ~openmp ~host', when='@0.4.0 +phist') + + depends_on('phist kernel_lib=tpetra', when='+trilinos +phist') + depends_on('phist kernel_lib=petsc', when='~trilinos +phist') + depends_on('phist@develop ~fortran ~scamac ~openmp ~host', when='@develop +phist') + depends_on('phist@1.8.0 ~fortran ~scamac ~openmp ~host', when='@0.5.0 +phist') + depends_on('phist@1.7.5 ~fortran ~scamac ~openmp ~host', when='@0.4.0 +phist') + + depends_on('ginkgo@develop ~openmp', when='@develop +ginkgo') + depends_on('ginkgo@develop ~openmp+cuda', when='@develop +ginkgo +cuda') + depends_on('ginkgo@1.1.0 ~openmp', when='@0.5.0 +ginkgo') + depends_on('ginkgo@1.1.0 ~openmp+cuda', when='@0.5.0 +cuda +ginkgo') + + depends_on('py-libensemble@develop+petsc4py', type='run', when='@develop +libensemble') + depends_on('py-libensemble@0.5.2+petsc4py', type='run', when='@0.5.0 +libensemble') + + depends_on('precice ~petsc', when='platform=cray +precice') + depends_on('precice@develop', when='@develop +precice') + depends_on('precice@1.6.1', when='@0.5.0 +precice') + + depends_on('butterflypack@master', when='@develop +butterflypack') + depends_on('butterflypack@1.1.0', when='@0.5.0 +butterflypack') # xSDKTrilinos depends on the version of Trilinos built with # +tpetra which is turned off for faster xSDK diff --git a/var/spack/repos/builtin/packages/xsdktrilinos/package.py b/var/spack/repos/builtin/packages/xsdktrilinos/package.py index c896e91134..b679ee7277 100644 --- a/var/spack/repos/builtin/packages/xsdktrilinos/package.py +++ b/var/spack/repos/builtin/packages/xsdktrilinos/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xset/package.py b/var/spack/repos/builtin/packages/xset/package.py index 128dfa1435..2cea9420c8 100644 --- a/var/spack/repos/builtin/packages/xset/package.py +++ b/var/spack/repos/builtin/packages/xset/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xsetmode/package.py b/var/spack/repos/builtin/packages/xsetmode/package.py index 39c2771075..547999fb06 100644 --- a/var/spack/repos/builtin/packages/xsetmode/package.py +++ b/var/spack/repos/builtin/packages/xsetmode/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xsetpointer/package.py b/var/spack/repos/builtin/packages/xsetpointer/package.py index 80ae9d996c..57775a6a19 100644 --- a/var/spack/repos/builtin/packages/xsetpointer/package.py +++ b/var/spack/repos/builtin/packages/xsetpointer/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xsetroot/package.py b/var/spack/repos/builtin/packages/xsetroot/package.py index d885514a52..4f0a49bd40 100644 --- a/var/spack/repos/builtin/packages/xsetroot/package.py +++ b/var/spack/repos/builtin/packages/xsetroot/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xsimd/package.py b/var/spack/repos/builtin/packages/xsimd/package.py index b4f8206761..fcb9d90a11 100644 --- a/var/spack/repos/builtin/packages/xsimd/package.py +++ b/var/spack/repos/builtin/packages/xsimd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xsm/package.py b/var/spack/repos/builtin/packages/xsm/package.py index 6d54a353dd..f3c80c0124 100644 --- a/var/spack/repos/builtin/packages/xsm/package.py +++ b/var/spack/repos/builtin/packages/xsm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xssp/package.py b/var/spack/repos/builtin/packages/xssp/package.py index 6d65369901..4a8149cb1b 100644 --- a/var/spack/repos/builtin/packages/xssp/package.py +++ b/var/spack/repos/builtin/packages/xssp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xstdcmap/package.py b/var/spack/repos/builtin/packages/xstdcmap/package.py index fc4a0621ae..5d203ff479 100644 --- a/var/spack/repos/builtin/packages/xstdcmap/package.py +++ b/var/spack/repos/builtin/packages/xstdcmap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xtensor-python/package.py b/var/spack/repos/builtin/packages/xtensor-python/package.py index 50ce72ed7b..781e8307bc 100644 --- a/var/spack/repos/builtin/packages/xtensor-python/package.py +++ b/var/spack/repos/builtin/packages/xtensor-python/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xtensor/package.py b/var/spack/repos/builtin/packages/xtensor/package.py index ff1ef0c018..740f17d4e3 100644 --- a/var/spack/repos/builtin/packages/xtensor/package.py +++ b/var/spack/repos/builtin/packages/xtensor/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xterm/package.py b/var/spack/repos/builtin/packages/xterm/package.py index 14ad9d207a..92bf2e5fbd 100644 --- a/var/spack/repos/builtin/packages/xterm/package.py +++ b/var/spack/repos/builtin/packages/xterm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xtl/package.py b/var/spack/repos/builtin/packages/xtl/package.py index e15f517655..15aa530a82 100644 --- a/var/spack/repos/builtin/packages/xtl/package.py +++ b/var/spack/repos/builtin/packages/xtl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xtrans/package.py b/var/spack/repos/builtin/packages/xtrans/package.py index 60656232a9..aaffcb447e 100644 --- a/var/spack/repos/builtin/packages/xtrans/package.py +++ b/var/spack/repos/builtin/packages/xtrans/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xtrap/package.py b/var/spack/repos/builtin/packages/xtrap/package.py index 052c3624e1..deca1170a7 100644 --- a/var/spack/repos/builtin/packages/xtrap/package.py +++ b/var/spack/repos/builtin/packages/xtrap/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xts/package.py b/var/spack/repos/builtin/packages/xts/package.py index 51507086f6..19149f9ec9 100644 --- a/var/spack/repos/builtin/packages/xts/package.py +++ b/var/spack/repos/builtin/packages/xts/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xvidtune/package.py b/var/spack/repos/builtin/packages/xvidtune/package.py index 0ccf033069..b2e41b6f60 100644 --- a/var/spack/repos/builtin/packages/xvidtune/package.py +++ b/var/spack/repos/builtin/packages/xvidtune/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xvinfo/package.py b/var/spack/repos/builtin/packages/xvinfo/package.py index 2ceb837c8d..4c6bf77a5f 100644 --- a/var/spack/repos/builtin/packages/xvinfo/package.py +++ b/var/spack/repos/builtin/packages/xvinfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xwd/package.py b/var/spack/repos/builtin/packages/xwd/package.py index 1978d6ec27..b874acbe73 100644 --- a/var/spack/repos/builtin/packages/xwd/package.py +++ b/var/spack/repos/builtin/packages/xwd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xwininfo/package.py b/var/spack/repos/builtin/packages/xwininfo/package.py index f946eef5e6..dce4cf8665 100644 --- a/var/spack/repos/builtin/packages/xwininfo/package.py +++ b/var/spack/repos/builtin/packages/xwininfo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xwud/package.py b/var/spack/repos/builtin/packages/xwud/package.py index 13ebeebf0a..4feff30d1d 100644 --- a/var/spack/repos/builtin/packages/xwud/package.py +++ b/var/spack/repos/builtin/packages/xwud/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xxhash/package.py b/var/spack/repos/builtin/packages/xxhash/package.py index 8222262394..421026f496 100644 --- a/var/spack/repos/builtin/packages/xxhash/package.py +++ b/var/spack/repos/builtin/packages/xxhash/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/xz/package.py b/var/spack/repos/builtin/packages/xz/package.py index e6579ee6dc..428993a816 100644 --- a/var/spack/repos/builtin/packages/xz/package.py +++ b/var/spack/repos/builtin/packages/xz/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/yajl/package.py b/var/spack/repos/builtin/packages/yajl/package.py index 4ad9af1364..ff7ed9ffef 100644 --- a/var/spack/repos/builtin/packages/yajl/package.py +++ b/var/spack/repos/builtin/packages/yajl/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/yambo/package.py b/var/spack/repos/builtin/packages/yambo/package.py index 29d84a20b7..df6d585557 100644 --- a/var/spack/repos/builtin/packages/yambo/package.py +++ b/var/spack/repos/builtin/packages/yambo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -45,20 +45,20 @@ class Yambo(AutotoolsPackage): # MPI dependencies are forced, until we have proper forwarding of variants # # Note that yambo is used as an application, and not linked as a library, - # thus there will be no case where another package pulls-in e.g. netcdf+mpi - # and wants to depend on yambo~mpi. + # thus there will be no case where another package pulls-in e.g. + # netcdf-c+mpi and wants to depend on yambo~mpi. depends_on('mpi', when='+mpi') - depends_on('netcdf+mpi', when='+mpi') + depends_on('netcdf-c+mpi', when='+mpi') depends_on('hdf5+mpi', when='+mpi') depends_on('fftw+mpi', when='+mpi') depends_on('scalapack', when='+mpi') - depends_on('netcdf~mpi', when='~mpi') + depends_on('netcdf-c~mpi', when='~mpi') depends_on('hdf5~mpi', when='~mpi') depends_on('fftw~mpi', when='~mpi') depends_on('hdf5+fortran') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-fortran') depends_on('libxc@2.0.3:') @@ -124,7 +124,7 @@ class Yambo(AutotoolsPackage): '--enable-netcdf-hdf5', '--enable-hdf5-compression', '--with-hdf5-libs={0}'.format(spec['hdf5'].libs), - '--with-netcdf-path={0}'.format(spec['netcdf'].prefix), + '--with-netcdf-path={0}'.format(spec['netcdf-c'].prefix), '--with-netcdff-path={0}'.format(spec['netcdf-fortran'].prefix) ]) diff --git a/var/spack/repos/builtin/packages/yaml-cpp/package.py b/var/spack/repos/builtin/packages/yaml-cpp/package.py index 49891b2a07..321792bd2e 100644 --- a/var/spack/repos/builtin/packages/yaml-cpp/package.py +++ b/var/spack/repos/builtin/packages/yaml-cpp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -17,6 +17,7 @@ class YamlCpp(CMakePackage): git = "https://github.com/jbeder/yaml-cpp.git" version('develop', branch='master') + version('0.6.3', sha256='77ea1b90b3718aa0c324207cb29418f5bced2354c2e483a9523d98c3460af1ed') version('0.6.2', sha256='e4d8560e163c3d875fd5d9e5542b5fd5bec810febdcba61481fe5fc4e6b1fd05') version('0.5.3', sha256='decc5beabb86e8ed9ebeb04358d5363a5c4f72d458b2c788cb2f3ac9c19467b2') diff --git a/var/spack/repos/builtin/packages/yara/package.py b/var/spack/repos/builtin/packages/yara/package.py index ec4df8b564..92fe48da0d 100644 --- a/var/spack/repos/builtin/packages/yara/package.py +++ b/var/spack/repos/builtin/packages/yara/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/yasm/package.py b/var/spack/repos/builtin/packages/yasm/package.py index 345f939b34..c6f757b453 100644 --- a/var/spack/repos/builtin/packages/yasm/package.py +++ b/var/spack/repos/builtin/packages/yasm/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/yorick/package.py b/var/spack/repos/builtin/packages/yorick/package.py index caffcfa11d..35d6e617a6 100644 --- a/var/spack/repos/builtin/packages/yorick/package.py +++ b/var/spack/repos/builtin/packages/yorick/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/z3/fix_1016_1.patch b/var/spack/repos/builtin/packages/z3/fix_1016_1.patch new file mode 100644 index 0000000000..181fa96035 --- /dev/null +++ b/var/spack/repos/builtin/packages/z3/fix_1016_1.patch @@ -0,0 +1,12 @@ +--- spack-src/src/util/hash.cpp.org 2019-11-14 11:12:11.233379342 +0900 ++++ spack-src/src/util/hash.cpp 2019-11-14 11:15:51.356519168 +0900 +@@ -75,8 +75,8 @@ + __fallthrough; + case 1 : + a+=str[0]; +- __fallthrough; + /* case 0: nothing left to add */ ++ break; + } + mix(a,b,c); + /*-------------------------------------------- report the result */ diff --git a/var/spack/repos/builtin/packages/z3/fix_1016_2.patch b/var/spack/repos/builtin/packages/z3/fix_1016_2.patch new file mode 100644 index 0000000000..95eccbf8cd --- /dev/null +++ b/var/spack/repos/builtin/packages/z3/fix_1016_2.patch @@ -0,0 +1,12 @@ +--- spack-src/src/util/hash.cpp.org 2019-11-13 13:25:33.317336437 +0900 ++++ spack-src/src/util/hash.cpp 2019-11-13 13:26:12.671491961 +0900 +@@ -83,8 +83,8 @@ + Z3_fallthrough; + case 1 : + a+=str[0]; +- Z3_fallthrough; + /* case 0: nothing left to add */ ++ break; + } + mix(a,b,c); + /*-------------------------------------------- report the result */ diff --git a/var/spack/repos/builtin/packages/z3/package.py b/var/spack/repos/builtin/packages/z3/package.py index b558fa010f..bd02c0c0db 100644 --- a/var/spack/repos/builtin/packages/z3/package.py +++ b/var/spack/repos/builtin/packages/z3/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -20,16 +20,30 @@ class Z3(MakefilePackage): phases = ['bootstrap', 'build', 'install'] - variant('python', default=False, description='Enable python support') - depends_on('python', when='+python') + variant('python', default=False, description='Enable python binding') + depends_on('python', type=('build', 'run')) + extends('python', when='+python') + + # Referenced: https://github.com/Z3Prover/z3/issues/1016 + patch('fix_1016_1.patch', when='@:4.4.1') + patch('fix_1016_2.patch', when='@4.5.0') build_directory = 'build' def configure_args(self): spec = self.spec - return [ - '--python' if '+python' in spec else '' - ] + + args = [] + + if spec.satisfies('+python'): + args.append('--python') + args.append( + '--pypkgdir=%s' % join_path( + prefix.lib, + 'python%s' % spec['python'].version.up_to(2), + 'site-packages')) + + return args def bootstrap(self, spec, prefix): options = ['--prefix={0}'.format(prefix)] + self.configure_args() diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py index 7eb5e511d0..44a659c193 100644 --- a/var/spack/repos/builtin/packages/zfp/package.py +++ b/var/spack/repos/builtin/packages/zfp/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/zip/package.py b/var/spack/repos/builtin/packages/zip/package.py index 6a9446a905..51cc012f43 100644 --- a/var/spack/repos/builtin/packages/zip/package.py +++ b/var/spack/repos/builtin/packages/zip/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/zlib/package.py b/var/spack/repos/builtin/packages/zlib/package.py index 034fad745a..82cdf73f25 100644 --- a/var/spack/repos/builtin/packages/zlib/package.py +++ b/var/spack/repos/builtin/packages/zlib/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) @@ -38,11 +38,11 @@ class Zlib(Package): ['libz'], root=self.prefix, recursive=True, shared=shared ) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if '+pic' in self.spec: - spack_env.append_flags('CFLAGS', self.compiler.pic_flag) + env.append_flags('CFLAGS', self.compiler.pic_flag) if '+optimize' in self.spec: - spack_env.append_flags('CFLAGS', '-O2') + env.append_flags('CFLAGS', '-O2') def install(self, spec, prefix): config_args = [] diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py index 9f70169970..b832dbc0f8 100644 --- a/var/spack/repos/builtin/packages/zoltan/package.py +++ b/var/spack/repos/builtin/packages/zoltan/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/zookeeper/package.py b/var/spack/repos/builtin/packages/zookeeper/package.py new file mode 100644 index 0000000000..bd4e09efd4 --- /dev/null +++ b/var/spack/repos/builtin/packages/zookeeper/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Zookeeper(Package): + """ + Apache ZooKeeper is an effort to develop and maintain an open-source + server which enables highly reliable distributed coordination. + """ + + homepage = "https://archive.apache.org" + url = "https://archive.apache.org/dist/zookeeper/zookeeper-3.4.11/zookeeper-3.4.11.tar.gz" + + version('3.4.11', sha256='f6bd68a1c8f7c13ea4c2c99f13082d0d71ac464ffaf3bf7a365879ab6ad10e84') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/zsh/package.py b/var/spack/repos/builtin/packages/zsh/package.py index 80d4cf9b31..60bb3cd3e7 100644 --- a/var/spack/repos/builtin/packages/zsh/package.py +++ b/var/spack/repos/builtin/packages/zsh/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/zstd/package.py b/var/spack/repos/builtin/packages/zstd/package.py index bfdd5d0d1a..1557cc8a07 100644 --- a/var/spack/repos/builtin/packages/zstd/package.py +++ b/var/spack/repos/builtin/packages/zstd/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/builtin/packages/zziplib/package.py b/var/spack/repos/builtin/packages/zziplib/package.py new file mode 100644 index 0000000000..c8f96738d3 --- /dev/null +++ b/var/spack/repos/builtin/packages/zziplib/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Zziplib(AutotoolsPackage): + """The zziplib provides read access to zipped files in a zip-archive, using + compression based solely on free algorithms provided by zlib. It also + provides a functionality to overlay the archive filesystem with the + filesystem of the operating system environment.""" + + homepage = "https://github.com/gdraheim/zziplib" + url = "https://github.com/gdraheim/zziplib/archive/v0.13.69.tar.gz" + + version('0.13.69', sha256='846246d7cdeee405d8d21e2922c6e97f55f24ecbe3b6dcf5778073a88f120544') + + patch('python2to3.patch') + + build_directory = 'spack-build' + + depends_on('python', type='build') + depends_on('zlib') + + def configure_args(self): + args = ['--with-zlib={0}'.format(self.spec['zlib'].prefix)] + return args diff --git a/var/spack/repos/builtin/packages/zziplib/python2to3.patch b/var/spack/repos/builtin/packages/zziplib/python2to3.patch new file mode 100644 index 0000000000..7e544f9e57 --- /dev/null +++ b/var/spack/repos/builtin/packages/zziplib/python2to3.patch @@ -0,0 +1,714 @@ +diff -ru a/docs/cpp2markdown-1.py b/docs/cpp2markdown-1.py +--- a/docs/cpp2markdown-1.py 2019-12-27 17:22:22.059961303 -0600 ++++ b/docs/cpp2markdown-1.py 2019-12-27 17:22:43.072910448 -0600 +@@ -39,7 +39,7 @@ + check2 = re.compile(r"^\s[*]\s+\b[Cc]opyright\b") + empty1 = re.compile(r"^\s[*]\s*$") + state = "intro" +- for i in xrange(1,len(lines)-1): ++ for i in range(1,len(lines)-1): + line = lines[i] + if state == "intro": + if empty1.match(line): +@@ -108,7 +108,7 @@ + def run(self, filename): + filetext = open(filename).read() + for line in self.process(filetext, filename): +- print line ++ print(line) + def process(self, filetext, filename=""): + section_ruler = "-----------------------------------------" + copyright = "" +@@ -136,7 +136,7 @@ + else: + if text: + yield "#### NOTES" +- print token, text.replace("\n", "\n ") ++ print(token, text.replace("\n", "\n ")) + if copyright: + yield section_ruler + yield "### COPYRIGHT" +diff -ru a/docs/cpp2markdown.py b/docs/cpp2markdown.py +--- a/docs/cpp2markdown.py 2019-12-27 17:22:22.059961303 -0600 ++++ b/docs/cpp2markdown.py 2019-12-27 17:22:43.140910284 -0600 +@@ -62,7 +62,7 @@ + def run(self, filename): + filetext = open(filename).read() + for line in self.process(filetext, filename): +- print line ++ print(line) + def process(self, filetext, filename=""): + for token, text in self.parse(filetext): + if token == FileInclude: +@@ -86,7 +86,7 @@ + else: + if text: + yield "#### NOTES" +- print token, text.replace("\n", "\n ") ++ print(token, text.replace("\n", "\n ")) + def isexported_function(self): + function = self.function_text.strip().replace("\n"," ") + logg.debug("@ --------------------------------------") +diff -ru a/docs/make-doc.py b/docs/make-doc.py +--- a/docs/make-doc.py 2019-12-27 17:22:22.059961303 -0600 ++++ b/docs/make-doc.py 2019-12-27 17:22:43.515909376 -0600 +@@ -3,7 +3,7 @@ + import sys + import re + import string +-import commands ++import subprocess + import warnings + + errors = 0 +@@ -23,7 +23,7 @@ + def m(string, pattern): + return re.match(pattern, string) + def sorted_keys(dict): +- keys = dict.keys() ++ keys = list(dict.keys()) + keys.sort() + return keys + +@@ -126,7 +126,7 @@ + class Options: + var = {} + def __getattr__(self, name): +- if not self.var.has_key(name): return None ++ if name not in self.var: return None + return self.var[name] + def __setattr__(self, name, value): + self.var[name] = value +@@ -135,15 +135,15 @@ + o = Options() + o.verbose = 0 + +-o.version = s( commands.getoutput( ++o.version = s( subprocess.getoutput( + """ grep -i "^version *:" *.spec 2>/dev/null | + sed -e "s/[Vv]ersion *: *//" """), r"\s*",r"") +-o.package = s(commands.getoutput( ++o.package = s(subprocess.getoutput( + """ grep -i "^name *:" *.spec 2>/dev/null | + sed -e "s/[Nn]ame *: *//" """), r"\s*",r"") + + if not len(o.version): +- o.version = commands.getoutput(""" date +%Y.%m.%d """) ++ o.version = subprocess.getoutput(""" date +%Y.%m.%d """) + if not len(o.package): + o.package = "_project" + +@@ -158,7 +158,7 @@ + self.copyright = "" + def __getattr__(self, name): + """ defend against program to break on uninited members """ +- if self.__dict__.has_key(name): return self.__dict__[name] ++ if name in self.__dict__: return self.__dict__[name] + warn("no such member: "+name); return None + def set_author(self, text): + if self.authors: +@@ -215,7 +215,7 @@ + #else + try: + input = open(name, "r") +- except IOError, error: ++ except IOError as error: + warn(#...... (scan_options) ............... + "can not open input file: "+name, error) + continue +@@ -294,12 +294,12 @@ + # return "" + def __getattr__(self, name): + """ defend against program exit on members being not inited """ +- if self.__dict__.has_key(name): return self.__dict__[name] ++ if name in self.__dict__: return self.__dict__[name] + warn("no such member: "+name); return None + def dict(self): + return self.__dict__ + def dict_sorted_keys(self): +- keys = self.__dict__.keys() ++ keys = list(self.__dict__.keys()) + keys.sort() + return keys + def parse(self, prototype): +@@ -376,7 +376,7 @@ + function.head = s(function.head, r"(.*)also:(.*)", lambda x + : set_seealso(function, x.group(2)) and x.group(1)) + if function.seealso and None: +- print "function[",function.name,"].seealso=",function.seealso ++ print("function[",function.name,"].seealso=",function.seealso) + examine_head_anchors(function_list) + + # =============================================================== HTML ===== +@@ -455,7 +455,7 @@ + s(ensure_name(this_function_link(section2html( func.body ), + func.name), func.name), + r"(?sx) (</?para>\s*) <br\s*\/>", r"\1")) +- return combined.values() ++ return list(combined.values()) + html_pages = combined_html_pages(function_list) + + def html_resolve_links_on_page(text, list): +@@ -495,7 +495,7 @@ + return T + def add_page_map(self, list): + """ generate the index-block at the start of the onepage-html file """ +- keys = list.keys() ++ keys = list(list.keys()) + keys.sort() + for name in keys: + self.toc += "<tr valign=\"top\">\n"+ \ +@@ -524,11 +524,11 @@ + # and finally print the html-formatted output + try: + F = open(o.libhtmlfile, "w") +-except IOError, error: ++except IOError as error: + warn(# ............. open(o.libhtmlfile, "w") .............. + "can not open html output file: "+o.libhtmlfile, error) + else: +- print >> F, html.page_text() ++ print(html.page_text(), file=F) + F.close() + #fi + +@@ -954,7 +954,7 @@ + if not header[file].authors and page.authors_list: + header[file].authors_list = page.authors_list + if not header[file].description: +- found = m(commands.getoutput("cat "+o.package+".spec"), ++ found = m(subprocess.getoutput("cat "+o.package+".spec"), + r"(?s)\%description\b([^\%]*)\%") + if found: + header[file].description = found.group(1) +@@ -987,40 +987,40 @@ + + try: + F = open(o.docbookfile,"w") +-except IOError, error: ++except IOError as error: + warn("can not open docbook output file: "+o.docbookfile, error) + else: +- print >> F, doctype, '<reference><title>Manual Pages</title>' ++ print(doctype, '<reference><title>Manual Pages</title>', file=F) + + for page in combined_pages: +- print >> F, page.refentry_text() ++ print(page.refentry_text(), file=F) + #od + +- for page in header_refpages.values(): ++ for page in list(header_refpages.values()): + if not page.refentry: continue +- print >> F, "\n<!-- _______ "+page.id+" _______ -->", +- print >> F, page.refentry_text() ++ print("\n<!-- _______ "+page.id+" _______ -->", end=' ', file=F) ++ print(page.refentry_text(), file=F) + #od + +- print >> F, "\n",'</reference>',"\n" ++ print("\n",'</reference>',"\n", file=F) + F.close() + #fi + + # _____________________________________________________________________ + try: + F = open( o.dumpdocfile, "w") +-except IOError, error: ++except IOError as error: + warn ("can not open"+o.dumpdocfile,error) + else: + for func in function_list: + name = func.name +- print >> F, "<fn id=\""+name+"\">"+"<!-- FOR \""+name+"\" -->\n" ++ print("<fn id=\""+name+"\">"+"<!-- FOR \""+name+"\" -->\n", file=F) + for H in sorted_keys(func.dict()): +- print >> F, "<"+H+" name=\""+name+"\">", +- print >> F, str(func.dict()[H]), +- print >> F, "</"+H+">" ++ print("<"+H+" name=\""+name+"\">", end=' ', file=F) ++ print(str(func.dict()[H]), end=' ', file=F) ++ print("</"+H+">", file=F) + #od +- print >> F, "</fn><!-- END \""+name+"\" -->\n\n"; ++ print("</fn><!-- END \""+name+"\" -->\n\n", file=F); + #od + F.close(); + #fi +diff -ru a/docs/makedocs.py b/docs/makedocs.py +--- a/docs/makedocs.py 2019-12-27 17:22:22.059961303 -0600 ++++ b/docs/makedocs.py 2019-12-27 17:22:43.644909064 -0600 +@@ -37,7 +37,7 @@ + return None + def print_list_mainheader(self): + for t_fileheader in self.headers: +- print t_fileheader.get_filename(), t_fileheader.src_mainheader() ++ print(t_fileheader.get_filename(), t_fileheader.src_mainheader()) + + class PerFunctionEntry: + def __init__(self, header, comment, prototype): +@@ -66,10 +66,10 @@ + functionprototype) ] + def print_list_titleline(self): + for funcheader in self.headers: +- print funcheader.get_filename(), "[=>]", funcheader.get_titleline() ++ print(funcheader.get_filename(), "[=>]", funcheader.get_titleline()) + def print_list_name(self): + for funcheader in self.prototypes: +- print funcheader.get_filename(), "[>>]", funcheader.get_name() ++ print(funcheader.get_filename(), "[>>]", funcheader.get_name()) + + class PerFunctionFamilyEntry: + def __init__(self, leader): +@@ -122,12 +122,12 @@ + for name in self.retarget: + into = self.retarget[name] + if into not in name_list: +- print ("function '"+name+"' retarget into '"+into+ +- "' does not exist - keep alone") ++ print(("function '"+name+"' retarget into '"+into+ ++ "' does not exist - keep alone")) + if into in self.retarget: + other = self.retarget[into] +- print ("function '"+name+"' retarget into '"+into+ +- "' which is itself a retarget into '"+other+"'") ++ print(("function '"+name+"' retarget into '"+into+ ++ "' which is itself a retarget into '"+other+"'")) + if into not in lead_list: + lead_list += [ into ] + for func in self.functions: +@@ -141,7 +141,7 @@ + entry.add(func) # the first + self.entries += [ entry ] + else: +- print "head function '"+name+" has no entry" ++ print("head function '"+name+" has no entry") + for func in self.functions: + name = func.get_name() + if name in self.retarget: +@@ -150,14 +150,14 @@ + if entry is not None: + entry.add(func) # will not add duplicates + else: +- print "into function '"+name+" has no entry" ++ print("into function '"+name+" has no entry") + def print_list_name(self): + for family in self.entries: + name = family.get_name() +- print name, ":", ++ print(name, ":", end=' ') + for item in family.functions: +- print item.get_name(), ",", +- print "" ++ print(item.get_name(), ",", end=' ') ++ print("") + class HtmlManualPageAdapter: + def __init__(self, entry): + """ usually takes a PerFunctionEntry """ +diff -ru a/docs/zzipdoc/commentmarkup.py b/docs/zzipdoc/commentmarkup.py +--- a/docs/zzipdoc/commentmarkup.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/commentmarkup.py 2019-12-27 17:22:43.674908991 -0600 +@@ -1,4 +1,4 @@ +-from match import Match ++from .match import Match + + def markup_link_syntax(text): + """ markup the link-syntax ` => somewhere ` in the text block """ +@@ -31,7 +31,7 @@ + comment = self.header.comment + try: + comment = self.header.get_otherlines() +- except Exception, e: ++ except Exception as e: + pass + mode = "" + text = "" +diff -ru a/docs/zzipdoc/dbk2htm.py b/docs/zzipdoc/dbk2htm.py +--- a/docs/zzipdoc/dbk2htm.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/dbk2htm.py 2019-12-27 17:22:43.685908965 -0600 +@@ -1,4 +1,4 @@ +-from match import Match ++from .match import Match + import string + + class dbk2htm_conversion: +diff -ru a/docs/zzipdoc/docbookdocument.py b/docs/zzipdoc/docbookdocument.py +--- a/docs/zzipdoc/docbookdocument.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/docbookdocument.py 2019-12-27 17:22:43.723908873 -0600 +@@ -1,6 +1,6 @@ + #! /usr/bin/env python + # -*- coding: UTF-8 -*- +-from match import Match ++from .match import Match + + class DocbookDocument: + """ binds some xml content page with additional markup - in this +@@ -23,14 +23,14 @@ + def get_title(self): + if self.title: return title + try: return self.text[0].get_title() +- except Exception, e: pass ++ except Exception as e: pass + return self.title + def _xml_doctype(self, rootnode): + return "<!DOCTYPE "+rootnode+self.docbook_dtd+">" + def _xml_text(self, xml): + """ accepts adapter objects with .xml_text() """ + try: return xml.xml_text() +- except Exception, e: print "DocbookDocument/text", e; pass ++ except Exception as e: print("DocbookDocument/text", e); pass + return str(xml) + def _fetch_rootnode(self, text): + fetch = Match(r"^[^<>]*<(\w+)\b") +@@ -47,7 +47,7 @@ + return filename + def save(self, filename = None): + filename = self._filename(filename) +- print "writing '"+filename+"'" ++ print("writing '"+filename+"'") + if len(self.text) > 1: + self.save_all(filename) + else: +@@ -58,12 +58,12 @@ + xml_text = self._xml_text(text) + rootnode = self._fetch_rootnode(xml_text) + doctype = self._xml_doctype(rootnode) +- print >>fd, doctype +- print >>fd, xml_text ++ print(doctype, file=fd) ++ print(xml_text, file=fd) + fd.close() + return True +- except IOError, e: +- print "could not open '"+filename+"'file", e ++ except IOError as e: ++ print("could not open '"+filename+"'file", e) + return False + def save_all(self, filename): + assert len(self.text) > 1 +@@ -76,20 +76,20 @@ + else: + rootnode = self.rootnode + doctype = self._xml_doctype(rootnode) +- print >>fd, doctype ++ print(doctype, file=fd) + title = self.get_title() + if title and self.rootnode in self.has_title_child: +- print >>fd, "<"+self.rootnode+'><title>'+title+'</title>' ++ print("<"+self.rootnode+'><title>'+title+'</title>', file=fd) + elif title: +- print >>fd, "<"+self.rootnode+' id="'+title+'">' ++ print("<"+self.rootnode+' id="'+title+'">', file=fd) + else: +- print >>fd, "<"+self.rootnode+'>' ++ print("<"+self.rootnode+'>', file=fd) + for text in self.text: + text = self._xml_text(text) +- print >>fd, text +- print >>fd, "</"+self.rootnode+">" ++ print(text, file=fd) ++ print("</"+self.rootnode+">", file=fd) + fd.close() + return True +- except IOError, e: +- print "could not open '"+filename+"'file", e ++ except IOError as e: ++ print("could not open '"+filename+"'file", e) + return False +diff -ru a/docs/zzipdoc/functionheader.py b/docs/zzipdoc/functionheader.py +--- a/docs/zzipdoc/functionheader.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/functionheader.py 2019-12-27 17:22:43.756908793 -0600 +@@ -1,4 +1,4 @@ +-from match import Match ++from .match import Match + + class FunctionHeader: + """ parsing the comment block that is usually presented before +diff -ru a/docs/zzipdoc/functionlisthtmlpage.py b/docs/zzipdoc/functionlisthtmlpage.py +--- a/docs/zzipdoc/functionlisthtmlpage.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/functionlisthtmlpage.py 2019-12-27 17:22:43.803908679 -0600 +@@ -1,5 +1,5 @@ +-from options import * +-from match import Match ++from .options import * ++from .match import Match + + class FunctionListHtmlPage: + """ The main part here is to create a TOC (table of contents) at the +@@ -35,7 +35,7 @@ + head_text = entry.head_xml_text() + body_text = entry.body_xml_text(name) + if not head_text: +- print "no head_text for", name ++ print("no head_text for", name) + return + try: + prespec = entry.head_get_prespec() +@@ -43,7 +43,7 @@ + callspec = entry.head_get_callspec() + head_text = ("<code><b><function>"+namespec+"</function></b>" + +callspec+" : "+prespec+"</code>") +- except Exception, e: ++ except Exception as e: + pass + try: + extraline = "" +@@ -56,7 +56,7 @@ + '<em><small>'+filename+'</small></em>'+ + '</td></table>') + body_text = extraline + body_text +- except Exception, e: ++ except Exception as e: + pass + def link(text): + return (text & Match("<function>(\w*)</function>") +@@ -102,7 +102,7 @@ + text &= (Match("(?s)<link>(\w+)</link>") + >> (lambda x: self.resolve_internal(x.group(1)))) + if len(self.not_found_in_anchors): +- print "not found in anchors: ", self.not_found_in_anchors ++ print("not found in anchors: ", self.not_found_in_anchors) + return (text & Match("(?s)<link>([^<>]*)</link>") + >> "<code>\\1</code>") + def resolve_external(self, func, sect): +diff -ru a/docs/zzipdoc/functionlistreference.py b/docs/zzipdoc/functionlistreference.py +--- a/docs/zzipdoc/functionlistreference.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/functionlistreference.py 2019-12-27 17:22:43.875908505 -0600 +@@ -1,7 +1,7 @@ + #! /usr/bin/env python + # -*- coding: UTF-8 -*- +-from match import Match +-from htm2dbk import * ++from .match import Match ++from .htm2dbk import * + + class FunctionListReference: + """ Creating a docbook-style <reference> list of <refentry> parts +@@ -19,7 +19,7 @@ + description = entry.body_xml_text(name) + funcsynopsis = entry.head_xml_text() + if not funcsynopsis: +- print "no funcsynopsis for", name ++ print("no funcsynopsis for", name) + return + if self.entry is None: + self.entry = FunctionListRefEntry(entry, self.o) +diff -ru a/docs/zzipdoc/functionprototype.py b/docs/zzipdoc/functionprototype.py +--- a/docs/zzipdoc/functionprototype.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/functionprototype.py 2019-12-27 17:22:43.898908449 -0600 +@@ -1,4 +1,4 @@ +-from match import Match ++from .match import Match + + class FunctionPrototype: + """ takes a single function prototype line (cut from some source file) +diff -ru a/docs/zzipdoc/htm2dbk.py b/docs/zzipdoc/htm2dbk.py +--- a/docs/zzipdoc/htm2dbk.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/htm2dbk.py 2019-12-27 17:22:43.946908333 -0600 +@@ -7,7 +7,7 @@ + present in the world of docbook-to-anything converters. """ + + from datetime import date +-import match ++from . import match + import sys + + m = match.Match +@@ -146,8 +146,8 @@ + doc.filename = filename + doc.add(f.read()) + f.close() +- except IOError, e: +- print >> sys.stderr, "can not open "+filename ++ except IOError as e: ++ print("can not open "+filename, file=sys.stderr) + return doc.value() + + def html2docbook(text): +@@ -155,4 +155,4 @@ + return htm2dbk_conversion().convert2(text) + + if __name__ == "__main__": +- print htm2dbk_files(sys.argv[1:]) ++ print(htm2dbk_files(sys.argv[1:])) +diff -ru a/docs/zzipdoc/htmldocument.py b/docs/zzipdoc/htmldocument.py +--- a/docs/zzipdoc/htmldocument.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/htmldocument.py 2019-12-27 17:22:43.990908227 -0600 +@@ -1,6 +1,6 @@ + #! /usr/bin/env python + # -*- coding: UTF-8 -*- +-from match import Match ++from .match import Match + + class HtmlDocument: + """ binds some html content page with additional markup - in this +@@ -29,31 +29,31 @@ + def get_title(self): + if self.title: return self.title + try: return self.text[0].get_title() +- except Exception, e: pass ++ except Exception as e: pass + return self.title + def _html_meta(self, meta): + """ accepts adapter objects with .html_meta() """ + try: return meta.html_meta() +- except Exception, e: pass ++ except Exception as e: pass + return str(meta) + def _html_style(self, style): + """ accepts adapter objects with .html_style() and .xml_style() """ + ee = None + try: return style.html_style() +- except Exception, e: ee = e; pass ++ except Exception as e: ee = e; pass + try: return style.xml_style() +- except Exception, e: print "HtmlDocument/style", ee, e; pass ++ except Exception as e: print("HtmlDocument/style", ee, e); pass + try: return str(style) +- except Exception, e: print "HtmlDocument/style", e; return "" ++ except Exception as e: print("HtmlDocument/style", e); return "" + def _html_text(self, html): + """ accepts adapter objects with .html_text() and .xml_text() """ + ee = None + try: return html.html_text() +- except Exception, e: ee = e; pass ++ except Exception as e: ee = e; pass + try: return html.xml_text() +- except Exception, e: print "HtmlDocument/text", ee, e; pass ++ except Exception as e: print("HtmlDocument/text", ee, e); pass + try: return str(html) +- except Exception, e: print "HtmlDocument/text", e; return " " ++ except Exception as e: print("HtmlDocument/text", e); return " " + def navigation(self): + if self.navi: + return self.navi +@@ -63,7 +63,7 @@ + self.navi = fd.read() + fd.close() + return self.navi +- except Exception, e: ++ except Exception as e: + pass + return None + def html_header(self): +@@ -103,15 +103,15 @@ + return filename + def save(self, filename = None): + filename = self._filename(filename) +- print "writing '"+filename+"'" ++ print("writing '"+filename+"'") + try: + fd = open(filename, "w") +- print >>fd, self.html_header() ++ print(self.html_header(), file=fd) + for text in self.text: +- print >>fd, self._html_text(text) +- print >>fd, self.html_footer() ++ print(self._html_text(text), file=fd) ++ print(self.html_footer(), file=fd) + fd.close() + return True +- except IOError, e: +- print "could not open '"+filename+"'file", e ++ except IOError as e: ++ print("could not open '"+filename+"'file", e) + return False +diff -ru a/docs/zzipdoc/match.py b/docs/zzipdoc/match.py +--- a/docs/zzipdoc/match.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/match.py 2019-12-27 17:23:03.216861711 -0600 +@@ -18,7 +18,7 @@ + MatchReplace.__call__(self, matching, template, count, flags) + def __call__(self, matching, template = None, count = 0, flags = None): + """ other than __init__ the template may be left off to be unchanged""" +- if isinstance(count, basestring): # count/flags swapped over? ++ if isinstance(count, str): # count/flags swapped over? + flags = count; count = 0 + if isinstance(matching, Match): + self.matching = matching +@@ -57,7 +57,7 @@ + def __call__(self, pattern, flags = None): + assert isinstance(pattern, str) or pattern is None + assert isinstance(flags, str) or flags is None +- str.__init__(self, pattern) ++ str.__init__(self) + self.replaced = 0 # set by subn() inside MatchReplace + self.found = None # set by search() to a MatchObject + self.pattern = pattern +@@ -90,14 +90,14 @@ + if __name__ == "__main__": + # matching: + if "foo" & Match("oo"): +- print "oo" ++ print("oo") + x = Match() + if "foo" & x("(o+)"): +- print x[1] ++ print(x[1]) + # replacing: + y = "fooboo" & Match("oo") >> "ee" +- print y ++ print(y) + r = Match("oo") >> "ee" +- print "fooboo" & r ++ print("fooboo" & r) + s = MatchReplace("oo", "ee") +- print "fooboo" & s ++ print("fooboo" & s) +diff -ru a/docs/zzipdoc/options.py b/docs/zzipdoc/options.py +--- a/docs/zzipdoc/options.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/options.py 2019-12-27 17:22:44.036908116 -0600 +@@ -3,13 +3,13 @@ + # @creator (C) 2003 Guido U. Draheim + # @license http://creativecommons.org/licenses/by-nc-sa/2.0/de/ + +-from match import Match ++from .match import Match + + # use as o.optionname to check for commandline options. + class Options: + var = {} + def __getattr__(self, name): +- if not self.var.has_key(name): return None ++ if name not in self.var: return None + return self.var[name] + def __setattr__(self, name, value): + self.var[name] = value +diff -ru a/docs/zzipdoc/textfileheader.py b/docs/zzipdoc/textfileheader.py +--- a/docs/zzipdoc/textfileheader.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/textfileheader.py 2019-12-27 17:22:44.071908031 -0600 +@@ -1,4 +1,4 @@ +-from match import Match ++from .match import Match + + class TextFileHeader: + """ scan for a comment block at the source file start and fill the +@@ -17,7 +17,7 @@ + x = Match() + text = self.textfile.get_src_text() + if not text: +- print "nonexistent file:", self.textfile.get_filename() ++ print("nonexistent file:", self.textfile.get_filename()) + return False + if text & x(r"(?s)[/][*]+(\s(?:.(?!\*\/))*.)\*\/" + r"(?:\s*\#(?:define|ifdef|endif)[ ]*\S*[ ]*\S*)*" +diff -ru a/docs/zzipdoc/textfile.py b/docs/zzipdoc/textfile.py +--- a/docs/zzipdoc/textfile.py 2019-12-27 17:22:22.058961305 -0600 ++++ b/docs/zzipdoc/textfile.py 2019-12-27 17:22:44.054908072 -0600 +@@ -17,7 +17,7 @@ + self.src_text = fd.read() + fd.close() + return True +- except IOError, e: ++ except IOError as e: + pass + return False + def assert_src_text(self): +@@ -41,7 +41,7 @@ + self._line(self.src_text, offset) + def _line(self, text, offset): + line = 1 +- for x in xrange(0,offset): ++ for x in range(0,offset): + if x == "\n": + line += 1 + return line diff --git a/var/spack/repos/tutorial/packages/armadillo/package.py b/var/spack/repos/tutorial/packages/armadillo/package.py index 3fca0bbcd5..13fabc20b3 100644 --- a/var/spack/repos/tutorial/packages/armadillo/package.py +++ b/var/spack/repos/tutorial/packages/armadillo/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/tutorial/packages/elpa/package.py b/var/spack/repos/tutorial/packages/elpa/package.py index f8c4ca7873..7fc10ef8fa 100644 --- a/var/spack/repos/tutorial/packages/elpa/package.py +++ b/var/spack/repos/tutorial/packages/elpa/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/tutorial/packages/hdf5/package.py b/var/spack/repos/tutorial/packages/hdf5/package.py index 1950f16969..9b0c683013 100644 --- a/var/spack/repos/tutorial/packages/hdf5/package.py +++ b/var/spack/repos/tutorial/packages/hdf5/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/tutorial/packages/mpich/package.py b/var/spack/repos/tutorial/packages/mpich/package.py index 6d127eed77..0acb31c217 100644 --- a/var/spack/repos/tutorial/packages/mpich/package.py +++ b/var/spack/repos/tutorial/packages/mpich/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/package.py b/var/spack/repos/tutorial/packages/netlib-lapack/package.py index 267cd2417f..e7edd9e23a 100644 --- a/var/spack/repos/tutorial/packages/netlib-lapack/package.py +++ b/var/spack/repos/tutorial/packages/netlib-lapack/package.py @@ -1,4 +1,4 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) |
