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2019-07-11test: Extra possible-dependencies coverage check (#11988)Tamara Dahlgren1-1/+10
2019-07-11New package: dimemas (#11979)Phil Tooley1-0/+34
2019-07-11OpenFOAM package: update download url (#11973)Mark Olesen1-2/+2
2019-07-11libfabric package: add support for tcp provider (#11965)Phil Carns1-1/+2
2019-07-11luit package: use autotools. (#11962)Toyohisa Kameyama1-8/+4
2019-07-11Rename build logs and make names consistent (#11806)Tamara Dahlgren14-104/+232
Fixes #11781 * Rename build log to spack-build-log.txt * Rename environment variables file to spack-build-env.txt * The name of the log and env files is now the same during the build and after the build completes * Update packages which referred to the build log/env files * For packages installed before this commit using older names for the build and env files, search for the older names
2019-07-10mpich: Add 3.3.1 (#11976)Michael Kuhn1-1/+4
2019-07-10bzip2: Add 1.0.7 (#11975)Michael Kuhn1-0/+1
2019-07-10tutorial: correct image link on tutorial pageTodd Gamblin1-1/+1
2019-07-10tutorial: updates slides for DOE/NSF workshop.Todd Gamblin1-9/+8
2019-07-09py-astropy: added latest version 3.2.1 (#11967)Reinhard1-0/+1
- correctly installs under python@3.5:3.7.3 - (partially) fixes https://github.com/spack/spack/issues/11966
2019-07-09package: Add powerapi package (#11845)Carson Woods1-0/+51
* Add powerapi package * Fix flake8 formatting * Fix download URL * Update powerapi version line * Fix how configure arguments are selected to improve readability * Bug Fixes * Fix trailing whitespace * Bug fixes * Remove incorrect configure flag
2019-07-09Ferret: add version 7.2 and adjust dependencies (#11921)Milton Woods1-24/+17
* ferret: use libx11 from spack * ferret: use mpi library with or without fortran support * ferret: add version 7.2 * ferret: no need to specify ~mpi * ferret: creating symlinks may fail for external packages; set include/lib paths instead
2019-07-08diffsplice package: remove -m64 on ARM. (#11899)Toyohisa Kameyama1-0/+5
2019-07-08zoltan: use autotools for new architecture host (#11924)Toyohisa Kameyama1-55/+71
* use autoreconf to regenerate configure script and config.guess for newer architectures * Add perl build dependency for older versions. The required perl version is constrained because the perl script uses syntax that is deprecated in older versions
2019-07-08motif package: fix the download url (#11939)Hironori-Yamaji1-1/+1
2019-07-08preCICE package: add version 1.5.2 (#11949)Frédéric Simonis1-0/+1
2019-07-08environment-modules package: add version 4.2.5 (#11953)Xavier Delaruelle1-0/+1
2019-07-08New package: r-grbase (starting at 1.8-3.4) (#11937)Justin S1-0/+26
2019-07-08r-graph: update R constraint to reflect DESCRIPTION (#11934)Justin S1-1/+1
2019-07-08r-rbgl: add 1.60.0 (#11936)Justin S1-0/+3
2019-07-08r-biocgenerics: add 0.30.0 (#11935)Justin S1-0/+2
2019-07-08bugfix: conflicts should print out the spec that has the conflict (#11947)Todd Gamblin1-1/+6
- Fix a bug introdcued by removing parse_anonymous_spec() - Conflicts' when specs are now *actually* anonymous, and the name of the package is implicit, so we need to remember to add it back to error messages.
2019-07-05travis: the sudo tag is now deprecated (#11933)cclauss1-10/+0
* Travis CI: The sudo tag is now deprecated in Travis __sudo: required__ no longer is. * Remove obsolete comment __travis_wait__ can help with long-running processes. * https://docs.travis-ci.com/user/common-build-problems/#build-times-out-because-no-output-was-received
2019-07-05bugfix: always generate a stack trace when spack is run with --debug (#11940)Todd Gamblin1-0/+5
- We weren't previously printing stack traces on SystemExit or KeyboardInterrupts. - Either raise or print the stacktrace in these cases.
2019-07-05tau: add conflicts for libelf/libdwarf variants (#11944)Kevin Huck1-0/+4
Declare a conflict for TAU versions older than 2.28.1, that they can't depend on libelf or libdwarf. The user can still install it by specifying tau@2.24~libelf~libdwarf.
2019-07-05cmake: add v3.14.5Christoph Junghans1-0/+1
2019-07-05setup-env.sh: make setup scripts work with `set -u`Todd Gamblin2-4/+11
- Add set -u to the setup-env.sh test script - Refactor lines in setup-env.sh that tested potentially undefined variables to use the `[ -z ${var+x} ]` construct
2019-07-05tests: add tests for setup-env.shTodd Gamblin5-29/+343
- tests use a shell-script harness and test all Spack commands that require special shell support. - tests work in bash, zsh, and dash - run setup-env.sh tests on macos and linux builds. - we run them on macos and linux
2019-07-05setup-env.sh: now compatible with bash, zsh, and dashTodd Gamblin1-65/+114
- replace use of [[ with [ - replace function foo { .. } with foo() { .. } - wrap some long lines - add lsof and /proc/fd magic so that we can find the sourced file even in dash - only do the complicated shell checks in one place; test $_sp_shell elsewhere.
2019-07-04py-stratify: vertical interpolation/stratification of atmos/ocean data (#11911)Milton Woods1-0/+22
* py-stratify: vertical interpolation/stratification of atmos/ocean data * py-stratify: download from pypi.io
2019-07-04py-scikit-image: include more dependencies (#11912)Milton Woods1-1/+4
* py-scikit-image: include more dependencies * py-scikit-image: limit some dependencies to recent versions
2019-07-04jdk: Add JDK 12.0.1 (#11903)Hironori-Yamaji1-0/+2
2019-07-04Added latest version, 0.7.1 (#11927)Paul1-0/+1
2019-07-04py-antlr4-python3-runtime: new package (#11890)Milton Woods1-0/+21
* py-antlr4-python3-runtime: new package * py-antlr4-python3-runtime: fix for flake8 * py-antlr4-python3-runtime: indent docstring * py-antlr4-python3-runtime: clarify role of this package vs ANTLR in docstring * py-antlr4-python3-runtime: remove whitespace at end of line
2019-07-03Set ignore files for py-reportlab (#11928)Glenn Johnson1-0/+6
The py-reportlab package includes binaries for easy_install and pip. That blocks activation if py-setuptools and/or py-pip are installed. This PR block the binaries from py-reportlab as easy_install and pip should be installed with their respective packages.
2019-07-03libtool: execute autoreconf at ver.2.4.2 (#11913)t-karatsu1-4/+4
Version 2.4.6 did not require running autoreconf, so this only does autoreconf for 2.4.2
2019-07-03libfabric package: add version 1.8.0 (#11918)shanedsnyder1-0/+2
2019-07-03coverage: remove sub-reports; only show project/patch on PRs (#11926)Todd Gamblin1-21/+1
- There's too much information on our PRs, and the Travis test results (which are arguably more important than coverage) get buried in coverage information - Remove coverage sub-categories, as you can browse codecov's file view to see roughly the same thing - show only project/patch on GitHub PRs.
2019-07-03py-cf-units: new package (#11891)Milton Woods1-0/+29
* py-cf-units: new package * py-cf-units: download from pypi.io * py-cf-units: include py-pytest-runner as build dep * py-cf-units: remove empty build_args function * py-cf-units: fix for flake8 * py-cf-units: indent docstring * py-cf-units: remove excess spaces * py-cf-units: list master branch ahead of numeric versions * py-cf-units: remove extension keyword from version
2019-07-03OpenMPI: add support for pbs/tm at configure. (#10620)Alberto Chiusole1-1/+24
2019-07-03turbine: Better auto-detection of R location (#11711)Justin M Wozniak1-2/+11
If R is provided by the system with a module (i.e. registered in packages.yaml with a "module" entry) and has no discernible prefix, this allows turbine to still make use of R.
2019-07-02py-pyke: new package (#11894)Milton Woods1-0/+20
* py-pyke: automatic python program generator * py-pyke: expand the package docstring
2019-07-02py-pyugrid: unstructured grids in netcdf files (#11900)Milton Woods1-0/+21
2019-07-02Add llvm as deps when static analyzer is enabled (#11888)ktsai71-15/+29
* dep llvm if static analyzer dep caliper if caliper * fix typo * adding variants for toggles
2019-07-02portcullis package: remove -m64 on aarch64. (#11905)Toyohisa Kameyama1-0/+5
GCC on aarch64 dose not support -m64. This patch removes the -m64 flag if target is aarch64.
2019-07-02opa-psm2 package: correct installation prefixes and add 11.2.77 (#11658)Phil Carns2-0/+84
This PR corrects a problem with the opa-psm2 package. It was installing headers into <prefix>/usr/include and libraries into <prefix>/usr/lib instead of <prefix>/include and <prefix>/lib. The extra level of usr/ subdirectories causes dependent packages like libfabric to fail to build.
2019-07-01openfoam: rename openfoam-com to openfoam (#11876)Mark Olesen16-30/+25
The original packaging, with openfoam as a virtual and with openfoam-com, openfoam-org and openfoam-extend as providers, adds an obfuscation layer without any benefit. - Rename `openfoam-com` to `openfoam`, and remove the `openfoam` virtual package.
2019-07-01specs: remove parse_anonymous_spec(); use Spec() insteadTodd Gamblin8-144/+224
- `parse_anonymous_spec()` is a vestige of the days when Spack didn't support nameless specs. We don't need it anymore because now we can write Spec() for a spec that will match anything, and satisfies() semantics work properly for anonymous specs. - Delete `parse_anonymous_spec()` and replace its uses with simple calls to the Spec() constructor. - make then handling of when='...' specs in directives more consistent. - clean up Spec.__contains__() - refactor directives and tests slightly to accommodate the change.
2019-07-01cray: use the cle-release file to determine CNL versionTodd Gamblin2-6/+72
- CNL OS previously used the *Cray PE* version to determine the OS version. Cray does not synchronize PE and CLE releases; you can run CLE7 with PrgEnv 6 (and NERSC currently does). - Fix Spack's OS detection by using the cle-release file to detect the OS version. This file is updated with every CLE OS release. - Add some tests for our parsing logic