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2023-08-04 julia: add v1.9.2 (#39269)Davide1-0/+1
2023-08-03salmon: update version (#39202)pabloaledo2-0/+20
* salmon: update version --------- Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-03adios2: add 2.9.1 release (#39257)Vicente Bolea1-2/+3
2023-08-03openssl: Update to 3.1.2, 3.0.10, 1.1.1v (#39216)Erik Schnetter1-3/+18
2023-08-03Revert checksum verification CI test (#39259)Tamara Dahlgren1-18/+1
2023-08-03sowing: add version 1.1.26-p8 (#39258)Satish Balay1-1/+4
* sowing: add version 1.1.26-p8 * add in maintainer
2023-08-03Automated deployment to update package flux-core 2023-08-03 (#39237)Vanessasaurus1-0/+1
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-08-03hpcviewer: add version 2023.07 (#39236)Mark W. Krentel1-1/+6
Add version 2023.07, adjust the line for deprecated (anything using java 8 is now deprecated).
2023-08-03patchelf@0.18.0 breaks intel compiler libraries (#39253)Stephen Sachs1-1/+2
2023-08-03kafka: new versions (#39249)Matthieu Dorier1-0/+9
* kafka: version 2.13-3.5.0 * kafka: version 2.13-3.5.1 and 2.13-3.4.1
2023-08-03librdkafka: version 2.2.0 (#39250)Matthieu Dorier1-0/+1
2023-08-03Add checksum CI test and verify with new versions for glab and gh (#39181)Alec Scott3-1/+21
2023-08-03gftl-shared: new version 1.6.1 (#39217)Matthew Thompson1-0/+1
This PR adds gFTL-shared v1.6.1
2023-08-03mapl: add package (#39227)Matthew Thompson4-0/+279
* mapl: add package * Fix style
2023-08-03py-sphinx-rtd-theme: avoid concretizing 0.5 with Sphinx 7.0 (#39212)Seth R. Johnson1-1/+1
* py-sphinx-rtd-theme: avoid concretizing 0.5 with Sphinx 7.0 * Update var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-03Add pika 0.17.0 (#39221)Auriane R1-0/+1
2023-08-03pfunit: add versions 4.7.1, 4.7.2, 4.7.3 (#39218)Matthew Thompson1-0/+3
This adds the latest versions of pFUnit
2023-08-03vecgeom: new version 1.2.5 (#39211)Seth R. Johnson1-2/+11
* vecgeom: new version 1.2.5 * Mark previous versions as deprecated * [@spackbot] updating style on behalf of sethrj * vecgeom: fix 1.2.4 checksum for change to git describe
2023-08-03ucsc-bedgraphtobigwig: add package (#39208)pabloaledo1-0/+50
Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-03R: fix build on macOS arm64 (#39228)Adam J. Stewart1-0/+2
2023-08-03repo cache: use -inf default instead of 0 (#39214)Harmen Stoppels2-28/+24
FastPackageChecker.modified_since should use a default number < 0 When the repo cache does not exist, Spack uses mtime 0. This causes the repo cache not to be generated when the repo has mtime 0. Some popular package managers such as spack use 0 mtime normalization for reproducible tarballs. So when installing spack with spack from a buildcache, the repo cache doesn't generate Also add some typehints
2023-08-03ucsc-bedclip: add package (#39209)pabloaledo3-0/+81
Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-03py-kornia: add v0.7.0 (#39233)Adam J. Stewart1-0/+2
2023-08-03Buildcache commands cleanup, again... (#39203)Harmen Stoppels6-158/+114
* Inform mypy that tty.die is noreturn * avoid temporary allocation in env * update spack buildcache save-specfile * fix spack buildcache check/download/get-buildcache-name - ensure that required args and mutually exclusive ones are marked as such in argparse for better error messages - deprecate --spec-file everywhere - use disambiguate for better error messages
2023-08-02nextdenovo: new package @2.5.2 (and py-paralleltask) (#39139)George Young2-0/+49
* py-paralleltask: new package @0.2.2 * adding hidden dependency * nextdenovo: new package @2.5.2 * style * Update var/spack/repos/builtin/packages/py-paralleltask/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-02py-melissa-core: add new versions and py-iterative-stats dependency (#38654)mschouler1-4/+13
* py-melissa-core: add new versions and py-iterative-stats dependency * Enhance dependency specification * Fix dependency specification * Fix comment alignment * Improve dependency specification style * Enhance dependencies * Fix mpi4py, py-cloudpickle and py-python-hostlist dependencies * Update var/spack/repos/builtin/packages/py-melissa-core/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-melissa-core/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-melissa-core/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Set develop version as preferred * Update var/spack/repos/builtin/packages/py-melissa-core/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Marc Schouler <marc.schouler@inria.fr> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-02py-libEnsemble: add v0.10.2 (#39074)Stephen Hudson1-2/+4
* libEnsemble: add v0.10.2 * Make setuptools build only dep * Update var/spack/repos/builtin/packages/py-libensemble/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-02Add qmake virtual provider (#38848)Adam J. Stewart4-1/+6
2023-08-02openmolcas: adding version 23.06 (#39195)snehring1-0/+1
2023-08-02bioconductor-dupradar, bioconductor-rsubread: add packages (#39206)pabloaledo2-0/+41
* bioconductor-dupradar, bioconductor-rsubread: add packages * [@spackbot] updating style on behalf of pabloaledo
2023-08-02tximeta: add package (#39207)pabloaledo1-0/+39
* tximeta: add package Signed-off-by: Pablo <pablo.aledo@seqera.io> * [@spackbot] updating style on behalf of pabloaledo --------- Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-02patchelf: 0.18 (#39215)Harmen Stoppels1-0/+1
2023-08-02CI: Refactor ci reproducer (#37088)kwryankrattiger5-95/+194
* CI: Refactor ci reproducer * Autostart container * Reproducer paths match CI paths * Generate start scripts for docker and reproducer * CI: Add interactive and gpg options to reproduce-build * Interactive will determine if the docker container persists after running reproduction. * GPG path/url allow downloading GPG keys needed for binary cache download validation. This is important for running reproducer for protected CI jobs. * Add exit_on_failure option to CI scripts * CI: Add runtime option for reproducer
2023-08-02version: move to module, avoid circular imports (#39077)Harmen Stoppels8-268/+358
2023-08-02buildcache extractall: extract directly into spec.prefix (#37441)Harmen Stoppels5-60/+159
- Run `mkdirp` on `spec.prefix` - Extract directly into `spec.prefix` 1. No need for `$store/tmp.xxx` where we extract the tarball directly, pray that it has one subdir `<name>-<version>-<hash>`, and then `rm -rf` the package prefix followed by `mv`. 2. No need to clean up this temp dir in `spack clean`. 3. Instead figure out package directory prefix from the tarball contents, and strip the tarinfo entries accordingly (kinda like tar --strip-components but more strict) - Set package dir permissions - Don't error during error handling when files cannot removed - No need to "enrich" spec.json with this tarball-toplevel-path After this PR, we can in fact tarball packages relative to `/` instead of `spec.prefix/..`, which makes it possible to use Spack tarballs as container layers, where relocation is impossible, and rootfs tarballs are expected.
2023-08-02feat: move -N/--namespace(s) to common args, allow in `buildcache list` (#36719)Wouter Deconinck9-45/+41
`spack buildcache list` did not have a way to display the namespace of packages in the buildcache. This PR adds that functionality. For consistency's sake, it moves the `-N/--namespace` arg definition to the `common/arguments.py` and modifies `find`, `solve`, `spec` to use the common definition. Previously, `find` was using `--namespace` (singular) to control whether to display the namespace (it doesn't restrict the search to that namespace). The other commands were using `--namespaces` (plural). For backwards compatibility and for consistency with `--deps`, `--tags`, etc, the plural `--namespaces` was chosen. The argument parser ensures that `find --namespace` will continue to behave as before. Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-08-02rust: disable build from downloading a version of LLVM from Rust CI (#39146)Alec Scott1-0/+3
2023-08-02Python: fix library/header error msg format (#39171)Adam J. Stewart1-4/+4
2023-08-01dcmtk: new version and pic configuration (#39161)Martin Aumüller1-8/+15
* dcmtk: checksum 3.6.7 compiles on macos * dcmtk: support pic configuration * [@spackbot] updating style on behalf of aumuell * dcmtk: use define_from_variant for shorter code * dcmtk: refine conflict it appears that dcmtk < 3.6.7 only fails on macos/aarch64: /Library/Developer/CommandLineTools/usr/lib/clang/14.0.3/include/xmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture" --------- Co-authored-by: aumuell <aumuell@users.noreply.github.com>
2023-08-01py-gevent: add 23.7.0 and py-greenlet: add 3.0.0a1 (#39164)Manuela Kuhn2-9/+18
* py-gevent: add 23.7.0 and py-greenlet: add 3.0.0a1 * Update var/spack/repos/builtin/packages/py-gevent/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Remove version 1.3.a2 --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-01py-openai, py-pandas-stubs (#38912)sid4-9/+109
* simple build of py-openai * added variants to py-openai * py-pandas-stubs is a dependency for py-openai * fixed format and flake8 errors for py-openai * black format error for py-pandas-stubs * [@spackbot] updating style on behalf of sidpbury * made style and format changes to py-openai * made style and format changes to py-pandas-stubs * py-types-pytz is a dependency for py-openai * [@spackbot] updating style on behalf of sidpbury * updated py-openpyxl for ver 3.0.7 and 3.1.2 * Update var/spack/repos/builtin/packages/py-pandas-stubs/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * ajs requested changes for py-openai * updated py-openpyxl for supported python * [@spackbot] updating style on behalf of sidpbury * updated py-openpyxl * removed requirement.txt dependencies in py-openpyxl * removed python depends on from openpyxl --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-01Add two latest versions (#39182)mschouler1-0/+2
Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
2023-08-01amrex: add 23.08 (#39190)Weiqun Zhang1-0/+1
2023-08-01Mongodb: Add new package (#39085)Dax Lynch2-0/+142
* Added the package * added dependency * Update package.py * Update package.py Added xz as a dependency
2023-08-01remove CMAKE_GENERATOR from the host-config because it cannot be overwritten ↵Chris White1-11/+0
on the command line (#39044)
2023-08-01Fix source bootstrapping for Debian and derivatives (#39107)vucoda1-1/+15
* Fix Python package.py for Debian and derivatives to find the system Python library location When bootstrapping from source, find_library() does not contain any paths that work for Debian and derivatives. fixes #36666 * Update to pass styling * Update to styling * Update python package.py with fake config value for LIBPL * Update python package.py libpl config_vars entry to follow double quote standard * styling update
2023-07-31petsc, py-petsc4py: add v3.19.4 (#39169)Satish Balay2-0/+2
2023-07-31qt-base: add conflict for 6.5+ with GCC < 9 (#39158)Martin Aumüller1-0/+3
2023-07-31py-numpy: add v1.25.2 (#39172)Adam J. Stewart1-0/+1
2023-07-31Add `spack checksum --verify`, fix `--add` (#38458)Alec Scott8-117/+272
* Add rewrite of spack checksum to include --verify and better add versions to package.py files * Fix formatting and remove unused import * Update checksum unit-tests to correctly test multiple versions and add to package * Remove references to latest in stage.py * Update bash-completion scripts to fix unit tests failures * Fix docs generation * Remove unused url_dict argument from methods * Reduce chance of redundant remote_versions work * Add print() before tty.die() to increase error readablity * Update version regular expression to allow for multi-line versions * Add a few unit tests to improve test coverage * Update command completion * Add type hints to added functions and fix a few py-lint suggestions * Add @no_type_check to prevent mypy from failing on pkg.versions * Add type hints to format.py and fix unit test * Black format lib/spack/spack/package_base.py * Attempt ignoring type errors * Add optional dict type hint and declare versions in PackageBase * Refactor util/format.py to allow for url_dict as an optional parameter * Directly reference PackageBase class instead of using TypeVar * Fix comment typo --------- Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
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