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2023-05-26py-datalad-metadata-model: add 0.3.10 (#37937)Manuela Kuhn1-1/+1
2023-05-26py-debugpy: add 1.6.7 (#37941)Manuela Kuhn1-0/+1
2023-05-26py-distro: add 1.8.0 (#37942)Manuela Kuhn1-1/+1
2023-05-26Update melissa build (#37609)mschouler3-3/+81
* Remove deprecated package * Add up-to-date melissa builds * Remove blank lines and FIXME comments * Use directive syntax for maintainers and remove unnecessary comments * Remove unused function * Deprecate former melissa recipe * Change melissa python package name * Update setuptools and rapidjson dependencies versions * Fix mypy error * Restore rapidjson version * Variant simplification * Make variants lower case * Deprecate former omitted version * Make torch version consistent with requirement file * Fix variants definition * Fix style error --------- Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
2023-05-26py-coloredlogs: add 15.0.1 and py-humanfriendly: add 10.0 (#37905)Manuela Kuhn2-1/+7
2023-05-26py-contourpy: add 1.0.7 (#37914)Manuela Kuhn1-1/+4
2023-05-26py-coverage: add 5.5 (#37922)Manuela Kuhn1-5/+2
2023-05-26Update py-pennylane ecosystem to support v0.30.0 (#37763)Lee James O'Riordan3-14/+28
* Update PennyLane ecosystem for 0.30 release * Update package dep versions * Fix formatting * Update dep versions * Remove PL hard pin and rely on PLQ to define version * Update var/spack/repos/builtin/packages/py-pennylane-lightning-kokkos/package.py Co-authored-by: Vincent Michaud-Rioux <vincent.michaud-rioux@xanadu.ai> * Convert pybind11 from build to link dep, and PL ver limit --------- Co-authored-by: Vincent Michaud-Rioux <vincent.michaud-rioux@xanadu.ai>
2023-05-26py-beautifulsoup4: add 4.12.2 (#37820)Manuela Kuhn1-3/+6
2023-05-26py-chardet: add 5.1.0 (#37879)Manuela Kuhn1-4/+3
* py-chardet: add 5.1.0 * Remove py-setuptools as run dependency
2023-05-26CI: Use relative path in default script (#36649)kwryankrattiger1-1/+1
2023-05-26picard: add 3.0.0, switch to java@17: (#37948)George Young1-1/+7
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26minimap2: adding 2.26 (#37945)George Young1-0/+1
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26hyphy: add 2.5.51hf, update dependencies for switch to MPI (#37938)George Young1-1/+4
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26Strip inactive maintainer. (#36048)Kai Torben Ohlhus1-1/+1
2023-05-26cdo: add 2.2.0 (#37244)Brian Spilner1-0/+5
2023-05-26PMIx and PRRTe: disabled use of sphinx (#37750)Howard Pritchard2-2/+2
Related to https://github.com/spack/spack/pull/37717 No need to be rebuilding openmpi man pages and other docs in spack as it almost always is used with release tarballs. See #37717 for more details. Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-05-25Windows MSVC: do not set sdk version if installing sdk (#37930)John W. Parent1-1/+5
Note the win-sdk package is not installable and reports an error which instructs the user how to add it. Without this fix, a (more confusing) error occurs before this message can be generated.
2023-05-25fastp: add version 0.23.3, add build dependencies (#37931)George Young1-0/+4
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-25gradle:add 7.3 (#37928)Leonard-Anderson-NNL1-0/+1
Co-authored-by: Cloud User <leonardanderson@leonardander001.hzterscemazurawp3xenxzahla.bx.internal.cloudapp.net>
2023-05-25Windows: fix "spack build-env" (#37923)John W. Parent3-3/+21
"spack build-env" was not generating proper environment variable definitions on Windows; this commit updates the generated commands to succeed with batch/PowerShell.
2023-05-25update ci ml darwin keypath (#37927)eugeneswalker1-3/+3
2023-05-25Windows CI: add paraview deps nightly build (#37924)John W. Parent1-0/+31
Add a nightly job to attempt building all Paraview dependencies and upload the results to cdash. This check doesn't affect the reported build/test status of Spack. We are using this to monitor the state of Windows support while working on more-robust checks (eventually the Windows build will have to succeed to merge PRs to Spack).
2023-05-25fix(protobuf-c): set version bound for protobuf dependency (#37917)H. Joe Lee1-1/+1
Fix #37887 GitLab CI failure.
2023-05-25fix(dpdk): add a new version 23.03. (#37919)H. Joe Lee1-1/+2
Fix E4S GitLab CI issue #37887.
2023-05-25sirius: add rocsolver/wannier90 (#37900)Simon Pintarelli1-1/+7
* sirius: add rocsolver dependency for 7.5: * add wannier90
2023-05-25Dyninst: add standalone test (#37876)Tim Haines1-0/+9
* Dyninst: add standalone test * Add docstring with description * Don't use join_path for builtin path objects * Whitespace * Update format of docstring
2023-05-25Protobuf package: CMake fix for Windows build (#37926)John W. Parent2-0/+15
Qualify reference with namespace. A pending upstream PR will eventually make this unnecessary, so the patch is only applied for 3.22. versions.
2023-05-25flecsi: disable cinch dependency for v1 release (#37857)Richard Berger1-4/+14
* flecsi: disable cinch dependency for v1 releases * [@spackbot] updating style on behalf of rbberger --------- Co-authored-by: rbberger <rbberger@users.noreply.github.com>
2023-05-25environment-modules: fix @main version requirements (#37807)Xavier Delaruelle1-0/+3
Some requirements for @main version of environment-modules were missing: * python (to build ChangeLog documentation file) * py-sphinx@1.0: (to build man-pages, etc) Also adding gzip, which is now required to build ChangeLog.gz (which is now shipped instead of ChangeLog). Other versions are not requiring these tools (as documentation is pre-built in dist tarball).
2023-05-25Bugfix/tests: write not append stand-alone test status (#37841)Tamara Dahlgren2-1/+26
2023-05-25fix(pmdk): add pkconfig as dependency (#37896)H. Joe Lee1-0/+1
Fix #37887 failure.
2023-05-25[devito] Move to version 4.8.1 (#37915)Stephen Sachs2-17/+31
* [devito] Move to version 4.8.1 * Fix: Adding patch file * Update var/spack/repos/builtin/packages/py-devito/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-devito/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Addressing @adamjstewart comments --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-25Add shared variant to geos package (#37899)Alex Richert1-0/+4
Co-authored-by: alexrichert <alexrichert@gmail.com>
2023-05-25Add macOS ML CI stacks (#36586)Adam J. Stewart6-172/+223
* Add macOS ML CI stacks * torchmeta is no longer maintained and requires ancient PyTorch * Add MXNet * update darwin aarch64 stacks * add darwin-aarch64 scoped config.yaml * remove unnecessary cleanup job * fix specifications * fix labels * fix labels * fix indent on tags specification * no tags for trigger jobs * try overriding tags in stack spack.yaml * do not use CI_STACK_CONFIG_SCOPES * incorporate config:install_tree:root: overrides and compiler defs * copy relevant ci-scoped config settings directly into stack spack.yaml * remove build-job-remove * spack ci generate: add debug flag * include cdash config directly in stack spack.yaml * customize build-job script section to avoid absolute paths * add any-job specification * tags: use aarch64-macos instead of aarch64 * generate tags: use aarch64-macos instead of aarch64 * do not add morepadding * use shared mirror; comment out known failures * remove any-job * nproc || true * comment out specs failing due to bazel from cache codesign issue --------- Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
2023-05-24Update for py-gmxapi for 0.4.1. (#37834)M. Eric Irrgang1-2/+3
* Update for py-gmxapi for 0.4.1. * Note 0.4.1 hash from PyPI. * Note relaxed dependencies for future versions. * Update var/spack/repos/builtin/packages/py-gmxapi/package.py
2023-05-24py-charset-normalizer: add 3.1.0 (#37880)Manuela Kuhn1-2/+1
2023-05-24py-bids-validator: add 1.11.0 (#37845)Manuela Kuhn1-0/+1
2023-05-24py-bottleneck: add 1.3.7 (#37847)Manuela Kuhn1-0/+1
2023-05-24py-certifi: add 2023.5.7 (#37848)Manuela Kuhn1-1/+1
2023-05-24py-attrs: add 23.1.0 (#37817)Manuela Kuhn1-2/+10
* py-attrs: add 23.1.0 * Add missing dependency
2023-05-24py-babel: add 2.12.1 (#37818)Manuela Kuhn1-3/+3
* py-babel: add 2.12.1 * Update var/spack/repos/builtin/packages/py-babel/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-24py-rasterio: add v1.3.7 (#37886)Adam J. Stewart1-0/+1
2023-05-24py-lightly: add v1.4.6 (#37885)Adam J. Stewart1-0/+1
2023-05-24starpu: add release 1.4.1 (#37883)Nathalie Furmento1-0/+1
2023-05-24paraview (protobuf failure) #37437 (#37440)QuellynSnead1-0/+6
When attempting to build paraview@5.10.1 using a recent Intel compiler (Classic or OneAPI) or the IBM XL compiler, the build fails if the version of protobuf used is > 3.18
2023-05-24sensei: Allow Paraview 5.11 for sensei develop version (#37719)willdunklin1-1/+1
2023-05-24Pcluster local buildcache (#37852)Stephen Sachs5-38/+23
* [pcluster pipeline] Use local buildcache instead of upstream spack Spack currently does not relocate compiler references from upstream spack installations. When using a buildcache we don't need an upstream spack. * gcc needs to be installed via postinstall to get correct deps * quantum-espresso@gcc@12.3.0 returns ICE on neoverse_{n,v}1 * Force gitlab to pull the new container * Revert "Force gitlab to pull the new container" This reverts commit 3af5f4cd88245138992deb2a46c17e6f85858d68. Seems the gitlab version does not yet support "pull_policy" in .gitlab-ci.yml * Gitlab keeps picking up wrong container. Renaming * Update containers once more after failed build
2023-05-24bugfix: env concretize after remove (#37877)Greg Becker2-0/+27
2023-05-24spack remove: fix traversal when user specs intersect (#37882)Harmen Stoppels1-21/+20
drop unnecessary double loop over the matching user specs.
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