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2023-10-06Make "minimal" the default duplicate strategy (#39621)Massimiliano Culpo20-120/+2984
* Allow branching out of the "generic build" unification set For cases like the one in https://github.com/spack/spack/pull/39661 we need to relax rules on unification sets. The issue is that, right now, nodes in the "generic build" unification set are unified together with their build dependencies. This was done out of caution to avoid the risk of circular dependencies, which would ultimately cause a very slow solve. For build-tools like Cython, however, the build dependencies is masked by a long chain of "build, run" dependencies that belong in the "generic build" unification space. To allow splitting on cases like this, we relax the rule disallowing branching out of the "generic build" unification set. * Fix issue with pure build virtual dependencies Pure build virtual dependencies were not accounted properly in the list of possible virtuals. This caused some facts connecting virtuals to the corresponding providers to not be emitted, and in the end lead to unsat problems. * Fixed a few issues in packages py-gevent: restore dependency on py-cython@3 jsoncpp: fix typo in build dependency ecp-data-vis-sdk: update spack.yaml and cmake recipe py-statsmodels: add v0.13.5 * Make dependency on "blt" of type "build"
2023-10-06python: add 3.12.0 (but keep 3.11 preferred) (#40282)Harmen Stoppels9-6/+318
2023-10-05ecFlow update (#40305)Alex Richert1-5/+41
* Support static openssl for ecflow * Update ecflow/static openssl * Update ssl settings in ecflow * add pic variant for ecflow * style fix * Update package.py * Update package.py
2023-10-05Revert "cray rhel: disable due to runner issues (#40324)" (#40335)eugeneswalker1-16/+16
This reverts commit bf7f54449ba8ed157c9ee258007e0a7a509600cf.
2023-10-05pbmpi: adding new version and maintainer (#40319)snehring1-0/+5
2023-10-05unparse: drop python 3.4 remnants (#40333)Harmen Stoppels1-15/+0
2023-10-05whizard: Make sure to detect LCIO if requested (#40316)Thomas Madlener1-0/+2
2023-10-05Add pika 0.19.0 (#40313)Auriane R1-0/+1
2023-10-05cray rhel: disable due to runner issues (#40324)Harmen Stoppels1-16/+16
2023-10-05exago: add and logging variant. (#40188)Cameron Rutherford2-5/+9
2023-10-04trilinos: add variant to build tests (#40284)eugeneswalker1-0/+7
* trilinos: add variant: testing * trilinos: rename +testing to +test
2023-10-04Improve build isolation in PythonPipBuilder (#40224)Harmen Stoppels1-1/+99
We run pip with `--no-build-isolation` because we don't wanna let pip install build deps. As a consequence, when pip runs hooks, it runs hooks of *any* package it can find in `sys.path`. For Spack-built Python this includes user site packages -- there shouldn't be any system site packages. So in this case it suffices to set the environment variable PYTHONNOUSERSITE=1. For external Python, more needs to be done, cause there is no env variable that disables both system and user site packages; setting the `python -S` flag doesn't work because pip runs subprocesses that don't inherit this flag (and there is no API to know if -S was passed) So, for external Python, an empty venv is created before invoking pip in Spack's build env ensures that pip can no longer see anything but standard libraries and `PYTHONPATH`. The downside of this is that pip will generate shebangs that point to the python executable from the venv. So, for external python an extra step is necessary where we fix up shebangs post install.
2023-10-04yaksa: Allow unsupported host compiler with CUDA (#40298)Ken Raffenetti1-0/+2
Fixes #40272.
2023-10-04Damaris release v1.9.2 (#40285)Josh Bowden1-2/+7
* Update to latest dot versions and improved installation of Damaris python module damaris4py * fix for visit dependency typo * whitespace check * whitespace check * fix for style issue * reviewer suggestions for integrating Python added * suggestion for boost depends statement added
2023-10-04Add new package awscli-v2 and its missing dependency awscrt (#40288)Dom Heinzeller2-0/+50
* Add new package awscli-v2 and its missing dependency awscrt * Remove boilerplate comments from awscli-v2 and awscrt packages * Fix typos in var/spack/repos/builtin/packages/awscli-v2/package.py * Update var/spack/repos/builtin/packages/awscli-v2/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/awscli-v2/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/awscli-v2/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/awscli-v2/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/awscli-v2/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Address reviewer comments * Remove py-pip version dependency from var/spack/repos/builtin/packages/awscli-v2/package.py --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-10-04py-isort: needs setuptools build dep before v5 (#40234)Harmen Stoppels2-1/+5
* py-isort: needs setuptools build dep before v5 Detected in #40224. In the past, system setuptools could be picked up when using an external python, so py-isort@4 would install fine. With the linked PR, pip can only consider packages that Spack controls from PYTHONPATH, so the issue of missing py-setuptools showed up. * py-importlib-metadata: fix lowerbounds on python * review * py-isort unconditionally add optional setuptools dep to prevent picking up user package at runtime * style * drop optional py-setuptools run dep
2023-10-04py-einops: add v0.7.0 (#40296)Adam J. Stewart1-0/+2
2023-10-04petsc: add conflict on rocm 5.6: for now (#40300)Harmen Stoppels1-0/+4
hipsparse@5.6.0 changed hipsparseSpSV_solve() API, but reverted in 5.6.1
2023-10-04ci: pull E4S images from github instead of dockerhub (#40307)Scott Wittenburg6-21/+21
2023-10-04e4s arm: disable bricks due to target=aarch64 not being respected (#40308)eugeneswalker1-6/+6
2023-10-03ADIOS2: v2.8 is not compatible with HDF5 v1.14: (#40258)kwryankrattiger1-0/+1
2023-10-03ci: Change how job names appear in gitlab (#39963)Scott Wittenburg2-38/+13
2023-10-03fix_qgis_build_with_pysip5 (#39941)Sinan1-8/+46
* fix_qgis_build_with_pysip5 * build fails with newer protobuf * somehow findgdal can figure this out. * Update var/spack/repos/builtin/packages/qgis/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * fix gdal lib again * qgis needs QtPositioning provided by qt+location option * fix FindPyQt5 cmake file * fix bug * fix qsci sip issue * fix bug * blackify * improve * add latest LTR * add build dep * revert until bug is fixed * specify proj version for qgis 3.28 * improve gdal libs search via indicating gdal-config * make flake happy * improve deps * add 3.28.11, improve style * fix style * [@spackbot] updating style on behalf of Sinan81 --------- Co-authored-by: Sinan81 <Sinan@world> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
2023-10-03falco: new package @1.2.1 (#40289)George Young1-0/+26
* falco: new package @1.2.1 * specifying gmake * Replacing homepage - readthedocs is empty --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-10-03py-tables: add v3.8.0 (#40295)Adam J. Stewart3-12/+69
2023-10-03[add] py-graphene: new recipe, required by py-cylc-flow (#39988)Lydéric Debusschère1-0/+23
2023-10-03Fix binutils regression on +gas~ld fix (#40292)Jordan Galby1-7/+9
2023-10-03e4s ci stacks: sync with e4s-23.08 (#40263)eugeneswalker6-289/+1212
* e4s amd64 gcc ci stack: sync with e4s-23.08 * e4s amd64 oneapi ci stack: sync with e4s-23.08 * e4s ppc64 gcc ci stack: sync with e4s-23.08 * add new ci stack: e4s amd64 gcc w/ external rocm * add new ci stack: e4s arm gcc ci * updates * py-scipy: -fvisibility issue is resolved in 2023.1.0: #39464 * paraview oneapi fails * comment out pkgs that fail to build on power * fix arm stack name * fix cabana +cuda specification * comment out failing spces * visit fails build on arm * comment out slepc arm builds due to make issue * comment out failing dealii arm builds
2023-10-03py-biom-format: Fix package file issues and bring up to date (#39962)Gavin John1-9/+19
* Fix python versioning issue for py-biom-format * Update deps according to feedback * Remove version requirement for py-cython Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Only depend on py-six for versions >=2.1.10 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add py-future as non-dependency for 2.1.15 * There we are. Everything anyone could ever want * Missed cython version change Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-10-03Adding dynaconf module (#39762)GeorgeJuniorGG1-0/+18
* Adding dynaconf module * Fixing style * Adding dependency
2023-10-03py-yarl: add 1.9.2 (#40277)Manuela Kuhn1-4/+4
2023-10-03py-dipy: Update version to support python@3.10 (#40229)Tom Payerle1-0/+6
* py-dipy: Update version to support python@3.10 py-dipy only adds support to python@3.10 in py-dipy@1.5.0 See #40228 * py-dipy: fix formatting issues * py-dipy: another formatting fix * py-dipy: Use depends instead of conflicts * py-dipy: formatting fix * py-dipy: Updating for @1.7.0 Added new minimum version requirements for py-cython py-numpy py-scipy py-h5py as suggested by @manuelakuhn (py-nibabel min version unchanged for @1.7.0)
2023-10-03py-wcwidth: add 0.2.7 (#40256)Manuela Kuhn1-0/+2
2023-10-03py-virtualenv: add 20.24.5 (#40255)Manuela Kuhn4-19/+32
* py-virtualenv: add 20.22.0 * py-platformdirs: add 3.5.3 * py-filelock: add 3.12.4 * py-distlib: add 0.3.7
2023-10-03py-websocket-client: add 1.6.3 (#40274)Manuela Kuhn1-19/+16
2023-10-03py-werkzeug: add 2.3.7 and 3.0.0 (#40275)Manuela Kuhn1-2/+15
2023-10-03py-wrapt: add 1.15.0 (#40276)Manuela Kuhn1-2/+1
2023-10-03py-libEnsemble: add v1.0.0 (#40203)Stephen Hudson1-15/+22
* py-libEnsemble: add v1.0.0 * Add version ranges for deps * Add comments to variants * Put when before type * Fix line lengths * Re-format * Update var/spack/repos/builtin/packages/py-libensemble/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * Update var/spack/repos/builtin/packages/py-libensemble/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> --------- Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-10-03[add] py-graphql-relay: new package (#39807)Lydéric Debusschère2-1/+27
* [add] py-graphql-relay: new package * py-graphql-relay: Update package.py Remove leftovers from version 3.2.0: * archive name in pypi * dependencies * [fix] py-graphql-relay: remove constraint on python version; add dependence py-rx because of ModuleNotFoundError during spack test * [fix] py-graphql-relay: remove py-rx dependence; py-graphql-core: add dependencies for version 2.3.2 * py-graphql-core: Update from review; set build backend, py-poetry for version 3: and py-setuptools for version 2 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-10-03[add] py-metomi-isodatetime: new recipe, required by py-cylc-flow (#39990)Lydéric Debusschère1-0/+19
* [add] py-metomi-isodatetime: new recipe, required by py-cylc-flow * py-metomi-isodatetime: use sources from pypi instead of github
2023-10-03build(deps): bump actions/setup-python from 4.7.0 to 4.7.1 (#40287)dependabot[bot]5-11/+11
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.0 to 4.7.1. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/61a6322f88396a6271a6ee3565807d608ecaddd1...65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-10-03build(deps): bump urllib3 from 2.0.5 to 2.0.6 in /lib/spack/docs (#40286)dependabot[bot]1-1/+1
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.5 to 2.0.6. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/v2.0.5...2.0.6) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-10-03Deactivate Cray sles, due to unavailable runner (#40291)Massimiliano Culpo1-12/+12
This reverts commit 027409120408eb4d41d8bdd82a13c34b3ac7fea9.
2023-10-03Buildcache tarballs with rootfs structure (#39341)Harmen Stoppels2-73/+162
Two changes in this PR: 1. Register absolute paths in tarballs, which makes it easier to use them as container image layers, or rootfs in general, outside of Spack. Spack supports this already on develop. 2. Assemble the tarfile entries "by hand", which has a few advantages: 1. Avoid reading `/etc/passwd`, `/etc/groups`, `/etc/nsswitch.conf` which `tar.add(dir)` does _for each file it adds_ 2. Reduce the number of stat calls per file added by a factor two, compared to `tar.add`, which should help with slow, shared filesystems where these calls are expensive 4. Create normalized `TarInfo` entries from the start, instead of letting Python create them and patching them after the fact 5. Don't recurse into subdirs before processing files, to avoid keeping nested directories opened. (this changes the tar entry order slightly, it's like sorting by `(not is_dir, name)`.
2023-10-02Add AdditiveFOAM package (#39295)Sam Reeve3-0/+68
* Add AdditiveFOAM package * Add AdditiveFOAM build and install Co-authored-by: kjrstory <kjrstory@gmail.com> Co-authored-by: Knapp, Gerry <knappgl@ornl.gov> --------- Co-authored-by: kjrstory <kjrstory@gmail.com> Co-authored-by: Knapp, Gerry <knappgl@ornl.gov>
2023-10-02py-torchgeo: add v0.5.0 (#40267)Adam J. Stewart1-97/+107
* py-torchgeo: add v0.5.0 * Better documentation of dependency quirks
2023-10-02vtk-m@2.0: depend on kokkos@3.7:3.9 per issue #40268 (#40281)eugeneswalker1-0/+1
2023-10-02Add ipm package (#40069)Christoph Weber2-0/+140
2023-10-02Rocm 5.6.0 & 5.6.1 release updates (#39673)renjithravindrankannath53-61/+4047
* 5.6.0 updates * Rocm 5.6.0 updates * Style and audit corrections for 5.6 * Patching smi path for tests. * Style correction * 5.6.1 updates * Updated hip tests for ci build failure Updated hiprand with the release tag Taken care the review comment rocsolver * Adding rocm-smi path for 5.6 * Adding the patch file * Setting library directory uniform * gl depends on mesa but it should not be llvm variant * Fix for the issue 39520 by setting CMAKE_INSTALL_LIBDIR=lib * i1 muls can sometimes happen after SCEV. They resulted in ISel failures because we were missing the patterns for them. * 5.6.0 & 5.6.1 updates for migraphx, miopen-hip, mivisionx * Revert "5.6.0 & 5.6.1 updates for migraphx, miopen-hip, mivisionx" This reverts commit f54c9c6c67a4e5a54859f59d6550eb8e542d6c26. * Revert operator mixup fix * Splitting compiler-rt-linkage-for-host and operator mixup patch * Adding missing patch for reverting operator mixup * 5.6 update for composable-kernel,migraphx,miopen-hip and mivisionx * Updating rvs, rcd and rccl for 5.6.1. adding comment for llvm patch
2023-10-02fix lhapdf package (#37384)Joseph Wang1-0/+9
* fix lhapdf package * [@spackbot] updating style on behalf of joequant --------- Co-authored-by: joequant <joequant@users.noreply.github.com>
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