dependabot[bot]
fb43cb8166
build(deps): bump sphinx-rtd-theme in /lib/spack/docs ( #38245 )
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Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme ) from 1.2.1 to 1.2.2.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst )
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.2.1...1.2.2 )
---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
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>
2023-06-11 13:35:03 -05:00
dependabot[bot]
28f68e5d11
build(deps): bump docker/build-push-action from 4.0.0 to 4.1.0 ( #38306 )
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Bumps [docker/build-push-action](https://github.com/docker/build-push-action ) from 4.0.0 to 4.1.0.
- [Release notes](https://github.com/docker/build-push-action/releases )
- [Commits](3b5e8027fc...44ea916f6c
2023-06-11 13:34:44 -05:00
dependabot[bot]
1199eeed0b
build(deps): bump docker/build-push-action from 4.0.0 to 4.1.0 ( #38306 )
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Bumps [docker/build-push-action](https://github.com/docker/build-push-action ) from 4.0.0 to 4.1.0.
- [Release notes](https://github.com/docker/build-push-action/releases )
- [Commits](3b5e8027fc...44ea916f6c
2023-06-11 13:34:33 -05:00
Manuela Kuhn
8ffeb4900b
py-multidict: add 6.0.4 ( #38284 )
2023-06-11 12:03:21 -05:00
Manuela Kuhn
456550da3f
py-mne: add 1.4.2 ( #38228 )
2023-06-11 11:52:01 -05:00
Olivier Cessenat
b2676fe2dd
Gxsview new version 2023.05.29 ( #38310 )
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* netpbm: new version 10.73.43
* gxsview: new version 2023.05.29
2023-06-11 09:48:04 -07:00
Jen Herting
8561ec6249
[py-spacy-legacy] New package ( #38276 )
2023-06-11 11:45:23 -05:00
Jen Herting
5b775d82ac
[py-spacy-loggers] new package ( #38275 )
2023-06-11 11:44:19 -05:00
Jen Herting
b43088cc16
[py-langcodes] new package ( #38273 )
2023-06-11 11:43:16 -05:00
Manuela Kuhn
237eab136a
py-nbclassic: add 1.0.0 and py-notebook-shim: add 0.2.3 ( #38289 )
2023-06-11 11:36:38 -05:00
Marie Houillon
ffffa2794b
New version for openCARP packages, v13.0 ( #37940 )
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* New version for openCARP packages
* Update carputils dependencies
* Update types of openCARP dependencies
* Add type "run" to setuptools dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add package py-common as carputils dependency
* Add setuptools dependency for py-common
* Remove spaces on blank line
* Restrict type of dependency setuptools to "build"
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: openCARP consortium <info@opencarp.org>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-11 11:25:41 -05:00
George Young
433b44403f
py-pybktree: new package ( #38209 )
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* py-pykbtree: new package
* py-pybktree: new package
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-11 11:16:33 -05:00
Manuela Kuhn
fa2e1c0653
py-pandas: exchange import_modules with skip_modules ( #38227 )
2023-06-11 11:14:56 -05:00
Manuela Kuhn
00257f6824
py-more-itertools: add 9.1.0 ( #38229 )
2023-06-11 11:14:43 -05:00
kjrstory
3b8366f3d3
slurm: add new version(23.02.2, 22.05.9) ( #38285 )
2023-06-10 18:48:48 -07:00
dependabot[bot]
a73f511404
build(deps): bump actions/checkout from 3.5.2 to 3.5.3 ( #38305 )
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Bumps [actions/checkout](https://github.com/actions/checkout ) from 3.5.2 to 3.5.3.
- [Release notes](https://github.com/actions/checkout/releases )
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md )
- [Commits](8e5e7e5ab8...c85c95e3d7
2023-06-10 18:45:37 -07:00
Vanessasaurus
c823e01baf
Automated deployment to update package flux-core 2023-06-10 ( #38308 )
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Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-06-10 18:30:10 -07:00
Carson Woods
4188080899
Add new Podman package versions and fix patch ( #38234 )
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* Add new podman versions and correct the versions which patch is applied to
* Replace the existing maintainer with alecbcs at maintainers request
2023-06-10 20:40:58 +02:00
Fabien Bruneval
ef6ea2c93f
correct SHA for ABINIT 9.8.3 and add ABINIT 9.8.4 ( #38283 )
2023-06-09 12:24:28 -07:00
Greg Becker
3c672905d0
install status arg: update to default true and add inverse ( #38252 )
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* install status arg: update to default true and add inverse
* update bash completion
* fix tests broken by output change
2023-06-09 10:38:05 -07:00
Jen Herting
ee106c747f
[py-typer] new package ( #38270 )
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* [py-typer] new package
* [py-typer] added version 0.7.0
2023-06-09 12:10:09 -05:00
Jen Herting
295726e6b8
[py-catalogue] added version 2.0.8 ( #38266 )
2023-06-09 12:01:04 -05:00
afzpatel
2654d64a3c
comgr: enable testing ( #35605 )
2023-06-09 18:04:19 +02:00
Stephen Sachs
d91ec8500f
[gromacs] Fix intel (classic) libstdc++ path ( #37822 )
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* [gromacs] Fix intel (classic) libstdc++ path
Gromacs's `cmake` run will look for `--gcc-toolchain` (e.g. LLVM, icpx) or
`--gcc-name` (e.g. icpc) in `CMAKE_CXX_FLAGS`. Only if it does not find a good
g++ candidate there it will look for `GMX_GPLUSPLUS_PATH`:
cb6b311c39/cmake/FindLibStdCpp.cmake (L97)
2023-06-09 09:17:49 -04:00
Jonathon Anderson
c354cc51d0
containerize: use an ENTRYPOINT script ( #37769 )
2023-06-09 09:25:13 +02:00
Massimiliano Culpo
d5747a61e7
Hotfix to avoid building compilers from sources in pcluster pipelines ( #38256 )
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The pcluster image has am internal buildcache without an index.
Also, we need to force reuse to avoid rebuilding GCC, since the default is
to only reuse dependencies - and that is subject to changes in the GCC
recipe.
2023-06-09 07:56:28 +02:00
Chris White
e88c747abc
BLT package: add version 0.5.3 ( #38247 )
2023-06-09 00:36:00 -04:00
Martin Pokorny
cfe9e5bca4
glab: add new versions ( #38236 )
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* glab: add new versions
* Update var/spack/repos/builtin/packages/glab/package.py
Co-authored-by: Alec Scott <alec@bcs.sh>
---------
Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-08 20:36:16 -07:00
Manuela Kuhn
48f7655a62
py-mako: add 1.2.4 ( #38194 )
2023-06-08 19:10:02 -04:00
Manuela Kuhn
a1111a9858
py-lxml: add 4.9.2 ( #38191 )
2023-06-08 19:09:41 -04:00
Manuela Kuhn
b8b9a798bf
py-looseversion: add 1.2.0 ( #38190 )
2023-06-08 19:03:05 -04:00
Manuela Kuhn
7a1e94c775
py-msgpack: add 1.0.5 ( #38230 )
2023-06-08 18:02:42 -04:00
Manuela Kuhn
8c4b2173d2
py-mistune: add 2.0.5 ( #38214 )
2023-06-08 17:43:51 -04:00
George Young
4c4cd7b3ea
py-llvmlite: add 0.40.0, update llvm dependency information ( #38171 )
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* py-llvmlite: add 0.40.0, update llvm dependency information
* Update var/spack/repos/builtin/packages/py-llvmlite/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/py-llvmlite/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/py-llvmlite/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/py-llvmlite/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-08 16:10:48 -05:00
George Young
e92554414b
gatk: add 4.4, update to java@17 ( #38211 )
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 16:01:56 -04:00
George Young
d165e2c94b
bowtie2: add 2.5.1 ( #38201 )
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 16:01:34 -04:00
George Young
a97bd31afe
trimgalore: add 0.6.10, adding variants ( #38206 )
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 15:55:03 -04:00
George Young
d7719b26f9
seqtk: add 1.4 ( #38193 )
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 15:48:54 -04:00
Manuela Kuhn
855c0fd9e0
py-markupsafe: add 2.1.3 ( #38198 )
2023-06-08 15:37:26 -04:00
Daniele Cesarini
4156397027
New packages: eprosima-fastdds and dependencies ( #38079 )
2023-06-08 12:27:06 -07:00
Juan Miguel Carceller
b4bbe5e305
ocaml: don't use the spack compiler ( #38251 )
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Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-06-08 12:17:29 -07:00
Adam J. Stewart
f5b595071e
py-lightning: add v2.0.3 ( #38260 )
2023-06-08 15:14:28 -04:00
George Young
b6f2184cce
bedtools2: patching to build with gcc@13 ( #38254 )
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* bedtools2: patching to build with gcc@13
* bedtools2: patching to build with gcc@13
* Update var/spack/repos/builtin/packages/bedtools2/package.py
Yep, sure. Makes sense.
Co-authored-by: Alec Scott <alec@bcs.sh>
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-08 14:59:01 -04:00
Axel Huebl
9288067380
Mold: 1.11.0 ( #38235 )
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* Mold: 1.11.0
Add the latest release of the `mold` linker.
* SHA for 1.7.1: zip to tar
2023-06-08 11:34:57 -07:00
Massimiliano Culpo
ddfc43be96
Forbid using env: as a top level environment attribute ( #38199 )
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* Remove "env" from environment schema
* Remove spack.env.schema.keys
* Remove spack.environment.config_dict
2023-06-08 14:34:17 -04:00
Adam J. Stewart
63cad5d338
py-lightly: add v1.4.7 ( #38259 )
2023-06-08 14:04:16 -04:00
Ivan Maidanski
436ecdfb19
bdw-gc: add v8.2.4 ( #37969 )
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* bdw-gc: add v8.2.4
* bdw-gc: Fix download URL for old package versions
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2023-06-08 14:03:57 -04:00
John W. Parent
06817600e4
CMake/Windows bugfix: Make CMAKE_INSTALL_PREFIX a posix path ( #36842 )
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CMake gives off a warning when passed Windows style paths as
install prefixes as the resultant path often causes invalid
escape sequences.
2023-06-08 10:05:38 -07:00
Wouter Deconinck
4ae1a73d54
(r-rcpp)ensmallen: new package ( #38249 )
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* ensmallen: new package
ensmallen is a high-quality C++ library for non-linear numerical optimization.
* r-rcppensmallen: new package
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-06-08 09:53:02 -07:00
Massimiliano Culpo
f29aab0d03
Fix compiler removal from command line ( #38057 )
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* Improve lib/spack/spack/test/cmd/compiler.py
* Use "tmp_path" in the "mock_executable" fixture
* Return a pathlib.Path from mock_executable
* Fix mock_executable fixture on Windows
"mock_gcc" was very similar to mock_executable, so use the latter to reduce code duplication
* Remove wrong compiler cache, fix compiler removal
fixes #37996
_CACHE_CONFIG_FILES was both unneeded and wrong, if called
subsequently with different scopes.
Here we remove that cache, and we fix an issue with compiler
removal triggered by having the same compiler spec in multiple
scopes.
2023-06-08 09:38:20 -07:00
