dependabot[bot]
9d005839af
build(deps): bump docker/setup-buildx-action from 2.5.0 to 2.6.0 ( #38242 )
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Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action ) from 2.5.0 to 2.6.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases )
- [Commits](4b4e9c3e2d...6a58db7e0d
2023-06-11 13:36:02 -05:00
dependabot[bot]
a7e5c73608
build(deps): bump docker/setup-qemu-action from 2.1.0 to 2.2.0 ( #38243 )
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Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action ) from 2.1.0 to 2.2.0.
- [Release notes](https://github.com/docker/setup-qemu-action/releases )
- [Commits](e81a89b173...2b82ce82d5
2023-06-11 13:35:42 -05:00
dependabot[bot]
7896625919
build(deps): bump urllib3 from 2.0.2 to 2.0.3 in /lib/spack/docs ( #38244 )
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Bumps [urllib3](https://github.com/urllib3/urllib3 ) from 2.0.2 to 2.0.3.
- [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/2.0.2...2.0.3 )
---
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>
2023-06-11 13:35:22 -05:00
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
