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 )
...
* 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 )
...
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 )
...
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 )
...
* 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
eugeneswalker
cea1b3123e
e4s oneapi ci: use official intel oneapi-derived runner image ( #38176 )
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* e4s oneapi ci: use official intel oneapi-derived runner image
* update oneapi image
* tau builds ok, but only with libdrm - comment out for now, follow up with pr later
2023-06-08 09:17:22 -07:00
Alec Scott
b22ccf279d
junit4: add v4.13.2 ( #38122 )
2023-06-08 11:54:09 -04:00
Wouter Deconinck
81e15ce36e
(r-rcpp)armadillo: new version 12.4.0 ( #38246 )
...
* armadillo: new version 12.4.0
No build system changes necessary, https://gitlab.com/conradsnicta/armadillo-code/-/compare/12.2.x...12.4.x
* r-rcpparmadillo: new version 0.12.4.0.0
2023-06-08 11:49:17 -04:00
George Young
8907e52933
bismark: add 0.24.1, add HISAT2 dependency ( #38210 )
...
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 11:49:00 -04:00
Carlos Bederián
80cefedac5
quantum-espresso: add 7.2 ( #38223 )
2023-06-08 11:23:54 -04:00
Seth R. Johnson
b85a66f77a
trilinos: drop preferred version ( #38086 )
2023-06-08 11:18:44 -04:00
Alec Scott
a0ba3d890a
cni-plugins: add v1.3.0 ( #38064 )
2023-06-08 10:27:20 +02:00
Manuela Kuhn
315873cbd3
py-keyring: add 23.13.1 ( #38183 )
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* py-keyring: add 23.13.1
* [@spackbot] updating style on behalf of manuelakuhn
2023-06-07 23:00:05 -05:00
Thomas Bouvier
e05095af90
py-nvidia-dali: update versions up to v1.26.0 (#38022 )
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* `py-nvidia-dali`: update versions up to v1.26.0
* Add proper `cuda` dependency version
2023-06-07 22:52:52 -05:00
Thomas Bouvier
e0d6a73f96
py-horovod: add versions v0.27.0 and v0.28.0 (#38016 )
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* `py-horovod`: add versions v0.27.0 and v0.28.0
* fix: typo
* Add upper version bound for `py-pyarrow`
2023-06-07 22:51:19 -05:00
Manuela Kuhn
6ebfb41ad9
py-json5: add 0.9.14 ( #38178 )
2023-06-07 22:16:28 -05:00
Manuela Kuhn
d0aa01c807
py-jaraco-classes: add 3.2.3 ( #38167 )
2023-06-07 21:48:58 -05:00
Manuela Kuhn
1265c7df47
py-jupyter-client: add 8.2.0 ( #38180 )
2023-06-07 21:48:12 -05:00
Alec Scott
91e3f14959
hbase: add v2.5.3 ( #38073 )
2023-06-07 18:11:21 -07:00
Alec Scott
5f03eb650d
chemfiles: add v0.10.4 ( #38063 )
2023-06-07 18:05:37 -07:00
Martin Pokorny
e0e6133444
casacore: add v3.5.0 ( #37806 )
2023-06-07 23:12:08 +02:00
Nate deVelder
ee68baf254
OpenFAST: add v3.3.0, v3.4.0 and v3.4.1 ( #37407 )
2023-06-07 23:10:39 +02:00
Christopher Kotfila
785c1a2070
Add documentation about package signing model ( #30939 )
...
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-07 23:05:44 +02:00
