Commit graph

31796 commits

Author SHA1 Message Date
Wouter Deconinck
4ae1a73d54
(r-rcpp)ensmallen: new package (#38249)
* 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)
* 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)
* 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)
* 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)
* `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)
* `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
Dan Lipsa
79656655ba
Guard for define in netcdf 4.9.0 and later. (#37853)
* Guard for define in netcdf 4.9.0 and later.

This code is already available in ParaView 5.11.0 so no patching
needed there.

* Add latest needed version (even if not in spack).

---------

Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
2023-06-07 14:20:27 -05:00
Sajid Ali
74921788a8
llvm: add new versions and set default for libomptarget according to os (#38092)
* llvm: add new versions and set default for libomptarget according to os

	modified:   var/spack/repos/builtin/packages/llvm/package.py

* Incorporate reviewer suggestions

Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>

---------

Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
2023-06-07 10:55:46 -05:00
Carlos Bederián
b313b28e64
nwchem: remove -mtune=native flags (#37892)
Co-authored-by: Edoardo Aprà <edoardo.apra@gmail.com>
2023-06-07 09:02:35 +02:00
eugeneswalker
5f1bc15e80
E4S Cray CI Stack (#37837)
* e4s cray ci stack

* e4s ci: add cray

* add zen4 tag

* WIP: new defintions just for cray

* updates

* remove ci signing job overrride, not necessary

* echo $PATH and show modules loaded

* add mirror

* add external def for cray-libsci

* comment out quantum-espresso

* use /etc/protected-runner as key path

* cray ci stack: do not remove tags: [spack, public]

* make cray stack composable

* generate job should run on public tagged runner, override default config:install_tree:root

* CI: Use relative path in default script

* CI: Use relative includes paths for shell runners

* Use concrete_env_dir for relpath

* ml-darwin-aarch64-mps: jax has bazel codesign issue

---------

Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
2023-06-06 18:41:32 -07:00
Mikael Simberg
fa9fb60df3
CachedCMakePackage: fix bug where CMAKE_CUDA_ARCHITECTURES=none is set (#38169)
#37592 updated cached cmake packages to set CMAKE_CUDA_ARCHITECTURES.
The condition `if archs != "none"` lead to `CMAKE_CUDA_ARCHITECTURES=none`
when cuda_arch=none (incorrect check on the value of a multi-valued
variant), i.e. CMAKE_CUDA_ARCHITECTURES is always set. This PR udpates
the condition to if archs[0] != "none" to ensure CMAKE_CUDA_ARCHITECTURES
is only set if cuda_arch is not none (which seems to be the pattern used
in other packages).

This does the same for HIP (although in general ROCmPackage disallows
amdgpu_target=none when +rocm).
2023-06-06 14:41:02 -07:00
Mosè Giordano
e759e6c410
julia: Update patch for llvm 14 without binary files (#37959) 2023-06-06 21:53:20 +02:00
Jonathon Anderson
f41446258a
containers: don't install epel-release on Fedora (#37766) 2023-06-06 21:50:46 +02:00
Erik Schnetter
268649654d
openssl: add versions 1.1.1u, 3.0.9, 3.1.1 (#38023) 2023-06-06 21:49:01 +02:00
Diego Alvarez S
12e249f64e
Add nextflow 23.04.1 (#38166) 2023-06-06 12:12:50 -07:00
Tamara Dahlgren
c34cd76f2a
perl: convert to new stand-alone test process (#37727) 2023-06-06 12:07:44 -07:00
Tamara Dahlgren
815b210fc8
tests/ginkgo: converted to new stand-alone test process (#35730)
* Ginkgo: converted to new stand-alone test process

* ginkgo: update string formatting, compiler setting
2023-06-06 11:58:53 -07:00
Tamara Dahlgren
e5d5efb4c1
tests/darshan-util: convert to new stand-alone test process (#37836) 2023-06-06 11:56:40 -07:00
Tamara Dahlgren
0aa4b4d990
tests/oommf: convert to new stand-alone test process (#38009)
* oommf: convert to new stand-alone test process

* oommf: Switch build-time tests to documented approach
2023-06-06 11:55:33 -07:00
Tamara Dahlgren
01c1d334ae
tests/mfem: convert to new stand-alone test process (#38011)
* mfem: convert to new stand-alone test process
* Restore make target, use config_mk property
2023-06-06 11:42:51 -07:00
Massimiliano Culpo
717fc11a46
Don't build rocky:9 images for ppc64le (#38202)
See https://docs.rockylinux.org/release_notes/9_2/
2023-06-06 17:46:53 +02:00
eugeneswalker
d21c49e329
@develop+stokhos: do not set Stokhos_ENABLE_PCE_Scalar_Type=False (#38187) 2023-06-06 08:32:21 -07:00
Tamara Dahlgren
6937d9dddc
eigenexa: convert to new stand-alone test process (#35745) 2023-06-06 15:08:51 +02:00
Thomas Bouvier
4c2531d5fb
libraqm: add missing fribidi dependency (#36125)
* `libraqm`: add missing `fribidi` dependency
* `libraqm`: add `sheenbidi` variant
* [@spackbot] updating style on behalf of thomas-bouvier

---------

Co-authored-by: thomas-bouvier <thomas-bouvier@users.noreply.github.com>
2023-06-05 18:13:42 -04:00
Alex Richert
62fd890c52
Rename fpic variant to pic for fms (#38101) 2023-06-05 14:58:52 -07:00
Alex Richert
4772fd7723
Add MADIS package (#38097)
* Add MADIS package
* madis update
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
* allow arg mismatch for gcc@10: for madis
2023-06-05 14:31:51 -07:00
snehring
7c11faceb0
ninja-phylogeny: adding new package ninja-phylogeny (#38182) 2023-06-05 16:44:51 -04:00
Alec Scott
053550e28a
asdcplib: add v2_10_38 (#37971) 2023-06-05 12:46:19 -07:00
Alec Scott
3ed7258447
fjcontrib: add v1.052 (#38116) 2023-06-05 14:25:30 -05:00
Manuela Kuhn
a5cf5baa9e
py-jupyterlab: add 4.0.1 incl. new dependencies (#38102) 2023-06-05 13:54:20 -05:00
Alec Scott
ec8039cc74
seal: add v4.1.1 (#38155) 2023-06-05 11:46:40 -07:00
snehring
9bfa840c27
ncbi-rmblastn: adding new version 2.14.0 (#38173)
* ncbi-rmblastn: adding new version 2.14.0
* ncbi-rmblastn: add maintainer
2023-06-05 11:45:15 -07:00
Alec Scott
9865f42335
azcopy: add v10.19.0 (#38106) 2023-06-05 10:56:34 -07:00
Alec Scott
dba2829871
hssp: add v3.1.5 (#38107) 2023-06-05 10:51:30 -07:00
Alec Scott
8c0e1fbed9
diamond: add v2.1.7 (#38115) 2023-06-05 10:46:39 -07:00
Alec Scott
187488b75b
optional-lite: add v3.5.0 (#38148) 2023-06-05 10:24:37 -07:00