Commit graph

35482 commits

Author SHA1 Message Date
Martin Diehl
f550262efb
update damask to 3.0.0-beta (#42259) 2024-01-29 09:33:22 -06:00
Harmen Stoppels
890ec8d71c
traverse: w/o deptype (#42345)
Add the empty deptype `spack.deptypes.NONE`.

Test the case `traverse_nodes(deptype=spack.deptypes.NONE)` to not
traverse dependencies, only de-duplicate.

Use the construct in environment views that otherwise would branch on
whether deps are enabled or not.
2024-01-29 16:31:50 +01:00
dependabot[bot]
62ed5ee318
build(deps): bump codecov/codecov-action from 3.1.4 to 3.1.5 (#42295)
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3.1.4 to 3.1.5.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](eaaf4bedf3...4fe8c5f003)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  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>
2024-01-29 16:27:44 +01:00
Mosè Giordano
0a10ff70bc
openblas: use ARMV8SVE when target supports SVE feature (#42107) 2024-01-29 08:20:32 -07:00
Harmen Stoppels
0718e3459a
filesystem: cleanup (#42342)
Type hints and removal of unused code
2024-01-29 14:43:17 +00:00
Rocco Meli
7ec93a496d
MDAnalysis: add v2.7.0 (#41907)
* ensure umpire~cuda~rocm when ~cuda~rocm

* MDAnalysis: add v2.7.0

* Apply suggestions from code review

* license

* review changes

* add gsd and py-cmake versions

* Update package.py

* py-cmake

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* fix and reorder

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-01-29 08:31:34 -06:00
Brian Vanderwende
2170386ad9
Improve NCL variant support and fix hdf-eos5 issues (#41259) 2024-01-29 15:28:32 +01:00
WuK
6c48effbf5
add py-vl-convert-python (#42073)
* add py-vl-convert-python

* code format

* Update package.py

add homepage

* Update var/spack/repos/builtin/packages/py-vl-convert-python/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* remove old versions, add todo

* Update var/spack/repos/builtin/packages/py-vl-convert-python/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* remove blank line

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-01-29 08:18:42 -06:00
Wouter Deconinck
97e3da0e3e
ncurses: fix 5.9 and 6.0 on modern compilers (#41982) 2024-01-29 15:18:25 +01:00
Alex Leute
d6ff81ab4d
py-metrics: Adding package py-metrics (#42220)
* New package: py-metrics

* [py-metrics] cleaned up extra comment

* Updated copyright and ran black

* py-pathspec: Added version 0.5.5

---------

Co-authored-by: vehrc <vehrc@rit.edu>
Co-authored-by: Jen Herting <jen@herting.cc>
Co-authored-by: Alex C Leute <aclrc@rit.edu>
2024-01-29 08:14:03 -06:00
Sam Grayson
6dfc2e7075
openldap: add findutils build dep (#42159) 2024-01-29 15:06:57 +01:00
Matthias Wolf
80e36d47c2
py-frozendict: patch up for Python 3.11 (#42192)
* py-frozendict: patch up for Python 3.11

See also Marco-Sulla/python-frozendict#68, rely on a pure Python
implementation when 3.11+ is used.

* mention related Github issue
2024-01-29 08:03:46 -06:00
snehring
e1826f89d4
tbl2asn: adding runtime dep libidn (#42171) 2024-01-29 14:59:10 +01:00
kjrstory
23df20fe6d
of-precice: add new versions, update run environment (#40479) 2024-01-29 14:57:16 +01:00
Wouter Deconinck
10ef7a0466
containers: switch to quay.io/almalinuxorg images (#42193) 2024-01-29 14:55:56 +01:00
Alec Scott
7eba7d4028
go: simplify dependency on git to only run (#42208) 2024-01-29 14:49:45 +01:00
Dani
b09d741aed
new builtin package: py-biobb-common (#41993)
* new builtin package: biobb-common

* removed whitespace for the style test

* replaced ' by " for the style test

* changed import line for the style test

* Update var/spack/repos/builtin/packages/biobb-common/package.py

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

* Update var/spack/repos/builtin/packages/biobb-common/package.py

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

* Update var/spack/repos/builtin/packages/biobb-common/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* removed test

* using pypi instead of git

I hope this is declared the right way.
I tried to test it locally but I am having problems with a dependency (openblas) thus I can not even try if this works.

* upgraded version

* Added py prefix

* removed biopython version restriction

* directory with new py-prefixed name

* Delete old non-prefixed package

* Update var/spack/repos/builtin/packages/py-biobb-common/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

---------

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-01-29 13:52:57 +01:00
Sergey Kosukhin
594069961a
netcdf-fortran: fix static linking in some cases (#35466)
* netcdf-fortran: enable building against static netcdf-c

* netcdf-fortran: strip the output of nc-config
2024-01-29 12:53:13 +01:00
Sean Koyama
9eb445f0a2
singularityce: add v3.11.4, v3.11.5 (#42251)
Co-authored-by: Servesh Muralidharan <smuralidharan@anl.gov>
2024-01-29 12:31:39 +01:00
Sean Koyama
e791f61c52
gnuplot: add v5.4.10, v6.0.0 (#42252)
Co-authored-by: Servesh Muralidharan <smuralidharan@anl.gov>
2024-01-29 12:30:47 +01:00
Thomas Madlener
b074e18402
py-jupytext: Add version 1.16 and update dependencies (#41552)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-01-29 12:26:58 +01:00
Alex Seaton
5b6a289d30
Added heyoka and mppp packages (#41839) 2024-01-29 11:03:48 +01:00
Jonathon Anderson
8e9bce44cc
opencl-c-headers: install with CMake (#42173) 2024-01-29 10:47:52 +01:00
Ye Luo
7242238a25
quantum_espresso: relax constrait to allow +openmp ^elpa~openmp (#42322) 2024-01-29 10:41:52 +01:00
Mikael Simberg
ef26ee3f1f
pika: Add 0.22.1 (#42338) 2024-01-29 02:37:56 -07:00
Adam J. Stewart
584ff9933a
py-pandas: add v2.2.0 (#42205) 2024-01-29 03:34:07 -06:00
dependabot[bot]
bb07776606
build(deps): bump black from 23.12.1 to 24.1.0 in /lib/spack/docs (#42328)
Bumps [black](https://github.com/psf/black) from 23.12.1 to 24.1.0.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.12.1...24.1.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2024-01-29 10:28:28 +01:00
Pramod Kumbhar
07df50fbdc
neuron: add new versions and clean-up the recipe (#41931)
* update tarball urls, add new versions and update maintainers
* remove unnecessary variant like cross-compile
* use self.define and self.define_from_variant
* improve regex / bug that matches with -DMPICH_SKIP_MPICXX=1

Co-authored-by: Matthias Wolf <matthias.wolf@epfl.ch>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-01-29 09:46:48 +01:00
Luc Grosheintz
fc731f28cb
highfive: add v2.9.0 (#42337) 2024-01-29 01:43:04 -07:00
Tom Payerle
6474d7ef00
hdf5: Make +subfiling variant depend on +mpi (#42324)
Based on CMakeLists.txt, the subfiling VFD requires a parallel HDF5 build.
So make +subfiling variant depend on +mpi

Should resolve #42323
2024-01-29 09:41:51 +01:00
Jonathon Anderson
0b23bbbbb0
hpctoolkit: update develop and add 2024.01.stable (#42309) 2024-01-29 09:05:02 +01:00
wspear
21406b119c
Update tau 2.33.1 hash (#42336) 2024-01-28 09:44:55 -08:00
Adam J. Stewart
2b51980904
Apply black 2024 style to Spack (#42317) 2024-01-27 16:15:35 +01:00
Robert Cohn
1865e228c4
[intel-oneapi-mkl] workaround linking issue for threads=openmp (#42327) 2024-01-26 22:22:51 -07:00
wspear
179a1e423e
pdt 3.25.2 (#42330)
Add support for -icpx for oneapi
2024-01-26 21:08:19 -07:00
wspear
bd8de5bf2d
Add tau 2.33.1 (#42331) 2024-01-26 20:52:44 -07:00
eugeneswalker
7c8c7eedca
xyce: break blis circularity in depends_on (#42321) 2024-01-26 20:22:55 -07:00
Massimiliano Culpo
8c1957c03e
gnupg: add v2.4.4 (#42320) 2024-01-26 14:33:48 -08:00
eugeneswalker
803ad69eb1
hydrogen@1.5.3: cmake patch with ESCAPE_QUOTES (#42325) 2024-01-26 13:56:16 -08:00
Chris White
29d784e5fa
Axom: Update/merge changes from Axom's repo (#42269)
* update axom package from axom's repo

Co-authored-by: white238 <white238@users.noreply.github.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
2024-01-26 11:08:21 -08:00
Dan LaManna
58b2201710
Stop passing manual AWS credentials to jobs (#42096) 2024-01-26 10:25:37 -07:00
Matthew Thompson
02605d577b
hdf5: fix build error on Apple Clang 15 (#42264) 2024-01-26 18:18:57 +01:00
Adam J. Stewart
42de252c12
py-black: add v24.1.0 (#42316) 2024-01-26 07:48:21 -07:00
m-shunji
6c3c06a571
pexsi: fix to build with fujitsu-ssl2 (#42234)
Co-authored-by: inada-yoshie <inada.yoshie@fujitsu.com>
2024-01-26 11:00:22 +01:00
Harmen Stoppels
6a4573ce5a
julia: patch for system lld and dsymutil (#42282) 2024-01-26 10:30:27 +01:00
Massimiliano Culpo
e77128dfa2
Run config audits in CI, add a new audit to detect wrongly named external specs (#42289) 2024-01-26 10:21:43 +01:00
Massimiliano Culpo
19df8e45ec
Merge virtuals= from duplicate dependencies (#42281)
Previously, for abstract specs like:
```
foo ^[virtuals=a] bar ^[virtuals=b] bar
```
the second requirement was silently discarded on concretization. Now they're merged, and the abstract spec is equivalent to:
```
foo ^[virtuals=a,b] bar
```
2024-01-26 09:48:53 +01:00
eugeneswalker
4c7a1f541c
e4s oneapi: use ghcr spack registry for runner image (#42267) 2024-01-26 02:02:58 +00:00
Daniele Cesarini
295e36efa3
COUNTDOWN package (#42123)
* Added countdown repo
* Added fixed version of COUNTDOWN
* Style fixes
* Changed mantainer syntax
* Variants listed in alphabetical order by name
* Added conflicts and some reordering
* Fixed conflicts syntax
* Style fixes
* [@spackbot] updating style on behalf of danielecesarini

---------

Co-authored-by: danielecesarini <danielecesarini@users.noreply.github.com>
2024-01-25 13:56:29 -08:00
eugeneswalker
3f47cc8d00
e4s neoverse-v2: use ghcr.io/spack image registry (#42268) 2024-01-25 13:45:29 -08:00