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Author SHA1 Message Date
nkgh77
8c0d947114 FrontISTR: relax the requirement on Trillinos (#38321) 2023-06-12 15:02:21 +02:00
Thomas Madlener
5ba4a2b83a podio: bump minimal version of catch2 (#38255) 2023-06-12 08:47:48 -04:00
Harmen Stoppels
da45073ef9 buildcache: remove deprecated api (#37246) 
The API was deprecated in v0.20 and is slated for removal in v0.21
 2023-06-12 14:33:26 +02:00
kwryankrattiger
61e17fb36d DaV: Use VTKm for all build configurations of ParaView (#38184) 2023-06-12 14:25:50 +02:00
Wouter Deconinck
9f13a90dd2 superlu: new version 6.0.0 (#38262) 
No changes to build system required. Changelog: https://github.com/xiaoyeli/superlu/compare/v5.3.0...v6.0.0

Since this new version adds "64-bit indexing support", and since at least one dependent package (`armadillo`) requires "32-bit integers" (faa6cbf895), the previous version remains preferred.

* [@spackbot] updating style on behalf of wdconinc

---------

Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
 2023-06-12 14:23:42 +02:00
Juan Miguel Carceller
ef4b35ea63 gaudi: remove the py-qmtest dependency (#38274) 
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
 2023-06-12 14:22:21 +02:00
George Young
66187c8a6e orthofinder: add 2.5.5, add variants (#38298) 
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
 2023-06-12 14:13:15 +02:00
Massimiliano Culpo
c8d95512fc bootstrap: add minimum versions required for flake8 and pytest (#38322) 2023-06-12 12:29:35 +02:00
George Young
c74fa648b9 fastq-screen: add 0.15.3, add variants (#38288) 
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
 2023-06-12 10:37:51 +02:00
snehring
4cc5e9cac6 ltr-retriever 2.9.4 (#38300) 2023-06-12 10:05:44 +02:00
snehring
41345d18f9 perl-libwww-perl: adding perl-clone dependency (#38301) 2023-06-12 10:04:29 +02:00
Alec Scott
0dd1316b68 alglib: add v4.00.0 (#38313) 2023-06-12 09:46:24 +02:00
Alec Scott
d8cc185e22 bismark: add v0.24.1 (#38315) 2023-06-12 09:45:53 +02:00
Alec Scott
061051270c blogbench: add v1.2 (#38316) 2023-06-12 09:45:42 +02:00
Alec Scott
61445159db consul: add v1.15.3 (#38317) 2023-06-12 09:45:30 +02:00
Christopher Christofi
7fa3c7f0fa Fix typo in example code block (#38318) 2023-06-11 22:12:36 -04:00
Manuela Kuhn
9c0fe30f42 py-mypy: add 1.3.0 (#38286) 
* py-mypy: add 1.3.0

* Remove redundant py-typed-ast dependency

* Read python@3.7 dep
 2023-06-11 15:22:55 -04:00
George Young
d00010819f py-deeptools: add 3.5.2, update dependency versions (#38287) 
* py-deeptools: add 3.5.2, update dependency versions

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

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

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

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

* Rearranging dependencies to match setup.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
 2023-06-11 15:17:52 -04:00
Manuela Kuhn
248b05b32a py-jedi: add 0.18.2 (#38177) 
* py-jedi: add 0.18.2

* Add setuptools as run dependency
 2023-06-11 15:12:56 -04:00
dependabot[bot]
8232e934e9 build(deps): bump docker/login-action from 2.1.0 to 2.2.0 (#38241) 
Bumps [docker/login-action](https://github.com/docker/login-action) from 2.1.0 to 2.2.0.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](f4ef78c080...465a07811f)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2023-06-11 13:36:31 -05:00
dependabot[bot]
9d005839af build(deps): bump docker/setup-buildx-action from 2.5.0 to 2.6.0 (#38242) 
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)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 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) 
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)

---
updated-dependencies:
- dependency-name: docker/setup-qemu-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2023-06-11 13:35:42 -05:00
dependabot[bot]
7896625919 build(deps): bump urllib3 from 2.0.2 to 2.0.3 in /lib/spack/docs (#38244) 
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) 
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) 
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)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 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) 
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)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 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) 
* 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) 
* 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) 
* 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) 
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)

---
updated-dependencies:
- dependency-name: actions/checkout
  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>
 2023-06-10 18:45:37 -07:00
Vanessasaurus
c823e01baf Automated deployment to update package flux-core 2023-06-10 (#38308) 
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) 
* Add new podman versions and correct the versions which patch is applied to
* Replace the existing maintainer with alecbcs at maintainers request
develop-2023-06-11 		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) 
* 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) 
* [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) 
* [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)

Spack installed intel compilers already define a g++ for std libs. But in
`icp{c,x}.cfg` instead of the compile line. If we use the pre-defined g++ we not
only have less chance of mixing g++ versions, but also don't need to explicitly
add `gcc` as dependency to `gromacs`.

* Fix format

* Use a variant

As there is no way to check if a file exists at depends_on stage

* Fix format

* New name and fail if variant is used with other compiler

* Line too long.
 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) 
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