Elsa Gonsiorowski, PhD
1711b6dee1
scr: fix @develop dependency versions ( #42379 )
2024-02-05 09:15:19 +01:00
Massimiliano Culpo
7fbd4afaaa
cp2k: fix self-referential dependencies ( #42472 )
2024-02-05 09:12:47 +01:00
Massimiliano Culpo
f396dbcb4f
berkeleygw: fix self-referential dependencies ( #42470 )
...
Also, remove a couple of duplicate directives
2024-02-05 09:04:32 +01:00
David Guibert
57fe3430fd
py-pymummer: init ( #42412 )
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* py-pymummer: init
* Update py-pymummer copyright date
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-04 06:27:46 -07:00
snehring
8428bef040
py-ete3: adding version 3.1.3 ( #42462 )
2024-02-04 06:12:19 -06:00
George Young
47c91c9163
ldsc: new package @2.0.1 ( #42430 )
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2024-02-04 06:06:45 -06:00
David Guibert
6c57360eac
py-pyfastaq: init ( #42413 )
2024-02-04 05:50:44 -06:00
George Young
624292d685
sicer2: new Python package @1.0.3 ( #42383 )
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2024-02-04 05:17:27 -06:00
Mike Renfro
55ecc47dce
fix ipyrad numpy dependencies ( #42098 )
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* fix ipyrad numpy depedencies
ipyrad versions through 0.9.90 use np.int, which is deprecated in numpy 1.20.
* fix whitespace
* Correct numpy dependency restrictions
2024-02-04 05:16:22 -06:00
Massimiliano Culpo
f2125882c5
flecsi: fix constraints on mpi providers ( #42447 )
2024-02-03 12:11:03 +01:00
Massimiliano Culpo
d23cb39a3f
quantum-espresso: fix self-referential dependencies ( #42458 )
2024-02-03 12:09:42 +01:00
Mosè Giordano
7f7d5b899a
py-alphafold: use permanent link for openmm patch ( #42461 )
2024-02-03 11:07:16 +01:00
Harmen Stoppels
c44e854d05
Environment views: dependents before dependencies, resolve identical file conflicts ( #42350 )
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Fix two separate problems:
1. We want to always visit parents before children while creating views
(when it comes to ignoring conflicts, the first instance generated in
the view is chosen, and we want the parent instance to have precedence).
Our preorder traversal does not guarantee that, but our topological-
order traversal does.
2. For copy style views with packages x depending on y, where
<x-prefix>/foo is a symlink to <y-prefix>/foo, we want to guarantee
that:
* A conflict is not registered
* <y-prefix>/foo is chosen (otherwise, the "foo" symlink would become
self-referential if relocated relative to the view root)
Note that
* This is an exception to [1] (in this case the dependency instance
overrides the dependent)
* Prior to this change, if "foo" was ignored as a conflict, it was
possible to create this self-referential symlink
Add tests for each of these cases
2024-02-03 11:05:45 +01:00
John W. Parent
8fa8dbc269
Sqlite package: export api symbols on Windows ( #42299 )
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* Sqlite requires the user to provide a command line arg (DYNAMIC_SHELL)
to export shared symbols to import lib from .def
* Add other options recommended by Sqlite docs:
https://github.com/sqlite/sqlite/blob/master/doc/compile-for-windows.md
* Some of these options mean we can restore variants that were
disabled for Windows (fts, functions, rtree).
2024-02-02 13:27:53 -08:00
jalcaraz
e59303d4ff
tau: update test functions ( #42432 )
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* Updated with generic test functions
* Added level_zero test
As the compiler is not installed by TAU, it should be loaded first and run with --dirty. Will check if there is a way to make it work without --dirty.
* Update var/spack/repos/builtin/packages/tau/package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-02-02 11:12:24 -08:00
Massimiliano Culpo
494d943a24
ascent: fix self-referential dependencies ( #42457 )
2024-02-02 19:25:56 +01:00
kwryankrattiger
d227da5554
CI: Call timing script in after_script ( #42166 )
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The main script body is over-written for power. Putting thet timing
aggregation in the after script allows it to be called on all of the
current pipelines.
2024-02-02 12:02:46 -06:00
Olivier Cessenat
714590426f
astyle: new version 4.1.11 and build using cmake ( #42390 )
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Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-02-02 18:58:27 +01:00
Massimiliano Culpo
9ffe179934
acts: fix self-referential dependencies ( #42455 )
2024-02-02 18:34:34 +01:00
dependabot[bot]
9c4e44a0ad
build(deps): bump codecov/codecov-action from 4.0.0 to 4.0.1 ( #42439 )
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Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action ) from 4.0.0 to 4.0.1.
- [Release notes](https://github.com/codecov/codecov-action/releases )
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md )
- [Commits](f30e4959ba...e0b68c6749
2024-02-02 12:20:29 +01:00
dependabot[bot]
1ef69a8bfb
build(deps): bump python-levenshtein in /lib/spack/docs ( #42440 )
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Bumps [python-levenshtein](https://github.com/rapidfuzz/python-Levenshtein ) from 0.23.0 to 0.24.0.
- [Release notes](https://github.com/rapidfuzz/python-Levenshtein/releases )
- [Changelog](https://github.com/rapidfuzz/python-Levenshtein/blob/main/HISTORY.md )
- [Commits](https://github.com/rapidfuzz/python-Levenshtein/compare/v0.23.0...v0.24.0 )
---
updated-dependencies:
- dependency-name: python-levenshtein
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>
2024-02-02 12:20:02 +01:00
Massimiliano Culpo
55db090206
Extract low-level clingo wrappers from spack.solver.asp ( #42429 )
2024-02-02 12:19:38 +01:00
Matthew Whitlock
f8ce84860c
Update packages_yaml.rst ( #42438 )
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Fix an incorrect example.
2024-02-02 11:05:26 +01:00
Mosè Giordano
795360fe48
openmm: Apply patch use FindCUDAToolkit ( #42437 )
2024-02-02 11:04:03 +01:00
Axel Huebl
3d3d075496
WarpX: Disable CCache ( #42434 )
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https://github.com/ECP-WarpX/WarpX/pull/4637
2024-02-02 11:02:00 +01:00
Frédéric Simonis
35630c219d
preCICE: add v3.0.0 ( #42426 )
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* preCICE: add version 3.0.0
* preCICE: add version conflict for libxml2 2.12.x
2024-02-01 22:56:18 -07:00
stefanfechter
5ef9bb7752
Bugfix: fix build of xforms ( #35391 )
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This additional patch fixes the build of the now unmaintained library
xforms.
2024-02-01 13:07:57 -08:00
kjrstory
5bd5a219a6
Add algorithmic differentiation packages for SU2 ( #39975 )
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* Add algorithmic differentiation packages for SU2
* Simplify checking boolean variants
* spack prefix and spec satisfies methos fix
* spelling fix
* style fix
2024-02-01 13:01:35 -08:00
fpruvost
c1450d26ff
Add new package Qrmumps ( #42393 )
2024-02-01 13:00:14 -08:00
Weiqun Zhang
10d826597a
amrex: add v24.02 ( #42431 )
2024-02-01 12:23:51 -07:00
Adam J. Stewart
00cbcd5dbc
py-lightly: add v1.4.25 ( #42421 )
2024-02-01 11:54:01 -07:00
George Young
6bd8fda597
foldseek: new package @8 ( #42422 )
...
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2024-02-01 11:33:28 -07:00
Rémi Lacroix
8b88255b43
pv: Add version 1.8.5. ( #42419 )
...
Switch to "tar.gz" source packages as the "tar.bz2" archives are not available for newer versions.
2024-02-01 09:54:53 -08:00
Rémi Lacroix
bcbd78cea9
ncdu: Add version 1.19 ( #42420 )
2024-02-01 09:49:57 -08:00
Adam J. Stewart
22ad28bb17
Python: add v3.12.1 ( #42397 )
2024-02-01 07:43:14 -07:00
Alberto Invernizzi
74bd8a9cf7
neovim: be more specific with lua dependencies ( #42401 )
2024-02-01 14:11:49 +01:00
Adam J. Stewart
023a6be67d
Update PyTorch ecosystem ( #42394 )
2024-02-01 06:42:13 -06:00
Harmen Stoppels
922a1983f3
docs: git version section title + highlight issues ( #42398 )
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* basic_usage: section title for git versions
* improve highlighting by using a comment instead of invalid syntax
2024-02-01 09:46:17 +01:00
Massimiliano Culpo
2758fc7e14
Remove caching in generated Dockerfiles ( #42405 )
2024-02-01 09:22:52 +01:00
dependabot[bot]
3541fcae01
build(deps): bump docker/metadata-action from 5.5.0 to 5.5.1 ( #42416 )
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Bumps [docker/metadata-action](https://github.com/docker/metadata-action ) from 5.5.0 to 5.5.1.
- [Release notes](https://github.com/docker/metadata-action/releases )
- [Commits](dbef88086f...8e5442c4ef
2024-02-01 09:14:31 +01:00
dependabot[bot]
eea06de6df
build(deps): bump codecov/codecov-action from 3.1.6 to 4.0.0 ( #42415 )
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Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action ) from 3.1.6 to 4.0.0.
- [Release notes](https://github.com/codecov/codecov-action/releases )
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md )
- [Commits](ab904c41d6...f30e4959ba
2024-02-01 09:13:52 +01:00
Alberto Invernizzi
29658eddcc
Lua: better specify providers in LuaPackage base class ( #42392 )
2024-02-01 08:57:12 +01:00
Tamara Dahlgren
2fc0d05a55
Environments: Add support for including views ( #42250 )
...
* Environments: Add support for including views (take 2)
* schema type hint fixes
2024-02-01 10:07:16 +09:00
Edward Hartnett
faf64f1a26
g2c: add v1.8.0 ( #40761 )
...
includes variant to build with future API for v2
2024-02-01 09:28:55 +09:00
Harmen Stoppels
d340523d68
jq: 1.7.1 ( #42409 )
2024-01-31 15:49:44 -08:00
Dave Sweeris
089fa12ff8
Update OpenSubdiv spec ( #42381 )
...
* Update package.py
Add support for OpenSubdiv 3.5.x
* Fixed Dependencies
I was getting errors about cmake not being able to find `xf86vm`, and adding a dependency on `libxxf86vm` fixes it.
2024-01-31 15:34:47 -08:00
Julius Plehn
d9528819a3
Adds nvhpc 24.1 ( #42388 )
2024-01-31 13:40:33 -08:00
Ben Wibking
e3d5ca2997
visit: set minimum silo version to 4.11 ( #42072 )
2024-01-31 22:05:17 +01:00
Sebastian Grimberg
8fc76ab325
Update recipe for Palace v0.12.0 ( #42400 )
2024-01-31 12:57:03 -08:00
Hector Martinez-Seara
e77678bd82
kim-api: added paths for bash/zsh completion ( #31691 )
...
Co-authored-by: Hector Mtz-Seara <hector@gmail.com>
Co-authored-by: Ryan S. Elliott <relliott@umn.edu>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: hseara <hseara@users.noreply.github.com>
2024-01-31 12:42:59 -07:00
