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Author SHA1 Message Date
Massimiliano Culpo
928ee7569c ecp-data-vis-sdk: remove self-referential dependencies (#42484) 
This shouldn't be an issue, but express this limitation
with a conflict.
 2024-02-05 15:17:46 +01:00
George Young
8190903821 motioncor2: add v1.6.4 (#42380) 
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
 2024-02-05 14:32:38 +01:00
George Young
473347df41 kentutils: update to @459, update download location & deps (#42448) 
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
 2024-02-05 04:23:33 -07:00
Adam J. Stewart
1ef52d7c8e py-pytest: add v8.0.0 (#42344) 2024-02-05 12:16:58 +01:00
Tom Payerle
561fe13bad cgal: add v5.3.2 (#42378) 2024-02-05 12:08:27 +01:00
George Young
c15ed38cef star: updating to 2.7.11a (#42011) 
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
 2024-02-05 12:06:01 +01:00
David Boehme
fa4568d9c9 kripke: add adiak dependency with Caliper enabled (#42414) 2024-02-05 11:17:24 +01:00
Nathalie Furmento
ef4f78a6cd starpu: add release 1.4.4 (#42446) 2024-02-05 11:12:50 +01:00
Adam J. Stewart
da36d069db py-lightly: fix conflict definition (#42449) 2024-02-05 11:11:23 +01:00
Cameron Rutherford
6ff3e17a7d hiop: require RAJA when cuda is enabled (#42407) 2024-02-05 11:04:08 +01:00
snehring
bb200be57d sentieon-genomics: add new version 202308.02 (#42465) 2024-02-05 11:01:00 +01:00
Olivier Cessenat
a238563fdb mpfr: add v4.2.1 (#42479) 2024-02-05 02:59:22 -07:00
Adam J. Stewart
bfc6f1d2a9 py-lightning: add v2.1.4 (#42468) 2024-02-05 10:59:00 +01:00
Olivier Cessenat
99b8a08366 stripack: sets the licence SPDX (#42473) 2024-02-05 10:45:23 +01:00
Olivier Cessenat
dba5ae939d visit-ffp and visit-unv: sets the licence SPDX (#42474) 2024-02-05 10:42:07 +01:00
Olivier Cessenat
7a4aa823d1 ngspice: new version 42 (#42475) 2024-02-05 10:41:06 +01:00
Olivier Cessenat
89e387cb67 latex2html: new version 2024 (#42476) 2024-02-05 10:38:24 +01:00
Olivier Cessenat
19c46de69f nlopt: new version 2.7.1 (#42477) 2024-02-05 10:27:01 +01:00
Michael Kuhn
e35fbfab77 gtkplus: add v3.24.41 and fix CUPS problems (#42480) 
Fixes #42297
 2024-02-05 10:23:57 +01:00
Massimiliano Culpo
478203dc68 asio: remove self-referential dependencies (#42469) 
These shouldn't be an issue, but they can be expressed
in terms of variants on the package.
 2024-02-05 10:10:58 +01:00
Massimiliano Culpo
5713ffd143 converge: fix self-referential dependencies (#42471) 2024-02-05 10:03:20 +01:00
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) 
* 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) 
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) 
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) 
* 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) develop-2024-02-04 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) 
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) 
* 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) 
* 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) 
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) 
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) 
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)

---
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>
 2024-02-02 12:20:29 +01:00
dependabot[bot]
1ef69a8bfb build(deps): bump python-levenshtein in /lib/spack/docs (#42440) 
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) 
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) 
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) 
* 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) 
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) 
* 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