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2024-02-05converge: fix self-referential dependencies (#42471)Massimiliano Culpo1-11/+3
2024-02-05scr: fix @develop dependency versions (#42379)Elsa Gonsiorowski, PhD1-8/+8
2024-02-05cp2k: fix self-referential dependencies (#42472)Massimiliano Culpo1-8/+7
2024-02-05berkeleygw: fix self-referential dependencies (#42470)Massimiliano Culpo1-4/+2
Also, remove a couple of duplicate directives
2024-02-04py-pymummer: init (#42412)David Guibert1-0/+29
* 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>
2024-02-04py-ete3: adding version 3.1.3 (#42462)snehring1-0/+1
2024-02-04ldsc: new package @2.0.1 (#42430)George Young1-0/+26
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2024-02-04py-pyfastaq: init (#42413)David Guibert1-0/+26
2024-02-04sicer2: new Python package @1.0.3 (#42383)George Young1-0/+21
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2024-02-04fix ipyrad numpy dependencies (#42098)Mike Renfro1-1/+7
* 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
2024-02-03flecsi: fix constraints on mpi providers (#42447)Massimiliano Culpo1-3/+3
2024-02-03quantum-espresso: fix self-referential dependencies (#42458)Massimiliano Culpo1-7/+7
2024-02-03py-alphafold: use permanent link for openmm patch (#42461)Mosè Giordano1-1/+1
2024-02-03Environment views: dependents before dependencies, resolve identical file ↵Harmen Stoppels12-40/+224
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
2024-02-02Sqlite package: export api symbols on Windows (#42299)John W. Parent1-16/+38
* 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).
2024-02-02tau: update test functions (#42432)jalcaraz1-37/+74
* 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>
2024-02-02ascent: fix self-referential dependencies (#42457)Massimiliano Culpo1-32/+34
2024-02-02CI: Call timing script in after_script (#42166)kwryankrattiger1-2/+2
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.
2024-02-02astyle: new version 4.1.11 and build using cmake (#42390)Olivier Cessenat1-6/+27
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-02-02acts: fix self-referential dependencies (#42455)Massimiliano Culpo1-6/+15
2024-02-02build(deps): bump codecov/codecov-action from 4.0.0 to 4.0.1 (#42439)dependabot[bot]3-7/+7
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](https://github.com/codecov/codecov-action/compare/f30e4959ba63075080d4f7f90cacc18d9f3fafd7...e0b68c6749509c5f83f984dd99a76a1c1a231044) --- 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>
2024-02-02build(deps): bump python-levenshtein in /lib/spack/docs (#42440)dependabot[bot]1-1/+1
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>
2024-02-02Extract low-level clingo wrappers from spack.solver.asp (#42429)Massimiliano Culpo2-218/+294
2024-02-02Update packages_yaml.rst (#42438)Matthew Whitlock1-4/+5
Fix an incorrect example.
2024-02-02openmm: Apply patch use `FindCUDAToolkit` (#42437)Mosè Giordano1-1/+10
2024-02-02WarpX: Disable CCache (#42434)Axel Huebl1-0/+4
https://github.com/ECP-WarpX/WarpX/pull/4637
2024-02-01preCICE: add v3.0.0 (#42426)Frédéric Simonis1-0/+2
* preCICE: add version 3.0.0 * preCICE: add version conflict for libxml2 2.12.x
2024-02-01Bugfix: fix build of xforms (#35391)stefanfechter2-0/+67
This additional patch fixes the build of the now unmaintained library xforms.
2024-02-01Add algorithmic differentiation packages for SU2 (#39975)kjrstory4-12/+141
* Add algorithmic differentiation packages for SU2 * Simplify checking boolean variants * spack prefix and spec satisfies methos fix * spelling fix * style fix
2024-02-01Add new package Qrmumps (#42393)fpruvost1-0/+50
2024-02-01amrex: add v24.02 (#42431)Weiqun Zhang1-0/+1
2024-02-01py-lightly: add v1.4.25 (#42421)Adam J. Stewart1-0/+5
2024-02-01foldseek: new package @8 (#42422)George Young1-0/+23
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2024-02-01pv: Add version 1.8.5. (#42419)Rémi Lacroix1-4/+6
Switch to "tar.gz" source packages as the "tar.bz2" archives are not available for newer versions.
2024-02-01ncdu: Add version 1.19 (#42420)Rémi Lacroix1-0/+1
2024-02-01Python: add v3.12.1 (#42397)Adam J. Stewart1-2/+4
2024-02-01neovim: be more specific with lua dependencies (#42401)Alberto Invernizzi4-7/+6
2024-02-01Update PyTorch ecosystem (#42394)Adam J. Stewart5-15/+39
2024-02-01docs: git version section title + highlight issues (#42398)Harmen Stoppels5-10/+14
* basic_usage: section title for git versions * improve highlighting by using a comment instead of invalid syntax
2024-02-01Remove caching in generated Dockerfiles (#42405)Massimiliano Culpo1-2/+0
2024-02-01build(deps): bump docker/metadata-action from 5.5.0 to 5.5.1 (#42416)dependabot[bot]1-1/+1
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](https://github.com/docker/metadata-action/compare/dbef88086f6cef02e264edb7dbf63250c17cef6c...8e5442c4ef9f78752691e2d8f8d19755c6f78e81) --- updated-dependencies: - dependency-name: docker/metadata-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>
2024-02-01build(deps): bump codecov/codecov-action from 3.1.6 to 4.0.0 (#42415)dependabot[bot]3-7/+7
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](https://github.com/codecov/codecov-action/compare/ab904c41d6ece82784817410c45d8b8c02684457...f30e4959ba63075080d4f7f90cacc18d9f3fafd7) --- updated-dependencies: - dependency-name: codecov/codecov-action 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>
2024-02-01Lua: better specify providers in LuaPackage base class (#42392)Alberto Invernizzi1-9/+6
2024-02-01Environments: Add support for including views (#42250)Tamara Dahlgren29-284/+590
* Environments: Add support for including views (take 2) * schema type hint fixes
2024-02-01g2c: add v1.8.0 (#40761)Edward Hartnett1-0/+12
includes variant to build with future API for v2
2024-01-31jq: 1.7.1 (#42409)Harmen Stoppels1-0/+1
2024-01-31Update OpenSubdiv spec (#42381)Dave Sweeris1-0/+3
* 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.
2024-01-31Adds nvhpc 24.1 (#42388)Julius Plehn1-0/+14
2024-01-31visit: set minimum silo version to 4.11 (#42072)Ben Wibking1-1/+2
2024-01-31Update recipe for Palace v0.12.0 (#42400)Sebastian Grimberg1-10/+32
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