Commit Graph

36394 Commits

Author SHA1 Message Date
WuK
0507c3c63d add new CUTLASS versions (#42715) 2024-02-16 09:23:50 -08:00
dependabot[bot]
59caa93571 build(deps): bump dorny/paths-filter from 3.0.0 to 3.0.1 (#42710)
Bumps [dorny/paths-filter](https://github.com/dorny/paths-filter) from 3.0.0 to 3.0.1.
- [Release notes](https://github.com/dorny/paths-filter/releases)
- [Changelog](https://github.com/dorny/paths-filter/blob/master/CHANGELOG.md)
- [Commits](0bc4621a31...ebc4d7e9eb)

---
updated-dependencies:
- dependency-name: dorny/paths-filter
  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>
2024-02-16 09:16:35 -08:00
Arne Becker
b4b53a9a9f perl-datetime-format-iso8601: New package (#42719)
Adds DateTime::Format::ISO8601
2024-02-16 09:15:54 -08:00
Todd Gamblin
be1cfffa45 clingo: add version 5.7.0 (#42707)
5.7.0 was just released. It includes a number of changes requested and/or
upstreamed by Spack developers, e.g.:

* API for accessing optimization priorities: https://github.com/potassco/clingo/pull/406
* Hash optimization: https://github.com/potassco/clingo/pull/441
* Contributing Guide: https://github.com/potassco/clingo/pull/465
* Hiding more ELF symbols:
  * https://github.com/potassco/clingo/pull/447
  * https://github.com/potassco/clingo/pull/449
2024-02-16 18:14:19 +01:00
Victor Lopez Herrero
75b7109222 dlb: add v3.4 (#42722) 2024-02-16 09:13:23 -08:00
Mikael Simberg
c56cf8c0d2 Add support for clang with OpenMP and other minor changes to oneapi build system (#42717)
* Add support for clang in oneapi packages with OpenMP

* Add fallback search for libomp in OneApi package with OpenMP threading

* Add requires for the compiler when using threads=openmp in intel-oneapi-mkl

* Cosmetic changes to messages in oneapi.py

* Update error message in oneapi.py

Co-authored-by: Robert Cohn <rscohn2@gmail.com>

* Update another error message in oneapi.py

Co-authored-by: Robert Cohn <rscohn2@gmail.com>

* Inline helper error function in oneapi.py

* Update one more error message in oneapi.py

* Wrap long line in oneapi.py

---------

Co-authored-by: Robert Cohn <rscohn2@gmail.com>
2024-02-16 11:39:31 -05:00
Robert Cohn
5c3df6e8ca [intel-oneapi-mkl] provide omp lib for threads=openmp (#42653) 2024-02-16 08:48:42 +01:00
Tim Fuller
79087d08d9 allow packages to request no submodules be updated (#40409)
* allow packages to request no submodules be updated when self.submodules is a
  callable function

* Extend the test added in Allow more fine-grained control over what submodules are
  updated: part 2 #27293 to include this case

* Update the type signature for the submodules arg of version() in directives.py

---------

Co-authored-by: tjfulle <tjfulle@users.noreply.github.com>
2024-02-15 22:36:37 -08:00
Victor Brunini
d31e503e5b develop: Add -b/--build-directory option to set build_directory package attribute (#39606)
* develop: Add -b/--build-directory option to set build_directory package attribute.

* Update docs

---------

Co-authored-by: psakievich <psakiev@sandia.gov>
Co-authored-by: vbrunini <vbrunini@users.noreply.github.com>
2024-02-16 06:30:58 +00:00
Eric Berquist
55b62c2168 SST: only run autoreconf for versions from Git branches (#42712) 2024-02-15 22:27:07 -06:00
Scott Wittenburg
6c3511ee1d Fix spack --profile|--pdb <cmd> (#42662) 2024-02-15 15:15:40 -07:00
Seth R. Johnson
d19fa74909 celeritas: new version 0.4.2 (#42702) 2024-02-15 16:41:10 +00:00
Jemma Stachelek
a2ad2d1c9f docs: fix typo (#42688) 2024-02-15 11:21:51 +01:00
Harmen Stoppels
55863bd680 compilers: fixup order of arguments to satisfies (#42682) 2024-02-15 10:21:06 +00:00
Harmen Stoppels
7d4dcd52d9 elpa: fix checksum (#42674) 2024-02-14 11:56:27 +01:00
Henrik Stooss
5e4e72ddd2 veclibfort: explicitly add platform=darwin as requirement (#42664) 2024-02-14 11:18:04 +01:00
John W. Parent
447c48e2fd VTK: limit patches to v8 (#42505)
* VTK: limit patches to v8

* Finer scrope on patch version applicability
2024-02-14 03:36:57 -06:00
Sreenivasa Murthy Kolam
3be4f4db86 Deprecate ROCm 5.1.0 till 5.2.3 (#41794) 2024-02-14 09:03:00 +01:00
John Pennycook
ca97a0fefb cmake: Enable compilation database generation (#42353)
* cmake: Enable CMAKE_EXPORT_COMPILE_COMMANDS

Enabling this option causes CMake to generate a compile_commands.json file
containing a compilation database that can be used to drive third-party tools.

CMAKE_EXPORT_COMPILE_COMMANDS only exists for CMake >= 3.5

Exporting compilation databases is only supported for Makefile and Ninja
generators, so check these conditions as well.

CMAKE_EXPORT_COMPILE_COMMANDS is only enabled in supported configurations
2024-02-13 16:47:40 -07:00
Jon Rood
59f56327fe Remove boost as dependency for trilinos+stk (#39556)
* Remove boost as dependency for trilinos+stk.

* Formatting.

* Put bounds on STK requirement of Boost.
2024-02-13 13:28:25 -07:00
Victor Brunini
e4c871489a boost: Add patch to workaround mpl compiler error with gcc 8.3 and c++17. (#39144)
Works around this issue: https://github.com/boostorg/mpl/issues/44

Co-authored-by: psakievich <psakiev@sandia.gov>
2024-02-13 12:23:13 -07:00
Nichols A. Romero
c048101d90 ELPA package: add patched version from Nov 2023 (#42539) 2024-02-13 10:47:28 -08:00
Alex Richert
e0304bf509 pdt: add aocc support (#42634) 2024-02-13 11:03:46 -07:00
Maciej Wójcik
0e2a9fe26a py-py-tes: add new package (#42531)
* py-py-tes: add new package

* py-py-tes: add constraint on Python
2024-02-13 10:31:11 -07:00
George Young
d1e01d5646 khmer: new package @2.1.1 (#42450)
* khmer: new package @2.1.1

* rationalising patch

* adding dep, modifying patch

* Update var/spack/repos/builtin/packages/khmer/package.py

Indeed!

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

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13 10:02:44 -07:00
George Young
7b04910f84 possvm: new package @1.2 (#42516)
* possvm: new package @1.2

* black!

* appeasing flake8

* Updating commit ID

* Adding graphing dep

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

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

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13 09:49:36 -07:00
Maciej Wójcik
0664a2cdb2 py-pysftp: add new package (#42525)
* py-pysftp: add new package

* py-pysftp: correct version

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13 09:49:14 -07:00
Jeremy Fix
fc38fe1c69 Adds the spack recipe for building the pynpm python package (#42582)
* Adds the spack recipe for building the pynpm python package

* fix license header

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13 09:42:11 -07:00
George Young
29cb1d0ce0 cellpose: new package @2.2.3 (#42403)
* py-fastremap: new package @1.14.1

* py-pyqtgraph: new package @0.13.3

* py-roifile: new package @2024.1.10

* py-superqt: new package @0.6.1

* cellpose: new package @2.2.3

* Appeasing black ...

* Dropping the cuda variant

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

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

* Adding python version dependency

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

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

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

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

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

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

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

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

* Adding missing dep & conflict

* Appeasing black

* Adding missing py- prefix for dep

* Switching over to py-pyqt6

* Switching over to py-pyqt6

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13 10:08:41 -06:00
Dani
ce777e3c89 py-biobb-structure-checking: new package (#42580)
* new builtin package: py-biobb-structure-checking

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

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

* dependencies are also build dependencies

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13 10:05:37 -06:00
Dani
bd44cedd0d new builtin package: py-biobb-io (#42451)
* new builtin package: py-biobb-io

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13 10:03:42 -06:00
Dani
316a9a5d11 py-biobb-gromacs: add new package (#42579)
* new builtin package: py-biobb-gromacs

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

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

* added setuptools dependency

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13 10:03:06 -06:00
Harmen Stoppels
4a04989bbb PythonExtension.add_files_to_view: link non-executable/non-shebang regular files (#42641) 2024-02-13 12:55:37 +01:00
Jordan Ogas
2c4b529896 squashfuse: add versions (#42589) 2024-02-13 09:03:49 +01:00
Henri Menke
e37c099ddb clfft: workaround compiler error (#42519) 2024-02-13 00:10:51 -07:00
George Young
4d7898a669 psipred: new package @4.02 (#42529)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2024-02-12 18:20:33 -08:00
Sreenivasa Murthy Kolam
91b0528abf ROCm packages and dependents: add 6.0.2 release (#42544)
* Bump up the version for rocm-6.0.2 release
* extend the patches that were created for apps for rocm-6.0.0 and rocm-6.0.2 releases
  (but apply hipfft patch for only 6.0.0)
2024-02-12 17:54:33 -08:00
Zack Galbreath
8ee3073350 More updates for GitLab CI memory requests (#42425)
* gitlab: remove requests for unreferenced packages

The packages removed in this commit are not built by any of
our current GitLab CI stacks.

* gitlab: update memory requests for "huge" packages

* gitlab: reduce memory requests for overprovisioned packages

* gitlab: more memory for py-torch (again)

* gitlab: update memory but keep CPU the same
2024-02-12 16:41:56 -06:00
Massimiliano Culpo
cb3c014a43 audit: detect self-referential depends_on (#42456) 2024-02-12 21:56:06 +01:00
Victoria Cherkas
2a01e9679a Adds latest releases of eccodes/eckit/metkit (#42618) 2024-02-12 13:41:15 -07:00
Harmen Stoppels
519deac544 Fix multiple issues with Python in views (#42601)
This fixes bugs, performance issues, and removes no longer necessary code.

Short version:

1. Creating views from Python extensions would error if the Spack `opt` dir itself was in some symlinked directory. Use of `realpath` would expand those, and keying into `merge_map` would fail.
2. Creating views from Python extensions (and Python itself, potentially) could fail if the `bin/` dir contains symlinks pointing outside the package prefix -- Spack keyed into `merge_map[target_of_symlink]` incorrectly.
3. In the `python` package the `remove_files_from_view` function was broken after a breaking API change two years ago (#24355). However, the entire function body was redundant anyways, so solved it by removing it.
4. Notions of "global view" (i.e. python extensions being linked into Python's own prefix instead of into a view) are completely outdated, and removed. It used to be supported but was removed years ago.
5. Views for Python extension would _always_ copy non-symlinks in `./bin/*`, which is a big mistake, since all we care about is rewriting shebangs of scripts; we don't want to copy binaries. Now we first check if the file is executable, and then read two bytes to check if it has a shebang, and only if so, copy the entire file and patch up shebangs.

The bug fixes for (1) and (2) basically consist of getting rid of `realpath` entirely, and instead simply keep track of file identifiers of files that are copied/modified in the view. Only after patching up regular files do we iterate over symlinks and check if they target one of those. If so, retarget it to the modified file in the view.
2024-02-12 19:52:52 +01:00
John Biddiscombe
c33a8dc223 h5hut: fix to work with latest hdf5 (H5_USE_110_API) (#42607) 2024-02-12 04:33:39 -07:00
Richard Berger
742e2fc7e4 caliper: allow newer papi to be used (#42501) 2024-02-12 11:53:57 +01:00
Jean Luca Bez
e90b616428 pdc: add v0.4 (#42508) 2024-02-12 11:52:54 +01:00
Brian Vanderwende
3d037c5150 nco: add v5.1.9 (#42512) 2024-02-12 11:46:07 +01:00
Ivan Maidanski
fd60e97784 bdw-gc: add v8.2.6 (#42524) 2024-02-12 11:38:12 +01:00
Thomas Madlener
c2cda6bc48 lcio: add v2.21 (#42514) 2024-02-12 11:37:10 +01:00
Thomas Madlener
1cd95a4bb7 podio: add 0.99 pre-release version and deprecate all older versions (#42526) 2024-02-12 11:36:30 +01:00
James Beal
727eaf3c82 samtools: add v1.19.2 (#42550)
Co-authored-by: James Beal <jb23@sanger.ac.uk>
2024-02-12 11:09:05 +01:00
Thomas Madlener
d014671bcb edm4hep: add v0.10.5, deprecate broken v0.10.4 (#42561) 2024-02-12 11:01:44 +01:00