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2023-06-15Remove experimental hdf5 versions 1.13.x and add hdf5 version 1.10.10. (#38013)Larry Knox5-12/+8
* Remove experimental hdf5 versions 1.13.x. Upgrade to 1.14 or remove dependencies on hdf5 1.13.x. * Revert change to netcdf-c/package.py.
2023-06-15star: add 2.7.10 (#38197)George Young1-4/+15
* star: add 2.7.10 * star: fix building for non-avx2 arch processors * convert to MakefilePackage, second take at fixing for aarch64 * style --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-15perl-gd: update to 2.77, update urls (#38413)George Young1-1/+9
* perl-gd: update to 2.77, update urls --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-15Enable build system guess tests on windows (#36971)markus-ferrell2-5/+1
2023-06-15MXNet: fix flag versions (#38402)Adam J. Stewart1-2/+2
2023-06-15Windows testing: enable graph, mark, and info cmd tests (#36977)markus-ferrell3-11/+0
2023-06-15Create package.py file for NIMROD abstract accelerated infrastructure. (#38405)Jacob King1-0/+58
Co-authored-by: jacobrking <jacobrking@users.noreply.github.com>
2023-06-15py-nibabel: add 5.1.0 (#38379)Manuela Kuhn1-2/+12
2023-06-15podio: Add py-tabulate as new run and test dependency (#38409)Thomas Madlener1-0/+1
2023-06-15py-numba: add 0.57.0, update dependency ranges (#38390)George Young1-5/+7
* py-numba: add 0.57.0, update dependency ranges * Update var/spack/repos/builtin/packages/py-numba/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * Update var/spack/repos/builtin/packages/py-numba/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * Update package.py --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-06-15py-datalad: add 0.18.4 (#37936)Manuela Kuhn1-1/+3
2023-06-15tests/py-horovod: convert to new stand-alone test process (#38366)Tamara Dahlgren1-3/+4
2023-06-15tests/py-libensemble: convert to new stand-alone test process (#38344)Tamara Dahlgren1-20/+16
2023-06-15tests/py-eccodes: convert to new stand-alone test process (#38346)Tamara Dahlgren1-9/+4
2023-06-15py-neurora: add 1.1.6.10 (#38378)Manuela Kuhn1-0/+1
2023-06-15Add virtual information on DAG edges (#34821)Massimiliano Culpo18-136/+290
* DependencySpec: add virtuals attribute on edges This works for both the new and the old concretizer. Also, added type hints to involved functions. * Improve virtual reconstruction from old format * Reconstruct virtuals when reading from Cray manifest * Reconstruct virtual information on test dependencies
2023-06-14test/dust: convert to new stand-alone test process (#38367)Tamara Dahlgren1-9/+5
2023-06-14py-nbclient: add 0.8.0 (#38325)Manuela Kuhn1-1/+3
2023-06-14py-nbconvert: add 7.4.0 (#38326)Manuela Kuhn1-19/+20
* py-nbconvert: add 7.4.0 * Move historical dependencies after variant
2023-06-14py-docutils: re-add python@3.7 (#38336)Manuela Kuhn1-0/+1
2023-06-14magma@master: add python dependency (#38341)Satish Balay1-0/+1
2023-06-14edm4hep: Add version 0.9 (#38205)Thomas Madlener1-0/+1
2023-06-14fairmq: Add v1.6.0 (#38392)Dennis Klein1-0/+7
2023-06-14ltp: add v20230516 (#38138)Alec Scott1-0/+1
2023-06-14subread: add 2.0.6, update download paths (#38200)George Young1-4/+4
* subread: add 2.0.6, update download paths * Update var/spack/repos/builtin/packages/subread/package.py --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-06-14openradioss-starter,engine: new package (#38291)kjrstory2-0/+256
* openradioss-starter,engine: new package * openradioss-engine: change version name develop to main * openradioss-starter: change version name develop to main
2023-06-14freeipmi: add v1.6.9 (#38349)Alec Scott1-0/+1
2023-06-14Add Binder spackage (#38371)Kim Liegeois1-0/+54
* Add Binder spackage * Format binder recipe * Format binder recipe
2023-06-14add bioconductor-ebseq (#38380)pabloaledo1-0/+29
* add buiconductor-ebseq Signed-off-by: Pablo <pablo.aledo@seqera.io> --------- Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-06-14ctffind: Add a patch to fix incorrect return types. (#38085)Rémi Lacroix2-0/+35
Prevent the code from crashing (cf. https://grigoriefflab.umassmed.edu/comment/1696#comment-1696).
2023-06-14dsqss: convert to new stand-alone test process (#38372)Tamara Dahlgren1-6/+15
2023-06-14lastz: add v1.04.22 (#38388)Alec Scott1-0/+2
* lastz: add v1.04.22 * Fix formatting of versions to include extra space
2023-06-14ipopt: add v3.14.9 (#38387)Alec Scott1-0/+1
2023-06-14imath: add v3.1.9 (#38386)Alec Scott1-0/+1
2023-06-14imagemagick: add v7.1.1-11 (#38385)Alec Scott1-0/+1
2023-06-14cgal: add v5.5.2 (#38384)Alec Scott1-0/+1
2023-06-14intel-xed: add version 2023.06.07 (#38373)Mark W. Krentel1-1/+2
Add version 2023.06.07, update python to 3.7.
2023-06-14hpcviewer: add version 2023.05 (#38374)Mark W. Krentel1-0/+5
2023-06-14cloc: add v1.96.1 (#38348)Alec Scott1-0/+1
2023-06-14DaV: Drop propagation of HDF5 to darshan (#38361)kwryankrattiger1-1/+1
Darshan Runtime does not properly link symols for HDF5 when using shared libraries.
2023-06-14hbase: add v2.5.4 (#38353)Alec Scott1-0/+1
2023-06-14fzf: add v0.41.1 (#38351)Alec Scott1-0/+1
2023-06-14hashcat: add v6.2.6 (#38352)Alec Scott1-0/+1
2023-06-14hyperfine: add v1.17.0 (#38354)Alec Scott1-0/+1
2023-06-14ftxui: add v4.1.1 (#38350)Alec Scott1-0/+1
2023-06-14Repeatmodeler 2.0.4 (#38337)snehring2-31/+69
* perl-devel-size: adding new package * repeatmodeler: adding new version 2.0.4 * perl-devel-size: adding proper description
2023-06-14dssp: convert to new stand-alone test process (#38368)Tamara Dahlgren1-10/+6
2023-06-14modules: use depends-on to autoload module with Lmod on Tcl (#38347)Xavier Delaruelle2-1/+36
Update Tcl modulefile template to use the `depends-on` command to autoload modules if Lmod is the current module tool. Autoloading modules with `module load` command in Tcl modulefile does not work well for Lmod at some extend. An attempt to unload then load designated module is performed each time such command is encountered. It may lead to a load storm that may not end correctly with large number of module dependencies. `depends-on` command should be used for Lmod instead of `module load`, as it checks if module is already loaded, and does not attempt to reload this module. Lua modulefile template already uses `depends_on` command to autoload dependencies. Thus it is already considered that to use Lmod with Spack, it must support `depends_on` command (version 7.6+). Environment Modules copes well with `module load` command to autoload dependencies (version 3.2+). `depends-on` command is supported starting version 5.1 (as an alias of `prereq-all` command) which was relased last year. This change introduces a test to determine if current module tool that evaluates modulefile is Lmod. If so, autoload dependencies are defined with `depends-on` command. Otherwise `module load` command is used. Test is based on `LMOD_VERSION_MAJOR` environment variable, which is set by Lmod starting version 5.1. Fixes #36764
2023-06-14build(deps): bump python-levenshtein in /lib/spack/docs (#38339)dependabot[bot]1-1/+1
Bumps [python-levenshtein](https://github.com/maxbachmann/python-Levenshtein) from 0.21.0 to 0.21.1. - [Release notes](https://github.com/maxbachmann/python-Levenshtein/releases) - [Changelog](https://github.com/maxbachmann/python-Levenshtein/blob/main/HISTORY.md) - [Commits](https://github.com/maxbachmann/python-Levenshtein/compare/v0.21.0...v0.21.1) --- updated-dependencies: - dependency-name: python-levenshtein 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>
2023-06-14build(deps): bump docker/build-push-action from 4.1.0 to 4.1.1 (#38369)dependabot[bot]1-1/+1
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.1.0 to 4.1.1. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/44ea916f6c540f9302d50c2b1e5a8dc071f15cdf...2eb1c1961a95fc15694676618e422e8ba1d63825) --- updated-dependencies: - dependency-name: docker/build-push-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>
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