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2023-06-12podio: bump minimal version of catch2 (#38255)Thomas Madlener1-1/+2
2023-06-12buildcache: remove deprecated api (#37246)Harmen Stoppels11-353/+72
The API was deprecated in v0.20 and is slated for removal in v0.21
2023-06-12DaV: Use VTKm for all build configurations of ParaView (#38184)kwryankrattiger1-1/+2
2023-06-12superlu: new version 6.0.0 (#38262)Wouter Deconinck1-1/+6
No changes to build system required. Changelog: https://github.com/xiaoyeli/superlu/compare/v5.3.0...v6.0.0 Since this new version adds "64-bit indexing support", and since at least one dependent package (`armadillo`) requires "32-bit integers" (https://gitlab.com/conradsnicta/armadillo-code/-/commit/faa6cbf895ba6f526473ed48779685919b36aa9f), the previous version remains preferred. * [@spackbot] updating style on behalf of wdconinc --------- Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-06-12gaudi: remove the py-qmtest dependency (#38274)Juan Miguel Carceller1-6/+1
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-06-12orthofinder: add 2.5.5, add variants (#38298)George Young1-1/+23
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-12bootstrap: add minimum versions required for flake8 and pytest (#38322)Massimiliano Culpo2-2/+3
2023-06-12fastq-screen: add 0.15.3, add variants (#38288)George Young1-6/+21
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-12ltr-retriever 2.9.4 (#38300)snehring2-1/+38
2023-06-12perl-libwww-perl: adding perl-clone dependency (#38301)snehring1-0/+1
2023-06-12alglib: add v4.00.0 (#38313)Alec Scott1-0/+1
2023-06-12bismark: add v0.24.1 (#38315)Alec Scott0-0/+0
2023-06-12blogbench: add v1.2 (#38316)Alec Scott1-0/+1
2023-06-12consul: add v1.15.3 (#38317)Alec Scott1-0/+1
2023-06-11Fix typo in example code block (#38318)Christopher Christofi1-1/+1
2023-06-11py-mypy: add 1.3.0 (#38286)Manuela Kuhn1-0/+2
* py-mypy: add 1.3.0 * Remove redundant py-typed-ast dependency * Read python@3.7 dep
2023-06-11py-deeptools: add 3.5.2, update dependency versions (#38287)George Young1-5/+7
* py-deeptools: add 3.5.2, update dependency versions * Update var/spack/repos/builtin/packages/py-deeptools/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * Update var/spack/repos/builtin/packages/py-deeptools/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * Rearranging dependencies to match setup.py --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-06-11py-jedi: add 0.18.2 (#38177)Manuela Kuhn1-13/+7
* py-jedi: add 0.18.2 * Add setuptools as run dependency
2023-06-11build(deps): bump docker/login-action from 2.1.0 to 2.2.0 (#38241)dependabot[bot]1-2/+2
Bumps [docker/login-action](https://github.com/docker/login-action) from 2.1.0 to 2.2.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/f4ef78c080cd8ba55a85445d5b36e214a81df20a...465a07811f14bebb1938fbed4728c6a1ff8901fc) --- updated-dependencies: - dependency-name: docker/login-action 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>
2023-06-11build(deps): bump docker/setup-buildx-action from 2.5.0 to 2.6.0 (#38242)dependabot[bot]1-1/+1
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.5.0 to 2.6.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/4b4e9c3e2d4531116a6f8ba8e71fc6e2cb6e6c8c...6a58db7e0d21ca03e6c44877909e80e45217eed2) --- updated-dependencies: - dependency-name: docker/setup-buildx-action 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>
2023-06-11build(deps): bump docker/setup-qemu-action from 2.1.0 to 2.2.0 (#38243)dependabot[bot]1-1/+1
Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2.1.0 to 2.2.0. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](https://github.com/docker/setup-qemu-action/compare/e81a89b1732b9c48d79cd809d8d81d79c4647a18...2b82ce82d56a2a04d2637cd93a637ae1b359c0a7) --- updated-dependencies: - dependency-name: docker/setup-qemu-action 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>
2023-06-11build(deps): bump urllib3 from 2.0.2 to 2.0.3 in /lib/spack/docs (#38244)dependabot[bot]1-1/+1
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.2 to 2.0.3. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/2.0.2...2.0.3) --- updated-dependencies: - dependency-name: urllib3 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>
2023-06-11build(deps): bump sphinx-rtd-theme in /lib/spack/docs (#38245)dependabot[bot]1-1/+1
Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.1 to 1.2.2. - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.2.1...1.2.2) --- updated-dependencies: - dependency-name: sphinx-rtd-theme 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>
2023-06-11build(deps): bump docker/build-push-action from 4.0.0 to 4.1.0 (#38306)dependabot[bot]0-0/+0
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.0.0 to 4.1.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/3b5e8027fcad23fda98b2e3ac259d8d67585f671...44ea916f6c540f9302d50c2b1e5a8dc071f15cdf) --- updated-dependencies: - dependency-name: docker/build-push-action 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>
2023-06-11build(deps): bump docker/build-push-action from 4.0.0 to 4.1.0 (#38306)dependabot[bot]1-1/+1
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.0.0 to 4.1.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/3b5e8027fcad23fda98b2e3ac259d8d67585f671...44ea916f6c540f9302d50c2b1e5a8dc071f15cdf) --- updated-dependencies: - dependency-name: docker/build-push-action 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>
2023-06-11py-multidict: add 6.0.4 (#38284)Manuela Kuhn1-4/+4
2023-06-11py-mne: add 1.4.2 (#38228)Manuela Kuhn1-0/+1
2023-06-11Gxsview new version 2023.05.29 (#38310)Olivier Cessenat1-0/+3
* netpbm: new version 10.73.43 * gxsview: new version 2023.05.29
2023-06-11[py-spacy-legacy] New package (#38276)Jen Herting1-0/+18
2023-06-11[py-spacy-loggers] new package (#38275)Jen Herting1-0/+18
2023-06-11[py-langcodes] new package (#38273)Jen Herting1-0/+18
2023-06-11py-nbclassic: add 1.0.0 and py-notebook-shim: add 0.2.3 (#38289)Manuela Kuhn2-4/+5
2023-06-11New version for openCARP packages, v13.0 (#37940)Marie Houillon4-16/+36
* New version for openCARP packages * Update carputils dependencies * Update types of openCARP dependencies * Add type "run" to setuptools dependency Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add package py-common as carputils dependency * Add setuptools dependency for py-common * Remove spaces on blank line * Restrict type of dependency setuptools to "build" Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: openCARP consortium <info@opencarp.org> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-11py-pybktree: new package (#38209)George Young1-0/+17
* py-pykbtree: new package * py-pybktree: new package --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-11py-pandas: exchange import_modules with skip_modules (#38227)Manuela Kuhn1-11/+1
2023-06-11py-more-itertools: add 9.1.0 (#38229)Manuela Kuhn1-7/+4
2023-06-10slurm: add new version(23.02.2, 22.05.9) (#38285)kjrstory1-0/+2
2023-06-10build(deps): bump actions/checkout from 3.5.2 to 3.5.3 (#38305)dependabot[bot]8-26/+26
Bumps [actions/checkout](https://github.com/actions/checkout) from 3.5.2 to 3.5.3. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/8e5e7e5ab8b370d6c329ec480221332ada57f0ab...c85c95e3d7251135ab7dc9ce3241c5835cc595a9) --- updated-dependencies: - dependency-name: actions/checkout 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>
2023-06-10Automated deployment to update package flux-core 2023-06-10 (#38308)Vanessasaurus1-0/+1
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-06-10Add new Podman package versions and fix patch (#38234)Carson Woods1-2/+4
* Add new podman versions and correct the versions which patch is applied to * Replace the existing maintainer with alecbcs at maintainers request
2023-06-09correct SHA for ABINIT 9.8.3 and add ABINIT 9.8.4 (#38283)Fabien Bruneval1-1/+2
2023-06-09install status arg: update to default true and add inverse (#38252)Greg Becker5-7/+26
* install status arg: update to default true and add inverse * update bash completion * fix tests broken by output change
2023-06-09[py-typer] new package (#38270)Jen Herting1-0/+21
* [py-typer] new package * [py-typer] added version 0.7.0
2023-06-09[py-catalogue] added version 2.0.8 (#38266)Jen Herting1-1/+4
2023-06-09comgr: enable testing (#35605)afzpatel1-0/+4
2023-06-09[gromacs] Fix intel (classic) libstdc++ path (#37822)Stephen Sachs1-3/+27
* [gromacs] Fix intel (classic) libstdc++ path Gromacs's `cmake` run will look for `--gcc-toolchain` (e.g. LLVM, icpx) or `--gcc-name` (e.g. icpc) in `CMAKE_CXX_FLAGS`. Only if it does not find a good g++ candidate there it will look for `GMX_GPLUSPLUS_PATH`: https://github.com/gromacs/gromacs/blob/cb6b311c39fc726a72170c4593b754c8d0a492ac/cmake/FindLibStdCpp.cmake#L97 Spack installed intel compilers already define a g++ for std libs. But in `icp{c,x}.cfg` instead of the compile line. If we use the pre-defined g++ we not only have less chance of mixing g++ versions, but also don't need to explicitly add `gcc` as dependency to `gromacs`. * Fix format * Use a variant As there is no way to check if a file exists at depends_on stage * Fix format * New name and fail if variant is used with other compiler * Line too long.
2023-06-09containerize: use an ENTRYPOINT script (#37769)Jonathon Anderson1-3/+9
2023-06-09Hotfix to avoid building compilers from sources in pcluster pipelines (#38256)Massimiliano Culpo5-5/+20
The pcluster image has am internal buildcache without an index. Also, we need to force reuse to avoid rebuilding GCC, since the default is to only reuse dependencies - and that is subject to changes in the GCC recipe.
2023-06-09BLT package: add version 0.5.3 (#38247)Chris White1-0/+1
2023-06-08glab: add new versions (#38236)Martin Pokorny1-0/+1
* glab: add new versions * Update var/spack/repos/builtin/packages/glab/package.py Co-authored-by: Alec Scott <alec@bcs.sh> --------- Co-authored-by: Alec Scott <alec@bcs.sh>
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