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* 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>
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Co-authored-by: openCARP consortium <info@opencarp.org>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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* py-pykbtree: new package
* py-pybktree: new package
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
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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>
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Co-authored-by: github-actions <github-actions@users.noreply.github.com>
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* Add new podman versions and correct the versions which patch is applied to
* Replace the existing maintainer with alecbcs at maintainers request
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* install status arg: update to default true and add inverse
* update bash completion
* fix tests broken by output change
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* [py-typer] new package
* [py-typer] added version 0.7.0
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* [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.
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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.
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* glab: add new versions
* Update var/spack/repos/builtin/packages/glab/package.py
Co-authored-by: Alec Scott <alec@bcs.sh>
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Co-authored-by: Alec Scott <alec@bcs.sh>
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* py-llvmlite: add 0.40.0, update llvm dependency information
* Update var/spack/repos/builtin/packages/py-llvmlite/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/py-llvmlite/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/py-llvmlite/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Update var/spack/repos/builtin/packages/py-llvmlite/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
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Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
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* bedtools2: patching to build with gcc@13
* bedtools2: patching to build with gcc@13
* Update var/spack/repos/builtin/packages/bedtools2/package.py
Yep, sure. Makes sense.
Co-authored-by: Alec Scott <alec@bcs.sh>
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
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* Mold: 1.11.0
Add the latest release of the `mold` linker.
* SHA for 1.7.1: zip to tar
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* Remove "env" from environment schema
* Remove spack.env.schema.keys
* Remove spack.environment.config_dict
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* bdw-gc: add v8.2.4
* bdw-gc: Fix download URL for old package versions
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Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
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CMake gives off a warning when passed Windows style paths as
install prefixes as the resultant path often causes invalid
escape sequences.
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* ensmallen: new package
ensmallen is a high-quality C++ library for non-linear numerical optimization.
* r-rcppensmallen: new package
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Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
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* Improve lib/spack/spack/test/cmd/compiler.py
* Use "tmp_path" in the "mock_executable" fixture
* Return a pathlib.Path from mock_executable
* Fix mock_executable fixture on Windows
"mock_gcc" was very similar to mock_executable, so use the latter to reduce code duplication
* Remove wrong compiler cache, fix compiler removal
fixes #37996
_CACHE_CONFIG_FILES was both unneeded and wrong, if called
subsequently with different scopes.
Here we remove that cache, and we fix an issue with compiler
removal triggered by having the same compiler spec in multiple
scopes.
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* e4s oneapi ci: use official intel oneapi-derived runner image
* update oneapi image
* tau builds ok, but only with libdrm - comment out for now, follow up with pr later
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* armadillo: new version 12.4.0
No build system changes necessary, https://gitlab.com/conradsnicta/armadillo-code/-/compare/12.2.x...12.4.x
* r-rcpparmadillo: new version 0.12.4.0.0
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Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
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