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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>
2023-06-08py-mako: add 1.2.4 (#38194)Manuela Kuhn1-3/+3
2023-06-08py-lxml: add 4.9.2 (#38191)Manuela Kuhn1-1/+2
2023-06-08py-looseversion: add 1.2.0 (#38190)Manuela Kuhn1-1/+3
2023-06-08py-msgpack: add 1.0.5 (#38230)Manuela Kuhn1-0/+1
2023-06-08py-mistune: add 2.0.5 (#38214)Manuela Kuhn1-0/+1
2023-06-08py-llvmlite: add 0.40.0, update llvm dependency information (#38171)George Young1-2/+6
* 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> --------- 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>
2023-06-08gatk: add 4.4, update to java@17 (#38211)George Young1-1/+3
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08bowtie2: add 2.5.1 (#38201)George Young1-0/+2
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08trimgalore: add 0.6.10, adding variants (#38206)George Young1-0/+8
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08seqtk: add 1.4 (#38193)George Young1-0/+1
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08py-markupsafe: add 2.1.3 (#38198)Manuela Kuhn1-3/+1
2023-06-08New packages: eprosima-fastdds and dependencies (#38079)Daniele Cesarini3-0/+58
2023-06-08ocaml: don't use the spack compiler (#38251)Juan Miguel Carceller1-1/+1
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-06-08py-lightning: add v2.0.3 (#38260)Adam J. Stewart2-3/+14
2023-06-08bedtools2: patching to build with gcc@13 (#38254)George Young2-0/+27
* 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> --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-08Mold: 1.11.0 (#38235)Axel Huebl1-3/+12
* Mold: 1.11.0 Add the latest release of the `mold` linker. * SHA for 1.7.1: zip to tar
2023-06-08Forbid using `env:` as a top level environment attribute (#38199)Massimiliano Culpo10-80/+60
* Remove "env" from environment schema * Remove spack.env.schema.keys * Remove spack.environment.config_dict
2023-06-08py-lightly: add v1.4.7 (#38259)Adam J. Stewart1-2/+7
2023-06-08bdw-gc: add v8.2.4 (#37969)Ivan Maidanski1-3/+12
* bdw-gc: add v8.2.4 * bdw-gc: Fix download URL for old package versions --------- Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2023-06-08CMake/Windows bugfix: Make CMAKE_INSTALL_PREFIX a posix path (#36842)John W. Parent1-2/+2
CMake gives off a warning when passed Windows style paths as install prefixes as the resultant path often causes invalid escape sequences.
2023-06-08(r-rcpp)ensmallen: new package (#38249)Wouter Deconinck2-0/+51
* ensmallen: new package ensmallen is a high-quality C++ library for non-linear numerical optimization. * r-rcppensmallen: new package --------- Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-06-08Fix compiler removal from command line (#38057)Massimiliano Culpo9-251/+200
* 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.
2023-06-08e4s oneapi ci: use official intel oneapi-derived runner image (#38176)eugeneswalker2-156/+131
* 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
2023-06-08junit4: add v4.13.2 (#38122)Alec Scott1-0/+1
2023-06-08(r-rcpp)armadillo: new version 12.4.0 (#38246)Wouter Deconinck2-0/+4
* 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
2023-06-08bismark: add 0.24.1, add HISAT2 dependency (#38210)George Young1-0/+2
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08quantum-espresso: add 7.2 (#38223)Carlos Bederián1-0/+1
2023-06-08trilinos: drop preferred version (#38086)Seth R. Johnson1-5/+1
2023-06-08cni-plugins: add v1.3.0 (#38064)Alec Scott1-0/+1
2023-06-07py-keyring: add 23.13.1 (#38183)Manuela Kuhn1-5/+9
* py-keyring: add 23.13.1 * [@spackbot] updating style on behalf of manuelakuhn
2023-06-07`py-nvidia-dali`: update versions up to v1.26.0 (#38022)Thomas Bouvier1-5/+120
* `py-nvidia-dali`: update versions up to v1.26.0 * Add proper `cuda` dependency version
2023-06-07`py-horovod`: add versions v0.27.0 and v0.28.0 (#38016)Thomas Bouvier1-2/+4
* `py-horovod`: add versions v0.27.0 and v0.28.0 * fix: typo * Add upper version bound for `py-pyarrow`
2023-06-07py-json5: add 0.9.14 (#38178)Manuela Kuhn1-1/+2
2023-06-07py-jaraco-classes: add 3.2.3 (#38167)Manuela Kuhn1-2/+1
2023-06-07py-jupyter-client: add 8.2.0 (#38180)Manuela Kuhn1-0/+1
2023-06-07hbase: add v2.5.3 (#38073)Alec Scott0-0/+0
2023-06-07chemfiles: add v0.10.4 (#38063)Alec Scott1-0/+1
2023-06-07casacore: add v3.5.0 (#37806)Martin Pokorny1-20/+22
2023-06-07OpenFAST: add v3.3.0, v3.4.0 and v3.4.1 (#37407)Nate deVelder1-0/+3
2023-06-07Add documentation about package signing model (#30939)Christopher Kotfila2-0/+485
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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