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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>
2023-06-07Guard for define in netcdf 4.9.0 and later. (#37853)Dan Lipsa2-0/+16
* Guard for define in netcdf 4.9.0 and later. This code is already available in ParaView 5.11.0 so no patching needed there. * Add latest needed version (even if not in spack). --------- Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
2023-06-07llvm: add new versions and set default for libomptarget according to os (#38092)Sajid Ali1-0/+5
* llvm: add new versions and set default for libomptarget according to os modified: var/spack/repos/builtin/packages/llvm/package.py * Incorporate reviewer suggestions Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com> --------- Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
2023-06-07nwchem: remove -mtune=native flags (#37892)Carlos Bederián1-0/+4
Co-authored-by: Edoardo Aprà <edoardo.apra@gmail.com>
2023-06-06E4S Cray CI Stack (#37837)eugeneswalker7-2/+503
* e4s cray ci stack * e4s ci: add cray * add zen4 tag * WIP: new defintions just for cray * updates * remove ci signing job overrride, not necessary * echo $PATH and show modules loaded * add mirror * add external def for cray-libsci * comment out quantum-espresso * use /etc/protected-runner as key path * cray ci stack: do not remove tags: [spack, public] * make cray stack composable * generate job should run on public tagged runner, override default config:install_tree:root * CI: Use relative path in default script * CI: Use relative includes paths for shell runners * Use concrete_env_dir for relpath * ml-darwin-aarch64-mps: jax has bazel codesign issue --------- Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com> Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
2023-06-06CachedCMakePackage: fix bug where CMAKE_CUDA_ARCHITECTURES=none is set (#38169)Mikael Simberg1-2/+2
#37592 updated cached cmake packages to set CMAKE_CUDA_ARCHITECTURES. The condition `if archs != "none"` lead to `CMAKE_CUDA_ARCHITECTURES=none` when cuda_arch=none (incorrect check on the value of a multi-valued variant), i.e. CMAKE_CUDA_ARCHITECTURES is always set. This PR udpates the condition to if archs[0] != "none" to ensure CMAKE_CUDA_ARCHITECTURES is only set if cuda_arch is not none (which seems to be the pattern used in other packages). This does the same for HIP (although in general ROCmPackage disallows amdgpu_target=none when +rocm).
2023-06-06julia: Update patch for llvm 14 without binary files (#37959)Mosè Giordano1-2/+2
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