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2022-08-04Adding JUBE 2.4.1, 2.4.2 and 2.4.3 (#31921)Filippo Spiga1-0/+15
2022-08-04Add checksum for py-arrow 1.2.1 and 1.2.2 (#31894)iarspider1-1/+6
* Add checksum for py-arror 1.2.1 and 1.2.2 * Update package.py * Update var/spack/repos/builtin/packages/py-arrow/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update package.py * Update package.py * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-08-03asp: refactor low level API to permit the injection of configurationMassimiliano Culpo5-78/+79
This allows writing extension commands that can benchmark different configurations in clingo, or try different configurations for a single test.
2022-08-03AMReX: 1D Option (#31913)Axel Huebl1-1/+1
Expose 1D support in AMREX_SPACEDIM.
2022-08-03sundials@6.1.0:6.2.0 +rocm: patch nvector to use pic (#31910)eugeneswalker3-0/+27
* sundials@6.1.0:6.2.0 +rocm: patch nvector to use pic * e4s ci: add sundials +rocm
2022-08-03ExaGO: disable Python with rocm+ipopt. HiOp: fix umpire+raja costraints. ↵Cameron Rutherford3-6/+13
RAJA: fix option naming for 0.14.0 (#31880)
2022-08-03New package: py-glymur (#31875)Jen Herting1-0/+24
* [py-glymur] New Package: py-glymur * [py-glymur] fixed copyright line * [py-glumur] update import ine * [@spackbot] updating style on behalf of qwertos Co-authored-by: James A Zilberman <jazrc@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-08-03Add checksum for py-smmap 3.0.5,4.0.0,5.0.0 (#31898)iarspider1-1/+6
2022-08-03py-torchgeo: lock down pytorch-lightning version (#31886)Adam J. Stewart1-2/+3
2022-08-03r-rhtslib: fix issue with git commit for v1.28 (#31653)Glenn Johnson1-1/+11
There is a problem with the git repo for rhtslib that apparently led to a bad version entry during the previous round of package updates. A git checkout on the commit also fails so use branch for most recent version.
2022-08-03AMReX: SYCL support (#31233)Erik1-0/+22
Add SYCL support, check CUDA-HIP-SYCL mutually exclusive. Require AMReX ver 21.06+ for SYCL. Co-authored-by: etpalmer63 <etpalmer63@users.noreply.github.com>
2022-08-03adios2: add v2.8.3 (#31885)Vicente Bolea1-1/+2
2022-08-03openssl: copy mozilla certs to work around symlink relocation issue (#31862)Harmen Stoppels1-5/+3
2022-08-03zopfli: add new package (#31879)Jen Herting1-0/+23
Co-authored-by: James A Zilberman <jazrc@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-08-03plasma: add code generation step for develop version (#31668)Piotr Luszczek1-0/+7
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-08-03Also set FC when building hypre+fortran (#31850)Peter Scheibel1-0/+1
2022-08-03QTLTools: add new package (#31881)dunatotatos1-0/+30
2022-08-03Match documentation of spack create with actual behavior. (#31892)dunatotatos1-1/+1
2022-08-03libspng: add new package (#31878)Jen Herting1-0/+17
Co-authored-by: James A Zilberman <jazrc@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-08-03Remove macOS 10.15 from bootstrap tests (#31890)Massimiliano Culpo1-1/+1
That version of the runners have been deprecated, see: https://github.blog/changelog/2022-07-20-github-actions-the-macos-10-15-actions-runner-image-is-being-deprecated-and-will-be-removed-by-8-30-22/
2022-08-03Make parmmg dependent on mmg and metis (#31838)Yang Zongze3-0/+17
1. copy source of mmg to its install tree for parmmg's build 2. add cmake args for parmmg 3. add '+mmg' when '+parmmg' for petsc
2022-08-03py-pytorch-lightning: add v1.7.0 (#31871)Adam J. Stewart1-1/+5
2022-08-03mpich: fix hwloc config option for version >= 4.0 (#31874)Ken Raffenetti1-4/+13
In MPICH 4.0, the config option for external hwloc changed from --with-hwloc-prefix to --with-hwloc
2022-08-03build(deps): bump actions/setup-python from 4.1.0 to 4.2.0 (#31882)dependabot[bot]4-19/+19
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.1.0 to 4.2.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/c4e89fac7e8767b327bbad6cb4d859eda999cf08...b55428b1882923874294fa556849718a1d7f2ca5) --- updated-dependencies: - dependency-name: actions/setup-python 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>
2022-08-02black: fix bootstrap for Python 3.6 (#31872)Chris Green1-0/+11
* py-platformdirs: sanitize UTF-8 setup.cfg on Python 3.6 * py-platformdirs: black compliance * Minimal fix per @adamjstewart
2022-08-02libedit: Make sure libedit linkes to the correct terminfo lib from spack ↵Chuck Atkins1-0/+10
(#31870)
2022-08-02e4s oneapi ci: build vtk-m ~openmp due to issue #31830 (#31840)eugeneswalker1-2/+3
2022-08-02ca-certificates-mozilla: add v2022-07-19 and v2022-04-26(#31863)Harmen Stoppels1-0/+10
2022-08-02butterflypack %oneapi: patch CMakeLists to solve issue #31818 (#31848)eugeneswalker3-3/+17
* butterflypack %oneapi: patch CMakeLists to solve issue #31818 * uncomment builds affected by failing butterflypack Co-authored-by: e <e>
2022-08-02new package: py-alphafold (#27849)Andrew W Elble14-2/+380
* new package: alphafold and related dependencies, depends on #27138 * [@spackbot] updating style on behalf of aweits * fix Co-authored-by: aweits <aweits@users.noreply.github.com>
2022-08-02Allow building with camp@0.2.3 for raja@0.14.0 and umpire@6.0.0 (#31853)Peter Scheibel2-2/+2
2022-08-02spack ci rebuild: Don't install in a login shell (#31771)Jonathon Anderson1-3/+2
On some systems the shell in login mode wipes important parts of the environment, such as PATH. This causes the build to fail since it can't find `spack`. For better robustness, don't use a login shell. In a full CI job the final spack install is run in an environment formed by scripts running in this order: export AWS_SECRET=... # 1. Load environment from GitLab project variables source spack/share/spack/setup-env.sh # 2. Load Spack into the environment (PATH) spack env activate -V concrete_env # 3. Activate the concrete environment source /etc/profile # 4. Bash login shell (from -l) spack install ... Whereas when a user launches their own container with (docker|podman) run -it, they end up running spack install in an environment formed in this order: source /etc/bash.bashrc # (not 4). Bash interactive shell (default with TTY) export AWS_SECRET=... #~1. Manually load environment from GitLab project variables source spack/share/spack/setup-env.sh # 2. Load Spack into the environment (PATH) spack env activate -V concrete_env # 3. Activate the concrete environment spack install ... The big problem being that (4) has a completely different position and content (on Leap 15 and possibly other containers). So in context, this PR removes (4) from the CI job case, leaving us with the simpler: export AWS_SECRET=... # 1. Load environment from GitLab project variables source spack/share/spack/setup-env.sh # 2. Load Spack into the environment (PATH) spack env activate -V concrete_env # 3. Activate the concrete environment spack install ...
2022-08-02Optimize reuse from buildcaches (#30806)Massimiliano Culpo2-11/+13
* database: don't sort on return from query_local * ASP-based solver: don't build the hash-lookup dictionary twice Building this dictionary twice and traversing all the specs might be time-consuming for large buildcaches.
2022-08-02Style fixesMassimiliano Culpo3-10/+11
2022-08-02Remove line that sets non-existing attribute?Massimiliano Culpo1-1/+0
2022-08-02Use __slots__ for fast attribute accessMassimiliano Culpo2-0/+12
2022-08-02Use __slots__ for fast attribute access during parsingMassimiliano Culpo2-0/+8
2022-08-02Document that reuse is higher priority than preferences in packages.yaml ↵Harmen Stoppels2-0/+35
(#31864) Resurrect Known issues, since users ask frequently about that.
2022-08-02py-pre-commit 2.20.0Harmen Stoppels1-0/+2
2022-08-02docs: Fix outdated pre-0.18 text on build dependencies (#31860)Todd Gamblin1-5/+13
2022-08-02gdb: add v12.1 (#31765)Melven Roehrig-Zoellner1-0/+1
2022-08-02Add mctc-lib v0.3.1 and toml-f v0.3.0 (#31847)Sebastian Ehlert2-0/+2
2022-08-02Add meson Python build backend (#31809)Adam J. Stewart4-36/+117
2022-08-02py-flake8: add v5.0 (#31854)Adam J. Stewart4-45/+62
2022-08-02spack checksum: black compliance (#31851)Adam J. Stewart1-1/+1
2022-08-01kokkos: set CMAKE_CXX_STANDARD instead of Kokkos_CXX_STANDARD (#31841)eugeneswalker1-1/+1
* kokkos@develop: set CMAKE_CXX_STANDARD instead of Kokkos_CXX_STANDARD * use CMAKE_CXX_STANDARD regardless of kokkos version
2022-08-01Add c++14 support flag for xl compiler (#31826)Peter Scheibel1-0/+8
2022-08-01lerc: add libs property (#31684)Adam J. Stewart1-0/+4
2022-08-01mxnet: prefer stable release (#31821)Adam J. Stewart1-1/+5
2022-08-01amrex: add v22.08 (#31844)Weiqun Zhang1-1/+2
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