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2022-08-04Add checksum for py-identify 2.5.3 (#31935)Jonathon Anderson1-0/+2
* Add checksum for py-identify 2.5.3 * Update package.py
2022-08-04Omnitrace version 1.3.1 (#31911)Jonathan R. Madsen1-0/+1
2022-08-04ruby-asciidoctor: adding version 2.0.17 (#31927)Olivier Cessenat1-0/+1
2022-08-04tassel: add version 3.0.174 (#31917)downloadico1-1/+6
* tassel: add version 3.0.174 fix naming of 5.2.39 from "2017-07-22" * changed single quotes to double quotes to appease the gods ;) * fixed style issues
2022-08-04HiOp: use ginkgo@glu_experimental with develop. (#31934)Cameron Rutherford2-1/+2
2022-08-04openblas%cce: patch to support -hnofortran (#31931)eugeneswalker2-0/+108
2022-08-04Move type hint to satisfy Python 3.6, 3.7 interpreters (#31932)Chris Green1-2/+2
2022-08-04Add documentation for git refs as versions (#31914)psakievich3-1/+133
* document git commit versions Include documentation for manually specifying associated known version * document spack develop command Co-authorerd-by: psakievich <psakiev@sandia.gov> Co-authored-by: Gregory Becker <becker33@llnl.gov> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-08-04Git Ref versions can be paired to defined versions in the spec (#30998)psakievich11-20/+179
The current use of git ref's as a version requires a search algorithm to pick the right matching version based on the tags in the git history of the package. This is less than ideal for the use case where users already know the specific version they want the git ref to be associated with. This PR makes a new version syntax [package]@[ref]=[version] to allow the users to specify the exact hash they wish to use.
2022-08-04Add checksums for py-onnx 1.10.1, 1.11.0, 1.12.0 (#31891)iarspider1-4/+11
* Add checksums for py-onnx 1.10.1, 1.11.0, 1.12.0 * Update package.py
2022-08-04Add checksum for py-notebook 6.4.12 (#31924)iarspider1-0/+1
2022-08-04Add checksum for py-ipython 7.31.1 (#31923)iarspider1-0/+1
2022-08-04pika: add v0.7.0 (#31906)Auriane R1-0/+1
2022-08-04New version for openCARP packages, v11.0 (#31652)Marie Houillon3-2/+5
Co-authored-by: openCARP consortium <info@opencarp.org>
2022-08-04Deprecate support for Python 3.5 (by removing it from CI) (#31908)Massimiliano Culpo6-9/+15
* Deprecate support for Python 3.5 (by removing it from CI) * Restore Python 3.9
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
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