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2022-02-07Support config variables in config.yaml extensions paths (#17772)Jordan Galby4-10/+32
2022-02-06py-torch: update dep constraints (#28743)Adam J. Stewart1-5/+7
The version of the ONNX submodule was updated between the PyTorch 1.9 and 1.10 releases, which fixed builds with newer protobuf but broke builds with older protobuf. Also this adds minimum version reqs for numpy/typing-extensions (which were not present before).
2022-02-06git: new versions (#28777)Harmen Stoppels1-3/+38
2022-02-06Fix GCC 8 build on macOS bigsur %apple-clang@12.0.5 (#28795)Seth R. Johnson1-2/+8
* gcc: revise patch range on darwin * gcc: add conflict to work around bootstrap failure closes #23296 . See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100340 . ``` Comparing stages 2 and 3 Bootstrap comparison failure! gcc/tree-ssa-operands.o differs gcc/tree-ssanames.o differs gcc/ipa-inline.o differs gcc/tree-ssa-pre.o differs gcc/gimple-loop-interchange.o differs ... ``` 639 total differences. * gcc: bump conflict up to correct later version
2022-02-04WarpX: add v22.02 (#28742)Axel Huebl3-2/+6
2022-02-04openfdtd: add version 2.6.3, 2.7.1, 2.7.3 and support Fujitsu Compiler. (#28472)Toyohisa Kameyama1-5/+22
2022-02-04wrf: Add New version, support fujitsu compiler, refactor and bug fix. (#28567)Toyohisa Kameyama10-102/+303
* wrf: Add version 4.3, support fujitsu compioler, output build log, and fix to build diffwrf.
2022-02-04atompaw: use autotoolsPackage and support Fujitsu compiler. (#28471)Toyohisa Kameyama2-10/+54
* atompaw: use autotoolsPackage and support Fujitsu compiler.
2022-02-04database: fix reindex with uninstalled deps (#28764)Harmen Stoppels4-42/+94
* Fix reindex with uninstalled deps When a prefix of a dep is removed, and the db is reindexed, it is added through the dependent, but until now it incorrectly listed the spec as 'installed'. There was also some questionable behavior in the db when the same spec was added multiple times, it would always be marked installed. * Always reserve path * Only add installed spec's prefixes to install prefixes set * Improve warning, and ensure ensure only ensures * test: reindex with every file system remnant removed except for the old index; it should give a database with nothing installed, including records with installed==False,external==False,ref_count==0,explicit=True, and these should be removable from the database
2022-02-04Use Spec.constrain to construct spec lists for stacks (#28783)Massimiliano Culpo4-40/+62
* stacks: add regression tests for matrix expansion * Use constrain semantics to construct spec lists for stacks * Fix semantics for constraining an anonymous spec. Add tests
2022-02-04WarpX/HiPACE: noacc PSATD also needs FFTW (#28756)Axel Huebl2-0/+9
Forgot to add that `compute=noacc` also needs FFTW3 for PSATD builds.
2022-02-04py-kubernetes: add new versions up to v21.7.0 (#28687)Valentin Volkl1-1/+7
* py-kubernetes: add new versions up to v21.7.0 * py-kubernetes: update python dependency
2022-02-04Adding new package: COSTA (#28727)Marko Kabic1-0/+57
2022-02-04cntk: fix build and add comments (#28676)Glenn Johnson1-2/+21
2022-02-04py-mpi4py: fix install_options (#28759)Adam J. Stewart1-0/+1
2022-02-04`py-warpx`: needs no `py-cmake` (#28761)Axel Huebl1-2/+4
Since in Spack we pull binaries out of the `warpx` package, we don't need `py-cmake` to build `py-warpx`. Generally, `py-cmake` in `pyproject.toml` is just a mean for us to tell `pip` to make a `cmake` CLI tool available.
2022-02-04e4s ci: uncomment variorum following pr #28754 (#28763)eugeneswalker2-2/+2
2022-02-04py-numpy: add v1.22.2 (#28771)Adam J. Stewart1-0/+2
2022-02-04flit: add version for development branch (#28773)Tim Haines1-0/+2
2022-02-04fpchecker: add version for master branch (#28774)Tim Haines1-0/+2
2022-02-03pruners-ninja: Add version for master branch (#28765)Tim Haines1-0/+2
2022-02-03amrex: add v22.02 (#28757)Weiqun Zhang1-1/+2
2022-02-03STRUMPACK new versions 6.3.0, 6.2.1, 6.2.0 (#28762)Pieter Ghysels1-0/+4
* Add new versions for STRUMPACK, newer ButterflyPACK dependency * small fix
2022-02-03Bump butterflypack versions to v.2.1.0 (#28758)liuyangzhuan1-1/+2
* added package gptune with all its dependencies: adding py-autotune, pygmo, py-pyaml, py-autotune, py-gpy, py-lhsmdu, py-hpbandster, pagmo2, py-opentuner; modifying superlu-dist, py-scikit-optimize * adding gptune package * minor fix for macos spack test * update patch for py-scikit-optimize; update test files for gptune * fixing gptune package style error * fixing unit tests * a few changes reviewed in the PR * improved gptune package.py with a few newly added/improved dependencies * fixed a few style errors * minor fix on package name py-pyro4 * fixing more style errors * Update var/spack/repos/builtin/packages/py-scikit-optimize/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * resolved a few issues in the PR * fixing file permissions * a few minor changes * style correction * minor correction to jq package file * Update var/spack/repos/builtin/packages/py-pyro4/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * fixing a few issues in the PR * adding py-selectors34 required by py-pyro4 * improved the superlu-dist package * improved the superlu-dist package * moree changes to gptune and py-selectors34 based on the PR * Update var/spack/repos/builtin/packages/py-selectors34/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * improved gptune package: 1. addressing comments of tldahlgren in PR 26936; 2. adding variant openmpi * fixing style issue of gptune * changing file mode * improved gptune package: add variant mpispawn which depends on openmpi; add variant superlu and hypre for installing the drivers; modified hypre package file to add a gptune variant * fixing style error * corrected pddrive_spawn path in gptune test; enforcing gcc>7 * fixing style error * setting environment variables when loading gptune * removing debug print in hypre/package.py * adding superlu-dist v7.2.0; fixing an issue with CMAKE_INSTALL_LIBDIR * changing site_packages_dir to python_platlib * not using python3.9 for py-gpy, which causes due to dropped support of tp_print * more replacement of site_packages_dir * fixing a few dependencies in gptune; added a gptune version * adding url for gptune * minor correction of gptune * updating versions in butterflypack Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-02-03[py-xonsh] added py-xonsh package (#28746)Matthieu Dorier1-0/+21
* [py-xonsh] added py-xonsh package * [py-xonsh] change dependency to python 3.6 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-02-03variorum: needs jansson (#28754)eugeneswalker1-0/+3
2022-02-03libblastrampoline: Add versions 4.1.0, 5.0.0, 5.0.1 (#28732)Mosè Giordano1-0/+4
2022-02-03Sundials: update version sha, add -D to cmake option (#28720)Chris White1-3/+3
2022-02-03petsc, py-petsc4py: add versions 3.16.4 (#28729)Satish Balay2-0/+2
2022-02-03libgit2: add mmap variant, disabling it makes it work on filesystems that do ↵Harmen Stoppels1-0/+7
not implement mmap (#28520)
2022-02-03gptune: add v2.1.0 (#28739)liuyangzhuan1-2/+4
2022-02-03conduit: convert HDF5 constaint to compile flag (#28735)kwryankrattiger1-7/+7
2022-02-03seacas: add v2022-01-27 (#28738)Greg Sjaardema1-0/+1
2022-02-03conduit: add v0.8.2 (#28730)Cyrus Harrison1-0/+1
2022-02-03julia: fix gfortran version detection (#28741)Harmen Stoppels2-0/+25
2022-02-02Change my name (#28737)Nils Vu4-4/+4
2022-02-02llvm: patch for gcc-11 (#28547)Glenn Johnson2-1/+12
* llvm: patch for gcc-11 - added llvm-gcc11.patch - adjusted version constraints on existing missing-includes patch. * remove unnecessary comment Co-authored-by: Tom Scogland <scogland1@llnl.gov>
2022-02-02py-torch: avoid build issue with newer protobuf (#28721)Adam J. Stewart1-1/+2
2022-02-02Revert "Deprecate Python 2 installations" (#28411)Adam J. Stewart109-397/+400
This reverts commit 7b76e3982f94ee952fe5d8fb0d19b389cc28228a.
2022-02-02Add a "sticky" property to variants (#28630)Massimiliano Culpo10-101/+196
* Add sticky variants * Add unit tests for sticky variants * Add documentation for sticky variants * Revert "Revert 19736 because conflicts are avoided by clingo by default (#26721)" This reverts commit 33ef7d57c1a09d6ce454503e9ff5638747e4f4a2. * Add stickiness to "allow-unsupported-compiler"
2022-02-02build(deps): bump docker/build-push-action from 2.8.0 to 2.9.0 (#28719)dependabot[bot]1-1/+1
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 2.8.0 to 2.9.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/1814d3dfb36d6f84174e61f4a4b05bd84089a4b9...7f9d37fa544684fb73bfe4835ed7214c255ce02b) --- updated-dependencies: - dependency-name: docker/build-push-action 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>
2022-02-02gromacs: Add versions 2021.4 and 2021.5 (#28722)Carlos Bederián1-0/+2
2022-02-02Snakemake: add v6.15.1 (#28724)Marcus Boden1-0/+1
2022-02-01new packages: py-rst2pdf and py-smartypants (#28697)Glenn Johnson2-0/+50
* new packages: py-rst2pdf and py-smartypants The py-smartypants package is a dependency of py-rst2pdf. * add missing dependencies
2022-02-01expat: Add latest release 2.4.4 with security fixes (#28692)Sebastian Pipping1-2/+3
2022-02-01py-argparse: skip dep for newer Python (#28718)Adam J. Stewart26-30/+26
2022-02-01Jali package: add version 1.1.6 (#28545)Rao Garimella1-2/+3
Boost dependency is only needed for @:1.1.5
2022-02-01TermStatusLine: fix python 2.7 and add test (#28715)Harmen Stoppels2-1/+12
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-02-01CI: macOS try to build latest GCC (#28709)Massimiliano Culpo1-1/+1
2022-02-01py-rich: fix installation with poetry (#28710)Nils Leif Fischer1-1/+1
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