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2023-12-26`spack gc`: add options for environments and build dependencies (#41731)Todd Gamblin10-78/+305
This adds a few options to `spack gc`. One to give you a little more control over dependencies: * `-b` / `--keep-build-dependencies`: By default, `spack gc` considers build dependencies to be "no longer needed" once their dependents are installed. With this option, we'll keep build dependencies of needed installations as well. And two more to make working with environments easier: * `-E` / `--except-any-environment`: Garbage collect anything NOT needed by an environment. `spack gc -E` and `spack gc -bE` are now easy ways to get rid of everytihng not used by some environment. * `-e` / `--except-environment` `ENV`: Instead of considering all environments, garbage collect everything not needed by a *specific* environment. Note that you can use this with `-E` to add directory environments to the list of considered envs, e.g.: spack gc -E -e /path/to/direnv1 -e /path/to/direnv2 #... - [x] rework `unused_specs()` method on DB to add options for roots and deptypes - [x] add `all_hashes()` method on DB - [x] rework `spack gc` command to add 3 more options - [x] tests
2023-12-26py-radiant-mlhub: older versions require typing_extensions (#41870)Adam J. Stewart1-1/+1
2023-12-26py-jupyter-server-terminals: disable import tests (#41862)Adam J. Stewart1-0/+2
2023-12-26py-greenlet: fix import tests (#41861)Adam J. Stewart1-0/+3
2023-12-26py-cppy: newer versions require setuptools at runtime (#41858)Adam J. Stewart1-3/+1
2023-12-26py-beautifulsoup4: fix import tests (#41857)Adam J. Stewart1-0/+3
2023-12-26py-black: add v23.12.1 (#41850)Adam J. Stewart2-2/+3
* py-black: add v23.12.1 * py-hatchling: add v1.21.0
2023-12-24arborx: new version 1.5 (#41796)Andrey Prokopenko1-0/+2
2023-12-24build(deps): bump mypy from 1.7.1 to 1.8.0 in /.github/workflows/style (#41820)dependabot[bot]1-1/+1
Bumps [mypy](https://github.com/python/mypy) from 1.7.1 to 1.8.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](https://github.com/python/mypy/compare/v1.7.1...v1.8.0) --- updated-dependencies: - dependency-name: mypy 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>
2023-12-24build(deps): bump mypy from 1.7.1 to 1.8.0 in /lib/spack/docs (#41821)dependabot[bot]1-1/+1
Bumps [mypy](https://github.com/python/mypy) from 1.7.1 to 1.8.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](https://github.com/python/mypy/compare/v1.7.1...v1.8.0) --- updated-dependencies: - dependency-name: mypy 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>
2023-12-24postgresql: 13.1 (#41825)Weizheng Lu1-0/+1
2023-12-24yosys: version update and added functionality (#41844)Dave Keeshan1-2/+38
* Add all versions back to 0.20, add more depends_on (flex, bison, libffi and ccache), add the ability to enable or disable both abc and ccache, abc is enabled by default, ccache is disabled by default * Fixed style with black * Removed unused f-string setups * Fixed style with black (again)
2023-12-24autoconf: add v2.72 (#41848)Michael Kuhn1-6/+4
2023-12-23py-pyomo: Update spec for newest major series (#41271)Miranda Mundt5-9/+180
* Add enum34, numdifftools, and updated pyomo packages * Syntax error * Apply black style * Trying to get around Python spec issue * All SHAs were somehow wrong * Change enum version * Change optional dependencies to be on run, not build * Add Pyomo 6.7.0 * Update SHA and version mismatch * Remove py-enum34 * Add three new packages to address comments * Fix linting errors; move casadi to py-casadi * Update license; add in dependency * Update setuptools version * Update class name to python class * Remove other boielerplate stuff * Update homepage addresses; update py-casadi
2023-12-23py-urllib3: add version 1.25.11 (#41756)Christopher Christofi1-0/+1
2023-12-23minimap2: Added option for paftools.js (#41765)Arne Becker1-0/+7
- Added an option for the Javascript paftools script - Added two slightly older versions
2023-12-23CUDNN: Add versions 8.8.x and 8.9.x. (#41790)Rémi Lacroix1-2/+44
NVIDIA changed the download URLs again so account for that.
2023-12-23py-apispec: add older version (#41798)Arne Becker1-0/+1
2023-12-23CI: Disable downloading artifacts from upstream jobs (#41846)kwryankrattiger1-0/+3
2023-12-23Revert "CI: Disable downloading artifacts from upstream jobs (#41432)" (#41843)Harmen Stoppels2-4/+0
This reverts commit a43156a86131a0b138f356a2721709a2070665ca.
2023-12-23Revert "Tcl: add nmake system for Windows (#41759)" (#41842)Harmen Stoppels1-88/+62
This reverts commit ecdf3ff297eda60180253c43a19a303a8b5a8bfd.
2023-12-23Revert "update an everywhere-but-windows check to include freebsd (#41819)" ↵Harmen Stoppels1-1/+1
(#41841) This reverts commit a2dc11acd3d368e7639e924a4e1d11e09b0b2f72.
2023-12-22Revert "sqlite: add NMake build system for Windows (#41761)" (#41840)Harmen Stoppels1-71/+36
This reverts commit 94fc2314f163b1f8dcdf072c4b66afccff9c83b4.
2023-12-22damask: add version 3.0.0-alpha8 (#41444)Martin Diehl4-0/+23
* damask 3.0.0-alpha8 * ensuring correct Python versions for py-damask
2023-12-22py-lightning: add v2.1.3 (#41809)Adam J. Stewart1-1/+3
2023-12-22Fftx final ecp update (#41812)Patrick Broderick4-4/+8
* build(deps): bump actions/setup-python from 2.2.2 to 2.3.1 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2.2.2 to 2.3.1. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/dc73133d4da04e56a135ae2246682783cc7c7cb6...f38219332975fe8f9c04cca981d674bf22aea1d3) --- 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> * build(deps): bump docker/build-push-action from 2.8.0 to 2.9.0 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> * build(deps): bump actions/upload-artifact from 2 to 3 Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 2 to 3. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v2...v3) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump actions/download-artifact from 2 to 3 Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 2 to 3. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v2...v3) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump actions/setup-python from 2 to 3.1.2 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 3.1.2. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v2...98f2ad02fd48d057ee3b4d4f66525b231c3e52b6) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump codecov/codecov-action from 2.1.0 to 3.1.0 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 2.1.0 to 3.1.0. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/master/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/f32b3a3741e1053eb607407145bc9619351dc93b...81cd2dc8148241f03f5839d295e000b8f761e378) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump actions/checkout from 2 to 3.0.2 Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3.0.2. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v2...2541b1294d2704b0964813337f33b291d3f8596b) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump docker/build-push-action from 2.10.0 to 4.0.0 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 2.10.0 to 4.0.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/ac9327eae2b366085ac7f6a2d02df8aa8ead720a...3b5e8027fcad23fda98b2e3ac259d8d67585f671) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump docker/setup-buildx-action from 2.2.1 to 2.4.1 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.2.1 to 2.4.1. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/8c0edbc76e98fa90f69d9a2c020dcb50019dc325...f03ac48505955848960e80bbb68046aa35c7b9e7) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump docutils from 0.18.1 to 0.20.1 in /lib/spack/docs Bumps [docutils](https://docutils.sourceforge.io/) from 0.18.1 to 0.20.1. --- updated-dependencies: - dependency-name: docutils dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Bump mypy from 1.5.0 to 1.5.1 in /lib/spack/docs Bumps [mypy](https://github.com/python/mypy) from 1.5.0 to 1.5.1. - [Commits](https://github.com/python/mypy/compare/v1.5.0...v1.5.1) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Bump sphinx-rtd-theme from 1.2.2 to 1.3.0 in /lib/spack/docs Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.2 to 1.3.0. - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.2.2...1.3.0) --- updated-dependencies: - dependency-name: sphinx-rtd-theme dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Bump actions/upload-artifact from 3.1.2 to 3.1.3 Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3.1.2 to 3.1.3. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/0b7f8abb1508181956e8e162db84b466c27e18ce...a8a3f3ad30e3422c9c7b888a15615d19a852ae32) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Bump docker/build-push-action from 4.1.1 to 5.0.0 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.1.1 to 5.0.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/2eb1c1961a95fc15694676618e422e8ba1d63825...0565240e2d4ab88bba5387d719585280857ece09) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * Bump docker/setup-qemu-action from 2.2.0 to 3.0.0 Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2.2.0 to 3.0.0. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](https://github.com/docker/setup-qemu-action/compare/2b82ce82d56a2a04d2637cd93a637ae1b359c0a7...68827325e0b33c7199eb31dd4e31fbe9023e06e3) --- updated-dependencies: - dependency-name: docker/setup-qemu-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * Bump docker/setup-buildx-action from 2.9.1 to 3.0.0 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.9.1 to 3.0.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/4c0219f9ac95b02789c1075625400b2acbff50b1...f95db51fddba0c2d1ec667646a06c2ce06100226) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * Bump actions/checkout from 3.5.3 to 4.1.0 Bumps [actions/checkout](https://github.com/actions/checkout) from 3.5.3 to 4.1.0. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/c85c95e3d7251135ab7dc9ce3241c5835cc595a9...8ade135a41bc03ea155e62e844d188df1ea18608) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * Bump pytest from 7.4.0 to 7.4.2 in /lib/spack/docs Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.0 to 7.4.2. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/7.4.0...7.4.2) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Bump sphinx from 6.2.1 to 7.2.6 in /lib/spack/docs Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 6.2.1 to 7.2.6. - [Release notes](https://github.com/sphinx-doc/sphinx/releases) - [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES.rst) - [Commits](https://github.com/sphinx-doc/sphinx/compare/v6.2.1...v7.2.6) --- updated-dependencies: - dependency-name: sphinx dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * Update tarball and version info for Final ECP versions of FFTX/Spiral repos --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-12-22update an everywhere-but-windows check to include freebsd (#41819)Peter Scheibel1-1/+1
2023-12-22Fix a couple typos in the docs (#41822)Alec Scott3-7/+7
2023-12-22py-keras: add v3.0.2 (#41827)Adam J. Stewart1-2/+3
2023-12-22py-mypy: add v1.8.0 (#41831)Adam J. Stewart1-0/+2
2023-12-22openfoam: add version 2312 (#41828)Mark Olesen1-0/+1
2023-12-22Add PAPI 7.0.1 and 7.1.0 (#38443)Wileam Y. Phan3-1/+81
* Add PAPI 7.0.1 * Add comment about skipping PAPI 7.0.0 * Add patch to avoid adding Intel ifort/ifx flag on Cray ftn * Modify patch to include Cray-specific flags * Adjust recipe to always apply patch for 7.0.1 * Expand Cray compiler checks in patch * Forgot to update recipe * Adjust recipe so it looks for hipcc in the correct path * Revert "Adjust recipe so it looks for hipcc in the correct path" This reverts commit 0db3df4fe2874cea7d0e31fee1709246db668499. * Patch HIP_PATH to work with Spack-built HIP * Patch LDFLAGS with llvm-amdgpu path * Forgot the depends_on line * libomptarget only builds with clang * Try a self-consistent build of llvm-amdgpu * Try making llvm-amdgpu depend on llvm for llvmoffloadarch library * Update prereq to use rocm-openmp-extras instead * Refactor llvm-amdgpu to use a version dict * Fix typo * Hack to exclude older versions without matching rocm-openmp-extras * Add PAPI 7.1.0 * Revert changes to llvm-amdgpu * Fix PAPI 7.1.0 checksum
2023-12-22Use white logo or dark backgrounds (#41836)Alec Scott1-1/+9
2023-12-22Update README.md formatting (#41813)Alec Scott1-10/+23
* Update README.md formatting * Add docs and bootstrapping status and left align * Update vertical badge spacing * Update vertical logo spacing
2023-12-22Remove deprecated versions from packages (#41031)Adam J. Stewart87-3424/+100
For now, this only includes packages that I personally maintain. Notable removals: * Anaconda 2 * Catalyst * Ancient numpy/scipy * Ancient PyTorch * Ancient Bazel/TF
2023-12-22Fix variant initialization logic to allow proper handling of values="*" (#40406)Tim Fuller2-1/+38
Co-authored-by: psakiev <psakiev@sandia.gov> Co-authored-by: tjfulle <tjfulle@users.noreply.github.com>
2023-12-22llvm: fix llvm@14 build with apple-clang-15 (#40191)Laurent Aphecetche2-0/+33
* llvm: fix llvm@14 build with apple-clang-15 * fix formatting --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-12-22costa: add missing dependency (#41829)Simon Pintarelli1-0/+1
2023-12-22GDAL: add v3.8.2 (#41795)Adam J. Stewart1-0/+1
2023-12-22ReSolve: Add version 0.99.1 (#41802)pelesh1-1/+6
* ReSolve: Add version 0.99.1 * [@spackbot] updating style on behalf of pelesh --------- Co-authored-by: pelesh <pelesh@users.noreply.github.com>
2023-12-22kealib: add version 1.5.3 (#41804)Sam Gillingham1-1/+2
2023-12-21Consolidate definition of Spack's extra `sys.path` components (#41816)Todd Gamblin1-7/+12
To work properly, Spack requires a few directories from its repository to be added to `sys.path`. Previously these were buried in `spack_installable.main.main()`, but it's sometimes useful to get the paths separately, e.g., if you want to set up your own functioning spack environment. With this change, adding the paths is much simpler: ```python import spack_installable sys.path[:0] = get_spack_sys_paths(spack_prefix) ``` - [x] Add `get_spack_sys_paths()` method with extra paths in order. - [x] Refactor `spack_installable.main.main()` to use it.
2023-12-21sqlite: add NMake build system for Windows (#41761)John W. Parent1-36/+71
2023-12-21Improve error reporting when Clingo install is broken (#41181)John W. Parent1-0/+33
With an improper/incomplete/broken installation of Clingo, it can be importable but not have any of the expected attributes Improve error reporting in this case
2023-12-21Tcl: add nmake system for Windows (#41759)John W. Parent1-62/+88
2023-12-21Compilers can inject first order rules into the solverMassimiliano Culpo12-95/+328
* Restore PackageBase class, and modify only ASP This prevents a noticeable slowdown in concretization due to the number of directives involved. * Fix issue with 'clang' being preferred to 'gcc', due to runtime version weights * Constraints on runtimes are declared by compilers The declaration of available runtime versions, and of their compatibility constraints are in the associated compiler class. Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-12-21gcc-runtime: add separate package for gcc runtime libsHarmen Stoppels6-1/+250
The gcc-runtime package adds a separate node for gcc's dynamic runtime libraries. This should help with: 1. binary caches where rpaths for compiler support libs cannot be relocated because the compiler is missing on the target system 2. creating "minimal" container images The package is versioned like `gcc` (in principle it could be unversioned, but Spack doesn't always guarantee not mixing compilers)
2023-12-21specs: Better error messages for badly quoted specs (#41805)Todd Gamblin4-25/+18
If you are calling Spack from the python API, you might have written something like this before #41529: ``` find = SpackCommand("find") find('--format={name}', 'saxpy@1.0.0', '+rocm', 'amdgpu_target="gfx90a"') ``` But with the breaking change in #41529, you should write: ``` find = SpackCommand("find") find('--format={name}', 'gromacs', '+rocm', 'amdgpu_target=gfx90a') ``` Note that we don't need quotes in Python strings, and that this is what would come in via argv if you typed a quoted variant on the CLI. The error messages for strings like this are not great -- you get something like this: ``` ==> No package matches the query: gromacs+rocm amdgpu_target="gfx90a" ``` Which doesn't indicate that the issue might be your quoting. This is because we were simply outputting the argv we got, instead of using spec.format() to output the error message. This PR fixes such errors to use `spec.format()` and to look like this: ``` ==> No package matches the query: gromacs+rocm amdgpu_target='"gfx90a"' ``` So users should have an easier time understanding that Spack considers the variant value to contain quotes here. - [x] update ConstraintAction to store parsed Specs - [x] refactor commands to display formatted parsed Specs instead of raw input
2023-12-21intel-oneapi-compilers and intel-oneapi-ccl: added new version to packages ↵Andrey Perestoronin2-2/+12
(#41807) * added new packages * compiler package * fix link in ccl * fix another links in ccl
2023-12-21ci: use "strong preference" idiom for compilers (#41806)Harmen Stoppels2-2/+5
to avoid duplication of conflicts / requirements in config
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