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2022-10-12gpi-space: add new version (#33184)Max Zeyen1-9/+20
* gpi-space: add new version * gpi-space: fix flake8 formatting issues * gpi-space: fix more flake8 issues
2022-10-12Added hash for version 2.7.0-6 (#33263)Brian Van Essen1-0/+1
2022-10-12env depfile: allow deps only install (#33245)Harmen Stoppels3-65/+69
* env depfile: allow deps only install - Refactor `spack env depfile` to use a Jinja template, making it a bit easier to follow as a human being. - Add a layer of indirection in the generated Makefile through an `<prefix>/.install-deps/<hash>` target, which allows one to specify different options when installing dependencies. For example, only verbose/debug mode on when installing some particular spec: ``` $ spack -e my_env env depfile -o Makefile --make-target-prefix example $ make example/.install-deps/<hash> -j16 $ make example/.install/<hash> SPACK="spack -d" SPACK_INSTALL_FLAGS=--verbose -j16 ``` This could be used to speed up `spack ci rebuild`: - Parallel install of dependencies from buildcache - Better readability of logs, e.g. reducing verbosity when installing dependencies, and splitting logs into deps.log and current_spec.log * Silence please!
2022-10-12NVIDIA HPC SDK: add v22.9 (#33258)Filippo Spiga1-0/+14
2022-10-12update Bioconductor R packages (#33224)Glenn Johnson29-1/+38
* Add bioc attribute to r-do-db * add version 1.38.1 to bioconductor package r-annotationforge * add version 1.30.4 to bioconductor package r-biocparallel * add version 2.64.1 to bioconductor package r-biostrings * add version 4.4.4 to bioconductor package r-clusterprofiler * add version 2.12.1 to bioconductor package r-complexheatmap * add version 1.18.1 to bioconductor package r-delayedmatrixstats * add version 3.22.1 to bioconductor package r-dose * add version 3.38.4 to bioconductor package r-edger * add version 1.16.2 to bioconductor package r-enrichplot * add version 2.20.2 to bioconductor package r-ensembldb * add version 1.32.4 to bioconductor package r-genomeinfodb * add version 1.32.1 to bioconductor package r-genomicalignments * add version 1.48.4 to bioconductor package r-genomicfeatures * add version 1.44.1 to bioconductor package r-ggbio * add version 3.4.4 to bioconductor package r-ggtree * add version 1.24.2 to bioconductor package r-hdf5array * add version 2.30.1 to bioconductor package r-iranges * add version 1.36.3 to bioconductor package r-keggrest * add version 3.52.4 to bioconductor package r-limma * add version 1.8.1 to bioconductor package r-matrixgenerics * update r-org-hs-eg-db * add version 1.38.1 to bioconductor package r-organismdbi * add version 1.36.1 to bioconductor package r-pathview * add version 1.56.1 to bioconductor package r-rtracklayer * add version 1.4.1 to bioconductor package r-scaledmatrix * add version 1.24.1 to bioconductor package r-scran * add version 1.6.3 to bioconductor package r-scuttle * add version 1.18.1 to bioconductor package r-singlecellexperiment * add version 1.20.2 to bioconductor package r-treeio * Revert "Add bioc attribute to r-do-db" This reverts commit 36be5c6072c98ec70bb16f9d613a6fe24407fee1. * Fix quotes on versions Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-10-12py-pythran: customize headers attribute (#33242)Massimiliano Culpo1-0/+9
2022-10-12Limit whip dependencies for pika (#33244)Auriane R1-1/+2
2022-10-12Add checksum for py-requests-oauthlib 1.3.1 (#33199)iarspider1-0/+1
2022-10-12Package slate: Added deps for +rocm smoke test (#33218)G-Ragghianti1-7/+4
* Added deps for slate+rocm smoke test * Style change
2022-10-12vtkm: add v1.9.0 (#33221)Vicente Bolea1-3/+3
2022-10-12Add checksum for py-awkward 1.9.0 (#33159)iarspider1-2/+8
2022-10-12oneapi: set -Wno-unused-command-line-argument (#33192)Harmen Stoppels1-0/+10
For older versions of intel-oneapi-compilers, running the compiler in preprocessor / compilation mode would trigger warnings that `-Wl,-rpath,...` flags were unused. This in turn caused certain configure scripts to fail as they did not expect output from the compiler (it's treated as an error). Notably cmake's bootstrap phase failed to detect c++ features of the compiler. As a workaround, add this flag to silence the warning, since I don't think we can scope the flags to compile+link mode.
2022-10-12neovim: add version 0.8.0 (#33238)Alberto Invernizzi2-2/+7
* bump version for libvterm, required by neovim * bump version for neovim and add related dep constraints see release note: https://github.com/neovim/neovim/commit/d367ed9b23d481998d297d812f54b950e5511c24 in particular: 'deps: Bump required libvterm to v0.3' https://github.com/neovim/neovim/pull/20222
2022-10-12Add checksum for py-prettytable 3.4.1 (#33138)iarspider1-0/+1
2022-10-12netcdf packages: filter compiler wrappers in the *-config files (#33025)Sergey Kosukhin3-0/+26
* netcdf packages: filter compiler wrappers in the *-config files * netcdf-c: provide dependent packages with unfiltered nc-config
2022-10-12man-db: fix gnulib issue (#33149)Harmen Stoppels2-0/+43
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-10-12py-sphinxcontrib-bibtex: new version 2.5.0 (#32902)Seth R. Johnson1-0/+2
2.4 seems to have issues with sphinx-rtd and sphinx 5.1: ``` AttributeError: 'Text' object has no attribute 'rawsource' ```
2022-10-12py-uproot: add v4.3.5 (#33151)iarspider1-0/+1
2022-10-12meson: add 0.63.3 (#33216)Michael Kuhn1-0/+1
2022-10-12ESMF package update (#33202)Jim Edwards2-7/+15
2022-10-12bear: fix RPATH handling (#33217)Jonathon Anderson2-0/+25
2022-10-12py-poetry-core: jail git to stage directory (#33181)Adam J. Stewart1-0/+7
2022-10-12Add new vtk 9.2.2 release (#33001)MicK71-8/+10
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-10-12Update CRAN packages (#33223)Glenn Johnson269-38/+527
2022-10-12infernal: add v1.1.4 (#33230)Luke Diorio-Toth1-0/+2
2022-10-12trnascan-se: add v2.0.11 (#33232)Luke Diorio-Toth1-1/+2
2022-10-12Fix typo in docs (#33182)Massimiliano Culpo1-1/+1
2022-10-11Add checksum for py-cryptography 37.0.4 (#33186)iarspider1-0/+1
2022-10-11Add checksum for py-frozenlist 1.3.1 (#33193)iarspider1-0/+4
2022-10-11Add checksum for py-yarl 1.8.1 (#33195)iarspider1-0/+2
2022-10-11Add checksum for py-immutables 0.18 (#33197)iarspider1-0/+1
2022-10-11Add checksum for py-google-auth-oauthlib 0.5.2 (#33198)iarspider1-0/+1
2022-10-11Add checksum for py-jupyter-server 1.18.1 (#33204)iarspider1-0/+1
2022-10-11Add checksum for py-websocket-client 1.4.1 (#33205)iarspider1-0/+2
2022-10-11Add checksum for py-requests-unixsocket 0.3.0 (#33206)iarspider1-1/+2
2022-10-11Add checksum for py-typed-ast 1.5.4 (#33207)iarspider1-0/+2
2022-10-11Add checksum for py-scinum 1.4.3 (#33208)iarspider1-0/+2
2022-10-11Add checksum for py-python-rapidjson@1.8 (#33210)iarspider1-0/+1
2022-10-11Add checksum for py-pysqlite3 0.4.7 (#33211)iarspider1-0/+1
2022-10-11version bump to 3.10.42 (#33220)Luke Diorio-Toth1-0/+1
2022-10-11py-rtree: add v1.0.1 (#33222)Adam J. Stewart1-0/+1
2022-10-11GCC: update Xcode 14 conflict (#33226)Adam J. Stewart1-1/+1
2022-10-11Specify GCC prefix in LLVM-based compilers (#33146)Harmen Stoppels6-35/+45
* spack.compiler.Compiler: introduce prefix property We currently don't really have something that gives the GCC install path, which is used by many LLVM-based compilers (llvm, llvm-amdgpu, nvhpc, ...) to fix the GCC toolchain once and for all. This `prefix` property is dynamic in the sense that it queries the compiler itself. This is necessary because it's not easy to deduce the install path from the `cc` property (might be a symlink, might be a filename like `gcc` which works by having the compiler load a module that sets the PATH variable, might be a generic compiler wrapper based on environment variables like on cray...). With this property introduced, we can clean up some recipes that have the logic repeated for GCC. * intel-oneapi-compilers: set --gcc-sysroot to %gcc prefix
2022-10-11Darshan variant cleanup (#33165)kwryankrattiger2-27/+13
* Darshan-Runtime: Cleanup version dependent variants * Darshan-Util: Cleanup version dependent variants.
2022-10-11Omega-H: Current constraint doesn't allow any cuda (#33164)kwryankrattiger1-4/+4
From the issue referenced, it seems later and earlier versions of cuda work.
2022-10-11Refactor a few classes related to package repositories (#32273)Massimiliano Culpo29-684/+485
Caches used by repositories don't reference the global spack.repo.path instance anymore, but get the repository they refer to during initialization. Spec.virtual now use the index, and computation done to compute the index use Repository.is_virtual_safe. Code to construct mock packages and mock repository has been factored into a unique MockRepositoryBuilder that is used throughout the codebase. Add debug print for pushing and popping config scopes. Changed spack.repo.use_repositories so that it can override or not previous repos spack.repo.use_repositories updates spack.config.config according to the modifications done Removed a peculiar behavior from spack.config.Configuration where push would always bubble-up a scope named command_line if it existed
2022-10-11`spack diff` any specs you want (#32737)Peter Scheibel1-4/+6
Resolves #31782 With this change, if a spec is concrete after parsing (e.g. spec.yaml or /hash-based), then it is not disambiguated (a process which requires (a) that the spec be installed and (b) that it be part of the currently-active environment). This commit allows you to: * Diff specs from an environment regardless of whether they have been installed (more useful for projection/matrix-based envs) * Diff specs read from .yaml files which may or may not be entirely different installations of Spack Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-10-11Bump actions/setup-python from 4.2.0 to 4.3.0 (#33166)dependabot[bot]4-12/+12
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.2.0 to 4.3.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/b55428b1882923874294fa556849718a1d7f2ca5...13ae5bb136fac2878aff31522b9efb785519f984) --- 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> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-10-11py-importlib-resources: add v5.9.0 (#33047)iarspider1-2/+4
2022-10-11e4s ci: add cabana +rocm (#33177)eugeneswalker1-0/+1
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