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2022-10-13Add missing upperbound to docs/spack.yaml (#33280)Harmen Stoppels1-0/+2
2022-10-13libcroco does not respect gtk-doc configure flag, so removing variant (#32890)Gregory Lee1-5/+7
* libcroco does not respect gtk-doc configure flag, so removing variant
2022-10-13py-meson: remove package (#33295)Adam J. Stewart2-27/+1
2022-10-13py-alive-progress, py-about-time, py-graphme: new packages (#33252)Luke Diorio-Toth3-0/+67
* new package + deps * Update var/spack/repos/builtin/packages/py-about-time/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-alive-progress/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * removed unnecessary python version dep Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-13Lua: Add versions and minor clean up (#33037)Chris White1-5/+14
* add new lua releases * split install phase and move it into a build phase, remove hardcoded standard flag * revert back to the original hardcoded std flag, guard patch against versions above 5.4
2022-10-13py-kornia: add v0.6.8 (#33287)Adam J. Stewart1-0/+1
2022-10-13py-shapely: add v1.8.5 (#33259)Adam J. Stewart1-0/+1
2022-10-13Add checksum for py-atomicwrites 1.4.1 (#33284)iarspider1-0/+1
2022-10-13Add checksum for py-asn1crypto 1.5.1 (#33283)iarspider1-0/+1
2022-10-13Fix ROCm constraints for ginkgo@glu_experimental in HiOp (#32499)Cameron Rutherford2-4/+4
* Remove ROCm constraints for ginkgo@glu_experimental. * Fix style. * Apply @tcojean suggestion. * Fix hip_repair_options in camp package. * Remvoe old ROCm logic. * Remove added whitespace. * Fix style issue. * Revert camp changes. * Revert camp whitespace change. * Set Ginkgo preferred version to 1.4.0
2022-10-13py-pyopenssl: add version 22.1.0 (#33189)Laurent Aphecetche1-1/+4
* py-pyopenssl: add version 22.1.0 * Update var/spack/repos/builtin/packages/py-pyopenssl/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-13Add checksum for py-bokeh 2.4.3 (#33236)iarspider1-6/+8
* Add checksum for py-bokeh 2.4.3 * [@spackbot] updating style on behalf of iarspider Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-13Add checksum for py-mpld3 0.5.8 (#33239)iarspider1-0/+1
2022-10-13Add checksum for py-cloudpickle 2.2.0 (#33240)iarspider1-0/+2
2022-10-13Add checksum for py-bottle 0.12.23 (#33241)iarspider1-0/+1
2022-10-13Add checksum for py-pymongo 4.2.0 (#33234)iarspider1-0/+2
2022-10-13Add checksum for py-keyring 23.9.1 (#33185)iarspider1-2/+4
* Add checksum for py-keyring 23.9.1 * Update package.py
2022-10-13Add checksum for py-setuptools-rust 1.5.1 (#33188)iarspider1-2/+3
* Add checksum for py-setuptools-rust 1.5.1 * Update package.py
2022-10-13Add checksum for py-jupyter-server-mathjax 0.2.6 (#33203)iarspider1-2/+4
* Add checksum for py-jupyter-server-mathjax 0.2.6 * Update package.py * Update package.py
2022-10-13Add checksum for py-regex 2022.8.17 (#33209)iarspider1-1/+4
* Add checksum for py-regex 2022.8.17 * Update var/spack/repos/builtin/packages/py-regex/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-13Add checksum for py-async-lru 1.0.3 (#33196)iarspider1-1/+10
* Add checksum for py-async-lru 1.0.3 * [@spackbot] updating style on behalf of iarspider * Update var/spack/repos/builtin/packages/py-async-lru/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py Co-authored-by: iarspider <iarspider@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-13Bump docker/login-action from 2.0.0 to 2.1.0 (#33268)dependabot[bot]1-2/+2
Bumps [docker/login-action](https://github.com/docker/login-action) from 2.0.0 to 2.1.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/49ed152c8eca782a232dede0303416e8f356c37b...f4ef78c080cd8ba55a85445d5b36e214a81df20a) --- updated-dependencies: - dependency-name: docker/login-action 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>
2022-10-13Bump docker/setup-buildx-action from 2.0.0 to 2.1.0 (#33267)dependabot[bot]1-1/+1
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.0.0 to 2.1.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/dc7b9719a96d48369863986a06765841d7ea23f6...95cb08cb2672c73d4ffd2f422e6d11953d2a9c70) --- 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> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-10-12exodusii: add fortran variant (#33074)William R Tobin1-0/+11
* add fortran variant, pass cmake options to build with fortran + specified compiler/mpi compiler wrapper (following existing style in the package), activate exodus fortran wrapper library compilation * change variant description, fix style
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
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