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2023-05-25Windows CI: add paraview deps nightly build (#37924)John W. Parent1-0/+31
Add a nightly job to attempt building all Paraview dependencies and upload the results to cdash. This check doesn't affect the reported build/test status of Spack. We are using this to monitor the state of Windows support while working on more-robust checks (eventually the Windows build will have to succeed to merge PRs to Spack).
2023-05-25fix(protobuf-c): set version bound for protobuf dependency (#37917)H. Joe Lee1-1/+1
Fix #37887 GitLab CI failure.
2023-05-25fix(dpdk): add a new version 23.03. (#37919)H. Joe Lee1-1/+2
Fix E4S GitLab CI issue #37887.
2023-05-25sirius: add rocsolver/wannier90 (#37900)Simon Pintarelli1-1/+7
* sirius: add rocsolver dependency for 7.5: * add wannier90
2023-05-25Dyninst: add standalone test (#37876)Tim Haines1-0/+9
* Dyninst: add standalone test * Add docstring with description * Don't use join_path for builtin path objects * Whitespace * Update format of docstring
2023-05-25Protobuf package: CMake fix for Windows build (#37926)John W. Parent2-0/+15
Qualify reference with namespace. A pending upstream PR will eventually make this unnecessary, so the patch is only applied for 3.22. versions.
2023-05-25flecsi: disable cinch dependency for v1 release (#37857)Richard Berger1-4/+14
* flecsi: disable cinch dependency for v1 releases * [@spackbot] updating style on behalf of rbberger --------- Co-authored-by: rbberger <rbberger@users.noreply.github.com>
2023-05-25environment-modules: fix @main version requirements (#37807)Xavier Delaruelle1-0/+3
Some requirements for @main version of environment-modules were missing: * python (to build ChangeLog documentation file) * py-sphinx@1.0: (to build man-pages, etc) Also adding gzip, which is now required to build ChangeLog.gz (which is now shipped instead of ChangeLog). Other versions are not requiring these tools (as documentation is pre-built in dist tarball).
2023-05-25Bugfix/tests: write not append stand-alone test status (#37841)Tamara Dahlgren2-1/+26
2023-05-25fix(pmdk): add pkconfig as dependency (#37896)H. Joe Lee1-0/+1
Fix #37887 failure.
2023-05-25[devito] Move to version 4.8.1 (#37915)Stephen Sachs2-17/+31
* [devito] Move to version 4.8.1 * Fix: Adding patch file * Update var/spack/repos/builtin/packages/py-devito/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-devito/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Addressing @adamjstewart comments --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-25Add shared variant to geos package (#37899)Alex Richert1-0/+4
Co-authored-by: alexrichert <alexrichert@gmail.com>
2023-05-25Add macOS ML CI stacks (#36586)Adam J. Stewart6-172/+223
* Add macOS ML CI stacks * torchmeta is no longer maintained and requires ancient PyTorch * Add MXNet * update darwin aarch64 stacks * add darwin-aarch64 scoped config.yaml * remove unnecessary cleanup job * fix specifications * fix labels * fix labels * fix indent on tags specification * no tags for trigger jobs * try overriding tags in stack spack.yaml * do not use CI_STACK_CONFIG_SCOPES * incorporate config:install_tree:root: overrides and compiler defs * copy relevant ci-scoped config settings directly into stack spack.yaml * remove build-job-remove * spack ci generate: add debug flag * include cdash config directly in stack spack.yaml * customize build-job script section to avoid absolute paths * add any-job specification * tags: use aarch64-macos instead of aarch64 * generate tags: use aarch64-macos instead of aarch64 * do not add morepadding * use shared mirror; comment out known failures * remove any-job * nproc || true * comment out specs failing due to bazel from cache codesign issue --------- Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
2023-05-24Update for py-gmxapi for 0.4.1. (#37834)M. Eric Irrgang1-2/+3
* Update for py-gmxapi for 0.4.1. * Note 0.4.1 hash from PyPI. * Note relaxed dependencies for future versions. * Update var/spack/repos/builtin/packages/py-gmxapi/package.py
2023-05-24py-charset-normalizer: add 3.1.0 (#37880)Manuela Kuhn1-2/+1
2023-05-24py-bids-validator: add 1.11.0 (#37845)Manuela Kuhn1-0/+1
2023-05-24py-bottleneck: add 1.3.7 (#37847)Manuela Kuhn1-0/+1
2023-05-24py-certifi: add 2023.5.7 (#37848)Manuela Kuhn1-1/+1
2023-05-24py-attrs: add 23.1.0 (#37817)Manuela Kuhn1-2/+10
* py-attrs: add 23.1.0 * Add missing dependency
2023-05-24py-babel: add 2.12.1 (#37818)Manuela Kuhn1-3/+3
* py-babel: add 2.12.1 * Update var/spack/repos/builtin/packages/py-babel/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-24py-rasterio: add v1.3.7 (#37886)Adam J. Stewart1-0/+1
2023-05-24py-lightly: add v1.4.6 (#37885)Adam J. Stewart1-0/+1
2023-05-24starpu: add release 1.4.1 (#37883)Nathalie Furmento1-0/+1
2023-05-24paraview (protobuf failure) #37437 (#37440)QuellynSnead1-0/+6
When attempting to build paraview@5.10.1 using a recent Intel compiler (Classic or OneAPI) or the IBM XL compiler, the build fails if the version of protobuf used is > 3.18
2023-05-24sensei: Allow Paraview 5.11 for sensei develop version (#37719)willdunklin1-1/+1
2023-05-24Pcluster local buildcache (#37852)Stephen Sachs5-38/+23
* [pcluster pipeline] Use local buildcache instead of upstream spack Spack currently does not relocate compiler references from upstream spack installations. When using a buildcache we don't need an upstream spack. * gcc needs to be installed via postinstall to get correct deps * quantum-espresso@gcc@12.3.0 returns ICE on neoverse_{n,v}1 * Force gitlab to pull the new container * Revert "Force gitlab to pull the new container" This reverts commit 3af5f4cd88245138992deb2a46c17e6f85858d68. Seems the gitlab version does not yet support "pull_policy" in .gitlab-ci.yml * Gitlab keeps picking up wrong container. Renaming * Update containers once more after failed build
2023-05-24bugfix: env concretize after remove (#37877)Greg Becker2-0/+27
2023-05-24spack remove: fix traversal when user specs intersect (#37882)Harmen Stoppels1-21/+20
drop unnecessary double loop over the matching user specs.
2023-05-24update nlcglib package (#37578)Simon Pintarelli2-28/+66
2023-05-24Add async vol v1.6 (#37875)Houjun Tang1-0/+1
2023-05-23hdf5-vol-daos: add a new package (#35653)H. Joe Lee1-0/+47
* hdf5-vol-daos: add a new package * hdf5-vol-daos: address @soumagne review --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-05-23julia: remove myself from maintainers list (#37868)Glenn Johnson1-1/+1
2023-05-23Updated hash for latest maintenance release (2022.2.1) (#37842)Laura Weber1-1/+1
2023-05-23gate: remove myself as maintainer (#37862)Glenn Johnson1-2/+0
2023-05-23Remove myself as maintainer of R packages (#37859)Glenn Johnson2-5/+1
* Remove myself as maintainer of R packages I will no longer have the time to properly maintain these packages. * fix flake8 test for import
2023-05-23bart: remove myself as maintainer (#37860)Glenn Johnson1-2/+0
2023-05-23heasoft: remove myself as maintainer (#37866)Glenn Johnson1-2/+0
2023-05-23opencv: remove myself from maintainers list (#37870)Glenn Johnson1-1/+1
2023-05-23e4s ci: add dealii (#32484)eugeneswalker1-0/+1
2023-05-23gatetools: remove myself as maintainer (#37863)Glenn Johnson1-2/+0
2023-05-23daos: add a new package (#35649)H. Joe Lee2-0/+112
2023-05-23reditools: remove myself as maintainer (#37871)Glenn Johnson1-2/+0
2023-05-23itk: remove myself as maintainer (#37867)Glenn Johnson1-2/+0
2023-05-23mumax: remove myself as maintainer (#37869)Glenn Johnson1-2/+0
2023-05-23gurobi: remove myself as maintainer (#37865)Glenn Johnson1-2/+0
2023-05-23fplo: remove myself as maintainer (#37861)Glenn Johnson1-2/+0
2023-05-23New package: FDS (#37850)kjrstory1-0/+94
2023-05-23py-bleach: add 6.0.0 (#37846)Manuela Kuhn1-4/+1
2023-05-23Bioc updates (#37297)Glenn Johnson193-24/+358
* add version 1.48.0 to bioconductor package r-a4 * add version 1.48.0 to bioconductor package r-a4base * add version 1.48.0 to bioconductor package r-a4classif * add version 1.48.0 to bioconductor package r-a4core * add version 1.48.0 to bioconductor package r-a4preproc * add version 1.48.0 to bioconductor package r-a4reporting * add version 1.54.0 to bioconductor package r-absseq * add version 1.30.0 to bioconductor package r-acde * add version 1.78.0 to bioconductor package r-acgh * add version 2.56.0 to bioconductor package r-acme * add version 1.70.0 to bioconductor package r-adsplit * add version 1.72.0 to bioconductor package r-affxparser * add version 1.78.0 to bioconductor package r-affy * add version 1.76.0 to bioconductor package r-affycomp * add version 1.58.0 to bioconductor package r-affycontam * add version 1.72.0 to bioconductor package r-affycoretools * add version 1.48.0 to bioconductor package r-affydata * add version 1.52.0 to bioconductor package r-affyilm * add version 1.70.0 to bioconductor package r-affyio * add version 1.76.0 to bioconductor package r-affyplm * add version 1.46.0 to bioconductor package r-affyrnadegradation * add version 1.48.0 to bioconductor package r-agdex * add version 3.32.0 to bioconductor package r-agilp * add version 2.50.0 to bioconductor package r-agimicrorna * add version 1.32.0 to bioconductor package r-aims * add version 1.32.0 to bioconductor package r-aldex2 * add version 1.38.0 to bioconductor package r-allelicimbalance * add version 1.26.0 to bioconductor package r-alpine * add version 2.62.0 to bioconductor package r-altcdfenvs * add version 2.24.0 to bioconductor package r-anaquin * add version 1.28.0 to bioconductor package r-aneufinder * add version 1.28.0 to bioconductor package r-aneufinderdata * add version 1.72.0 to bioconductor package r-annaffy * add version 1.78.0 to bioconductor package r-annotate * add version 1.62.0 to bioconductor package r-annotationdbi * add version 1.24.0 to bioconductor package r-annotationfilter * add version 1.42.0 to bioconductor package r-annotationforge * add version 3.8.0 to bioconductor package r-annotationhub * add version 3.30.0 to bioconductor package r-aroma-light * add version 1.32.0 to bioconductor package r-bamsignals * add version 2.16.0 to bioconductor package r-beachmat * add version 2.60.0 to bioconductor package r-biobase * add version 2.8.0 to bioconductor package r-biocfilecache * add version 0.46.0 to bioconductor package r-biocgeneric * add version 1.10.0 to bioconductor package r-biocio * add version 1.18.0 to bioconductor package r-biocneighbors * add version 1.34.0 to bioconductor package r-biocparallel * add version 1.16.0 to bioconductor package r-biocsingular * add version 2.28.0 to bioconductor package r-biocstyle * add version 3.17.1 to bioconductor package r-biocversion * add version 2.56.0 to bioconductor package r-biomart * add version 1.28.0 to bioconductor package r-biomformat * add version 2.68.0 to bioconductor package r-biostrings * add version 1.48.0 to bioconductor package r-biovizbase * add version 1.10.0 to bioconductor package r-bluster * add version 1.68.0 to bioconductor package r-bsgenome * add version 1.36.0 to bioconductor package r-bsseq * add version 1.42.0 to bioconductor package r-bumphunter * add version 2.66.0 to bioconductor package r-category * add version 2.30.0 to bioconductor package r-champ * add version 2.32.0 to bioconductor package r-champdata * add version 1.50.0 to bioconductor package r-chipseq * add version 4.8.0 to bioconductor package r-clusterprofiler * add version 1.36.0 to bioconductor package r-cner * add version 1.32.0 to bioconductor package r-codex * add version 2.16.0 to bioconductor package r-complexheatmap * add version 1.74.0 to bioconductor package r-ctc * add version 2.28.0 to bioconductor package r-decipher * add version 0.26.0 to bioconductor package r-delayedarray * add version 1.22.0 to bioconductor package r-delayedmatrixstats * add version 1.40.0 to bioconductor package r-deseq2 * add version 1.46.0 to bioconductor package r-dexseq * add version 1.42.0 to bioconductor package r-dirichletmultinomial * add version 2.14.0 to bioconductor package r-dmrcate * add version 1.74.0 to bioconductor package r-dnacopy * add version 3.26.0 to bioconductor package r-dose * add version 2.48.0 to bioconductor package r-dss * add version 3.42.0 to bioconductor package r-edger * add version 1.20.0 to bioconductor package r-enrichplot * add version 2.24.0 to bioconductor package r-ensembldb * add version 1.46.0 to bioconductor package r-exomecopy * add version 2.8.0 to bioconductor package r-experimenthub * add version 1.26.0 to bioconductor package r-fgsea * add version 2.72.0 to bioconductor package r-gcrma * add version 1.36.0 to bioconductor package r-gdsfmt * add version 1.82.0 to bioconductor package r-genefilter * add version 1.36.0 to bioconductor package r-genelendatabase * add version 1.72.0 to bioconductor package r-genemeta * add version 1.78.0 to bioconductor package r-geneplotter * add version 1.22.0 to bioconductor package r-genie3 * add version 1.36.0 to bioconductor package r-genomeinfodb * update r-genomeinfodbdata * add version 1.36.0 to bioconductor package r-genomicalignments * add version 1.52.0 to bioconductor package r-genomicfeatures * add version 1.52.0 to bioconductor package r-genomicranges * add version 2.68.0 to bioconductor package r-geoquery * add version 1.48.0 to bioconductor package r-ggbio * add version 3.8.0 to bioconductor package r-ggtree * add version 2.10.0 to bioconductor package r-glimma * add version 1.12.0 to bioconductor package r-glmgampoi * add version 5.54.0 to bioconductor package r-globaltest * update r-go-db * add version 1.20.0 to bioconductor package r-gofuncr * add version 2.26.0 to bioconductor package r-gosemsim * add version 1.52.0 to bioconductor package r-goseq * add version 2.66.0 to bioconductor package r-gostats * add version 1.78.0 to bioconductor package r-graph * add version 1.62.0 to bioconductor package r-gseabase * add version 1.32.0 to bioconductor package r-gtrellis * add version 1.44.0 to bioconductor package r-gviz * add version 1.28.0 to bioconductor package r-hdf5array * add version 1.72.0 to bioconductor package r-hypergraph * add version 1.36.0 to bioconductor package r-illumina450probevariants-db * add version 0.42.0 to bioconductor package r-illuminaio * add version 1.74.0 to bioconductor package r-impute * add version 1.38.0 to bioconductor package r-interactivedisplaybase * add version 2.34.0 to bioconductor package r-iranges * add version 1.60.0 to bioconductor package r-kegggraph * add version 1.40.0 to bioconductor package r-keggrest * add version 3.56.0 to bioconductor package r-limma * add version 2.52.0 to bioconductor package r-lumi * add version 1.76.0 to bioconductor package r-makecdfenv * add version 1.78.0 to bioconductor package r-marray * add version 1.12.0 to bioconductor package r-matrixgenerics * add version 1.8.0 to bioconductor package r-metapod * add version 2.46.0 to bioconductor package r-methylumi * add version 1.46.0 to bioconductor package r-minfi * add version 1.34.0 to bioconductor package r-missmethyl * add version 1.80.0 to bioconductor package r-mlinterfaces * add version 1.12.0 to bioconductor package r-mscoreutils * add version 2.26.0 to bioconductor package r-msnbase * add version 2.56.0 to bioconductor package r-multtest * add version 1.38.0 to bioconductor package r-mzid * add version 2.34.0 to bioconductor package r-mzr * add version 1.62.0 to bioconductor package r-oligoclasses * update r-org-hs-eg-db * add version 1.42.0 to bioconductor package r-organismdbi * add version 1.40.0 to bioconductor package r-pathview * add version 1.92.0 to bioconductor package r-pcamethods * update r-pfam-db * add version 1.44.0 to bioconductor package r-phyloseq * add version 1.62.0 to bioconductor package r-preprocesscore * add version 1.32.0 to bioconductor package r-protgenerics * add version 1.34.0 to bioconductor package r-quantro * add version 2.32.0 to bioconductor package r-qvalue * add version 1.76.0 to bioconductor package r-rbgl * add version 2.40.0 to bioconductor package r-reportingtools * add version 2.44.0 to bioconductor package r-rgraphviz * add version 2.44.0 to bioconductor package r-rhdf5 * add version 1.12.0 to bioconductor package r-rhdf5filters * add version 1.22.0 to bioconductor package r-rhdf5lib * add version 1.76.0 to bioconductor package r-roc * add version 1.28.0 to bioconductor package r-rots * add version 2.16.0 to bioconductor package r-rsamtools * add version 1.60.0 to bioconductor package r-rtracklayer * add version 0.38.0 to bioconductor package r-s4vectors * add version 1.8.0 to bioconductor package r-scaledmatrix * add version 1.28.0 to bioconductor package r-scater * add version 1.14.0 to bioconductor package r-scdblfinder * add version 1.28.0 to bioconductor package r-scran * add version 1.10.0 to bioconductor package r-scuttle * add version 1.66.0 to bioconductor package r-seqlogo * add version 1.58.0 to bioconductor package r-shortread * add version 1.74.0 to bioconductor package r-siggenes * add version 1.22.0 to bioconductor package r-singlecellexperiment * add version 1.34.0 to bioconductor package r-snprelate * add version 1.50.0 to bioconductor package r-snpstats * add version 2.36.0 to bioconductor package r-somaticsignatures * add version 1.12.0 to bioconductor package r-sparsematrixstats * add version 1.40.0 to bioconductor package r-spem * add version 1.38.0 to bioconductor package r-sseq * add version 1.30.0 to bioconductor package r-summarizedexperiment * add version 3.48.0 to bioconductor package r-sva * add version 1.38.0 to bioconductor package r-tfbstools * add version 1.22.0 to bioconductor package r-tmixclust * add version 2.52.0 to bioconductor package r-topgo * add version 1.24.0 to bioconductor package r-treeio * add version 1.28.0 to bioconductor package r-tximport * add version 1.28.0 to bioconductor package r-tximportdata * add version 1.46.0 to bioconductor package r-variantannotation * add version 3.68.0 to bioconductor package r-vsn * add version 2.6.0 to bioconductor package r-watermelon * add version 2.46.0 to bioconductor package r-xde * add version 1.58.0 to bioconductor package r-xmapbridge * add version 0.40.0 to bioconductor package r-xvector * add version 1.26.0 to bioconductor package r-yapsa * add version 1.26.0 to bioconductor package r-yarn * add version 1.46.0 to bioconductor package r-zlibbioc * Revert "add version 1.82.0 to bioconductor package r-genefilter" This reverts commit 1702071c6d3ab83b75e0fcf493622113957223bb. * Revert "add version 0.38.0 to bioconductor package r-s4vectors" This reverts commit 58a7df23872ac8035fdac75c93cedf6dd7819dd0. * add version 0.38.0 to bioconductor package r-s4vectors * Revert "add version 1.28.0 to bioconductor package r-aneufinder" This reverts commit 0a1f59de6c17fe6aa62bcf807826f9d2023280e6. * add version 1.28.0 to bioconductor package r-aneufinder * Revert "add version 2.16.0 to bioconductor package r-beachmat" This reverts commit cd49fb8e4c84763a063f1b2d0b3bdc0179161568. * add version 2.16.0 to bioconductor package r-beachmat * Revert "add version 4.8.0 to bioconductor package r-clusterprofiler" This reverts commit 6e9a951cbe08042ca5100f47b8b1680cae26cc14. * add version 4.8.0 to bioconductor package r-clusterprofiler * Fix syntax error * r-genefilter: add version 1.82.0 * new package: r-basilisk-utils * new package: r-basilisk * new package: r-densvis * new package: r-dir-expiry * r-affyplm: add zlib dependency * r-cner: add zlib dependency * r-mzr: add zlib dependency * r-rhdf5filters: add zstd dependency * r-shortread: add zlib dependency * r-snpstats: add zlib dependency --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-05-23usalign: new package (#37646)snehring1-0/+47
* usalign: adding new package * usalign: updating shasum, adding note about distribution
generated by cgit v1.2.3-60-g2f50 (git 2.42.0) at 2024-07-16 23:53:28 +0000