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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
2023-05-23hpcg: apply patch with openmp pragma changes for intel and oneapi compilers ↵Andrey Parfenov1-0/+12
(#37856) Signed-off-by: Andrey Parfenov <andrey.parfenov@intel.com>
2023-05-23libgcrypt: patch 1.10.2 on macos (#37844)Todd Gamblin2-0/+38
macOS doesn't have `getrandom`, and 1.10.2 fails to compile because of this. There's an upstream fix at https://dev.gnupg.org/T6442 that will be in the next `libgcrypt` release, but the patch is available now.
2023-05-23dd4hep: add LD_LIBRARY_PATH for plugins for Gaudi (#37824)Juan Miguel Carceller1-0/+2
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-23gaudi: add gaudi to LD_LIBRARY_PATH (#37821)Juan Miguel Carceller1-0/+2
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-23dd4hep: restrict podio versions (#37699)Juan Miguel Carceller1-0/+1
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-22py-pastml: adding version for compatibility with py-topiary-asr (#37828)snehring2-2/+5
2023-05-22py-asttokens: add 2.2.1 (#37816)Manuela Kuhn1-0/+1
2023-05-22py-dask: add v2023.4.1 (#37550)genric4-4/+36
* py-dask: add v2023.4.1 * address review comments
2023-05-22py-huggingface-hub: add v0.14.1, cli variant (#37815)Adam J. Stewart3-2/+52
2023-05-22py-fiona: add v1.9.4 (#37780)Adam J. Stewart1-3/+5
2023-05-22azcopy: add new package (#37693)Adam J. Stewart1-0/+22
2023-05-22gaudi: fix issue with fmt::format (#37810)Juan Miguel Carceller2-0/+23
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-22tau %oneapi: -Wno-error=implicit-function-declaration (#37829)eugeneswalker1-0/+3
2023-05-22deleted package.py better error message (#37814)simonleary-umass-edu1-1/+1
adds the namespace to the exception object's string representation
2023-05-22swig: convert to new stand-alone test process (#37786)Tamara Dahlgren1-37/+31
2023-05-22llvm: Fix hwloc@1 and hwloc@:2.3 compatibility (#35387)Jordan Galby1-1/+8
2023-05-21arborx: new version 1.4 (#37809)Andrey Prokopenko1-2/+5
2023-05-21Update `CHANGELOG.md` for v0.20.0Todd Gamblin1-0/+218
2023-05-20py-argcomplete: add 3.0.8 (#37797)Manuela Kuhn1-2/+5
* py-argcomplete: add 3.0.8 * Update var/spack/repos/builtin/packages/py-argcomplete/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * [@spackbot] updating style on behalf of manuelakuhn --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-20Mochi-Margo: Add patch for pthreads detection (#36109)kwryankrattiger2-0/+567
2023-05-19libtiff: disable use of sphinx (#37803)Manuela Kuhn1-0/+2
2023-05-19py-anyio: add 3.6.2 (#37796)Manuela Kuhn1-1/+3
2023-05-19py-alabaster: add 0.7.13 (#37798)Manuela Kuhn1-0/+2
2023-05-19New patch release SLEPc 3.19.1 (#37675)Jose E. Roman2-0/+3
* New patch release SLEPc 3.19.1 * py-slepc4py: add explicit dependency on py-numpy
2023-05-19Automated deployment to update package flux-security 2023-05-16 (#37696)Vanessasaurus1-0/+1
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-05-19fix binutils dep of spack itself (#37738)Harmen Stoppels1-3/+2
2023-05-19aml: v0.2.1 (#37621)Swann Perarnau1-7/+11
* aml: v0.2.1 * add version 0.2.1 * fix hip variant bug * [fix] pkgconf required for all builds On top of needing pkgconf for autoreconf builds, the release configure scripts needs pkgconf do detect dependencies if any of the hwloc, ze, or opencl variants are active. * Remove deprecation for v0.2.0 based on PR advise.
2023-05-19intel-xed: add version 2023.04.16 (#37582)Mark W. Krentel2-12/+55
* intel-xed: add version 2023.04.16 1. add version 2023.04.16 2. adjust the mbuild resource to better match the xed version at the time 3. replace three conflicts() with one new requires() for x86_64 target 4. add patch for libxed-ild for some new avx512 instructions * [@spackbot] updating style on behalf of mwkrentel * Fix the build for 2023.04.16. XED requires its source directory to be exactly 'xed', so add a symlink. 5. move the mbuild resource up one level, xed wants it to be in the same directory as the xed source dir 6. deprecate 10.2019.03 * semantic style fix: add OSError to except * [@spackbot] updating style on behalf of mwkrentel --------- Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
2023-05-19spack env create: generate a view when newly created env has concrete specs ↵Harmen Stoppels2-1/+23
(#37799)
2023-05-19hipsycl: add v0.9.4 (#37247)Thomas-Ulrich1-0/+4
2023-05-19updates for the libpressio ecosystem (#37764)Robert Underwood10-0/+25
* updates for the libpressio ecosystem * [@spackbot] updating style on behalf of robertu94 * style fix: remove FIXME --------- Co-authored-by: Robert Underwood <runderwood@anl.gov> Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
2023-05-19archspec: fix entry in the JSON file (#37793)Massimiliano Culpo2-2/+2
2023-05-19fortrilinos: convert to new stand-alone test process (#37783)Tamara Dahlgren1-18/+11
2023-05-19formetis: converted to new stand-alone test process (#37785)Tamara Dahlgren1-19/+12
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-11-09 20:11:24 +0000