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Sync with upstream #72
Sync with upstream #72
Commits on Nov 11, 2022
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libxcrypt: 4.4.30 (spack#33845)
* libxcrypt: 4.4.30 * libxcrypt.so.2 by default * add libs prop, since libxcrypt provides libcrypt
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Commits on Nov 12, 2022
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magma: add version 2.7.0 (spack#33814)
* magma: add version 2.7.0 Co-authored-by: Stan Tomov <tomov@icl.utk.edu>
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Update ExaGO for 1.5.0 release. (spack#33853)
* Update ExaGO for 1.5.0 release
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use spack.version_info as source of version truth for spack tutorial …
…command (spack#33860) * Use spack.spack_version_info as source of truth Co-authored-by: Todd Gamblin <gamblin2@llnl.gov>
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Commits on Nov 13, 2022
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Speed-up bootstrap and architecture unit tests (spack#33865)
* Speed-up bootstrap mirror unit test The unit test doesn't need to concretize, since it checks only metadata for the mirror. * architecture.py: use "default_mock_concretization" for slow test
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hotfix: ensure that schema is compatible with tutorial VM config
We added a hotfix to releases/v0.19 with a feature flag, but the flag is incompatible with the config schema on `develop`. - [x] Ensure schema is compatible on develop even though config option is unused.
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[sundials] fix cmake argument generation for '+magma' (spack#33858)
[dealii] force cmake to accept Scalapack settings from Spack
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GDAL: add v3.6.0 (spack#33856)
* GDAL: add v3.6.0 * Explicitly control BASISU * More reasonable variant defaults
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Commits on Nov 14, 2022
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Remove support for running with Python 2.7 (spack#33063)
* Remove CI jobs related to Python 2.7 * Remove Python 2.7 specific code from Spack core * Remove externals for Python 2 only * Remove llnl.util.compat
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Update CHANGELOG.md for v0.19.0
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
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rocm: add all GFX9, GFX10 and GFX11 amdgpu_targets (spack#33871)
This change adds all documented AMDGPU processors from GFX9 through GFX11 and sorts the list.
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Add
$date
option to the list of config variables (spack#33875)I'm finding I often want the date in my paths and it would be nice if spack had a config variable for this. Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
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Ginkgo 1.5.0 version, new MPI variant, related fixes (spack#33838)
* Ginkgo 1.5.0 release, new MPI variant * Fix ROCTHRUST/ROCPRIM issues * Fix deal.II issue with Ginkgo 1.5.0 * Also fix hipRAND+rocRAND RPATH settings * Turn off CCACHE for spack builds. Co-authored-by: Veselin Dobrev <dobrev@llnl.gov> Co-authored-by: Veselin Dobrev <dobrev@llnl.gov>
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Commits on Nov 15, 2022
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[py-pmw-patched] needs setuptools to build (spack#33902)
Error message: ``` ModuleNotFoundError: No module named 'setuptools' ``` Co-authored-by: Stephen Sachs <stesachs@amazon.com>
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gitlab: Add shared PR mirror to places pipelines look for binaries. (s…
…pack#33746) While binaries built for PRs that get merged must still be rebuilt in develop pipelines, they can be used by other PRs that find they would otherwise need to rebuild them. Now that spackbot is managing copying PR binaries from merged PRs into a shared location, keeping it pruned to a reasonable size, and making sure the indices are up to date, spack can use these mirrors as a potential source of binaries.
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Stop using
six
in Spack (spack#33905)Since we dropped support for Python 2.7, there's no need so use `six` anymore. We still need to vendor it until we update our vendored dependencies.
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Revert "fix perl libxcrypt.so dep (spack#33846)" (spack#33909)
This reverts commit bf1b2a8, as libxcrypt's configure script requires Perl, leading to a circular dependency.
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Since they cause --backtrace to report backtraces even with exit code 0
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python: missing libxcrypt dep (spack#33847)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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External find now searches all dynamic linker paths (spack#33800)
Add spack.ld_so_conf.host_dynamic_linker_search_paths Retrieve the current host runtime search paths for shared libraries; for GNU and musl Linux we try to retrieve the dynamic linker from the current Python interpreter and then find the corresponding config file (e.g. ld.so.conf or ld-musl-<arch>.path). Similar can be done for BSD and others, but this is not implemented yet. The default paths are always returned. We don't check if the listed directories exist. Use this in spack external find for libraries. Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
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Fix incorrect timer (spack#33900)
Revamp the timer so we always have a designated begin and end. Fix a bug where the phase timer was stopped before the phase started, resulting in incorrect timing reports in timers.json.
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depfile: improve tab completion (spack#33773)
This PR allows you to do: ``` spack env create -d . spack -e . add python spack -e . concretize spack -e . env depfile -o Makefile make in<tab> # -> install make install-<tab> # -> install-deps/ make install-deps/py<tab> # -> install-deps/python-x.y.z-hash make install/zl<tab> # -> install/zlib-x.y.z-hash make SP<tab> # -> make SPACK make SPACK_<tab> # -> make SPACK_INSTALL_FLAGS= ```
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thepeg: make rivet dependency optional... (spack#33912)
* thepeg: make rivet dependency optional... * add "libs" variant, move compiler flags to flag_handler Co-authored-by: iarspider <iarspider@users.noreply.github.com>
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nsimd: Update Python requirements (spack#33879)
We need Python 3.0:3.9
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New Package: Prime95/Mprime (spack#33895)
* New Package: Prime95/Mprime * Fix trailing whitespaces in prime95 * Fix checksum for prime95 Signed-off-by: saqibkh <saqibkhan@utexas.edu>
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spectre: add v2022.11.15 (spack#33921)
Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
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Update BML versions list in package.py (spack#33920)
* Update BML versions list in package.py * Update package.py
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xsdk: add version @0.8.0 (spack#33794)
- enable sundials+magma+ginkgo - enable dealii+sundials - disable dealii~cgal due to build errors - enable petsc+rocm - enable slepc+cuda+rocm - enable strumpack+cuda+slate - enable slate build with non-gcc compilers - enable pumi+shared - enable mfem+shared - enable ginkgo+mpi - add hiop - and exago - use exago~ipopt due to mumps~mpi conflict with mpi.h) - add raja variant [used by exago/hiop] ~raja builds exago in pflow-only mode - i.e exago~hiop~ipopt~python~cuda ^hiop~cuda [Default on MacOS] Co-authored-by: Cody Balos <balos1@llnl.gov>
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zfp: update for version 1.0.0 (spack#33452)
* zfp: updates and many fixes for version 1.0.0 Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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Commits on Nov 16, 2022
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neovim: fix build dependencies (spack#33935)
Buildin neovim@0.8.0 complains (for me) about Lua's lpeg and mpack packages not being available at build time. Removing the link-only setting in the dependencies for these two packages fixes the build for me.
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py-isal: use external libisal (spack#33932)
* py-isal: adding some missing build deps * py-isal: use external libisal
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add sz3 and mdz smoke test for inclusion in e4s (spack#33864)
* add sz3 and mdz smoke test Co-authored-by: Robert Underwood <runderwood@anl.gov>
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SIP build system: fix "python not defined in builder" (spack#33906)
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
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Windows bootstrapping: remove unneeded call to add dll to PATH (spack…
…#33622) spack#32942 fixed bootstrapping on Windows by having the core Spack code explicitly add the Clingo package bin/ directory as a DLL path. Since then, spack#33400 has been merged, which ensures that the Python module installed by the Spack `clingo` package can find the DLLs in bin/. Note that this only works for Spack instances which have been bootstrapped after spack#33400: for installations bootstrapped before then, you will need to run `spack clean -b` (this would only be needed for Spack instances running on Windows).
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Clean unit-test workflow file (spack#33945)
Delete statements related to Python 2.7, and avoid installing patchelf since now we can bootstrap it.
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Commits on Nov 17, 2022
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* ninja: Set min. required version of re2c dependency, fixes spack#33127
(spack#33128) Reviewed-by: haampie, bernhardkaindl
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[xz] icc does not support attribute __symver__ (spack#33839)
xz have added attribute __symver__ for compilers that identify as GCC>=10.0 via __GNUC__. Intels `icc` sets __GNUC__ but currently does not support this attribute: https://community.intel.com/t5/Intel-C-Compiler/symver-not-supported/m-p/1429028/emcs_t/S2h8ZW1haWx8dG9waWNfc3Vic2NyaXB0aW9ufExBQVRWMjIyUFFZTlZTfDE0MjkwMjh8U1VCU0NSSVBUSU9OU3xoSw#M40459
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zlib, openssl: return to
http
URLs (spack#33324)In spack#3113, `https` was removed to ensure that `curl` can be bootstrapped without SSL being present. This was lost in spack#25672 which aimed to use `https` where possible. Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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Python: fix bug detection, trying to access self (spack#33955)
Typo introduced in spack#33847
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Octopus : Separate serial and MPI dependencies (spack#33836)
* replace mpi as a variant instead of dependency * separate serial and MPI dependencies * configure args depending on serial or mpi variant * reformat with black
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Remove deprecated subcommands from "spack bootstrap" (spack#33964)
These commands are slated for removal in v0.20
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Python: do not set PYTHONHOME during build (spack#33956)
Setting PYTHONHOME is rarely needed (since each interpreter has various ways of setting it automatically) and very often it is difficult to get right manually. For instance, the change done to set PYTHONHOME to sysconfig["base_prefix"] broke bootstrapping dev dependencies of Spack for me, when working inside a virtual environment in Linux.
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Waf build system: fix typo in legacy_attributes (spack#33958)
Fix erroneous duplication of `build_time_test_callbacks` in `legacy_attributes`: one of the duplicates should be `install_time_test_callbacks`
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Update CMake version to 3.25.0 (spack#33957)
CMake had official release 3.25.0, update package version to reflect Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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Hdf5 package: build on Windows (spack#31141)
* Enable hdf5 build (including +mpi) on Windows * This includes updates to hdf5 dependencies openssl (minor edit) and bzip2 (more-extensive edits) * Add binary-based installation of msmpi (this is currently the only supported MPI implementation in Spack for Windows). Note that this does not install to the Spack-specified prefix. This implementation will be replaced with a source-based implementation Co-authored-by: John Parent <john.parent@kitware.com>
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Spack Bioconductor package updates (spack#33852)
* add version 1.46.0 to bioconductor package r-a4 * add version 1.46.0 to bioconductor package r-a4base * add version 1.46.0 to bioconductor package r-a4classif * add version 1.46.0 to bioconductor package r-a4core * add version 1.46.0 to bioconductor package r-a4preproc * add version 1.46.0 to bioconductor package r-a4reporting * add version 1.52.0 to bioconductor package r-absseq * add version 1.28.0 to bioconductor package r-acde * add version 1.76.0 to bioconductor package r-acgh * add version 2.54.0 to bioconductor package r-acme * add version 1.68.0 to bioconductor package r-adsplit * add version 1.70.0 to bioconductor package r-affxparser * add version 1.76.0 to bioconductor package r-affy * add version 1.74.0 to bioconductor package r-affycomp * add version 1.58.0 to bioconductor package r-affycompatible * add version 1.56.0 to bioconductor package r-affycontam * add version 1.70.0 to bioconductor package r-affycoretools * add version 1.46.0 to bioconductor package r-affydata * add version 1.50.0 to bioconductor package r-affyilm * add version 1.68.0 to bioconductor package r-affyio * add version 1.74.0 to bioconductor package r-affyplm * add version 1.44.0 to bioconductor package r-affyrnadegradation * add version 1.46.0 to bioconductor package r-agdex * add version 3.30.0 to bioconductor package r-agilp * add version 2.48.0 to bioconductor package r-agimicrorna * add version 1.30.0 to bioconductor package r-aims * add version 1.30.0 to bioconductor package r-aldex2 * add version 1.36.0 to bioconductor package r-allelicimbalance * add version 1.24.0 to bioconductor package r-alpine * add version 2.60.0 to bioconductor package r-altcdfenvs * add version 2.22.0 to bioconductor package r-anaquin * add version 1.26.0 to bioconductor package r-aneufinder * add version 1.26.0 to bioconductor package r-aneufinderdata * add version 1.70.0 to bioconductor package r-annaffy * add version 1.76.0 to bioconductor package r-annotate * add version 1.60.0 to bioconductor package r-annotationdbi * add version 1.22.0 to bioconductor package r-annotationfilter * add version 1.40.0 to bioconductor package r-annotationforge * add version 3.6.0 to bioconductor package r-annotationhub * add version 3.28.0 to bioconductor package r-aroma-light * add version 1.30.0 to bioconductor package r-bamsignals * add version 2.14.0 to bioconductor package r-beachmat * add version 2.58.0 to bioconductor package r-biobase * add version 2.6.0 to bioconductor package r-biocfilecache * add version 0.44.0 to bioconductor package r-biocgenerics * add version 1.8.0 to bioconductor package r-biocio * add version 1.16.0 to bioconductor package r-biocneighbors * add version 1.32.1 to bioconductor package r-biocparallel * add version 1.14.0 to bioconductor package r-biocsingular * add version 2.26.0 to bioconductor package r-biocstyle * add version 3.16.0 to bioconductor package r-biocversion * add version 2.54.0 to bioconductor package r-biomart * add version 1.26.0 to bioconductor package r-biomformat * add version 2.66.0 to bioconductor package r-biostrings * add version 1.46.0 to bioconductor package r-biovizbase * add version 1.8.0 to bioconductor package r-bluster * add version 1.66.1 to bioconductor package r-bsgenome * add version 1.34.0 to bioconductor package r-bsseq * add version 1.40.0 to bioconductor package r-bumphunter * add version 2.64.0 to bioconductor package r-category * add version 2.28.0 to bioconductor package r-champ * add version 2.30.0 to bioconductor package r-champdata * add version 1.48.0 to bioconductor package r-chipseq * add version 4.6.0 to bioconductor package r-clusterprofiler * add version 1.34.0 to bioconductor package r-cner * add version 1.30.0 to bioconductor package r-codex * add version 2.14.0 to bioconductor package r-complexheatmap * add version 1.72.0 to bioconductor package r-ctc * add version 2.26.0 to bioconductor package r-decipher * add version 0.24.0 to bioconductor package r-delayedarray * add version 1.20.0 to bioconductor package r-delayedmatrixstats * add version 1.38.0 to bioconductor package r-deseq2 * add version 1.44.0 to bioconductor package r-dexseq * add version 1.40.0 to bioconductor package r-dirichletmultinomial * add version 2.12.0 to bioconductor package r-dmrcate * add version 1.72.0 to bioconductor package r-dnacopy * add version 3.24.1 to bioconductor package r-dose * add version 2.46.0 to bioconductor package r-dss * add version 3.40.0 to bioconductor package r-edger * add version 1.18.0 to bioconductor package r-enrichplot * add version 2.22.0 to bioconductor package r-ensembldb * add version 1.44.0 to bioconductor package r-exomecopy * add version 2.6.0 to bioconductor package r-experimenthub * add version 1.24.0 to bioconductor package r-fgsea * add version 2.70.0 to bioconductor package r-gcrma * add version 1.34.0 to bioconductor package r-gdsfmt * add version 1.80.0 to bioconductor package r-genefilter * add version 1.34.0 to bioconductor package r-genelendatabase * add version 1.70.0 to bioconductor package r-genemeta * add version 1.76.0 to bioconductor package r-geneplotter * add version 1.20.0 to bioconductor package r-genie3 * add version 1.34.3 to bioconductor package r-genomeinfodb * update r-genomeinfodbdata * add version 1.34.0 to bioconductor package r-genomicalignments * add version 1.50.2 to bioconductor package r-genomicfeatures * add version 1.50.1 to bioconductor package r-genomicranges * add version 2.66.0 to bioconductor package r-geoquery * add version 1.46.0 to bioconductor package r-ggbio * add version 3.6.2 to bioconductor package r-ggtree * add version 2.8.0 to bioconductor package r-glimma * add version 1.10.0 to bioconductor package r-glmgampoi * add version 5.52.0 to bioconductor package r-globaltest * update r-go-db * add version 1.18.0 to bioconductor package r-gofuncr * add version 2.24.0 to bioconductor package r-gosemsim * add version 1.50.0 to bioconductor package r-goseq * add version 2.64.0 to bioconductor package r-gostats * add version 1.76.0 to bioconductor package r-graph * add version 1.60.0 to bioconductor package r-gseabase * add version 1.30.0 to bioconductor package r-gtrellis * add version 1.42.0 to bioconductor package r-gviz * add version 1.26.0 to bioconductor package r-hdf5array * add version 1.70.0 to bioconductor package r-hypergraph * add version 1.34.0 to bioconductor package r-illumina450probevariants-db * add version 0.40.0 to bioconductor package r-illuminaio * add version 1.72.0 to bioconductor package r-impute * add version 1.36.0 to bioconductor package r-interactivedisplaybase * add version 2.32.0 to bioconductor package r-iranges * add version 1.58.0 to bioconductor package r-kegggraph * add version 1.38.0 to bioconductor package r-keggrest * add version 3.54.0 to bioconductor package r-limma * add version 2.50.0 to bioconductor package r-lumi * add version 1.74.0 to bioconductor package r-makecdfenv * add version 1.76.0 to bioconductor package r-marray * add version 1.10.0 to bioconductor package r-matrixgenerics * add version 1.6.0 to bioconductor package r-metapod * add version 2.44.0 to bioconductor package r-methylumi * add version 1.44.0 to bioconductor package r-minfi * add version 1.32.0 to bioconductor package r-missmethyl * add version 1.78.0 to bioconductor package r-mlinterfaces * add version 1.10.0 to bioconductor package r-mscoreutils * add version 2.24.0 to bioconductor package r-msnbase * add version 2.54.0 to bioconductor package r-multtest * add version 1.36.0 to bioconductor package r-mzid * add version 2.32.0 to bioconductor package r-mzr * add version 1.60.0 to bioconductor package r-oligoclasses * update r-org-hs-eg-db * add version 1.40.0 to bioconductor package r-organismdbi * add version 1.38.0 to bioconductor package r-pathview * add version 1.90.0 to bioconductor package r-pcamethods * update r-pfam-db * add version 1.42.0 to bioconductor package r-phyloseq * add version 1.60.0 to bioconductor package r-preprocesscore * add version 1.30.0 to bioconductor package r-protgenerics * add version 1.32.0 to bioconductor package r-quantro * add version 2.30.0 to bioconductor package r-qvalue * add version 1.74.0 to bioconductor package r-rbgl * add version 2.38.0 to bioconductor package r-reportingtools * add version 2.42.0 to bioconductor package r-rgraphviz * add version 2.42.0 to bioconductor package r-rhdf5 * add version 1.10.0 to bioconductor package r-rhdf5filters * add version 1.20.0 to bioconductor package r-rhdf5lib * add version 2.0.0 to bioconductor package r-rhtslib * add version 1.74.0 to bioconductor package r-roc * add version 1.26.0 to bioconductor package r-rots * add version 2.14.0 to bioconductor package r-rsamtools * add version 1.58.0 to bioconductor package r-rtracklayer * add version 0.36.0 to bioconductor package r-s4vectors * add version 1.6.0 to bioconductor package r-scaledmatrix * add version 1.26.0 to bioconductor package r-scater * add version 1.12.0 to bioconductor package r-scdblfinder * add version 1.26.0 to bioconductor package r-scran * add version 1.8.0 to bioconductor package r-scuttle * add version 1.64.0 to bioconductor package r-seqlogo * add version 1.56.0 to bioconductor package r-shortread * add version 1.72.0 to bioconductor package r-siggenes * add version 1.20.0 to bioconductor package r-singlecellexperiment * add version 1.32.0 to bioconductor package r-snprelate * add version 1.48.0 to bioconductor package r-snpstats * add version 2.34.0 to bioconductor package r-somaticsignatures * add version 1.10.0 to bioconductor package r-sparsematrixstats * add version 1.38.0 to bioconductor package r-spem * add version 1.36.0 to bioconductor package r-sseq * add version 1.28.0 to bioconductor package r-summarizedexperiment * add version 3.46.0 to bioconductor package r-sva * add version 1.36.0 to bioconductor package r-tfbstools * add version 1.20.0 to bioconductor package r-tmixclust * add version 2.50.0 to bioconductor package r-topgo * add version 1.22.0 to bioconductor package r-treeio * add version 1.26.0 to bioconductor package r-tximport * add version 1.26.0 to bioconductor package r-tximportdata * add version 1.44.0 to bioconductor package r-variantannotation * add version 3.66.0 to bioconductor package r-vsn * add version 2.4.0 to bioconductor package r-watermelon * add version 2.44.0 to bioconductor package r-xde * add version 1.56.0 to bioconductor package r-xmapbridge * add version 0.38.0 to bioconductor package r-xvector * add version 1.24.0 to bioconductor package r-yapsa * add version 1.24.0 to bioconductor package r-yarn * add version 1.44.0 to bioconductor package r-zlibbioc * make version resource consistent for r-bsgenome-hsapiens-ucsc-hg19 * make version resource consistent for r-go-db * make version resource consistent for r-kegg-db * make version resource consistent for r-org-hs-eg-db * make version resource consistent for r-pfam-db * new package: r-ggrastr * Patches not needed for new version * new package: r-hdo-db * new package: r-ggnewscale * new package: r-gson * Actually depends on ggplot2@3.4.0: * Fix formatting of r-hdo-db * Fix dependency version specifiers * Clean up duplicate dependency references
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fixes for ndzip and sperr (spack#33882)
* fixes for ndzip * fix commits in spack * new and fixed sperr release Co-authored-by: Robert Underwood <runderwood@anl.gov>
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Commits on Nov 18, 2022
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[lerc] added version 4.0.0 (spack#33974)
* [lerc] added version 4.0.0 * [@spackbot] updating style on behalf of qwertos Co-authored-by: qwertos <qwertos@users.noreply.github.com>
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libxml2: make older versions depend on python@:3.9 (spack#33952)
Add a dependency on python versions less than 3.10 in order to work around a bug in libxml2's configure script that fails to parse python version strings with more than one character for the minor version. The bug is present in v2.10.1, but has been fixed in 2.10.2. Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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Update libjpeg-turbo using new multibuildsystem approach (spack#33971)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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openblas: Fix build on ARM Neoverse with gcc@:9 (no sve2+bf16) (spack…
…#33968) Also improve the InstallError message when +fortran but no FC was added. Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
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py-cutadapt: adding version 4.1 (spack#33959)
* py-dnaio: adding version 0.9.1 py-cutadapt: adding version 4.1 * py-cutadapt: remove old python versions * py-dnaio: remove old python versions * py-cutadapt: add cython dep
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py-mypy: add new versions; add new py-types packages (spack#34002)
* py-mypy: add new versions * Add new packages
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LibPressio support for MGARD (spack#33999)
Co-authored-by: Robert Underwood <runderwood@anl.gov>
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gcc: Ensure matching assembler/binutils on RHEL8 (spack#33994)
gcc@10: Newer binutils than RHEL7/8's are required to for guaranteed operaton. Therefore, on RHEL7/8, reject ~binutils. You need to add +binutils to be sure to have binutils which are recent enough. See this discussion with the OpenBLAS devs for reference: OpenMathLib/OpenBLAS#3805 (comment) Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
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Updating faiss with new versions (spack#33983)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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PackageBase should not define builder legacy attributes (spack#33942)
* Add a regression test for 33928 * PackageBase should not set `(build|install)_time_test_callbacks` * Fix audits by preserving the current semantic Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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PackageBase should not define builder legacy attributes (spack#33942)
* Add a regression test for 33928 * PackageBase should not set `(build|install)_time_test_callbacks` * Fix audits by preserving the current semantic Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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Commits on Nov 19, 2022
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mercury: add version 2.2.0 (spack#31966)
add psm, psm2 and hwloc variants Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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graphviz: remove 1. cyclic dep when +pangocairo and 2. error with pop…
…pler+glib (spack#32120) * graphviz: remove cyclic dep to svg when pangocairo and poppler+glib failure * graphviz: remove cyclic dep to svg when pangocairo and poppler+glib failure
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OpenMC: add v0.13.2 (spack#33903)
* openmc: add v0.13.2 * Fix style formatting * Update Python version dependency * Update numpy version dependency
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New package: py-ahpy (spack#34008)
* first build of ahpy * updated to limit python to >4 * added from spack.package import * to >4 Co-authored-by: Sid Pendelberry <sid@rit.edu>
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Commits on Nov 20, 2022
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Update dask and related packages (spack#33925)
* Update dask and related packages * Update package dependency specs * Run spack style * Add new version of locket * Respond to comments * Added constraints * Add version constraints for py-dask+distributed * Run spack style * Update var/spack/repos/builtin/packages/py-dask/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Deprecated dask versions * Deprecated more dask and distirbuted * spack style --fix Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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krb5: Add new versions 1.19.4 and 1.20.1 (spack#34021)
Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
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Commits on Nov 21, 2022
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qt6: new packages (spack#29555)
* qt6: initial commit of several basic qt6 packages * Qt6: fix style issues * [qt6] fix style issues, trailing spaces * [qt6] rename to qt-* ecosystem; remove imports * [qt6] rename dependencies; change version strings * [qt6] list_urls * [qt6] homepage links * [qt6] missing closing quotes failed style check * qt-declarative: use private _versions Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> * qt-quick3d, qt-quicktimeline, qt-shadertools: use private _versions * qt-base: rework feature defines and use run_tests * qt: new version 6.2.4 * flake8 whitespace before comma * qt-base: variant opengl when +gui Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> * qt6: rebase and apply new black style * qt6: apply style isort fixes * qt6: new version 6.3.0 and 6.3.1 * qt6: add 6.3.0 and 6.3.1 to versions list * qt6: multi-argument join_path Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * qt-base: fix isort * qt-shadertools: no cmake_args needed * qt-declarative: imports up front * qt-quick3d: fix import * qt-declarative: remove useless cmake_args * qt-shadertools: imports and join_path fixes * qt-quick3d: join_path fixes * qt-declarative: join_path fixes * Update features based on gui usage * Update dependencies, cmake args, mac support * Update features based on linux * More updates * qt-base: fix style * qt-base: archive_files join_path * qt-base: new version 6.3.2 * qt-{declarative,quick3d,quicktimeline,shadertools}@6.3.2 * qt-base: require libxcb@1.13: and use system xcb_xinput when on linux Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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texinfo: require also
makeinfo
executable (spack#33370)* texinfo: require also `makeinfo` executable * texinfo: add versions 6.6, 6.7, 6.8 * texinfo: add `info` and `makeinfo` sanity checks
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uninstall: fix accidental cubic complexity (spack#34005)
* uninstall: fix accidental cubic complexity Currently spack uninstall runs in worst case cubic time complexity thanks to traversal during traversal during traversal while collecting the specs to be uninstalled. Also brings down the number of error messages printed to something linear in the amount of matching specs instead of quadratic.
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Speed-up a few unit-tests (spack#34044)
* test_suite.py: speed up slow test by using mock packages * Don't resolve the sha during unit-tests * Skip long-running test that fails, instead of executing it
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Commits on Nov 22, 2022
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Spec traversal: add option for topological ordering (spack#33817)
Spec traversals can now specify a topological ordering. A topologically- ordered traversal with input specs X1, X2... will * include all of X1, X2... and their children * be ordered such that a given node is guaranteed to appear before any of its children in the traversal Other notes: * Input specs can be children of other input specs (this is useful if a user specifies a set of specs to uninstall: some of those specs might be children of others) * `direction="parents"` will produce a reversed topological order (children always come before parents). * `cover="edges"` will generate a list of edges L such that (a) input edges will always appear before output edges and (b) if you create a list with the destination of each edge in L the result is topologically ordered
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Windows: add registry query and SDK/WDK packages (spack#33021)
* Add a WindowsRegistryView class, which can query for existing package installations on Windows. This is particularly important because some Windows packages (including those added here) do not allow two simultaneous installs, and this can be queried in order to provide a clear error message. * Consolidate external path detection logic for Windows into WindowsKitExternalPaths and WindowsCompilerExternalPaths objects. * Add external-only packages win-sdk and wgl * Add win-wdk (including external detection) which depends on win-sdk * Replace prior msmpi implementation with a source-based install (depends on win-wdk). This install can control the install destination (unlike the binary installation). * Update MSVC compiler to choose vcvars based on win-sdk dependency * Provide "msbuild" module-level variable to packages during build * When creating symlinks on Windows, need to explicitly specify when a symlink target is a directory * executables_in_path no-longer defaults to using PATH (this is now expected to be taken care of by the caller)
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Warn about removal of deprecated format strings (spack#33829)
Co-authored-by: becker33 <becker33@users.noreply.github.com>
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Revert "Warn about removal of deprecated format strings (spack#33829)" (
spack#34056) This reverts commit 7f9af8d.
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eckit: add v1.20.2, v1.16.3 (spack#33200)
Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
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cpu-features: Fix appending -DBUILD_SHARED_LIBS (spack#34055)
Also: * Use the release tarball for v0.7.0 to fix spack warning Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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Python: drop EOL versions (spack#33898)
This PR removes [end of life](https://endoflife.date/python) versions of Python from Spack. Specifically, this includes all versions of Python older than 3.7. See spack#31824 for rationale. Deprecated in spack#32615. And spack#28003. For anyone using software that relies on Python 2, you have a few options: * Upgrade the software to support Python 3. The `3to2` tool may get you most of the way there, although more complex libraries may need manual tweaking. * Add Python 2 as an [external package](https://spack.readthedocs.io/en/latest/build_settings.html#external-packages). Many Python libraries do not support Python 2, but you may be able to add older versions that did once upon a time. * Use Spack 0.19. Spack 0.19 is the last release to officially support Python 3.6 and older * Create and maintain your own [custom repository](https://spack.readthedocs.io/en/latest/repositories.html). Basically, you would need a package for Python 2 and any other Python 2-specific libraries you need.
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Commits on Nov 23, 2022
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cmd/checksum: allow adding new versions to package (spack#24532)
This adds super-lazy maintainer mode to `spack checksum`: Instead of only printing the new checksums to the terminal, `-a` and `--add-to-package` will add the new checksums to the `package.py` file and open it in the editor afterwards for final checks.
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New package: py-rasterstats (spack#34070)
* Fixed dependencies for rasterstats * Fixed flake8 errors * Fix flake8 error * Cleans up package desc., adds build dependency on setuptools. * Fixes flake8 error Co-authored-by: Bailey Brown <bobits@rit.edu>
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boost: At least with older Xcode, boost can't build with lzma (spack#…
…34075) Reference: https://lists.boost.org/Archives/boost/2019/11/247380.php As reported at the end of spack#33998 and this link, liblzma on older Xcode on MacOSX 10 misses _lzma_cputhreads, so boost's can't use liblzma on those.
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capnproto: update to v0.10.2 (spack#34063)
Co-authored-by: Alexander Knieps <a.knieps@fz-juelich.de>
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berkelygw: use mpi variant for scalapack (spack#33948)
The package.py assumed "+mpi" in many places, without checking for the variant. This problem went undetected, as a hard dependency on scalapack pulled an mpi implementation into the dependency chain (this is also fixed). Also, the +mpi variant is used select between serial and parallel mode: It has to enable MPI and ScaLAPACK: They are inter-dependent. Compile fails because of checks for the other if the other is not enabled. Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
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New package: py-imagecodecs (spack#34098)
* [libjpeg-turbo] Added version 2.1.3 * [imagecodecs] Added jpeg deependency commented outconglicting libraries * [WIP] * [py-imagecodecs] modifying setup.py to work with spack install locations * [py-imagecodecs] Removed comments and unneeded dependencies * [py-imagecodecs] removed some comments and fixed up some flake8 complaints * [py-imagecodecs] flake8 * [py-imagecodecs] fixed import * [@spackbot] updating style on behalf of qwertos Co-authored-by: James A Zilberman <jazrc@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
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Revert "gitlab: Add shared PR mirror to places pipelines look for bin…
…aries. (spack#33746)" (spack#34087) This reverts commit 5c4137b.
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E4S: Conservatively add ecp-data-vis-sdk (spack#33621)
* E4S: Conservatively add ecp-data-vis-sdk * Remove ascent from CUDA SDK stack to stop hanging on Dray * Adios2: Newer FindPython uses Python_EXECUTABLE
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url_exists
related improvements (spack#34095)For reasons beyond me Python thinks it's a great idea to upgrade HEAD requests to GET requests when following redirects. So, this PR adds a better `HTTPRedirectHandler`, and also moves some ad-hoc logic around for dealing with disabling SSL certs verification. Also, I'm stumped by the fact that Spack's `url_exists` does not use HEAD requests at all, so in certain cases Spack awkwardly downloads something first to see if it can download it, and then downloads it again because it knows it can download it. So, this PR ensures that both urllib and botocore use HEAD requests. Finally, it also removes some things that were there to support currently unsupported Python versions. Notice that the HTTP spec [section 10.3.2](https://datatracker.ietf.org/doc/html/rfc2616.html#section-10.3.2) just talks about how to deal with POST request on redirect (whether to follow or not): > If the 301 status code is received in response to a request other > than GET or HEAD, the user agent MUST NOT automatically redirect the > request unless it can be confirmed by the user, since this might > change the conditions under which the request was issued. > Note: When automatically redirecting a POST request after > receiving a 301 status code, some existing HTTP/1.0 user agents > will erroneously change it into a GET request. Python has a comment about this, they choose to go with the "erroneous change". But they then mess up the HEAD request while following the redirect, probably because they were too busy discussing how to deal with POST. See python/cpython#99731
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[py-antlr4-python3-runtime] Added versions 4.9.3 and 4.10 (spack#34102)
* Working updates to py-antlr4-python3-runtime and py-omegaconf * [py-antlr4-python3-runtime] added version 4.9.3 * [@spackbot] updating style on behalf of qwertos Co-authored-by: Benjamin Meyers <bsmits@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
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Control Werror by converting to Wno-error (spack#30882)
Using `-Werror` is good practice for development and testing, but causes us a great deal of heartburn supporting multiple compiler versions, especially as newer compiler versions add warnings for released packages. This PR adds support for suppressing `-Werror` through spack's compiler wrappers. There are currently three modes for the `flags:keep_werror` setting: * `none`: (default) cancel all `-Werror`, `-Werror=*` and `-Werror-*` flags by converting them to `-Wno-error[=]*` flags * `specific`: preserve explicitly selected warnings as errors, such as `-Werror=format-truncation`, but reverse the blanket `-Werror` * `all`: keeps all `-Werror` flags These can be set globally in config.yaml, through the config command-line flags, or overridden by a particular package (some packages use Werror as a proxy for determining support for other compiler features). We chose to use this approach because: 1. removing `-Werror` flags entirely broke *many* build systems, especially autoconf based ones, because of things like checking `-Werror=feature` and making the assumption that if that did not error other flags related to that feature would also work 2. Attempting to preserve `-Werror` in some phases but not others caused similar issues 3. The per-package setting came about because some packages, even with all these protections, still use `-Werror` unsafely. Currently there are roughly 3 such packages known.
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Commits on Nov 24, 2022
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Add py-urwid@2.1.2 (spack#34103)
* Add py-urwid@2.1.2 * [@spackbot] updating style on behalf of meyersbs
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New package: py-kt-legacy (spack#34104)
* first build of keras-tuner with dataset kt-legacy * [py-kt-legacy] fixed homepage * [py-kt-legacy] depends on setuptools * [py-kt-legacy] fixed import * [@spackbot] updating style on behalf of qwertos Co-authored-by: Sid Pendelberry <sid@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
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Arbor: Yank v0.5 (spack#34094)
v0.5 does not build due to a change in setting `arch` introduced in v0.5.2, compatibility with which was not kept in `arbor/package.py`. Since v0.5.2 is compatible with `arbor/package.py`, and is API compatible with v0.5, any users relying on v0.5 can rely on v0.5.2.
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Commits on Nov 25, 2022
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ffmpeg: adding version 5.1.2 (spack#33758)
* ffmpeg: add version 5.1.2 and switch to conditional variants Also: py-torchvision: restrict ffmpeg dependency
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Update TotalView versions and website (spack#33418)
Co-authored-by: Peter Thompson <thompson81@llnl.gov> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
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Commits on Nov 26, 2022
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Revert "
url_exists
related improvements (spack#34095)" (spack#34144)This reverts commit d06fd26. The problem is that Bitbucket's API forwards download requests to an S3 bucket using a temporary URL. This URL includes a signature for the request, which embeds the HTTP verb. That means only GET requests are allowed, and HEAD requests would fail verification, leading to 403 erros. The same is observed when using `curl -LI ...`
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nvtop: Add 2.0.3, 2.0.4, 3.0.0 and 3.0.1 (spack#34145)
* And add the option to compile support for Intel GPU's
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Octopus: branch for Octopus development is now "main" (spack#34128)
Historically, development of the Octopus code was done on the "develop" branch on https://gitlab.com/octopus-code/octopus but now development takes place on "main" (since Q3 2022). The suggestion in this PR to solve the issue is to keep the spack label `octopus@develop` as this better indicates this is the development branch on git than `octopus@main`, but of course to use the `main` branch (there is no choice here - the `develop` branch is not touched anymore). Sticking to `octopus@develop` as the version label also keeps backwards compatibility.
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py-fastpath: new package (spack#34142)
* py-fastpath: new package * Update var/spack/repos/builtin/packages/py-fastpath/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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Commits on Nov 27, 2022
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Revert "Revert "gitlab: Add shared PR mirror to places pipelines look…
… for binaries. (spack#33746)" (spack#34087)" (spack#34153) This reverts commit 63e4406.
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Use a module-like object to propagate changes in the MRO, when settin…
…g build env (spack#34059) This fixes an issue introduced in spack#32340, which changed the semantics of the "module" object passed to the "setup_dependent_package" callback.
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warn about removal of deprecated format strings (spack#34101)
* warn about removal of deprecated format strings Co-authored-by: becker33 <becker33@users.noreply.github.com>
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py-bidskit: new package and dcm2niix: add 1.0.20220720 (spack#34162)
* py-bidskit: new package and dcm2niix: add 1.0.20220720 * Remove list_url
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Add checksum for py-rsa 4.9 (spack#34115)
* Add checksum for py-rsa 4.9 * Update package.py * Update var/spack/repos/builtin/packages/py-rsa/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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Commits on Nov 29, 2022
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