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Sync with upstream #72

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Commits on Nov 11, 2022

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  2. libxcrypt: 4.4.30 (spack#33845)

    * libxcrypt: 4.4.30
    
    * libxcrypt.so.2 by default
    
    * add libs prop, since libxcrypt provides libcrypt
    haampie committed Nov 11, 2022
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Commits on Nov 12, 2022

  1. magma: add version 2.7.0 (spack#33814)

    * magma: add version 2.7.0
    
    Co-authored-by: Stan Tomov <tomov@icl.utk.edu>
    balay and stomov committed Nov 12, 2022
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  2. Update ExaGO for 1.5.0 release. (spack#33853)

    * Update ExaGO for 1.5.0 release
    cameronrutherford committed Nov 12, 2022
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  4. 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>
    becker33 and tgamblin committed Nov 12, 2022
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Commits on Nov 13, 2022

  1. 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
    alalazo committed Nov 13, 2022
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  2. 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.
    tgamblin committed Nov 13, 2022
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  3. [sundials] fix cmake argument generation for '+magma' (spack#33858)

    [dealii] force cmake to accept Scalapack settings from Spack
    v-dobrev committed Nov 13, 2022
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  5. GDAL: add v3.6.0 (spack#33856)

    * GDAL: add v3.6.0
    
    * Explicitly control BASISU
    
    * More reasonable variant defaults
    adamjstewart committed Nov 13, 2022
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  6. tau: checksum (spack#33873)

    haampie committed Nov 13, 2022
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Commits on Nov 14, 2022

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  4. 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
    alalazo committed Nov 14, 2022
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  7. Bump version to v0.20.0.dev0

    tgamblin committed Nov 14, 2022
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  8. Update SECURITY.md for v0.19

    tgamblin committed Nov 14, 2022
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  9. Update CHANGELOG.md for v0.19.0

    Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
    tgamblin and haampie committed Nov 14, 2022
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  12. fix perl libxcrypt.so dep (spack#33846)

    Detected using spack#28109
    haampie committed Nov 14, 2022
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  14. 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.
    cgmb committed Nov 14, 2022
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  15. 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>
    psakievich and tldahlgren committed Nov 14, 2022
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  17. 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>
    tcojean and v-dobrev committed Nov 14, 2022
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Commits on Nov 15, 2022

  1. [py-pmw-patched] needs setuptools to build (spack#33902)

    Error message:
    ```
    ModuleNotFoundError: No module named 'setuptools'
    ```
    
    Co-authored-by: Stephen Sachs <stesachs@amazon.com>
    stephenmsachs and stephenmsachs committed Nov 15, 2022
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  2. 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.
    scottwittenburg committed Nov 15, 2022
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  3. 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.
    alalazo committed Nov 15, 2022
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  4. fixup

    alalazo committed Nov 15, 2022
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  7. 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.
    blue42u committed Nov 15, 2022
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  8. Remove exit(0) (spack#33896)

    Since they cause --backtrace to report backtraces even with exit code 0
    haampie committed Nov 15, 2022
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  9. python: missing libxcrypt dep (spack#33847)

    Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
    haampie and adamjstewart committed Nov 15, 2022
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  10. 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>
    bvanessen and haampie committed Nov 15, 2022
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  13. 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.
    haampie committed Nov 15, 2022
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  15. 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=
    ```
    haampie committed Nov 15, 2022
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  16. 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>
    iarspider and iarspider committed Nov 15, 2022
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  17. nsimd: Update Python requirements (spack#33879)

    We need Python 3.0:3.9
    eschnett committed Nov 15, 2022
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  19. 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>
    saqibkh committed Nov 15, 2022
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  22. spectre: add v2022.11.15 (spack#33921)

    Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
    sxs-bot and sxs-bot committed Nov 15, 2022
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  24. Update BML versions list in package.py (spack#33920)

    * Update BML versions list in package.py
    * Update package.py
    jeanlucf22 committed Nov 15, 2022
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  25. 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>
    balay and balos1 committed Nov 15, 2022
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  26. 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>
    GarrettDMorrison and bernhardkaindl committed Nov 15, 2022
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Commits on Nov 16, 2022

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  3. Automated deployment to update package flux-core 2022-11-09 (spack#33780

    )
    
    Co-authored-by: github-actions <github-actions@users.noreply.github.com>
    vsoch and github-actions committed Nov 16, 2022
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  7. 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.
    matz-e committed Nov 16, 2022
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  10. py-isal: use external libisal (spack#33932)

    * py-isal: adding some missing build deps
    
    * py-isal: use external libisal
    snehring committed Nov 16, 2022
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  11. 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>
    robertu94 and Robert Underwood committed Nov 16, 2022
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  13. SIP build system: fix "python not defined in builder" (spack#33906)

    Co-authored-by: Stephen Sachs <stesachs@amazon.com>
    stephenmsachs and stephenmsachs committed Nov 16, 2022
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  14. 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).
    johnwparent committed Nov 16, 2022
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  18. Clean unit-test workflow file (spack#33945)

    Delete statements related to Python 2.7, and avoid installing
    patchelf since now we can bootstrap it.
    alalazo committed Nov 16, 2022
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Commits on Nov 17, 2022

  1. gettext: On ppc64le, for older versions, use system cdefs.h (spack#33411

    )
    
    Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
    blue42u and bernhardkaindl committed Nov 17, 2022
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  2. * ninja: Set min. required version of re2c dependency, fixes spack#33127

     (spack#33128)
    
    Reviewed-by: haampie, bernhardkaindl
    picsel2 committed Nov 17, 2022
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  8. [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
    stephenmsachs committed Nov 17, 2022
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  9. 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>
    mathstuf and bernhardkaindl committed Nov 17, 2022
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  13. 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
    iamashwin99 committed Nov 17, 2022
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  14. Remove deprecated subcommands from "spack bootstrap" (spack#33964)

    These commands are slated for removal in v0.20
    alalazo committed Nov 17, 2022
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  18. 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.
    alalazo committed Nov 17, 2022
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  19. 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`
    greenc-FNAL committed Nov 17, 2022
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  20. 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>
    3 people committed Nov 17, 2022
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  21. 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>
    jpopelar and johnwparent committed Nov 17, 2022
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  23. glib: fix URLs (spack#33919)

    heerener committed Nov 17, 2022
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  24. 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
    glennpj committed Nov 17, 2022
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  25. 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>
    robertu94 and Robert Underwood committed Nov 17, 2022
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  27. julia: 1.8.3 (spack#33976)

    haampie committed Nov 17, 2022
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Commits on Nov 18, 2022

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  2. [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>
    qwertos and qwertos committed Nov 18, 2022
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  4. 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>
    3 people committed Nov 18, 2022
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  6. Update libjpeg-turbo using new multibuildsystem approach (spack#33971)

    Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
    iarspider and bernhardkaindl committed Nov 18, 2022
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  7. 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>
    bernhardkaindl and bernhardkaindl committed Nov 18, 2022
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  9. 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
    snehring committed Nov 18, 2022
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  10. py-mypy: add new versions; add new py-types packages (spack#34002)

    * py-mypy: add new versions
    * Add new packages
    adamjstewart committed Nov 18, 2022
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  11. LibPressio support for MGARD (spack#33999)

    Co-authored-by: Robert Underwood <runderwood@anl.gov>
    robertu94 and Robert Underwood committed Nov 18, 2022
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  13. 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>
    bernhardkaindl and bernhardkaindl committed Nov 18, 2022
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  17. Updating faiss with new versions (spack#33983)

    Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
    rblake-llnl and alalazo committed Nov 18, 2022
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  18. 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>
    greenc-FNAL and alalazo committed Nov 18, 2022
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  19. Revert "Merge pull request spack#66 from chissg/bugfix/PackageBase-te…

    …st-callbacks"
    
    This reverts commit 9c020da, reversing
    changes made to 74a8c30.
    greenc-FNAL committed Nov 18, 2022
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  20. 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>
    greenc-FNAL and alalazo committed Nov 18, 2022
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  2. 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>
    soumagne and bernhardkaindl committed Nov 19, 2022
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  5. 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
    cessenat committed Nov 19, 2022
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  10. OpenMC: add v0.13.2 (spack#33903)

    * openmc: add v0.13.2
    
    * Fix style formatting
    
    * Update Python version dependency
    
    * Update numpy version dependency
    paulromano committed Nov 19, 2022
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  11. 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>
    qwertos and sidpbury committed Nov 19, 2022
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  3. 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>
    charmoniumQ and adamjstewart committed Nov 20, 2022
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  4. krb5: Add new versions 1.19.4 and 1.20.1 (spack#34021)

    Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
    bernhardkaindl and bernhardkaindl committed Nov 20, 2022
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Commits on Nov 21, 2022

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  2. 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>
    3 people committed Nov 21, 2022
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  5. 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
    giordano committed Nov 21, 2022
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  8. 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.
    haampie committed Nov 21, 2022
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  13. 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
    alalazo committed Nov 21, 2022
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Commits on Nov 22, 2022

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  2. 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
    haampie committed Nov 22, 2022
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  3. qiskit: updates (spack#33877)

    aweits committed Nov 22, 2022
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  7. 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)
    johnwparent committed Nov 22, 2022
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  8. Warn about removal of deprecated format strings (spack#33829)

    Co-authored-by: becker33 <becker33@users.noreply.github.com>
    becker33 and becker33 committed Nov 22, 2022
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  10. eckit: add v1.20.2, v1.16.3 (spack#33200)

    Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
    Dominic Hofer and bernhardkaindl committed Nov 22, 2022
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  11. 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>
    iarspider and bernhardkaindl committed Nov 22, 2022
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  14. 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.
    adamjstewart committed Nov 22, 2022
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Commits on Nov 23, 2022

  1. 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.
    michaelkuhn committed Nov 23, 2022
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  7. 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>
    qwertos and Bailey Brown committed Nov 23, 2022
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  9. 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.
    bernhardkaindl committed Nov 23, 2022
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  10. capnproto: update to v0.10.2 (spack#34063)

    Co-authored-by: Alexander Knieps <a.knieps@fz-juelich.de>
    alexrobomind and Alexander Knieps committed Nov 23, 2022
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  16. 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>
    glaweh and bernhardkaindl committed Nov 23, 2022
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  21. 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>
    3 people committed Nov 23, 2022
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  23. 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
    kwryankrattiger committed Nov 23, 2022
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  24. 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
    haampie committed Nov 23, 2022
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  25. [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>
    3 people committed Nov 23, 2022
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  26. 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.
    trws committed Nov 23, 2022
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Commits on Nov 24, 2022

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  3. Add py-urwid@2.1.2 (spack#34103)

    * Add py-urwid@2.1.2
    
    * [@spackbot] updating style on behalf of meyersbs
    meyersbs committed Nov 24, 2022
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  6. 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>
    3 people committed Nov 24, 2022
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  9. 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.
    brenthuisman committed Nov 24, 2022
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Commits on Nov 25, 2022

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  5. 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
    snehring committed Nov 25, 2022
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  6. 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>
    3 people committed Nov 25, 2022
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Commits on Nov 26, 2022

  1. 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 ...`
    balay committed Nov 26, 2022
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  2. 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
    marcost2 committed Nov 26, 2022
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  3. 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.
    fangohr committed Nov 26, 2022
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  8. 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>
    luke-dt and adamjstewart committed Nov 26, 2022
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Commits on Nov 27, 2022

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Commits on Nov 28, 2022

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  4. Revert "Revert "gitlab: Add shared PR mirror to places pipelines look…

    … for binaries. (spack#33746)" (spack#34087)" (spack#34153)
    
    This reverts commit 63e4406.
    haampie committed Nov 28, 2022
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  5. 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.
    alalazo committed Nov 28, 2022
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  10. 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>
    becker33 and becker33 committed Nov 28, 2022
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  12. 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
    manuelakuhn committed Nov 28, 2022
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  16. 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>
    iarspider and adamjstewart committed Nov 28, 2022
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Commits on Nov 29, 2022

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