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2023-09-12r-piggyback: Add `R` package `piggyback` (#39932)Johann Gaebler1-0/+53
2023-09-12r-pl94171: Add R package PL94171 (#39926)Johann Gaebler1-0/+37
2023-09-12binutils: add v2.41 (#39483)Massimiliano Culpo1-0/+1
2023-09-12bam-readcount: add 1.0.1, correct build flags (#39950)George Young1-0/+4
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-12CI/Add superlu-dist to broken stand-alone tests due to hang (#38908)Tamara Dahlgren2-0/+16
* Add superlu-dist to broken stand-alone CI tests * Revert "disable superlu test (#38894)" This reverts commit e16397b5d865d402c749482d05bb2bdc09b96661.
2023-09-12mpifileutils: switch to main branch (#39525)Adam Moody1-1/+1
2023-09-12libjpeg-turbo: Fix Darwin lib install name (#39834)Dom Heinzeller1-0/+6
* Fix Darwin lib install name in var/spack/repos/builtin/packages/libjpeg-turbo/package.py * Update var/spack/repos/builtin/packages/libjpeg-turbo/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-12Filter spack compiler wrappers for h4cc in ↵Dom Heinzeller1-0/+4
var/spack/repos/builtin/packages/hdf/package.py (#39870)
2023-09-12g2 package bugfix (#39923)Alex Richert1-16/+31
* g2 package bugfix * g2: fix w3emc dep * fix setup_run_environment * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * style fix * Update var/spack/repos/builtin/packages/g2/package.py Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Update var/spack/repos/builtin/packages/g2/package.py Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> --------- Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-09-12amrex: add v23.09 (#39788)Weiqun Zhang1-0/+1
2023-09-12openexr: add 2.4.3, 2.5.9, 3.1.11 & 3.2.0 (#39863)Martin Aumüller1-21/+19
* openexr: add 2.4.3, 2.5.9, 3.1.11 & 3.2.0 - 2.5.9 is the latest version compatible with OpenScenGraph - improved compatibility with GCC 13 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * openexr: drop unsupported debug variant --disable/enable-debug is not supported by ./configure in 1.3, 1.7, 2.0, 2.2 and 2.3 * openexr: transform into multi-build system package simplifies package considerably, as nothing special seems to be required * openexr: pkg-config is also used by @3 * openexr: use system libdeflate instead of internal if no libdeflate is found, openexr would download and build its own starting with 3.2.0 * openexr: disable tests would download lots of data during cmake and make build times noticably longer --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-12Update PennyLane packages to v0.32. (#39688)Vincent Michaud-Rioux3-16/+24
* Update PennyLane packages to v0.32. * Reformat. * Couple small fixes. * Fix Lightning cmake_args. * Couple dep fixes in py-pennylane + plugins. * Fix scipy condition. * Add comment on conflicting requirement.
2023-09-12openssl: deprecate 1.1.1 (#39942)Harmen Stoppels1-11/+7
2023-09-12asp.py: fix deprecation warning (#39943)Harmen Stoppels1-3/+2
2023-09-12Add gperftools 2.13 (#39940)Mikael Simberg1-0/+1
2023-09-12filtlong: add v0.2.1, patch for %gcc@13: (#39775)George Young2-0/+14
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-12build(deps): bump black from 23.7.0 to 23.9.1 in /lib/spack/docs (#39937)dependabot[bot]1-1/+1
Bumps [black](https://github.com/psf/black) from 23.7.0 to 23.9.1. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/compare/23.7.0...23.9.1) --- updated-dependencies: - dependency-name: black dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-12lbann: make two variants sticky (#39710)Brian Van Essen1-2/+12
* Make the state of the Python Front End (PFE) and Python data reader support sticky so that the concretizer does not arbitrarily disable them. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-09-11[gromacs] Fix 2021.2 build error (#39722)Stephen Sachs1-0/+6
* [gromacs] Fix 2021.2 build error See https://gromacs.bioexcel.eu/t/compilation-failure-for-gromacs-2021-1-and-2021-2-with-cmake-3-20-2/2129 * Update var/spack/repos/builtin/packages/gromacs/package.py Co-authored-by: Andrey Alekseenko <al42and@gmail.com> --------- Co-authored-by: Andrey Alekseenko <al42and@gmail.com>
2023-09-11fish: add 3.6.0, 3.6.1, update cmake requirement (#39899)Caetano Melone1-1/+4
2023-09-11py-build: add v1 (#39930)Adam J. Stewart1-7/+12
2023-09-11Add awscli@1.29.41 and its dependency py-botocore@1.31.41 (#39878)Dom Heinzeller2-5/+9
* Add awscli@1.29.41 and its dependency py-botocore@1.31.41 * Update var/spack/repos/builtin/packages/awscli/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> --------- Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-09-11package_qscintilla_build_with_qt6 (#39544)Sinan1-114/+78
* package_qscintilla_build_with_qt6 * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * improve * fix Qsci.abi3.so install * simplify, fix, tidy * fix style * fix style * fix style * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * improve * improve style * fix style * make black happy * add ver 2.14.1 * update * make black happy * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * improve --------- Co-authored-by: Sinan81 <Sinan@world> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11py-black: add v23.9 (#39931)Adam J. Stewart1-0/+2
2023-09-11py-tifffile: add 2023.8.30 (#39918)Manuela Kuhn1-1/+5
2023-09-11py-tinycss2: add 1.2.1 (#39921)Manuela Kuhn1-1/+2
2023-09-11py-tomlkit: add 0.12.1 (#39922)Manuela Kuhn1-2/+2
2023-09-11tidynamics: add v1.1.2 (#39911)Rocco Meli1-0/+2
* ensure umpire~cuda~rocm when ~cuda~rocm * update tydynamics
2023-09-11correct py-bx-python@0.8.8 python dependency (#39766)Mike Renfro1-1/+5
* correct python dependency for 0.8.8 * add missing zlib dependency * restore missing whitespace * correct versions for 0.9.0, clarify rules for future releases * Update package.py * Remove whitespace for black check
2023-09-11fpchecker: add version 0.4.0 (#39924)Tim Haines1-0/+1
2023-09-11cuda: add versions 12.2.0 and 12.2.1 (#39684)Richard Berger1-0/+28
2023-09-11py-fairscale and dependencies py-pgzip libgit2 py-pygit2 (#39220)sid4-16/+83
* simple build of py-openai * added variants to py-openai * py-pandas-stubs is a dependency for py-openai * fixed format and flake8 errors for py-openai * black format error for py-pandas-stubs * [@spackbot] updating style on behalf of sidpbury * made style and format changes to py-openai * made style and format changes to py-pandas-stubs * py-types-pytz is a dependency for py-openai * [@spackbot] updating style on behalf of sidpbury * updated py-openpyxl for ver 3.0.7 and 3.1.2 * Update var/spack/repos/builtin/packages/py-pandas-stubs/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * ajs requested changes for py-openai * updated py-openpyxl for supported python * [@spackbot] updating style on behalf of sidpbury * updated py-openpyxl * removed requirement.txt dependencies in py-openpyxl * removed python depends on from openpyxl * updated package to support newer versions * updated version of py-pygit2 * py-fairscale is a new package in support of torch * py-pgzip is a dependency for py-fairscale * switch fairscale pypi, added extra variant for convenience * removed python dependency * changed multiple requirement versions * changes for upstream py-fairscale * changes for upsteam py-pygit2 * Update package.py * Update package.py * sorted out some of the dependency versions * removed version 1.12.2 because dependency could not be met * updated py-cached-property dependency * suggested changes from adamjstewart --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11spectre: add v2023.08.18 and v2023.09.07 (#39925)Nils Vu1-0/+6
2023-09-11Update MDAnalysis (#39787)Rocco Meli2-3/+19
* ensure umpire~cuda~rocm when ~cuda~rocm * update mdanalysis * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-mdanalysis/package.py --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11update q-e-sirius package (#39744)Simon Pintarelli1-9/+37
2023-09-11Add another url for whizard (#37354)Juan Miguel Carceller1-1/+4
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-09-11gdrcopy: inherit from CudaPackage, update dependencies (#39596)Scot Halverson1-1/+8
2023-09-11py-pipdeptree: add new package; py-hatchling: add 1.18.0 (#39697)Fábio de Andrade Barboza2-0/+22
* py-hatchling: add 1.18.0 * py-pipdeptree: add new package * py-hatchling: add Python 3.8 dependency * Apply suggestion from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Fábio de Andrade Barboza <f168817@dac.unicamp.br> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11SLEPc: add v3.19.2 (#39805)Jose E. Roman2-0/+2
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2023-09-11py-enum-tools: add new package and dependencies (#39672)Fábio de Andrade Barboza14-0/+305
* Adds package 'enum-tools' * Fixes syntax * py-enum-tools: update pypi link and dependencies * py-whey: add new package * py-consolekit: add new package * py-shippinglabel: add new package * py-project-parser: add new package * py-handy-archives: add new package * py-domdf-python-tools: add new package * py-dom-toml: add new package * py-dist-meta: add new package * py-deprecation-alias: add new package * py-pygments: add versions 2.16.0 and 2.16.1 * py-mistletoe: add new package * py-apeye: add new package * py-apeye-core: add new package * Fix dependencies' names and remove redundancies * Fix style * py-enum-tools: fix dependencies * py-mistletoe: update dependencies * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * py-whey: fix dependencies * py-whey: fix style * py-apeye: fix dependencies --------- Co-authored-by: Fábio de Andrade Barboza <f168817@dac.unicamp.br> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11dakota: add v6.18 (#39882)Travis1-0/+14
Co-authored-by: Travis Drayna <tdrayna@loki.local>
2023-09-11dd4hep: make sure to find libraries correctly (#39516)Thomas Madlener1-1/+8
2023-09-11ctffind: extend a Power 9 patch to AArch64 (#39137)dslarm2-1/+2
2023-09-11MALT: add v1.2.2 (#39890)Sébastien Valat1-1/+2
2023-09-11NUMAPROF: add v1.1.5 (#39891)Sébastien Valat1-0/+1
2023-09-11py-dunamai: add 1.18.0 (#39849)Manuela Kuhn1-1/+2
2023-09-11glibc: fix deps, drop pre 2.17 (#39806)Harmen Stoppels7-232/+23
* glibc: add missing deps, drop < 2.17 Building glibc 2.17 requires linking libgcc_{s,eh}.a, which themselves depend on whatever glibc the current gcc uses for its runtime libraries. Newer gcc depends on gnu extensions of libdl it seems, so that means you simply cannot build old glibc with gcc-using-new-glibc. The relevant fix in glibc is this commit: commit 95f5a9a866695da4e038aa4e6ccbbfd5d9cf63b7 Author: Joseph Myers <joseph@codesourcery.com> Date: Tue Jul 3 19:14:59 2012 +0000 Avoid use of libgcc_s and libgcc_eh when building glibc. See also references to that commit in the glibc mailing list. * update the gmake bound * add --without-selinux
2023-09-11Update archspec to latest commit (#39920)Massimiliano Culpo4-10/+119
- [x] Intel flags for old architectures - [x] Support for Sapphire Rapids - [x] Cache the "ancestors" computation
2023-09-11Support of versions of cp2k below 7 marked as deprecated (#39652)Taillefumier Mathieu1-7/+22
SIRIUS was introduced in version 7 of cp2k but could be used in practice in version 9 (input format and functionalities). SIRIUS with version 6 and below are marked as a dependency conflict until CP2K version 9. Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
2023-09-11elpa: Add --enable-scalapack-tests to configure when +autotune (#39728)Tom Payerle1-0/+2
When building elpa +autotune, we apparently need to add the configure option --enable-scalapack-tests
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