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2023-07-09Automated deployment to update package flux-core 2023-07-08 (#38790)Vanessasaurus1-0/+1
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-07-09Don’t call spec.format in Database._get_matching_spec_key (#38792)Harmen Stoppels1-1/+15
`"%s" % spec` formats the spec with deps included, which produces sometimes KBs of data and is slow to run in pure Python. It can delay otherwise very short-lived read/write locks on the database. Discovered in #38762 where profile output showed about 2 seconds is spent in `spec.format`, which is significant overhead when using multiprocessing to install from binary cache in parallel (installation often takes <5s for small packages). With this change, `spec.format` no longer shows up in profile output. (This line hasn't changed since Spack v0.9 ;p) * move format() call to custom NoSuchSpecError exception * add a comment saying why, so we can eventually change `Spec.__str__`
2023-07-09pkgconf: Update to new upstream URL (#38800)Jonathon Anderson1-1/+1
See https://github.com/pkgconf/pkgconf/commit/437c2a3218bfcb1cae7fa38a4ccd0cb29575ff07
2023-07-09gcc: add 10.5.0 (#38784)Michael Kuhn1-1/+2
2023-07-08qt-* (Qt6 pkgs): new versions 6.5.0, 6.5.1 (#36705)Wouter Deconinck5-0/+10
* qt-base: new version 6.5.0 * qt-declarative: new version 6.5.0 * qt-quick3d: new version 6.5.0 * qt-quicktimeline: new version 6.5.0 * qt-shadertools: new version 6.5.0 * qt-*: new version 6.5.1 * qt-base: new version 6.5.1
2023-07-07PyNVTX: added new package (#38763)Dax Lynch1-0/+26
2023-07-07py-pyarrow: disable dataset variant by default (#38775)Manuela Kuhn1-1/+4
* py-pyarrow: enable parquet variant by default * Disable parquet variant by default * Add conflict to enable parquet when dataset is active * Disable dataset variant by default
2023-07-07py-matplotlib: add v3.7.2 (#38745)Adam J. Stewart1-0/+3
* py-matplotlib: add v3.7.2 * Update dep versions
2023-07-07New package: py-nanobind (#38327)Chris Richardson1-0/+34
* initial commit of nanobind package * style fixes * Update package.py Typo * addressed PR comments * add v1.4.0 * Update var/spack/repos/builtin/packages/py-nanobind/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Matthew Archer <ma595@cam.ac.uk> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-07py-astropy: fix import tests and restrict py-pip version (#38731)Manuela Kuhn7-25/+151
* py-astropy: fix import tests and restrict py-pip version * Fix --install-option name in comments * Rename variant and fix variant dependencies * Remove parquet variant from py-pyarrow
2023-07-07Remove "node_compiler" from the list of unknown atoms (#38753)Massimiliano Culpo1-0/+1
2023-07-07Fix multiple quadratic complexity issues in environments (#38771)Harmen Stoppels3-63/+57
1. Fix O(n^2) iteration in `_get_overwrite_specs` 2. Early exit `get_by_hash` on full hash 3. Fix O(n^2) double lookup in `all_matching_specs` with hashes 4. Fix some legibility issues
2023-07-07Prevent "spack external find" to error out on wrong permissions (#38755)Massimiliano Culpo2-4/+36
fixes #38733
2023-07-07add info about spack env from spack-configs for oneAPI build tools (#38751)Andrey Parfenov1-0/+47
Signed-off-by: Andrey Parfenov <andrey.parfenov@intel.com>
2023-07-06add cgns 4.4.0 (#38530)Mickael PHILIT1-0/+1
2023-07-06freesurfer: add 7.4.1, 7.4.0, 7.3.2 (#38544)Carlos Bederián1-0/+3
2023-07-06mlpack: new package (#38277)Wouter Deconinck1-0/+81
* mlpack: new package mlpack is an intuitive, fast, and flexible header-only C++ machine learning library with bindings to other languages. It is meant to be a machine learning analog to LAPACK, and aims to implement a wide array of machine learning methods and functions as a "swiss army knife" for machine learning researchers. * mlpack: upstream merged patch to allow python installation in spack
2023-07-06Curl Package: Fixup bugs preventing build on Win (#38757)John W. Parent1-4/+1
2023-07-06Add new version 5.0.0 of PyAMG (#38674)Ben Cowan2-1/+7
* Added v5.0.0 of PyAMG. This required v7.1.0 of setuptools_scm due to a bug in 7.0.5. * Added comment about version requirement. * Loosened dependency based on build experiments. * Updated tomli deps. * Update var/spack/repos/builtin/packages/py-setuptools-scm/package.py Dependence for 7.0 only. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyamg/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Swapped lines. --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-06Disable fortran in openblas for darwin ci, fix variant default value (#38752)Harmen Stoppels2-1/+3
2023-07-06`py-torch`: fix build (#38730)Thomas Bouvier1-0/+14
2023-07-06py-scikit-learn: add v1.3.0 (#38660)Adam J. Stewart1-9/+13
2023-07-06openfoam.org: add a maintainer(#37280) (#37697)kjrstory1-0/+1
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
2023-07-06[py-blis] added versions 0.7.9 and 0.9.1 (#38269)Jen Herting1-0/+3
* [py-blis] added version 0.7.9 * [py-blis] added version 0.9.1 * [py-blis] - removed type run for dependency py-cython
2023-07-06namd: add maintainer (#38740)Jim Phillips1-0/+2
2023-07-06py-abipy: add 0.9.3 (#38716)Manuela Kuhn1-16/+39
* py-abipy: add 0.9.3 * Remove py-cython dependency * Remove dep version restrictions for new release
2023-07-06[py-cymem] added version 2.0.7 (#38267)Jen Herting1-1/+3
* [py-cymem] added version 2.0.3 * [py-cymem] added restriction to py-wheel limitation
2023-07-06`py-dm-tree`: add v0.1.8 (#38606)Thomas Bouvier1-2/+5
* `py-dm-tree`: add v0.1.8 * Update dependencies * Fix hash
2023-07-05`py-horovod`: update to v0.28.1 (#38732)Thomas Bouvier1-0/+1
2023-07-05py-pip: add 23.1.2 (#38608)Manuela Kuhn13-5/+35
* py-pip: add 23.1.2 * Restrict py-pip version for py-protobuf * Restrict py-pip version for straightforward packages * Restrict py-pip version for nrm * Fix --install-option name in comments * Simplify py-pip restriction for py-scs * nrm: fix wrong comment
2023-07-05perl: add 5.38.0, 5.36.1; prefer all even minor versions over development ↵Harmen Stoppels3-15/+123
versions (#38690) * perl: add 5.38.0, 5.36.1; prefer all even minor versions over development versions * fix libxcrypt build with new perl * fix libxcrypt with a patch
2023-07-05py-spglib: add 2.0.2 (#38715)Manuela Kuhn1-4/+4
* py-spglib: add 2.0.2 * Update var/spack/repos/builtin/packages/py-spglib/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Remove py-setuptools as run dependency --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-05acts: new variant cxxstd (#38682)Wouter Deconinck1-6/+21
* acts: allow ^root cxxstd=20 * acts: new variant cxxstd, pass through to root * acts: always args.append CMAKE_CXX_STANDARD from variant * acts: remove unused import * acts: fix self.define_from_variant
2023-07-05Drop Python 2 super syntax (#38718)Adam J. Stewart117-318/+270
2023-07-05Drop Python 2 object subclassing (#38720)Adam J. Stewart110-233/+233
2023-07-05salmon: patching to build with %gcc@13: (#38553)George Young1-0/+9
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-07-05plumed: deprecate non-buildable versions, patch Python makefile only when ↵Harmen Stoppels1-9/+47
supported (#38713)
2023-07-05Update cosma and a few related recipes (#35615)Taillefumier Mathieu4-28/+128
* Add maintainers * Updated cosma archive checksum and costa version - updated cosma version (in the cosma build system) - updated costa version - use the default generic url for downloading packages - do not build tiled-mm when the cpu only version is needed Signed-off-by: Dr. Mathieu Taillefumier <mathieu.taillefumier@free.fr> Co-authored-by: Rocco Meli <r.meli@bluemail.ch> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-07-05damask: fix build of alpha release (#38457)Martin Diehl3-0/+16
2023-07-05Add version 1.8.23 that fixes a compilation bug on clang-15. (#38541)Tom Epperly1-0/+5
2023-07-05tk: convert to new stand-alone test process (#38575)Tamara Dahlgren1-5/+8
2023-07-05ip: add v4.1.0, and additional variants (#38526)Alex Richert1-2/+43
2023-07-05tests/qthreads: convert to new stand-alone test process (#38600)Tamara Dahlgren1-43/+35
2023-07-05tests/papyrus: convert to new stand-alone test process (#38627)Tamara Dahlgren1-65/+80
2023-07-05Build NAMD with Tcl by default (#38645)Jim Phillips1-1/+1
NAMD users expect the Tcl scripting interface to be enabled as it is used in many examples and tutorials in addition to being required for features such as multi-copy algorithms.
2023-07-05git-annex: add latest version 10.20230408 (#38728)Rémi Lacroix1-1/+10
2023-07-05xrootd: add _STAT_VER patch (#38547)Juan Miguel Carceller1-0/+7
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-07-05Installations: don't set group permissions when they match what is desired ↵Peter Scheibel2-0/+36
(#38036) * When installing a package Spack will attempt to set group permissions on the install prefix even when the configuration does not specify a group. Co-authored-by: David Gomez <dvdgomez@users.noreply.github.com>
2023-07-05hcoll: ucx version requirements (#38665)Carlos Bederián1-0/+15
2023-07-05py-pyqt4: stricter dependency versions (#38673)Adam J. Stewart1-3/+6
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