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2023-06-22py-networkx: add 3.1 (#38377)Manuela Kuhn1-19/+35
* py-networkx: add 3.1 * Update var/spack/repos/builtin/packages/py-networkx/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add default variant --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-22opencascade: typo in `True` (#38487)Wouter Deconinck1-1/+1
Not sure why flake8 didn't catch this as an undefined name, e.g. https://www.flake8rules.com/rules/F823.html.
2023-06-22Add VecGeom 1.2.3 and mark old versions as deprecated (#38483)Seth R. Johnson1-21/+107
Co-authored-by: Ben Morgan <drbenmorgan@users.noreply.github.com>
2023-06-22add new package: daemonize (#38477)miheer vaidya1-0/+24
2023-06-22IQ-TREE: Add version 2.2.2.7 (#38481)Rémi Lacroix1-0/+1
2023-06-22celeritas: new version 0.3.0 (#38438)Seth R. Johnson1-1/+3
2023-06-22geant4: new version 11.1.2 (#38475)Wouter Deconinck1-0/+1
No changes required to the geant4 package.py file. Changes: https://gitlab.cern.ch/geant4/geant4/-/compare/v11.1.1...v11.1.2 Release notes: https://geant4.web.cern.ch/download/release-notes/notes-v11.1.2.txt Co-authored-by: Ben Morgan <drbenmorgan@users.noreply.github.com>
2023-06-22tests/py-chainer: convert to new stand-alone test process (#38365)Tamara Dahlgren1-22/+20
* tests/py-chainer: convert to new stand-alone test process * py-chainer: add skip_modules entry for onnx_chainer
2023-06-21py-pycairo: add 1.24.0 (#38503)Manuela Kuhn1-6/+10
* py-pycairo: add 1.24.0 * Change python dependency to 3.8 * Remove upper bound for python dependency * Update var/spack/repos/builtin/packages/py-pycairo/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-21tetranscripts: new package @2.2.3 (#38485)George Young1-0/+23
* tetranscripts: new package @2.2.3 * tidying up --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-21[tclap] Adds new versions to tclap package (#38508)Matthieu Dorier1-0/+3
2023-06-21darshan-runtime,darshan-util,py-darshan: add 3.4.3 releases (#38359)shanedsnyder3-13/+16
* add darshan 3.4.3 releases * darshan-runtime 3.4.3 * darshan-util 3.4.3 * py-darshan 3.4.3.0 - add py-humanize as new dependency * py-darshan has strict darshan-util version reqs darshan-util version required is based on the first 3 parts of the py-darshan version string * remove support for python3.6 * py-humanize dependency for 3.4.3+ versions * only enforce scipy dependency for 3.4.0.1 * drop optional lxml dependency * drop matplotlib pinning * importlib-resources not a dep in python-3.7+ * drop unnecessary numpy pin * add build dep for pytest-runner * fix typo in pytest-runner package name * pip setuptools to match pydarsan setup.py * spack style fix
2023-06-21neovim: add v0.9.(0|1) (#38463)miheer vaidya1-0/+4
2023-06-21py-prometheus-client: add 0.17.0 (#38471)Manuela Kuhn1-11/+7
2023-06-21py-gsutil: add 5.24, fix and add dependencies (#38450)Manuela Kuhn7-6/+74
* py-gsutil: add 5.24, fix and add dependencies * Update var/spack/repos/builtin/packages/py-httplib2/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add httplib2@0.20.4 and pin it in py-gsutil * Add py-cryptography conflict * Update var/spack/repos/builtin/packages/py-httplib2/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * py-pyopenssl: fix py-cryptography conflict --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-21mpich: undefined variable dso_suffix (#37373)Erik Heeren1-0/+1
* mpich: undefined variable dso_suffix * mpich: formatting --------- Co-authored-by: Nichols A. Romero <naromero77@users.noreply.github.com>
2023-06-21py-lightly: add v1.4.8 (#38397)Adam J. Stewart3-3/+13
* py-lightly: add v1.4.8 * Fix typo * Update deps as well * typing-extensions dep needed earlier Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * Runtime dep on setuptools removed in master --------- Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-06-21py-pygments: add 2.15.1 (#38505)Manuela Kuhn1-3/+4
2023-06-21py-pydicom: add 2.4.1 (#38504)Manuela Kuhn1-1/+6
2023-06-21py-psutil: add 5.9.5 (#38479)Manuela Kuhn1-4/+1
* py-psutil: add 5.9.5 * Remove unneeded windows dependencies
2023-06-21bulker: new package @0.7.3 (#38437)George Young1-0/+24
* py-bulker: new package at 0.7.3 * bulker: renaming package --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-21Add MDAnalysis and MDAnalysisTests to 2.5.0 (#37968)Rocco Meli2-114/+27
* update mda and mdatests * black * 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> * polish * Update var/spack/repos/builtin/packages/py-mdanalysistests/package.py * fixes --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-21py-tensorboard(-plugin-wit): remove unused patch files (#38360)Christian Mauch4-65/+0
2023-06-21py-numpy: add v1.25.0 (#38461)Adam J. Stewart2-3/+8
2023-06-20kokkos-nvcc-wrapper: add new versions (#38446)Martin Pokorny1-0/+13
2023-06-20tests/superlu: convert to new stand-alone test process (#38404)Tamara Dahlgren1-97/+67
* superlu: convert to new stand-alone test process * Bugfix/superlu: add BaseBuilder and move post-install work to it
2023-06-20[mochi-margo] margo version 0.14.0 added (#38473)Matthieu Dorier1-0/+1
2023-06-20[WRF] Always use compiler wrappers for FFLAGS/FCFLAGS (#38470)Stephen Sachs1-12/+3
`FFLAGS` and `FCFLAGS` are being ignored by WRF build system. Not only in version `3.9.1.1`, but also `4.x`. Also, I see no reason to explicitly add `-w` and `-O2` to compile lines when using `gcc@10:`. Tested for version `3.9.1.1`, `4.2.2`, & `4.5.0`. Tagging original authors of this part @MichaelLaufer and @giordano in case they want to chime in.
2023-06-20fastjet: add v3.4.1, update patch (#38467)Valentin Volkl1-1/+8
2023-06-20mpiwrapper: New version 2.10.4 (#38448)Erik Schnetter1-0/+1
2023-06-20mpitrampoline: New version 5.3.1 (#38449)Erik Schnetter1-0/+1
2023-06-20ncbi-rmblastn: switching urls from ftp to https (#38490)snehring1-3/+7
2023-06-20ncbi-rmblastn: patching to support building with %gcc@13: (#38382)George Young2-0/+13
* ncbi-rmblastn: patching to support building with %gcc@13: * ncbi-rmblastn: patching to build with %gcc@13: --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-20py-umi-tools: add 1.1.4, add py-pybktree dependency (#38394)George Young1-2/+2
* py-umi-tools: add 1.1.4, add py-pybktree dependency * remove python spec * Remove `six` dependency --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-20apptainer: adding version 1.1.9 (#38492)snehring1-0/+1
2023-06-20py-pybids: add 0.16.1 (#38480)Manuela Kuhn1-5/+16
2023-06-20root: fix variant detection (#38436)Valentin Volkl1-2/+5
2023-06-19py-pre-commit: add 3.3.3 (#38468)Manuela Kuhn1-11/+16
* py-pre-commit: add 3.3.3 * Update var/spack/repos/builtin/packages/py-pre-commit/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-19py-nodeenv: add 1.8.0 (#38383)Manuela Kuhn1-1/+2
* py-nodeenv: add 1.8.0 * Remove python@3.7 restriction
2023-06-19py-pkginfo: add 1.9.6 (#38434)Manuela Kuhn1-2/+2
* py-pkginfo: add 1.9.6 * Remove py-setuptools as run dependency
2023-06-19gsl: set GSL_ROOT_DIR (#38464)Juan Miguel Carceller1-0/+5
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-19repeatmasker: adding version 4.1.5 (#38445)snehring1-0/+1
2023-06-19py-pooch: add 1.7.0 (#38466)Manuela Kuhn1-3/+11
2023-06-19spdlog: patch for fmt::basic_runtime when ^fmt@10 (#38082)Wouter Deconinck1-0/+7
2023-06-18cc: Ensure that user-specified flags take precedence over others (#37376)Andrey Parfenov2-195/+256
Spack flags supplied by users should supersede flags from package build systems and other places in Spack. However, Spack currently adds user-supplied flags to the beginning of the compile line, which means that in some cases build system flags will supersede user-supplied ones. The right place to add a flag to ensure it has highest precedence for the compiler really depends on the type of flag. For example, search paths like `-L` and `-I` are examined in order, so adding them first is highest precedence. Compilers take the *last* occurrence of optimization flags like `-O2`, so those should be placed *after* other such flags. Shim libraries with `-l` should go *before* other libraries on the command line, so we want user-supplied libs to go first, etc. `lib/spack/env/cc` already knows how to split arguments into categories like `libs_list`, `rpath_dirs_list`, etc., so we can leverage that functionality to merge user flags into the arg list correctly. The general rules for injected flags are: 1. All `-L`, `-I`, `-isystem`, `-l`, and `*-rpath` flags from `spack_flags_*` to appear before their regular counterparts. 2. All other flags ordered with the ones from flags after their regular counterparts, i.e. `other_flags` before `spack_flags_other_flags` - [x] Generalize argument categorization into its own function in the `cc` shell script - [x] Apply the same splitting logic to injected flags and flags from the original compile line. - [x] Use the resulting flag lists to merge user- and build-system-supplied flags by category. - [x] Add tests. Signed-off-by: Andrey Parfenov <andrey.parfenov@intel.com> Co-authored-by: iermolae <igor.ermolaev@intel.com>
2023-06-18fix oneapi modules (#38400)simonleary-umass-edu1-1/+1
2023-06-18py-vermin: add latest version 1.5.2 (#38460)Morten Kristensen1-3/+3
* py-vermin: add latest version 1.5.2 * Removed obsolete dep and setuptools is only for build-time - setuptools are not used as runtime - py27 isn't strictly necessary
2023-06-17Add latest enzyme release (#38442)William Moses1-3/+5
2023-06-16unparser: drop Python 2, fix testing bugs with newer Pythons (#38424)Greg Becker2-129/+20
The `unparser` that Spack uses for package hashing had several tweaks to ensure compatibility with Python 2.7: 1. Currently, the unparser automatically moves `*` and `**` args to the end to preserve compatibility with `python@:3.4` 2. `print a, b, c` statements and single-tuple `print((a, b, c))` function calls were remapped to `print(a, b, c)` in the unparsed output for consistency across versions. (1) is causing issues in our tests because a recent patch to the Python source code (https://github.com/python/cpython/pull/102953/files#diff-7972dffec6674d5f09410c71766ac6caacb95b9bccbf032061806ae304519c9bR813-R823) has a `**` arg before an named argument, and we round-trip the core python source code as a test of our unparser. This isn't actually a break with our consistent unpausing -- it's still consistent, the python source just doesn't unparse to the same thing anymore. It does makes it harder to test, so it's not worth maintaining the Python2-specific stuff anymore. Since we only support `python@3.6:`, this PR removes (1) and (2) from the unparser, but keeps one last tweak for unicode AST inconsistencies, as it's still needed for Python 3.5-3.7. This fixes the CI error we've been seeing on `python@3.11.4` and `python@3.10.12`. Again, that bug exists only in the test system and doesn't affect our canonical hashing of Python code.
2023-06-16py-aiohttp: add 3.8.4 (#38451)Manuela Kuhn1-15/+18
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