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2023-03-03Update python linting packages (#35811)MicK72-2/+8
* add 2.14.2 py-astroid version * add py-pylint 2.26.2 * fix black * fix py-dill depends_on Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * fix py-astroid minor versionning Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * modify typing_extensions depends_on --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-03-03Start using paths found in extra_rpaths in compilers.yaml when building (#35376)MatthewLieber1-1/+7
* Start using paths found in extra_rpaths in compilers.yaml when building * running black and changing maintainer list * changing import order to pass isort --------- Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
2023-03-03snakemake: added versions 7.19.0-7.22.0 (#35535)Lucas Frérot1-3/+13
* snakemake: added versions 7.19.0-7.22.0 * snakemake: corrected +reports dependencies
2023-03-03py-ipdb: updating versions (#35654)Loïc Pottier1-16/+12
* py-ipdb: updating versions Signed-off-by: Loïc Pottier <pottier1@llnl.gov> * py-ipdb: fixing versions problem and deleting 10.1 which is too old for Python > 3.6 Signed-off-by: Loïc Pottier <pottier1@llnl.gov> * Update var/spack/repos/builtin/packages/py-ipdb/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * py-ipdb: removed useless dependencies Signed-off-by: Loïc Pottier <pottier1@llnl.gov> * Update var/spack/repos/builtin/packages/py-ipdb/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-ipdb/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * py-ipdb: missing @ Signed-off-by: Loïc Pottier <pottier1@llnl.gov> * Update var/spack/repos/builtin/packages/py-ipdb/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Signed-off-by: Loïc Pottier <pottier1@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-03-03update github URL (#35789)Jean Luca Bez1-2/+2
2023-03-03Update pyprecice v2.5.0.2 (#35788)Ishaan Desai1-0/+1
* Update versions 2.5.0.0 and 2.5.0.1 * Applying review changes * Updating incorrect checksum for v2.4.0.0 * Add for loop to define depends_on for preCICE versions and bindings versions * Formatting * Missing comma * Add pyprecice v2.5.0.2
2023-03-03py-jupyter-server-proxy: fix dependency condition (#35784)Erik Heeren1-2/+2
Too much copypasta
2023-03-02scons: add a new version (#35652)H. Joe Lee1-6/+2
* scons: add a new version * scons: address @adamjstewart review
2023-03-02Add e3sm scorpio (#35794)downloadico1-0/+54
* e3sm-scorpio: add e3sm-scorpio package This is the Scorpio package from the e3sm.org site. * fixed style errors * removed unneeded dependency on cmake
2023-03-02py-nbstripout: add new package (#35786)Adam J. Stewart1-0/+18
2023-03-02py-rtoml: add new package (#35780)Adam J. Stewart2-0/+40
2023-03-02julia: fix for libuv and Julia (#35776)Robert Underwood2-1/+8
Use correct `shlib_symbol_version` for Julia 1.8, work around issue where libuv-julia's git checkout has arbitrary mtime, causing make to regenerate configure scripts, sometimes.
2023-03-02py-chart-studio: new package (#35759)Erik Heeren1-0/+22
* py-chart-studio: new package * py-chart-studio: add missing six dependency
2023-03-02Add a `py-gmxapi` package. (#35738)M. Eric Irrgang1-0/+48
* Add a `py-gmxapi` package. This package provides the Python package for the GROMACS public API. The Python package is not strongly coupled to a specific GROMACS _version_, but its compiled extension module is strongly coupled to a specific GROMACS _installation_. * Update conflict info. In order to allow `^gromacs@2022.1` while rejecting `^gromacs@2022`, we need to compare to `gromacs@2022.0`. * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Apply suggestions from code review. * Simplify build system structure. * Update dependencies for completeness. * Update var/spack/repos/builtin/packages/py-gmxapi/package.py Per code review, pretend gmxapi <0.4 doesn't exist, for simplicity. * Update var/spack/repos/builtin/packages/py-gmxapi/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-gmxapi/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-03-02WarpX: add v23.03 (#35775)Axel Huebl2-2/+5
Update `warpx` & `py-warpx` to the latest release.
2023-03-02py-kornia: add v0.6.10 (#35554)Adam J. Stewart1-0/+1
2023-03-02py-pytorch-lightning: add v1.9.3 (#35629)Adam J. Stewart1-0/+1
2023-03-01Add py-mpi4py as a dependency for henson (#35743)Dmitriy1-0/+3
* Add py-mpi4py as a dependency * Add maintainers per spackbot's request * Add type=(build,run) per adamjstewart's suggestion
2023-03-01py-torchgeo: kornia backwards-incompatible change (#35570)Adam J. Stewart1-4/+5
2023-03-01py-scipy: add v1.10.1 (#35581)Adam J. Stewart1-1/+3
2023-03-01py-pygments 2.12; fix py-docutils, again (#35394)Harmen Stoppels2-1/+5
* py-pygments 2.12; fix py-docutils, again `2.12` is the latest for which our style hack works, beyond that we need our own package to make a plugin. Old docutils needs old setuptools * py-setuptools is always a dep Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update the range Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-03-01Add capitalized symlinks for libesmf.{a,so} (#35774)Alex Richert1-1/+8
* Add capitalized symlinks for libesmf.{a,so} * Add import of lib suffixes
2023-03-01GitHub CLI: Add version 2.23.0 (#35761)Rémi Lacroix1-0/+1
2023-03-01papi: more fixes for Intel OneAPI compiler (#34048)Howard Pritchard2-0/+43
The Intel OneAPI's extreme pickiness continues to bring out buggy/noncompliant code. This patch fixes an error in the configure.in embedded 'c' test code and also in a file with an initialized, but unused, variable. Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-03-01Update FEniCSx libraries to v0.6 (#35600)Garth N. Wells7-36/+63
* Updates to release 0.6. * Dep updates * Dep version fix * Another version fix * Fix typo * UFL version fix * Update var/spack/repos/builtin/packages/py-fenics-dolfinx/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fenics-ffcx/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Some updates following review * Update var/spack/repos/builtin/packages/py-fenics-dolfinx/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * More updates * More updates * build/run updates * Small fix * Fix version number. * specify lower bounds for python dependencies * address style issues * address style issues * address PR comments * amend setuptools dependency to be of type build only * amend setuptools dependency to be of type run and build for ffcx and ufl * add build dependency to ensure import tests pass --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Matthew Archer <ma595@cam.ac.uk>
2023-03-01cp2k: fix builds on macOS, workaround reported issue with __contains__ (#35584)Tiziano Müller4-36/+39
Co-authored-by: Robert Cohn <rscohn2@gmail.com> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-03-01py-dbf: new versions and dependency (#35760)Erik Heeren1-0/+4
2023-03-01Fix superlu-dist package for cray fortran (#35728)luker1-1/+1
The superlu-dist code developers modified the code such that the patch is no longer needer for `@7.2.0:` (the patch will actually fail)
2023-03-01Py dask mpi (#35679)Erik Heeren3-0/+76
* py-dask-mpi: new package with dependencies * py-hatch-jupyter-builder is not needed after all * skip_modules seems cleaner * Update var/spack/repos/builtin/packages/py-jupyter-server-proxy/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-simpervisor/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-03-01py-fiona: add upper bounds to Python versions (#35658)Adam J. Stewart1-3/+18
* py-fiona: add upper bounds to Python versions * Add error msg
2023-03-01wrf: Fix compilation with GCC 10+ (#35177)Mosè Giordano1-1/+11
Flags `-fallow-argument-mismatch -fallow-invalid-boz` set in `FFLAGS`/`FCFLAGS` environment variables don't really have effect in older versions of WRF, we need to force them in the compiler wrappers. Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-03-01py-particle: new versions 0.16.*, 0.20.*, 0.21.* (#35547)Wouter Deconinck1-2/+18
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-03-01sartre: new package (#32713)Wouter Deconinck1-0/+46
2023-03-01vc: improvements for testing (#28887)Valentin Volkl2-55/+25
2023-03-01mvapich2-gdr/mvapich2x: add v2.3.7, update package config (#33066)MatthewLieber2-14/+40
Co-authored-by: Nick Contini <contini.26@osu.edu>
2023-03-01hdf5-vol-async: add v1.5 (#35636)Houjun Tang1-0/+1
2023-03-01dd4hep: depends_on root +webgui when +ddeve ^root @6.28: (#35624)Wouter Deconinck1-1/+4
2023-03-01dpdk: add a new build system and version (#35647)H. Joe Lee1-4/+29
2023-03-01isa-l_crypto: add a new package (#35651)H. Joe Lee1-0/+46
2023-03-01isa-l: add a new package (#35650)H. Joe Lee1-0/+49
2023-03-01upp: add v10.0.8 (#35667)Alex Richert1-0/+2
2023-03-01grib-util: fix dependency constraints (#35668)Alex Richert1-2/+3
2023-03-01OOMMF: set preferred version (#35675)Hans Fangohr1-1/+3
With the last merge request for OOMMF [1], the intention was to have version 20b0_20220930 as the preferred version, and provide 20b0_20220930-vanilla as an additional version for the unlikely case anybody needed that. I made the (wrong) assumption that the `version` listed first in the `package.py` file would be the preferred version. This merge request is to correct that by explicitly tagging the preferred version with `preferred=True`. [1] https://github.com/spack/spack/pull/33072/files
2023-03-01docbook: resolve conflict in spack env view (#35682)Glenn Johnson2-2/+2
If the docbook packages - docbook-xml - docbook-xsl are installed in a spack environment view the catalog files will be in conflict in the view directory. This PR resolves that by adding an appropriate prefix to each catalog name so that they are unique in the view. The resulting XML_CATALOG_FILES environment variable will then be able to point to both of them.
2023-03-01dd4hep: new versions 1.25, 1.25.1 (#35665)Wouter Deconinck1-0/+2
2023-03-01elk: add v8.3.22 and fix a few issues (#35678)acastanedam1-17/+29
2023-03-01mbedtls: new versions and deprecations [CVE-2022-46392] (#35715)Harmen Stoppels1-9/+52
* Add new versions and deprecations [CVE-2022-46392] * remove maintainer, order versions by major no
2023-03-01cbench: renamed test_blas_linkage to check_blas_linkage (#35690)Tamara Dahlgren1-1/+1
2023-03-01py-uproot: new versions 4.3.*, 5.0.* (#35548)Wouter Deconinck1-2/+12
2023-03-01py-torchmetrics: add v0.11.2-3 (#35755)Adam J. Stewart1-0/+2
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