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2023-03-07aspell: add v0.60.8 (#35834)Alec Scott1-0/+1
2023-03-07Update biopython, gsd, and griddataformats (#35827)Rocco Meli3-8/+44
* update mda dependencies * apply black * Update var/spack/repos/builtin/packages/py-gsd/package.py * Update var/spack/repos/builtin/packages/py-griddataformats/package.py * Update var/spack/repos/builtin/packages/py-griddataformats/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * remove numpy upper bound * Update var/spack/repos/builtin/packages/py-griddataformats/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-gsd/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-03-07beforelight: add v1.0.6 (#35843)Alec Scott1-0/+1
2023-03-07busybox: add v1.36.0 (#35840)Alec Scott1-0/+1
2023-03-07bitmap: add v1.1.0 (#35839)Alec Scott1-0/+1
2023-03-07blktrace: add v1.3.0 (#35842)Alec Scott1-0/+1
2023-03-07bmake: add v20230303 (#35841)Alec Scott1-0/+1
2023-03-07atk: add v2.38.0 (#35833)Alec Scott1-0/+1
2023-03-07appres: add v1.0.6 (#35831)Alec Scott1-0/+1
2023-03-07ace: add v7.1.0 (#35829)Alec Scott1-0/+1
2023-03-07alglib: add v3.20.0 (#35830)Alec Scott1-0/+1
2023-03-06py-matplotlib: add v3.7.1 (#35822)Adam J. Stewart1-0/+1
2023-03-06Proj: to CMake (#35108)John W. Parent1-17/+39
* update proj * re-add autotools support * style * Setup env in builders * Drop direct windows conflict for older versions * Default to CMake Add new style class definiton * Proj: setup_run_environment in package not builder * Proj: move run env changes to pkg, rm cmake arg * Set PROJ_LIB during build * Style * Rm redundant configure arg
2023-03-06py-elasticsearch: new versions (#35764)Erik Heeren2-1/+29
* py-elasticsearch: new versions Also add py-elastic-transport as a new dependency * py-elasticsearch: py-urllib3 is no longer a dependency * Update var/spack/repos/builtin/packages/py-elasticsearch/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-03-05Add Hugo v0.111.1 (#35824)Alec Scott1-0/+1
2023-03-05curl: add v7.88.1 and deprecate previous versions due to CVEs (#35825)Alec Scott1-38/+198
* curl: add v7.88.1 and deprecate previous versions due to CVEs * Add self as a maintainer to curl
2023-03-05libarchive: add v3.6.2 and deprecate previous versions due to CVE-2022-36227 ↵Alec Scott1-8/+45
(#35826)
2023-03-05windows: use `sys.platform == "win32"` instead of `is_windows` (#35640)Todd Gamblin7-49/+39
`mypy` only understands `sys.platform == "win32"`, not indirect assignments of that value to things like `is_windows`. If we don't use the accepted platform checks, `mypy` registers many Windows-only symbols as not present on Linux, when it should skip the checks for platform-specific code.
2023-03-04py-simpervisor: correct pypi (#35785)Erik Heeren1-1/+1
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>
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