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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
2023-03-06compiler flags: fix multiple compilers with different flags (#35721)Greg Becker3-2/+27
Currently, if two compilers with the same spec differ on the flags, the concretizer will: 1. mix both sets of flags for the spec in the ASP program 2. error noting that the set of flags from the compiler (both of them) doesn't match the set from the lower priority compiler This PR fixes both -- only flags from the highest priority compiler with a given spec are considered.
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 Gamblin37-196/+133
`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>
2023-03-03Polish `spack.util.environment` (#35812)Massimiliano Culpo7-336/+341
Update `spack.util.environment` to remove legacy idioms. * Remove kwargs from method signature and use a class for traces * Uppercase a few global variables * spack.util.environment: add type-hints * Improve docstrings * Fixed most style issues reported by pylint
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>
2023-03-03CI: Fix timeout for VisIt and ParaView (#35787)kwryankrattiger1-0/+2
ref. #35400
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
2023-03-01Detection of Cray's slingshot detection has relied on the presence of (#35779)Brian Van Essen1-1/+1
a shared library /lib64/libcxi.so, which seems to also appear on other non-slingshot systems. This patch also checks to make sure that there is a Cray programming enviornment in /opt/cray/pe in addition to the shared library.
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>
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