Commit graph

29830 commits

Author SHA1 Message Date
Alec Scott
973bc92813
libarchive: add v3.6.2 and deprecate previous versions due to CVE-2022-36227 (#35826) 2023-03-05 18:22:41 +01:00
Todd Gamblin
42a02411b4
windows: use sys.platform == "win32" instead of is_windows (#35640)
`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.
2023-03-05 07:58:05 -08:00
Erik Heeren
4561536403
py-simpervisor: correct pypi (#35785) 2023-03-04 10:44:03 -06:00
MicK7
6b694749d3
Update python linting packages (#35811)
* 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>
2023-03-03 16:06:56 -06:00
MatthewLieber
c0f48b30cf
Start using paths found in extra_rpaths in compilers.yaml when building (#35376)
* 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>
2023-03-03 13:29:59 -08:00
Massimiliano Culpo
046416479a
Polish spack.util.environment (#35812)
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
2023-03-03 16:17:27 -05:00
Lucas Frérot
b17113b63d
snakemake: added versions 7.19.0-7.22.0 (#35535)
* snakemake: added versions 7.19.0-7.22.0

* snakemake: corrected +reports dependencies
2023-03-03 12:46:29 -06:00
Loïc Pottier
479f5a74a3
py-ipdb: updating versions (#35654)
* 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>
2023-03-03 05:28:40 -05:00
kwryankrattiger
895886959f
CI: Fix timeout for VisIt and ParaView (#35787)
ref. #35400
2023-03-03 09:13:14 +01:00
Jean Luca Bez
0bdb0b07fd
update github URL (#35789) 2023-03-03 00:23:23 -05:00
Ishaan Desai
817b59900a
Update pyprecice v2.5.0.2 (#35788)
* 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
2023-03-03 00:19:17 -05:00
Erik Heeren
2ddd66ca48
py-jupyter-server-proxy: fix dependency condition (#35784)
Too much copypasta
2023-03-03 00:18:31 -05:00
H. Joe Lee
7ddd796f89
scons: add a new version (#35652)
* scons: add a new version

* scons: address @adamjstewart review
2023-03-02 15:14:59 -06:00
downloadico
1e2ef16b39
Add e3sm scorpio (#35794)
* e3sm-scorpio: add e3sm-scorpio package
   This is the Scorpio package from the e3sm.org site.
* fixed style errors
* removed unneeded dependency on cmake
2023-03-02 15:48:55 -05:00
Adam J. Stewart
77355fd348
py-nbstripout: add new package (#35786) 2023-03-02 10:47:48 -07:00
Adam J. Stewart
1facf99f51
py-rtoml: add new package (#35780) 2023-03-02 09:43:36 -08:00
Robert Underwood
07c8939679
julia: fix for libuv and Julia (#35776)
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.
2023-03-02 16:36:55 +01:00
Erik Heeren
28f4b5729a
py-chart-studio: new package (#35759)
* py-chart-studio: new package

* py-chart-studio: add missing six dependency
2023-03-02 08:40:37 -06:00
M. Eric Irrgang
dd7af323ed
Add a py-gmxapi package. (#35738)
* 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>
2023-03-02 08:37:17 -06:00
Axel Huebl
2ba1f700e6
WarpX: add v23.03 (#35775)
Update `warpx` & `py-warpx` to the latest release.
2023-03-02 04:19:08 -08:00
Adam J. Stewart
739ab89b65
py-kornia: add v0.6.10 (#35554) 2023-03-02 01:08:39 -08:00
Adam J. Stewart
7e5099627f
py-pytorch-lightning: add v1.9.3 (#35629) 2023-03-02 00:23:34 -08:00
Brian Van Essen
eb29889f6e
Detection of Cray's slingshot detection has relied on the presence of (#35779)
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.
2023-03-01 23:19:20 -08:00
Dmitriy
ae27df4113
Add py-mpi4py as a dependency for henson (#35743)
* Add py-mpi4py as a dependency

* Add maintainers per spackbot's request

* Add type=(build,run) per adamjstewart's suggestion
2023-03-01 22:43:31 -08:00
Adam J. Stewart
ae2c8c02a2
py-torchgeo: kornia backwards-incompatible change (#35570) 2023-03-01 22:13:23 -08:00
Adam J. Stewart
caff9e4292
py-scipy: add v1.10.1 (#35581) 2023-03-01 16:04:23 -08:00
Harmen Stoppels
beb3414b4d
py-pygments 2.12; fix py-docutils, again (#35394)
* 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>
2023-03-01 15:53:41 -08:00
Alex Richert
ed07cee852
Add capitalized symlinks for libesmf.{a,so} (#35774)
* Add capitalized symlinks for libesmf.{a,so}
* Add import of lib suffixes
2023-03-01 15:28:46 -08:00
Rémi Lacroix
7c1a164219
GitHub CLI: Add version 2.23.0 (#35761) 2023-03-01 13:59:28 -08:00
Howard Pritchard
18e0b893f2
papi: more fixes for Intel OneAPI compiler (#34048)
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>
2023-03-01 13:33:55 -08:00
Garth N. Wells
df5b25764b
Update FEniCSx libraries to v0.6 (#35600)
* 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>
2023-03-01 13:18:23 -08:00
Tiziano Müller
44705b0a6e
cp2k: fix builds on macOS, workaround reported issue with __contains__ (#35584)
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-03-01 12:01:00 -08:00
Erik Heeren
3bb03ea7d1
py-dbf: new versions and dependency (#35760) 2023-03-01 10:49:27 -08:00
luker
3c411bf135
Fix superlu-dist package for cray fortran (#35728)
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)
2023-03-01 10:49:06 -08:00
Erik Heeren
f2363c1cb5
Py dask mpi (#35679)
* 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>
2023-03-01 11:35:55 -06:00
Adam J. Stewart
7188eeb604
py-fiona: add upper bounds to Python versions (#35658)
* py-fiona: add upper bounds to Python versions

* Add error msg
2023-03-01 09:53:20 -06:00
Adam J. Stewart
583d89e95a
Simplify spack help --spec output (#35626) 2023-03-01 16:26:59 +01:00
Mosè Giordano
4a24401ed0
wrf: Fix compilation with GCC 10+ (#35177)
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>
2023-03-01 07:14:42 -08:00
Wouter Deconinck
2796794b19
py-particle: new versions 0.16.*, 0.20.*, 0.21.* (#35547)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-03-01 14:49:37 +01:00
Wouter Deconinck
dd854e86d9
sartre: new package (#32713) 2023-03-01 14:36:16 +01:00
Valentin Volkl
1500246ab7
vc: improvements for testing (#28887) 2023-03-01 14:29:43 +01:00
MatthewLieber
206cd94c0b
mvapich2-gdr/mvapich2x: add v2.3.7, update package config (#33066)
Co-authored-by: Nick Contini <contini.26@osu.edu>
2023-03-01 14:24:34 +01:00
Houjun Tang
ff1a425c8d
hdf5-vol-async: add v1.5 (#35636) 2023-03-01 14:16:56 +01:00
Wouter Deconinck
ab999d5af9
dd4hep: depends_on root +webgui when +ddeve ^root @6.28: (#35624) 2023-03-01 14:13:50 +01:00
H. Joe Lee
513ff34e66
dpdk: add a new build system and version (#35647) 2023-03-01 14:08:41 +01:00
H. Joe Lee
b59c8e9a43
isa-l_crypto: add a new package (#35651) 2023-03-01 14:06:37 +01:00
H. Joe Lee
9483e34d15
isa-l: add a new package (#35650) 2023-03-01 14:06:22 +01:00
Alex Richert
7e02139cad
upp: add v10.0.8 (#35667) 2023-03-01 14:00:27 +01:00
Alex Richert
a08d86c201
grib-util: fix dependency constraints (#35668) 2023-03-01 13:59:45 +01:00
Hans Fangohr
4e70532cd1
OOMMF: set preferred version (#35675)
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
2023-03-01 13:53:59 +01:00