Commit graph

33118 commits

Author SHA1 Message Date
Scott Wittenburg
fa9acb6a98
ci: Tag reindex job to match the image architecture (#39958) 2023-09-12 16:33:56 -04:00
Johann Gaebler
621d42d0c7
r-piggyback: Add R package piggyback (#39932) 2023-09-12 12:53:47 -07:00
Johann Gaebler
cfdaee4725
r-pl94171: Add R package PL94171 (#39926) 2023-09-12 12:51:23 -07:00
Massimiliano Culpo
306ba86709
binutils: add v2.41 (#39483) 2023-09-12 21:15:45 +02:00
George Young
b47fd61f18
bam-readcount: add 1.0.1, correct build flags (#39950)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-12 11:26:30 -07:00
Tamara Dahlgren
c10ff27600
CI/Add superlu-dist to broken stand-alone tests due to hang (#38908)
* Add superlu-dist to broken stand-alone CI tests
* Revert "disable superlu test (#38894)"
  This reverts commit e16397b5d8.
2023-09-12 11:09:25 -07:00
Adam Moody
9056f31f11
mpifileutils: switch to main branch (#39525) 2023-09-12 10:57:29 -07:00
Dom Heinzeller
513232cdb3
libjpeg-turbo: Fix Darwin lib install name (#39834)
* Fix Darwin lib install name in var/spack/repos/builtin/packages/libjpeg-turbo/package.py

* Update var/spack/repos/builtin/packages/libjpeg-turbo/package.py

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-12 10:49:30 -07:00
Dom Heinzeller
30893dd99a
Filter spack compiler wrappers for h4cc in var/spack/repos/builtin/packages/hdf/package.py (#39870) 2023-09-12 10:41:04 -07:00
Alex Richert
b7c2411b50
g2 package bugfix (#39923)
* g2 package bugfix

* g2: fix w3emc dep

* fix setup_run_environment

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* style fix

* Update var/spack/repos/builtin/packages/g2/package.py

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

* Update var/spack/repos/builtin/packages/g2/package.py

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

---------

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-09-12 10:40:37 -07:00
Weiqun Zhang
002e833993
amrex: add v23.09 (#39788) 2023-09-12 10:39:56 -07:00
Martin Aumüller
02c9296db4
openexr: add 2.4.3, 2.5.9, 3.1.11 & 3.2.0 (#39863)
* openexr: add 2.4.3, 2.5.9, 3.1.11 & 3.2.0

- 2.5.9 is the latest version compatible with OpenScenGraph
- improved compatibility with GCC 13

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* openexr: drop unsupported debug variant

--disable/enable-debug is not supported by ./configure in 1.3, 1.7, 2.0, 2.2 and 2.3

* openexr: transform into multi-build system package

simplifies package considerably, as nothing special seems to be required

* openexr: pkg-config is also used by @3

* openexr: use system libdeflate instead of internal

if no libdeflate is found, openexr would download and build its own starting with 3.2.0

* openexr: disable tests

would download lots of data during cmake and make build times noticably longer

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-12 10:37:48 -07:00
Vincent Michaud-Rioux
562065c427
Update PennyLane packages to v0.32. (#39688)
* Update PennyLane packages to v0.32.

* Reformat.

* Couple small fixes.

* Fix Lightning cmake_args.

* Couple dep fixes in py-pennylane + plugins.

* Fix scipy condition.

* Add comment on conflicting requirement.
2023-09-12 12:19:29 -05:00
Harmen Stoppels
9d00bcb286
openssl: deprecate 1.1.1 (#39942) 2023-09-12 12:45:51 +02:00
Harmen Stoppels
a009a1a62a
asp.py: fix deprecation warning (#39943) 2023-09-12 09:27:03 +00:00
Mikael Simberg
f7692d5699
Add gperftools 2.13 (#39940) 2023-09-12 11:26:19 +02:00
George Young
12e1768fdb
filtlong: add v0.2.1, patch for %gcc@13: (#39775)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-12 04:03:02 -04:00
dependabot[bot]
28a3be3eca
build(deps): bump black from 23.7.0 to 23.9.1 in /lib/spack/docs (#39937)
Bumps [black](https://github.com/psf/black) from 23.7.0 to 23.9.1.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.7.0...23.9.1)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-12 07:44:19 +02:00
Brian Van Essen
33500b5169
lbann: make two variants sticky (#39710)
* Make the state of the Python Front End (PFE) and Python data reader
support sticky so that the concretizer does not arbitrarily disable
them.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-09-12 01:42:48 -04:00
Stephen Sachs
91011a8c5f
[gromacs] Fix 2021.2 build error (#39722)
* [gromacs] Fix 2021.2 build error

See https://gromacs.bioexcel.eu/t/compilation-failure-for-gromacs-2021-1-and-2021-2-with-cmake-3-20-2/2129

* Update var/spack/repos/builtin/packages/gromacs/package.py

Co-authored-by: Andrey Alekseenko <al42and@gmail.com>

---------

Co-authored-by: Andrey Alekseenko <al42and@gmail.com>
2023-09-11 19:49:18 -04:00
Caetano Melone
4570c9de5b
fish: add 3.6.0, 3.6.1, update cmake requirement (#39899) 2023-09-11 19:34:33 -04:00
Adam J. Stewart
e7507dcd08
py-build: add v1 (#39930) 2023-09-11 19:04:32 -04:00
Dom Heinzeller
4711758593
Add awscli@1.29.41 and its dependency py-botocore@1.31.41 (#39878)
* Add awscli@1.29.41 and its dependency py-botocore@1.31.41

* Update var/spack/repos/builtin/packages/awscli/package.py

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

---------

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-09-11 18:02:46 -04:00
Sinan
b55e9e8248
package_qscintilla_build_with_qt6 (#39544)
* package_qscintilla_build_with_qt6

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* improve

* fix Qsci.abi3.so install

* simplify, fix, tidy

* fix style

* fix style

* fix style

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* improve

* improve style

* fix style

* make black happy

* add ver 2.14.1

* update

* make black happy

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* improve

---------

Co-authored-by: Sinan81 <Sinan@world>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11 16:58:28 -05:00
Adam J. Stewart
2e62cfea3e
py-black: add v23.9 (#39931) 2023-09-11 16:36:16 -05:00
Manuela Kuhn
286e1147d6
py-tifffile: add 2023.8.30 (#39918) 2023-09-11 16:34:20 -05:00
Manuela Kuhn
7e3d228d19
py-tinycss2: add 1.2.1 (#39921) 2023-09-11 16:32:42 -05:00
Manuela Kuhn
a1ab42c8c0
py-tomlkit: add 0.12.1 (#39922) 2023-09-11 16:31:55 -05:00
Rocco Meli
57a2f2ddde
tidynamics: add v1.1.2 (#39911)
* ensure umpire~cuda~rocm when ~cuda~rocm

* update tydynamics
2023-09-11 16:17:17 -05:00
Mike Renfro
b7b7b2fac4
correct py-bx-python@0.8.8 python dependency (#39766)
* correct python dependency for 0.8.8

* add missing zlib dependency

* restore missing whitespace

* correct versions for 0.9.0, clarify rules for future releases

* Update package.py

* Remove whitespace for black check
2023-09-11 16:16:28 -05:00
Tim Haines
5ac1167250
fpchecker: add version 0.4.0 (#39924) 2023-09-11 17:16:20 -04:00
Richard Berger
fcc4185132
cuda: add versions 12.2.0 and 12.2.1 (#39684) 2023-09-11 23:13:06 +02:00
sid
943c8091c2
py-fairscale and dependencies py-pgzip libgit2 py-pygit2 (#39220)
* simple build of py-openai

* added variants to py-openai

* py-pandas-stubs is a dependency for py-openai

* fixed format and flake8 errors for py-openai

* black format error for py-pandas-stubs

* [@spackbot] updating style on behalf of sidpbury

* made style and format changes to py-openai

* made style and format changes to py-pandas-stubs

* py-types-pytz is a dependency for py-openai

* [@spackbot] updating style on behalf of sidpbury

* updated py-openpyxl for ver 3.0.7 and 3.1.2

* Update var/spack/repos/builtin/packages/py-pandas-stubs/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* ajs requested changes for py-openai

* updated py-openpyxl for supported python

* [@spackbot] updating style on behalf of sidpbury

* updated py-openpyxl

* removed requirement.txt dependencies in  py-openpyxl

* removed python depends on from openpyxl

* updated package to support newer versions

* updated version of py-pygit2

* py-fairscale is a new package in support of torch

* py-pgzip is a dependency for py-fairscale

* switch fairscale pypi, added extra variant for convenience

* removed python dependency

* changed multiple requirement versions

* changes for upstream py-fairscale

* changes for upsteam py-pygit2

* Update package.py

* Update package.py

* sorted out some of the dependency versions

* removed version 1.12.2 because dependency could not be met

* updated py-cached-property dependency

* suggested changes from adamjstewart

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11 16:11:02 -05:00
Nils Vu
a7a6f2aaef
spectre: add v2023.08.18 and v2023.09.07 (#39925) 2023-09-11 17:10:28 -04:00
Rocco Meli
5aaa82fb69
Update MDAnalysis (#39787)
* ensure umpire~cuda~rocm when ~cuda~rocm

* update mdanalysis

* 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>
2023-09-11 16:06:20 -05:00
Simon Pintarelli
bc33d5f421
update q-e-sirius package (#39744) 2023-09-11 22:48:19 +02:00
Juan Miguel Carceller
0e4e232ad1
Add another url for whizard (#37354)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-09-11 22:45:21 +02:00
Scot Halverson
145d44cd97
gdrcopy: inherit from CudaPackage, update dependencies (#39596) 2023-09-11 22:36:20 +02:00
Fábio de Andrade Barboza
e797a89fe1
py-pipdeptree: add new package; py-hatchling: add 1.18.0 (#39697)
* py-hatchling: add 1.18.0

* py-pipdeptree: add new package

* py-hatchling: add Python 3.8 dependency

* Apply suggestion from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

---------

Co-authored-by: Fábio de Andrade Barboza <f168817@dac.unicamp.br>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11 15:14:33 -05:00
Jose E. Roman
254a2bc3ea
SLEPc: add v3.19.2 (#39805)
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2023-09-11 22:13:21 +02:00
Fábio de Andrade Barboza
873652a33e
py-enum-tools: add new package and dependencies (#39672)
* Adds package 'enum-tools'

* Fixes syntax

* py-enum-tools: update pypi link and dependencies

* py-whey: add new package

* py-consolekit: add new package

* py-shippinglabel: add new package

* py-project-parser: add new package

* py-handy-archives: add new package

* py-domdf-python-tools: add new package

* py-dom-toml: add new package

* py-dist-meta: add new package

* py-deprecation-alias: add new package

* py-pygments: add versions 2.16.0 and 2.16.1

* py-mistletoe: add new package

* py-apeye: add new package

* py-apeye-core: add new package

* Fix dependencies' names and remove redundancies

* Fix style

* py-enum-tools: fix dependencies

* py-mistletoe: update dependencies

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* py-whey: fix dependencies

* py-whey: fix style

* py-apeye: fix dependencies

---------

Co-authored-by: Fábio de Andrade Barboza <f168817@dac.unicamp.br>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11 15:12:46 -05:00
Travis
3f686734ab
dakota: add v6.18 (#39882)
Co-authored-by: Travis Drayna <tdrayna@loki.local>
2023-09-11 22:06:16 +02:00
Thomas Madlener
e1373d5408
dd4hep: make sure to find libraries correctly (#39516) 2023-09-11 16:04:42 -04:00
dslarm
a2054564d8
ctffind: extend a Power 9 patch to AArch64 (#39137) 2023-09-11 16:04:20 -04:00
Sébastien Valat
ea75dbf7bd
MALT: add v1.2.2 (#39890) 2023-09-11 21:57:36 +02:00
Sébastien Valat
63a67e525b
NUMAPROF: add v1.1.5 (#39891) 2023-09-11 21:57:04 +02:00
Manuela Kuhn
95aaaeb5af
py-dunamai: add 1.18.0 (#39849) 2023-09-11 14:56:34 -05:00
Harmen Stoppels
a0bd53148b
glibc: fix deps, drop pre 2.17 (#39806)
* glibc: add missing deps, drop < 2.17

Building glibc 2.17 requires linking libgcc_{s,eh}.a, which themselves
depend on whatever glibc the current gcc uses for its runtime libraries.

Newer gcc depends on gnu extensions of libdl it seems, so that means you
simply cannot build old glibc with gcc-using-new-glibc.

The relevant fix in glibc is this commit:

commit 95f5a9a866695da4e038aa4e6ccbbfd5d9cf63b7
Author: Joseph Myers <joseph@codesourcery.com>
Date:   Tue Jul 3 19:14:59 2012 +0000

    Avoid use of libgcc_s and libgcc_eh when building glibc.

See also references to that commit in the glibc mailing list.

* update the gmake bound

* add --without-selinux
2023-09-11 10:45:53 -07:00
Massimiliano Culpo
3302b176fd
Update archspec to latest commit (#39920)
- [x] Intel flags for old architectures
- [x] Support for Sapphire Rapids
- [x] Cache the "ancestors" computation
2023-09-11 10:03:35 -07:00
Taillefumier Mathieu
4672346d9c
Support of versions of cp2k below 7 marked as deprecated (#39652)
SIRIUS was introduced in version 7 of cp2k but could be used
in practice in version 9 (input format and functionalities).
SIRIUS with version 6 and below are marked as a dependency
conflict until CP2K version 9.

Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
2023-09-11 18:46:52 +02:00