Commit graph

34715 commits

Author SHA1 Message Date
Harmen Stoppels
374fda1063
Don’t call spec.format in Database._get_matching_spec_key (#38792)
`"%s" % spec` formats the spec with deps included, which produces sometimes KBs
of data and is slow to run in pure Python. It can delay otherwise very short-lived
read/write locks on the database.

Discovered in #38762 where profile output showed about 2 seconds is spent in
`spec.format`, which is significant overhead when using multiprocessing to install
from binary cache in parallel (installation often takes <5s for small packages). With
this change, `spec.format` no longer shows up in profile output.

(This line hasn't changed since Spack v0.9 ;p)

* move format() call to custom NoSuchSpecError exception
* add a comment saying why, so we can eventually change `Spec.__str__`
2023-07-09 11:27:38 -04:00
Jonathon Anderson
3c14569b8e
pkgconf: Update to new upstream URL (#38800)
See 437c2a3218
2023-07-09 16:12:47 +02:00
Michael Kuhn
841402c57a
gcc: add 10.5.0 (#38784) 2023-07-09 12:13:04 +02:00
Wouter Deconinck
09e1258ed4
qt-* (Qt6 pkgs): new versions 6.5.0, 6.5.1 (#36705)
* qt-base: new version 6.5.0

* qt-declarative: new version 6.5.0

* qt-quick3d: new version 6.5.0

* qt-quicktimeline: new version 6.5.0

* qt-shadertools: new version 6.5.0

* qt-*: new version 6.5.1

* qt-base: new version 6.5.1
2023-07-08 15:36:27 -05:00
Dax Lynch
b2dcd9bd42
PyNVTX: added new package (#38763) 2023-07-07 20:02:21 -05:00
Manuela Kuhn
2dc76248d3
py-pyarrow: disable dataset variant by default (#38775)
* py-pyarrow: enable parquet variant by default

* Disable parquet variant by default

* Add conflict to enable parquet when dataset is active

* Disable dataset variant by default
2023-07-07 16:27:32 -05:00
Adam J. Stewart
bf6eb832ae
py-matplotlib: add v3.7.2 (#38745)
* py-matplotlib: add v3.7.2

* Update dep versions
2023-07-07 14:43:41 -05:00
Chris Richardson
e8e6d69af5
New package: py-nanobind (#38327)
* initial commit of nanobind package

* style fixes

* Update package.py

Typo

* addressed PR comments

* add v1.4.0

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

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

---------

Co-authored-by: Matthew Archer <ma595@cam.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-07 12:02:45 -04:00
Manuela Kuhn
050d8df5a5
py-astropy: fix import tests and restrict py-pip version (#38731)
* py-astropy: fix import tests and restrict py-pip version

* Fix --install-option name in comments

* Rename variant and fix variant dependencies

* Remove parquet variant from py-pyarrow
2023-07-07 10:19:02 -05:00
Massimiliano Culpo
6958b49c2f
Remove "node_compiler" from the list of unknown atoms (#38753) 2023-07-07 13:19:53 +02:00
Harmen Stoppels
a1d33e97ec
Fix multiple quadratic complexity issues in environments (#38771)
1. Fix O(n^2) iteration in `_get_overwrite_specs`
2. Early exit `get_by_hash` on full hash
3. Fix O(n^2) double lookup in `all_matching_specs` with hashes
4. Fix some legibility issues
2023-07-07 10:51:58 +00:00
Massimiliano Culpo
ca9b52bbc5
Prevent "spack external find" to error out on wrong permissions (#38755)
fixes #38733
2023-07-07 12:05:32 +02:00
Andrey Parfenov
ae00d7c358
add info about spack env from spack-configs for oneAPI build tools (#38751)
Signed-off-by: Andrey Parfenov <andrey.parfenov@intel.com>
2023-07-07 03:47:54 +00:00
Mickael PHILIT
1071c1d8e0
add cgns 4.4.0 (#38530) 2023-07-06 17:52:03 -07:00
Carlos Bederián
5f6c832020
freesurfer: add 7.4.1, 7.4.0, 7.3.2 (#38544) 2023-07-06 17:51:01 -07:00
Wouter Deconinck
9e4c4be3f5
mlpack: new package (#38277)
* mlpack: new package

mlpack is an intuitive, fast, and flexible header-only C++ machine learning library with bindings to other languages. It is meant to be a machine learning analog to LAPACK, and aims to implement a wide array of machine learning methods and functions as a "swiss army knife" for machine learning researchers.

* mlpack: upstream merged patch to allow python installation in spack
2023-07-06 13:42:56 -07:00
John W. Parent
6c325a2246
Curl Package: Fixup bugs preventing build on Win (#38757) 2023-07-06 14:59:42 -04:00
Ben Cowan
28b884ace5
Add new version 5.0.0 of PyAMG (#38674)
* Added v5.0.0 of PyAMG.  This required v7.1.0 of setuptools_scm due to a bug in 7.0.5.

* Added comment about version requirement.

* Loosened dependency based on build experiments.

* Updated tomli deps.

* Update var/spack/repos/builtin/packages/py-setuptools-scm/package.py

Dependence for 7.0 only.

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

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

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

* Swapped lines.

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-06 13:54:29 -04:00
Harmen Stoppels
a13687f022
Disable fortran in openblas for darwin ci, fix variant default value (#38752) 2023-07-06 17:47:20 +02:00
Thomas Bouvier
bd81676e3c
py-torch: fix build (#38730) 2023-07-06 09:35:11 -05:00
Adam J. Stewart
7eaa99eabc
py-scikit-learn: add v1.3.0 (#38660) 2023-07-06 08:55:00 -05:00
kjrstory
5cb0b57b30
openfoam.org: add a maintainer(#37280) (#37697)
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
2023-07-06 13:44:24 +02:00
Jen Herting
c6867649b9
[py-blis] added versions 0.7.9 and 0.9.1 (#38269)
* [py-blis] added version 0.7.9

* [py-blis] added version 0.9.1

* [py-blis]

- removed type run for dependency py-cython
2023-07-06 05:09:11 -04:00
Jim Phillips
c129603192
namd: add maintainer (#38740) 2023-07-06 04:28:54 -04:00
Manuela Kuhn
4e456992e4
py-abipy: add 0.9.3 (#38716)
* py-abipy: add 0.9.3

* Remove py-cython dependency

* Remove dep version restrictions for new release
2023-07-06 04:23:55 -04:00
Jen Herting
10876736e0
[py-cymem] added version 2.0.7 (#38267)
* [py-cymem] added version 2.0.3

* [py-cymem] added restriction to py-wheel limitation
2023-07-06 04:13:44 -04:00
Thomas Bouvier
982cdd7988
py-dm-tree: add v0.1.8 (#38606)
* `py-dm-tree`: add v0.1.8

* Update dependencies

* Fix hash
2023-07-06 00:12:04 -05:00
Thomas Bouvier
095e48f399
py-horovod: update to v0.28.1 (#38732) 2023-07-05 23:56:47 -05:00
Manuela Kuhn
833db65fa3
py-pip: add 23.1.2 (#38608)
* py-pip: add 23.1.2

* Restrict py-pip version for py-protobuf

* Restrict py-pip version for straightforward packages

* Restrict py-pip version for nrm

* Fix --install-option name in comments

* Simplify py-pip restriction for py-scs

* nrm: fix wrong comment
2023-07-05 23:37:16 -04:00
Harmen Stoppels
06268f7b72
perl: add 5.38.0, 5.36.1; prefer all even minor versions over development versions (#38690)
* perl: add 5.38.0, 5.36.1; prefer all even minor versions over development versions

* fix libxcrypt build with new perl

* fix libxcrypt with a patch
2023-07-05 18:08:54 -04:00
Manuela Kuhn
f884e71a03
py-spglib: add 2.0.2 (#38715)
* py-spglib: add 2.0.2

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

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

* Remove py-setuptools as run dependency

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-05 15:24:31 -05:00
Wouter Deconinck
ea1439dfa1
acts: new variant cxxstd (#38682)
* acts: allow ^root cxxstd=20

* acts: new variant cxxstd, pass through to root

* acts: always args.append CMAKE_CXX_STANDARD from variant

* acts: remove unused import

* acts: fix self.define_from_variant
2023-07-05 12:56:06 -07:00
Adam J. Stewart
45838cee0b
Drop Python 2 super syntax (#38718) 2023-07-05 09:04:29 -05:00
Adam J. Stewart
95847a0b37
Drop Python 2 object subclassing (#38720) 2023-07-05 14:37:44 +02:00
George Young
8861fe0294
salmon: patching to build with %gcc@13: (#38553)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-07-05 14:36:55 +02:00
Harmen Stoppels
12427c6974
plumed: deprecate non-buildable versions, patch Python makefile only when supported (#38713) 2023-07-05 05:48:13 -04:00
Taillefumier Mathieu
a412403d7b
Update cosma and a few related recipes (#35615)
* Add maintainers 

* Updated cosma archive checksum and costa version

- updated cosma version (in the cosma build system)
- updated costa version
- use the default generic url for downloading packages
- do not build tiled-mm when the cpu only version is needed


Signed-off-by: Dr. Mathieu Taillefumier <mathieu.taillefumier@free.fr>
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-07-05 11:02:50 +02:00
Martin Diehl
6a258c148f
damask: fix build of alpha release (#38457) 2023-07-05 10:59:05 +02:00
Tom Epperly
8b13440038
Add version 1.8.23 that fixes a compilation bug on clang-15. (#38541) 2023-07-05 10:56:18 +02:00
Tamara Dahlgren
632f840d8a
tk: convert to new stand-alone test process (#38575) 2023-07-05 10:55:07 +02:00
Alex Richert
8372726a88
ip: add v4.1.0, and additional variants (#38526) 2023-07-05 10:45:38 +02:00
Tamara Dahlgren
5dc84b64e9
tests/qthreads: convert to new stand-alone test process (#38600) 2023-07-05 10:41:25 +02:00
Tamara Dahlgren
8d72b8dd63
tests/papyrus: convert to new stand-alone test process (#38627) 2023-07-05 10:34:15 +02:00
Jim Phillips
adde84e663
Build NAMD with Tcl by default (#38645)
NAMD users expect the Tcl scripting interface to be enabled as it is used in many examples and tutorials in addition to being required for features such as multi-copy algorithms.
2023-07-05 10:29:11 +02:00
Rémi Lacroix
f863066b7e
git-annex: add latest version 10.20230408 (#38728) 2023-07-05 04:27:46 -04:00
Juan Miguel Carceller
082afe04b8
xrootd: add _STAT_VER patch (#38547)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-07-05 10:14:18 +02:00
Peter Scheibel
f365386447
Installations: don't set group permissions when they match what is desired (#38036)
* When installing a package Spack will attempt to set group permissions on
the install prefix even when the configuration does not specify a group.

Co-authored-by: David Gomez <dvdgomez@users.noreply.github.com>
2023-07-05 09:54:04 +02:00
Carlos Bederián
a90200528f
hcoll: ucx version requirements (#38665) 2023-07-05 09:48:58 +02:00
Adam J. Stewart
1ce6feef94
py-pyqt4: stricter dependency versions (#38673) 2023-07-05 09:45:24 +02:00
Weiqun Zhang
84010108b1
amrex: add v23.07 (#38676) 2023-07-05 09:43:37 +02:00