Commit graph

33064 commits

Author SHA1 Message Date
Jen Herting
19e1d10cdf
[py-marshmallow] added version 3.19.0 (#38972) 2023-08-07 19:44:44 -05:00
Jen Herting
7caf2a512d
[py-srsly] added version 2.4.6 (#38970)
* [py-srsly] added version 2.4.6

* [py-srsly] added dependency on py-catalogue

* [py-srsly] added conflict on newer versions of py-cython
2023-08-07 19:44:34 -05:00
Jen Herting
1f6e3cc8cb
[py-pathy] new package (#38968)
* [py-pathy] new package

* [py-pathy] removed lines for unsupported versions of python
2023-08-07 19:41:21 -05:00
Jen Herting
169c4245e0
[py-gensim] added version 4.3.1 (#38272)
* [py-gensim] added version 4.3.1

* [py-gensim] flake8

* [py-gensim] removed version limitation on py-cython
2023-08-07 18:56:53 -05:00
Jen Herting
ee1982010f
[py-clean-text] added version 0.6.0 (#38271)
* [py-clean-text] added missing dependency on py-poetry

* [py-clean-text] added version 0.6.0

* [py-clean-text] Made required changes
2023-08-07 18:52:22 -05:00
Melven Roehrig-Zoellner
dd396c4a76
freeglut: set correct library name (#39300) 2023-08-07 19:08:08 -04:00
Jean Luca Bez
235802013d
h5bench: include tests for E4S and new version (#37830)
* include tests for h5bench
* update to new test format
* update path
* improve description and detect MPI runner
* fix test name
* Include new release
* update with corrections
* include SLURM dependency and reduce test to one process
* fixes on filters
* fix on oversubscribe
* suggested fixes

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-08-07 11:43:32 -07:00
Harmen Stoppels
e1f07e98ae
libdeflate: new versions, switch to cmake (#39062) 2023-08-07 13:48:12 -04:00
Adam J. Stewart
60aee6f535
py-torchmetrics: add v1.0.2 (#39274) 2023-08-07 10:43:43 -07:00
Adam J. Stewart
2510dc9e6e
py-timm: add v0.9.5 (#39275) 2023-08-07 10:42:14 -07:00
Christopher Christofi
5607dd259b
samtools: add 1.17 (#39287) 2023-08-07 10:29:03 -07:00
Harmen Stoppels
7bd5d1fd3c
use {%compiler.name}{@compiler.version} in matching_specs (#39247) 2023-08-07 18:54:10 +02:00
Harmen Stoppels
f6104cc3cb
spack: bump package (#39184) 2023-08-07 18:52:14 +02:00
kwryankrattiger
b54d286b4a
CI: remove redundant sections (#38514)
Refactor gitlab ci configs so that mac and cray jobs can reuse as much higher level
configuration as possible.

* CI: remove redundant sections
* CI: Include base linux CI configs in cray stacks

Relocation and runner mapping is consistent between cray and linux runners.

* Export user cache path in before script
* CI: add GPG root for mac runners
* Disable user configs

Metal runners share a ~ directory

* Disable user config and add configs in activate env
2023-08-07 10:23:16 -06:00
Seth R. Johnson
ea9c488897
celeritas: new version 0.3.1 (#39288) 2023-08-07 12:16:30 +01:00
Massimiliano Culpo
ba1d295023
Extract prefix locks and failure markers from Database (#39024)
This PR extracts two responsibilities from the `Database` class:
1. Managing locks for prefixes during an installation
2. Marking installation failures

and pushes them into their own class (`SpecLocker` and `FailureMarker`). These responsibilities are also pushed up into the `Store`, leaving to `Database` only the duty to manage `index.json` files.

`SpecLocker` classes no longer share a global list of locks, but locks are per instance. Their identifier is simply `(dag hash, package name)`, and not the spec prefix path, to avoid circular dependencies across Store / Database / Spec.
2023-08-07 06:47:52 -04:00
Harmen Stoppels
27f04b3544
Picklable HTTPError (#39285) 2023-08-07 10:48:35 +02:00
Brian Van Essen
8cd9497522
Bugfix spack module files (#39282)
* Fixed the LD_LIBRARY_PATH to use the lib64 directory.
* On AMD systems the llvm/lib directory is not properly put into the LD_LIBRARY_PATH.
* Added both lib and lib64 paths for libfabric.
* Split the prepend statements.
2023-08-05 20:26:00 -07:00
Harmen Stoppels
ef544a3b6d
Add a more detailed HTTPError (#39187) 2023-08-05 11:16:51 +02:00
Adam J. Stewart
4eed832653
py-pyqt6: add new package (#32696) 2023-08-04 18:49:54 -05:00
Wouter Deconinck
5996aaa4e3
acts: new versions 23.[3-5].0, 24.0.0, 25.0.[0-1], 26.0.0, 27.[0-1].0, 28.0.0 (#37055)
* acts: new version 23.[3-5].0, 24.0.0
- https://github.com/acts-project/acts/compare/v23.2.1...v23.3.0
- https://github.com/acts-project/acts/compare/v23.3.0...v23.4.0
- https://github.com/acts-project/acts/compare/v23.4.0...v23.5.0
- https://github.com/acts-project/acts/compare/v23.5.0...v24.0.0
* acts: update dependencies
* acts: new versions 25.0.0, 25.0.1, 26.0.0, 27.0.0
* [@spackbot] updating style on behalf of wdconinc
* acts: rm duplicate edm4hep variant definition
* acts: depends_on podio 0.6: open ended range
* acts: new version 27.1.0
* acts: depends_on mlpack when +mlpack
* acts: new version 28.0.0
* actsvg: new version 0.4.35
* acts: depends_on actsvg@0.4.35: when @28:

---------

Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-08-04 16:47:15 -07:00
Brian Van Essen
4957607005
FIX libfabric module file (#39271)
* Add support to export the LD_LIBRARY_PATH for the libfabric package
and subsequent module files.

Fix the AWS OFI RCCL package so that it prepends the enviornment
variables.

* Fixed comment
2023-08-04 15:04:54 -07:00
Matt Drozt
78bca131fb
[py-smartredis] New Package (#39098)
* Create a spack package for smartredis python client

* make py-SR deps versions match docs

* tie SR v0.4.0 to redis-plus-plus v1.3.5

* looser extension lib deps for concretization

* Apply suggestions from code review

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

* Address reviewer feedback

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-04 09:44:23 -05:00
Brian Van Essen
045c5cea53
Replace code that captures a recipes generator statement in the cached (#39192)
cmake build.
2023-08-04 05:38:12 -07:00
Alex Richert
ea256145d9
Add MET, METplus packages (#39238)
* Add metplus package
* Add met package
* add metplus develop version
* copyright year var/spack/repos/builtin/packages/met/package.py
* copyright year var/spack/repos/builtin/packages/metplus/package.py

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-08-04 06:53:44 -04:00
Davide
0b2098850c
julia: add v1.9.2 (#39269) 2023-08-04 10:53:59 +02:00
pabloaledo
d2df0a29ce
salmon: update version (#39202)
* salmon: update version

---------

Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-03 17:57:17 -07:00
Vicente Bolea
92e9daec9b
adios2: add 2.9.1 release (#39257) 2023-08-03 17:28:55 -04:00
Erik Schnetter
d65437114a
openssl: Update to 3.1.2, 3.0.10, 1.1.1v (#39216) 2023-08-03 23:22:35 +02:00
Tamara Dahlgren
9a6e98e729
Revert checksum verification CI test (#39259) 2023-08-03 23:21:39 +02:00
Satish Balay
6515c16432
sowing: add version 1.1.26-p8 (#39258)
* sowing: add version 1.1.26-p8
* add in maintainer
2023-08-03 16:34:19 -04:00
Vanessasaurus
2826ab36f0
Automated deployment to update package flux-core 2023-08-03 (#39237)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-08-03 11:07:41 -07:00
Mark W. Krentel
c035512930
hpcviewer: add version 2023.07 (#39236)
Add version 2023.07, adjust the line for deprecated (anything using
java 8 is now deprecated).
2023-08-03 10:52:58 -07:00
Stephen Sachs
cfadba47d3
patchelf@0.18.0 breaks intel compiler libraries (#39253) 2023-08-03 13:33:48 -04:00
Matthieu Dorier
95391dfe94
kafka: new versions (#39249)
* kafka: version 2.13-3.5.0
* kafka: version 2.13-3.5.1 and 2.13-3.4.1
2023-08-03 10:14:48 -07:00
Matthieu Dorier
382ba99631
librdkafka: version 2.2.0 (#39250) 2023-08-03 10:05:35 -07:00
Alec Scott
f8e25c79bf
Add checksum CI test and verify with new versions for glab and gh (#39181) 2023-08-03 09:53:05 -07:00
Matthew Thompson
93b54b79d3
gftl-shared: new version 1.6.1 (#39217)
This PR adds gFTL-shared v1.6.1
2023-08-03 11:32:17 -04:00
Matthew Thompson
ff30efcebc
mapl: add package (#39227)
* mapl: add package
* Fix style
2023-08-03 09:40:34 -04:00
Seth R. Johnson
54514682d4
py-sphinx-rtd-theme: avoid concretizing 0.5 with Sphinx 7.0 (#39212)
* py-sphinx-rtd-theme: avoid concretizing 0.5 with Sphinx 7.0

* Update var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-03 09:31:05 -04:00
Auriane R
92a75717f0
Add pika 0.17.0 (#39221) 2023-08-03 09:26:55 -04:00
Matthew Thompson
b9be8e883e
pfunit: add versions 4.7.1, 4.7.2, 4.7.3 (#39218)
This adds the latest versions of pFUnit
2023-08-03 09:26:33 -04:00
Seth R. Johnson
da838a7d10
vecgeom: new version 1.2.5 (#39211)
* vecgeom: new version 1.2.5
* Mark previous versions as deprecated
* [@spackbot] updating style on behalf of sethrj
* vecgeom: fix 1.2.4 checksum for change to git describe
2023-08-03 08:59:41 -04:00
pabloaledo
85e5fb9ab7
ucsc-bedgraphtobigwig: add package (#39208)
Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-03 14:16:30 +02:00
Adam J. Stewart
c0c300d773
R: fix build on macOS arm64 (#39228) 2023-08-03 14:15:06 +02:00
Harmen Stoppels
6e933ac7df
repo cache: use -inf default instead of 0 (#39214)
FastPackageChecker.modified_since should use a default number < 0

When the repo cache does not exist, Spack uses mtime 0. This causes the repo
cache not to be generated when the repo has mtime 0.

Some popular package managers such as spack use 0 mtime normalization for
reproducible tarballs. So when installing spack with spack from a buildcache, the
repo cache doesn't generate

Also add some typehints
2023-08-03 14:13:13 +02:00
pabloaledo
be679759be
ucsc-bedclip: add package (#39209)
Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-03 14:04:37 +02:00
Adam J. Stewart
eace479b1e
py-kornia: add v0.7.0 (#39233) 2023-08-03 13:59:31 +02:00
Harmen Stoppels
2069a42ba3
Buildcache commands cleanup, again... (#39203)
* Inform mypy that tty.die is noreturn

* avoid temporary allocation in env

* update spack buildcache save-specfile

* fix spack buildcache check/download/get-buildcache-name

- ensure that required args and mutually exclusive ones are marked as
  such in argparse for better error messages
- deprecate --spec-file everywhere
- use disambiguate for better error messages
2023-08-03 10:44:02 +02:00
George Young
41d2161b5b
nextdenovo: new package @2.5.2 (and py-paralleltask) (#39139)
* py-paralleltask: new package @0.2.2

* adding hidden dependency

* nextdenovo: new package @2.5.2

* style

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

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

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-02 19:11:18 -04:00