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Author SHA1 Message Date
Harmen Stoppels
668879141f
remove a few redundant calls to setup_run_environment (#42718) 
Any package `X` used as `depends_on("x", type="build")` will have
`X.setup_run_environment(env)` called, because it has to be able to
"run" in the build environment.

So there is no point in calling `setup_run_environment` from
`setup_dependent_build_environment`.

Also it's redundant to call `setup_run_environment` in
`setup_dependent_run_environment`, cause (a) the latter is called _for
every parent edge_ instead of once per node, and (b) it's only called
after `setup_run_environment` is called anyways. Better to call
`setup_run_environment` once and only once.
 2024-02-19 11:43:45 +01:00
Adam J. Stewart
267defd9d3
py-matplotlib: add v3.8.3 (#42698) 2024-02-19 11:40:18 +01:00
Ken Raffenetti
603d3f2283
mpich: Remove invalid pmi option (#42686) 
pmi=off is not a valid configuration option. MPICH cannot function
without a PMI library. Fixes #42685.
 2024-02-19 11:38:49 +01:00
James Beal
02bfbbe269
Bump for new version of bedtools2 (#42034) 
Co-authored-by: James Beal <jb23@sanger.ac.uk>
 2024-02-19 11:35:26 +01:00
Alec Scott
44d08d2c24
gnupg: make discoverable as external (#42736) 2024-02-19 11:27:39 +01:00
AMD Toolchain Support
c6faab10aa
CP2K: fix multiple use of spec["fftw"] (#42724) 
fftw object was originally created with spec["fftw:openmp"], but
referencing spec["fftw"] overwrites the 'last_query' in the spec object,
so later use of fftw.libs was not returing FFTW OpenMP libs.

Also allow the post-install fixup to support amdfftw as well as fftw.

Co-authored-by: Branden Moore <branden.moore@amd.com>
Co-authored-by: Phil Tooley <phil.tooley@amd.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
 2024-02-19 11:21:11 +01:00
Geoffrey Lentner
baa203f115
duckdb: add v0.9.2 (#42374) 2024-02-19 03:02:43 -07:00
Alec Scott
575a33846f
bfs: add v3.1.1 (#42740) 2024-02-19 10:54:00 +01:00
Adam J. Stewart
79df065730
py-shapely: add v2.0.3 (#42738) 2024-02-18 21:29:18 +01:00
William Moses
953ee2d0ca
Bump enzyme to 0.0.100 (#42626) 2024-02-18 08:48:21 -08:00
Nai-Yuan Chiang
6796b581ed
hiop new release, v1.0.3 (#42730) 2024-02-18 08:45:44 -08:00
Christoph Junghans
f49a5519b7
byfl: initial commit (#42731) 2024-02-18 08:43:56 -08:00
Tom Drever
e07a6f51dc
Add py-click-option-group (#42678) 
* Add py-click-option-group

* Specify dependency versions
 2024-02-18 08:22:25 -06:00
Dani
cb73d71cf1
new builtin package: py-biobb-model (#42681) 
* new builtin package: py-biobb-model

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2024-02-18 03:18:03 -06:00
Jonas Eschle
5949fc2c88
add package py-jacobi (#42672) 
* add package py-jacobi

* fix:  add description

* fix:  add description

* fix:  add description

* [@spackbot] updating style on behalf of jonas-eschle

* Update package.py

* Update package.py

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

I don't think that numpy is used in "build"? But not important

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

---------

Co-authored-by: jonas-eschle <jonas-eschle@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2024-02-18 03:17:35 -06:00
Jonas Eschle
fd10cfdebf
add package py dotmap (#42665) 
* add package py dotmap

* add maintainer

* [@spackbot] updating style on behalf of jonas-eschle

* fix:  add description

* [@spackbot] updating style on behalf of jonas-eschle

* Update package.py

---------

Co-authored-by: jonas-eschle <jonas-eschle@users.noreply.github.com>
 2024-02-18 03:16:32 -06:00
Maciej Wójcik
32506e222d
py-sysrsync: add new package (#42492) 
* py-sysrsync: add new package

* py-sysrsync: specify dependency type

* py-sysrsync: add constraint for Python
 2024-02-18 03:15:42 -06:00
Maciej Wójcik
a7d5cc6d68
py-google-...: add new versions and few new packages (#42671) 
* py-google-cloud-storage: add new versions

* py-google-api-core: add new versions

* py-proto-plus: add new package

* py-google-api-core: add grpc variant

* py-google-api-core: add grpc variant

* py-google-api-core: add missing prefix

* py-google-cloud-batch: add new package

* py-google-cloud-logging: add new package

* py-google-cloud-appengine-logging: add new package

* py-google-cloud-audit-log: add new package

* py-grpc-google-iam-v1: add new package

* py-proto-plus: remove obvious dependency

* Whitespace

* Whitespace

* py-google-cloud-audit-log: correct conflict

* py-proto-plus: correct dependency type

* Whitespace

* py-google-auth: add new version

* py-google-resumable-media: add new version

* py-google-cloud-storage: constrain version of dependency

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

* py-grpcio-status: use newer version

* py-google-resumable-media: add upper bound of dependency

* Add types of dependencies.

* py-grpcio: add new version

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2024-02-18 03:15:02 -06:00
Vanessasaurus
222241f232
flux-core: add uuid (#42635) 
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
 2024-02-18 08:54:11 +01:00
Sinan
aa1820eb5c
pdal: new package (#42714) 
* new package pdal

* [@spackbot] updating style on behalf of Sinan81

* fix style

* add license

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

Co-authored-by: Alec Scott <alec@bcs.sh>

* [@spackbot] updating style on behalf of Sinan81

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

Co-authored-by: Alec Scott <alec@bcs.sh>

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

Co-authored-by: Alec Scott <alec@bcs.sh>

* improve dependency spec

* add maintainer

* add conflict

* fix bug

* improve

* improve

* [@spackbot] updating style on behalf of Sinan81

* fix style

* specify cmake dependency version

---------

Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
Co-authored-by: Alec Scott <alec@bcs.sh>
 2024-02-17 13:40:40 -08:00
George Young
16ea5f68ba
cryodrgn: new package @2.3.0 (#42443) 
* cryodrgn: new package @2.3.0

* correcting dependency ranges

* correcting dependency ranges

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
 2024-02-17 15:07:56 -06:00
Dani
aeec515b4f
new builtin package: py-biobb-structure-utils (#42683) 2024-02-17 14:42:10 -06:00
Maciej Wójcik
6e2ec2950b
py-kubernetes: add new versions (#42670) 
* py-kubernetes: add new versions

* py-oauthlib: add new version
 2024-02-17 14:32:20 -06:00
Maciej Wójcik
fe5772898d
py-azure-... and py-msrest: add new versions (#42624) 
* py-azure-batch: add new versions

* py-azure-core: add new versions

* py-azure-identity: add new versions

* py-azure-mgmt-batch: add new versions

* py-azure-mgmt-core: add new versions

* py-azure-storage-blob: add new versions

* py-msrest: add new versions

* Whitespace

* Whitespace

* py-msrest: add a note

* py-msrest: version-dependent URL

* py-azure-mgmt-batch: correct version of dependency
 2024-02-17 14:24:11 -06:00
Alex Leute
384ddf8e93
py-smote-variants: Added package py-smote-variants (#42502) 
* py-smote-variants: Added package py-smote-variants

Also added py-minisom and py-metric-learn as dependencies

* py-metric-learn: Added build dependency on setuptools

* py-smote-variants: Added a dependency on py-pytest-runner

As well as a comment about why statistics isn't included

* [@spackbot] updating style on behalf of alex391

---------

Co-authored-by: Alex C Leute <aclrc@rit.edu>
 2024-02-17 14:20:03 -06:00
Tom Vander Aa
32c2e240f8
py-charm4py: needs Cython<3.0 (#42491) 
* py-charm4py: needs Cython<3.0

* Update var/spack/repos/builtin/packages/py-charm4py/package.py

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2024-02-17 14:16:31 -06:00
dependabot[bot]
b88c4792a7
build(deps): bump clingo from 5.6.2 to 5.7.1 in /.github/workflows/style (#42732) 
Bumps [clingo](https://github.com/potassco/clingo) from 5.6.2 to 5.7.1.
- [Release notes](https://github.com/potassco/clingo/releases)
- [Changelog](https://github.com/potassco/clingo/blob/master/CHANGES.md)
- [Commits](https://github.com/potassco/clingo/compare/v5.6.2...v5.7.1)

---
updated-dependencies:
- dependency-name: clingo
  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>
 2024-02-16 22:24:10 -08:00
dependabot[bot]
ac92e94b00
build(deps): bump pytest from 8.0.0 to 8.0.1 in /lib/spack/docs (#42733) 
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.0.0 to 8.0.1.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.0.0...8.0.1)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2024-02-16 22:23:13 -08:00
Luc Berger
4a01865f7b
Kokkos Ecosystem: update for release 4.2.01 (#42711) 
* Kokkos Ecosystem: update for release 4.2.01

Will rebase this on top of develop once Kokkos Core PR merges.

* Kokkos Ecosystem: update license statement to reflect current license
 2024-02-16 17:28:29 -07:00
Sebastian Pipping
025165e22e
expat: Add latest release 2.6.0 with security fixes (#42680) 
* expat: Add latest release 2.6.0 with security fixes

* expat: Deprecate vulnerable 2.5.0

* expat: Add past CVEs and where they were fixed
 2024-02-16 17:23:46 -07:00
SXS Bot
cda9bc3e1d
spectre: add v2024.02.05 (#42496) 
* spectre: add v2024.02.05

* [@spackbot] updating style on behalf of sxs-bot

---------

Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
 2024-02-16 15:49:06 -07:00
Lydéric Debusschère
caf21dda42
rust: enable vendor (#42365) 
* rust: enable vendor

* rust: modify vendor description; move the call of variant

* rust: fix style

* rust: typo

* rust: remove variant 'vendor' to let vendoring as default fonctionality

---------

Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
 2024-02-16 14:13:44 -08:00
HELICS-bot
e1779a2884
helics: Add version 3.5.0 (#42572) 
* helics: Add version 3.5.0

* helics: define CMAKE_CXX_STANDARD=20 when GCC>=13 is used to compile

---------

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Ryan Mast <mast9@llnl.gov>
 2024-02-16 14:12:50 -08:00
Adam J. Stewart
f55a018fd9
py-torchmetrics: add v1.3.1 (#42638) 2024-02-16 14:00:43 -08:00
dependabot[bot]
f5964e1dde
build(deps): bump black in /.github/workflows/style (#42631) 
Bumps [black](https://github.com/psf/black) from 24.1.1 to 24.2.0.
- [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/24.1.1...24.2.0)

---
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>
 2024-02-16 13:52:38 -08:00
dependabot[bot]
23e0fe2e21
build(deps): bump black from 24.1.1 to 24.2.0 in /lib/spack/docs (#42629) 
Bumps [black](https://github.com/psf/black) from 24.1.1 to 24.2.0.
- [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/24.1.1...24.2.0)

---
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>
 2024-02-16 13:51:50 -08:00
dependabot[bot]
44438e6171
build(deps): bump python-levenshtein in /lib/spack/docs (#42630) 
Bumps [python-levenshtein](https://github.com/rapidfuzz/python-Levenshtein) from 0.24.0 to 0.25.0.
- [Release notes](https://github.com/rapidfuzz/python-Levenshtein/releases)
- [Changelog](https://github.com/rapidfuzz/python-Levenshtein/blob/main/HISTORY.md)
- [Commits](https://github.com/rapidfuzz/python-Levenshtein/compare/v0.24.0...v0.25.0)

---
updated-dependencies:
- dependency-name: python-levenshtein
  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>
 2024-02-16 13:51:12 -08:00
Martin Lang
af8e000a93
bigdft-futile: new versions 1.9.3, 1.9.4 (#42646) 2024-02-16 13:41:18 -08:00
Adam J. Stewart
375b82a593
py-black: add v24.2.0 (#42639) 2024-02-16 13:39:16 -08:00
Adam J. Stewart
2030e2b089
py-jsonargparse: add v4.27.5 (#42640) 2024-02-16 13:38:17 -08:00
Carlos Bederián
34aba94148
openmpi: add ucc to fabrics (#41889) 2024-02-16 22:37:00 +01:00
Nicolas Morales
43c909e19c
Update maintainers for Kokkos and add Kokkos 4.2.1 (#42690) 
* update kokkos spack package maintainers

* add Kokkos 4.2.01

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

Co-authored-by: Luc Berger <lberge@sandia.gov>

---------

Co-authored-by: Alec Scott <alec@bcs.sh>
Co-authored-by: Luc Berger <lberge@sandia.gov>
 2024-02-16 11:12:36 -07:00
Martin Lang
7c011d304f
nfft: new versions 3.5.1, 3.5.2, 3.5.3 (#42645) 2024-02-16 09:58:03 -08:00
Martin Lang
1546fc7e5f
dftbplus: new versions 22.2, 23.1 (#42647) 2024-02-16 09:55:53 -08:00
Rob Falgout
75a134f085
Update package.py for hypre release 2.31.0 (#42689) 2024-02-16 11:46:29 -06:00
Alex Richert
d0c4675a9b
Add aocc support to ESMF (#42708) 
* Add aocc support to ESMF

* Update package.py
 2024-02-16 09:33:47 -08:00
WuK
0507c3c63d
add new CUTLASS versions (#42715) 2024-02-16 09:23:50 -08:00
dependabot[bot]
59caa93571
build(deps): bump dorny/paths-filter from 3.0.0 to 3.0.1 (#42710) 
Bumps [dorny/paths-filter](https://github.com/dorny/paths-filter) from 3.0.0 to 3.0.1.
- [Release notes](https://github.com/dorny/paths-filter/releases)
- [Changelog](https://github.com/dorny/paths-filter/blob/master/CHANGELOG.md)
- [Commits](0bc4621a31...ebc4d7e9eb)

---
updated-dependencies:
- dependency-name: dorny/paths-filter
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2024-02-16 09:16:35 -08:00
Arne Becker
b4b53a9a9f
perl-datetime-format-iso8601: New package (#42719) 
Adds DateTime::Format::ISO8601
 2024-02-16 09:15:54 -08:00
Todd Gamblin
be1cfffa45
clingo: add version 5.7.0 (#42707) 
5.7.0 was just released. It includes a number of changes requested and/or
upstreamed by Spack developers, e.g.:

* API for accessing optimization priorities: https://github.com/potassco/clingo/pull/406
* Hash optimization: https://github.com/potassco/clingo/pull/441
* Contributing Guide: https://github.com/potassco/clingo/pull/465
* Hiding more ELF symbols:
  * https://github.com/potassco/clingo/pull/447
  * https://github.com/potassco/clingo/pull/449
 2024-02-16 18:14:19 +01:00