Commit graph

31984 commits

Author SHA1 Message Date
Adam J. Stewart
5ba40913af
py-numpy: add v1.25.1 (#38799) 2023-07-10 21:18:39 -05:00
Jen Herting
7288f11cf9
[arrow] tuple has no method append (#38820) 2023-07-10 18:12:08 -07:00
Wouter Deconinck
d5b01e45ce
mlpack: remove go variant from cmake_args (#38821) 2023-07-10 18:10:02 -07:00
Manuela Kuhn
8827f01865
py-minkowskiengine: add missing openblas dependency (#38742)
* py-minkowskiengine: add missing openblas dependency

* Add comment about blas
2023-07-10 17:21:16 -05:00
renjithravindrankannath
2163c3701c
Setting library path as lib similar to other rocm packages. (#37568)
* Setting library path as lib similar to other rocm packages.
* Fix style check failure
* Restricting changes to 5.4.3 and above
* Including comgr change
2023-07-10 14:55:39 -07:00
afzpatel
db23fd055c
new hip-examples package (#35891)
* initial commit for adding hip-examples package
* adding test to hip-examples
* fixed compile error on add4
* change standalone test to use new syntax
2023-07-10 13:05:46 -07:00
Sangu Mbekelu
73acf110ff
py-sacrebleu (#37159)
* new mosesdecoder package

* "new py-sacrebleu package"

* Delete package.py

* [@spackbot] updating style on behalf of Sangu-Mbekelu

* Update package.py

updating package based on review

---------

Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
2023-07-10 12:16:42 -07:00
kjrstory
ff49969264
Package:Openfoam-org version url using function (#37587)
* Package:Openfoam-org version url using function
* Package:Openfoam-org small style fix
* openfoam-org: url_for_function
2023-07-10 11:19:29 -07:00
eugeneswalker
eb94d830e1
legion +rocm: set HIP_PATH to {hip.prefix}/hip (#38819) 2023-07-10 10:35:12 -07:00
Chris Green
8fdd8fcf63
Perl package: detect opcode support in externals (#38618)
Spack-installed Perl always has opcode support, but external Perl
installations might not. This commit adds a +opcode variant and
updates the external detection logic to check for opcode support.

The postgresql package is updated to require perl+opcode (in
combination with the above, this helps detect when an external
Perl instance is sufficient for a Spack build of postgreqsql, or
if Spack needs to build its own Perl).
2023-07-10 10:01:20 -07:00
Michael Kuhn
30b077e63c
glib: add 2.76.4 (#38813) 2023-07-10 09:06:05 -07:00
Taillefumier Mathieu
64c6d63675
Update cp2k recipe to use cmake or the current build system (#35718)
* Update cp2k recipe to use cmake or the current build system

Offers the possibility to build cp2k with the new cmake build system. commands like this are now supported

spack install cp2k@master build_system=cmake +.....

the recipe supports the following optional functionalities

- superlu, cosma, sirius, spglib, metis, spglib, libxc, libint, cuda/rocm, mkl/openblas/sci (and others), mpi, openmp, dbcsr
- dbcsr is built separately using the currently available recipe.

Two PRs need to be merged to be fully functional (cosma update in spack + one PR in cp2k github).

* Fix indentation

* Fix indentation

* Update libvori

* More typos

* Simplify BLAS/LAPACK

* Simplify BLAS/LAPACK

* Add A100 gpu value

* Fix typo

* Add the enable_regtests option

if -DCP2K_ENABLE_REGTESTS=ON (+enable_regtests with spack) then the location of the binary executables will be in the cp2k root directory under exe/build-cmake-*. This option is needed to run the regtests afterwards.

* Minor update

* more fixes

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>

* small changes

* Remove any reference to nvidia architecture in the rocm list

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>

* Final reformating

* Update py-fypp

---------

Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
2023-07-10 14:02:52 +02:00
Massimiliano Culpo
0ed6ff3823
Removing inactive maintainer (#38773) 2023-07-10 11:31:09 +02:00
Todd Gamblin
757f8ae59c
find: add --hashes shortcut for piping to other commands (#38663)
People frequently ask us how to pipe `spack find` output to other commands, and we tell
them to do things like this:

```console
$ spack find --format "/{hash}" | spack uninstall -ay
```

Sometimes users don't know about hash references and come up with potentially ambiguous
formulations like this:

```console
spack find --format {name}@{version}%{compiler} | spack uninstall -ay
```

Since this is a common enough thing to want to do, and to make it more obvious how, this
PR adds a `-H` / `--hashes` as a shortcut, so you can now just do:

```console
spack find -H | spack uninstall -ay
```
2023-07-10 09:43:37 +02:00
Dax Lynch
27c62b981a
Added package py-bitstruct (#38761)
* Added packages bitstruct, callmonitor, and PYnvtx

* Revert "Added packages bitstruct, callmonitor, and PYnvtx"

This reverts commit 76d25aa76bf4655a85c78725fe5c76c1792717c9.

* py-bitstruct: This module is intended to have a similar interface as the python struct module, but working on bits instead of primitive data types (char, int, …)

* Update package.py

To pass the style prechecks

* PyNVTX: new package

* Delete package.py

Accidentally added this package.

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

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

---------

Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-09 20:19:07 -05:00
Manuela Kuhn
1ed934c710
py-triangle: restrict Python version (#38808) 2023-07-09 20:12:42 -04:00
Harmen Stoppels
eef14ddcad
openssl: prefer 3.x (#36729)
* openssl: prefer 3.x

This PR is not intended to be merged immediately, but it would be good
to see what packages fail to build in CI so that we can get proper
version constraints on openssl (before all packages update and support
both openssl 1 and 3)

* Disable assembly for 3.x %oneapi

* cmake: depend on spack curl, to deal with curl - openssl compat

* also make zlib external

* remove overly strict & unsafe requirement on py-cryptographty patch version number

* update openssl compat bounds in py-cryptography

* smaller diff

* Make libssh2 an autotools/cmake package

* fix weird upperbound in libssh2 as there is not openssl v2

* libssh2: pc file lists plain -lssl -lcrypto w/o leading -L flag, confusing libgit2 parsing of pkg-config output

* Actually fix the issue in libssh2: its pc file looks broken
2023-07-09 17:48:00 -04:00
Jonathon Anderson
db879a5679
ci: Fix broken SPACK_CHECKOUT_VERSION (#38778) 2023-07-09 12:37:36 -07:00
Vanessasaurus
d0804c44f1
Automated deployment to update package flux-core 2023-07-08 (#38790)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-07-09 12:12:55 -07:00
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