Commit graph

34896 commits

Author SHA1 Message Date
George Young
6bd8fda597
foldseek: new package @8 (#42422)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2024-02-01 11:33:28 -07:00
Rémi Lacroix
8b88255b43
pv: Add version 1.8.5. (#42419)
Switch to "tar.gz" source packages as the "tar.bz2" archives are not available for newer versions.
2024-02-01 09:54:53 -08:00
Rémi Lacroix
bcbd78cea9
ncdu: Add version 1.19 (#42420) 2024-02-01 09:49:57 -08:00
Adam J. Stewart
22ad28bb17
Python: add v3.12.1 (#42397) 2024-02-01 07:43:14 -07:00
Alberto Invernizzi
74bd8a9cf7
neovim: be more specific with lua dependencies (#42401) 2024-02-01 14:11:49 +01:00
Adam J. Stewart
023a6be67d
Update PyTorch ecosystem (#42394) 2024-02-01 06:42:13 -06:00
Harmen Stoppels
922a1983f3
docs: git version section title + highlight issues (#42398)
* basic_usage: section title for git versions

* improve highlighting by using a comment instead of invalid syntax
2024-02-01 09:46:17 +01:00
Massimiliano Culpo
2758fc7e14
Remove caching in generated Dockerfiles (#42405) 2024-02-01 09:22:52 +01:00
dependabot[bot]
3541fcae01
build(deps): bump docker/metadata-action from 5.5.0 to 5.5.1 (#42416)
Bumps [docker/metadata-action](https://github.com/docker/metadata-action) from 5.5.0 to 5.5.1.
- [Release notes](https://github.com/docker/metadata-action/releases)
- [Commits](dbef88086f...8e5442c4ef)

---
updated-dependencies:
- dependency-name: docker/metadata-action
  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>
2024-02-01 09:14:31 +01:00
dependabot[bot]
eea06de6df
build(deps): bump codecov/codecov-action from 3.1.6 to 4.0.0 (#42415)
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3.1.6 to 4.0.0.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](ab904c41d6...f30e4959ba)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2024-02-01 09:13:52 +01:00
Alberto Invernizzi
29658eddcc
Lua: better specify providers in LuaPackage base class (#42392) 2024-02-01 08:57:12 +01:00
Tamara Dahlgren
2fc0d05a55
Environments: Add support for including views (#42250)
* Environments: Add support for including views (take 2)

* schema type hint fixes
2024-02-01 10:07:16 +09:00
Edward Hartnett
faf64f1a26
g2c: add v1.8.0 (#40761)
includes variant to build with future API for v2
2024-02-01 09:28:55 +09:00
Harmen Stoppels
d340523d68
jq: 1.7.1 (#42409) 2024-01-31 15:49:44 -08:00
Dave Sweeris
089fa12ff8
Update OpenSubdiv spec (#42381)
* Update package.py
   Add support for OpenSubdiv 3.5.x
* Fixed Dependencies
   I was getting errors about cmake not being able to find `xf86vm`, and adding a dependency on `libxxf86vm` fixes it.
2024-01-31 15:34:47 -08:00
Julius Plehn
d9528819a3
Adds nvhpc 24.1 (#42388) 2024-01-31 13:40:33 -08:00
Ben Wibking
e3d5ca2997
visit: set minimum silo version to 4.11 (#42072) 2024-01-31 22:05:17 +01:00
Sebastian Grimberg
8fc76ab325
Update recipe for Palace v0.12.0 (#42400) 2024-01-31 12:57:03 -08:00
Hector Martinez-Seara
e77678bd82
kim-api: added paths for bash/zsh completion (#31691)
Co-authored-by: Hector Mtz-Seara <hector@gmail.com>
Co-authored-by: Ryan S. Elliott <relliott@umn.edu>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: hseara <hseara@users.noreply.github.com>
2024-01-31 12:42:59 -07:00
Richard Berger
dafd8dbe87
Add sol2 package (#42402) 2024-01-31 12:09:07 -07:00
Chris White
5034919d23
add new release versions (#42362) 2024-01-31 10:58:07 -08:00
Harmen Stoppels
2bcfb72d38
environment/view: small cleanup (#42395) 2024-01-31 17:22:20 +01:00
Harmen Stoppels
f27bff81ba
spack reproduce-build: accept URLs from web interface (#42261)
Sometimes the logs are too long and the copy & paste command is not
shown. In that case I'd like to just copy the failing GitLab job URL in
my browser to `spack reproduce-build <url>`.
2024-01-31 15:58:51 +01:00
Massimiliano Culpo
5c49bb45c7
ASP-based solver: decouple setup phase from clingo.backend (#41952)
Currently, the `SpackSolverSetup` and the `PyclingoDriver` are more coupled than necessary:
1. The driver object needs a setup object to be injected during a solve, 
2. And the setup object will get a reference back to the driver

This design is necessary because we use the low-level `clingo.backend` interface to setup our problem. This interface though is meant to bypass the grounder and add symbols directly in the grounded table, which is a feature we don't currently use.

The PR simplifies the encoding by having the setup object returning the problem-specific facts / rules as a list of strings, and the driver ingesting them using the [clingo.Control.add](https://potassco.org/clingo/python-api/5.6/clingo/control.html#clingo.control.Control.add) method. This removes any use of the low level interface.

Using this encoding makes it easy to hash the output of the setup phase, since it is returned as a string.
2024-01-31 15:37:59 +01:00
Alex Richert
97fb9565ee
py-nbconvert: avoid install-time downloads (#42024)
* py-nbconvert: avoid install-time downloads

* install css files as resources for py-nbconvert

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

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

* Update package.py

* py-nbconvert: update dependencies for 7.14.1

* [@spackbot] updating style on behalf of AlexanderRichert-NOAA

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

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

* Update resources & remove style.min.css file

* Update package.py

* [@spackbot] updating style on behalf of AlexanderRichert-NOAA

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-01-31 08:28:41 -06:00
Alberto Invernizzi
72eaca23fe
environments: develop paths were not getting expanded (#34986) 2024-01-31 15:18:25 +01:00
kwryankrattiger
1f11b3844a
CI: Add OIDC capability for deprecated CI (#42371)
This "breaks" the deprecated schema by allowing unknown attributes
to the attributes section of the job types. The breaking change here is
that deprecated stacks will no longer ignore attributes that are unknown
but rather assume the new CI schema behavior of injecting them into the
generated CI configuration. This change is required to secure
authentication in Spack CI.
2024-01-31 15:05:57 +01:00
Rocco Meli
e129a6f47a
Add +dlaf variant to cp2k in CI (#42346) 2024-01-31 11:54:45 +01:00
Harmen Stoppels
d983ac35fe
ci: bump ghcr.io/spack/linux-ubuntu22.04-x86_64_v2 tag (#42357) 2024-01-31 09:59:03 +01:00
dependabot[bot]
2dcf4f709b
build(deps): bump urllib3 from 2.1.0 to 2.2.0 in /lib/spack/docs (#42384)
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.1.0 to 2.2.0.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/2.1.0...2.2.0)

---
updated-dependencies:
- dependency-name: urllib3
  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>
2024-01-31 09:55:26 +01:00
dependabot[bot]
a171fe3565
build(deps): bump codecov/codecov-action from 3.1.5 to 3.1.6 (#42385)
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3.1.5 to 3.1.6.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](4fe8c5f003...ab904c41d6)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  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>
2024-01-31 09:54:11 +01:00
Jonathon Anderson
c9aeab58e6
hpctoolkit: refine dependencies (#42354)
* Force Dyninst <=12 before @2024.01

* Remove some +pic requirements

* Use virtual tbb dep
2024-01-31 08:27:05 +01:00
Harmen Stoppels
517dac6ff8
compression.py: refactor + bug fix (#42367)
Improve naming, so it's clear file "extensions" are not taken in the
`PurePath(path).suffix` sense as the original function name suggests,
but rather that the files are opened and their magic bytes are
classified.

Add type hints.

Fix a bug where `stream.read(num_bytes)` was run on the compressed
stream instead of the uncompressed stream, which can potentially break
detection of tar.bz2 files.

Ensure that when peeking into streams for magic bytes, they are reset to
their original position upon return.

Use new API in `spack logs`.
2024-01-31 07:59:07 +01:00
jalcaraz
376653ec3d
Updated last commit of TAU package with Dyninst test (#42387)
* Updated last commit of TAU package with Dyninst test

* The path to dyninst was missing when loading TAU
2024-01-30 19:07:33 -08:00
Harmen Stoppels
28eea2994f
elf: relocate PT_INTERP (#42318)
Relocation of `PT_INTERP` in ELF files already happens to work from long to short path, thanks to generic binary relocation (i.e. find and replace). This PR improves it:

1. Adds logic to grow `PT_INTERP` strings through patchelf (which is only useful if the interpreter and rpath paths are the _only_ paths in the binary that need to be relocated)
2. Makes shrinking `PT_INTERP` cleaner. Before this PR when you would use Spack-built glibc as link dep, and relocate
executables using its dynamic linker, you'd end up with

   ```
   $ file exe
   exe: ELF 64-bit LSD pie executable, ..., interpreter /////////////////////////////////////////////////path/to/glibc/lib/ld-linux.so
   ```

   With this PR you get something sensible:

   ```
   $ file exe
   exe: ELF 64-bit LSD pie executable, ..., interpreter /path/to/glibc/lib/ld-linux.so
   ```

When Spack cannot modify the interpreter or rpath strings in-place, it errors out without modifying the file, and leaves both tasks to patchelf instead.

Also add type hints to `elf.py`.
2024-01-30 22:36:49 +01:00
Frédéric Simonis
6d55caabe8
precice: add release v2.5.1 (#42376) 2024-01-30 12:47:59 -08:00
Benjamin Fovet
d8260907df
add gmsh v4.12.2 (#42375) 2024-01-30 12:13:07 -08:00
Wileam Y. Phan
9474f4bb33
gtpin: add versions 3.4 and 3.7 (#42373) 2024-01-30 12:05:43 -08:00
Rémi Lacroix
698b71e2fd
autoconf: Fix patches' URLs (#42372) 2024-01-30 11:33:48 -08:00
John W. Parent
749301d133
MSVC: Broken ifx needs new $TMP (#42155)
Certain versions of ifx (the majority of those available) have an issue
where they are not compatible with TMP directories with dot chars
This precludes their use with CMake.
Remap TMP to point to the stage directory rather than whatever the TMP
default is
2024-01-30 10:18:54 -08:00
Massimiliano Culpo
a20c0de6d8
ns-3-dev: rewrite the package to use CMake (#34207) 2024-01-30 17:57:27 +01:00
dependabot[bot]
ad2ae63745
build(deps): bump pytest from 7.4.4 to 8.0.0 in /lib/spack/docs (#42361)
Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.4 to 8.0.0.
- [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/7.4.4...8.0.0)

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2024-01-30 08:23:50 -07:00
dependabot[bot]
d56ca4f107
build(deps): bump black from 24.1.0 to 24.1.1 in /lib/spack/docs (#42360)
Bumps [black](https://github.com/psf/black) from 24.1.0 to 24.1.1.
- [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/24.1.0...24.1.1)

---
updated-dependencies:
- dependency-name: black
  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>
2024-01-30 15:23:42 +00:00
dependabot[bot]
e09c3ddec2
build(deps): bump black in /.github/workflows/style (#42359)
Bumps [black](https://github.com/psf/black) from 24.1.0 to 24.1.1.
- [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/24.1.0...24.1.1)

---
updated-dependencies:
- dependency-name: black
  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>
2024-01-30 15:23:30 +00:00
Massimiliano Culpo
1882920c97
elsi: cleanup recipe (#42355) 2024-01-30 14:08:10 +01:00
Matthias Wolf
b70cb60b65
py-bluepyefe, py-igor2: new version, new package igor2 (#42191) 2024-01-30 03:29:07 -07:00
Adam J. Stewart
6a1e64f531
py-black: add v24.1.1 (#42343) 2024-01-30 03:14:02 -07:00
Nathalie Furmento
5217b20901
starpu: add release 1.4.3 (#42339) 2024-01-30 03:09:21 -07:00
James Beal
ed37969925
singularityce: add v4.x (#42347)
Co-authored-by: James Beal <jb23@sanger.ac.uk>
2024-01-30 03:08:57 -07:00
Henrik Finsberg
32230e6520
Add fenics development version and ufl-legacy (#42182)
* Add fenics development version and ufl-legacy

* Make sure python and setuptools are added to ufl-legacy and add version 2022.3.0 as well

* Run black and add maintainer to fenics package

* Fix typo

* Use Fiat version 2019.1.0

* Run black

* Add back master branch of fiat

* Remove master from the list of dolfin versions and add one extra line of each deps instead

* Run black

* Do not specify python version in ufl-legacy

* Remove python dependency from ufl-legacy

* Remove python dependency from ffc

* Add special case for master in ffc

* Run black

* Remove master from loop in ffc

* Run black again
2024-01-30 02:49:51 -07:00