Commit graph

34185 commits

Author SHA1 Message Date
Dom Heinzeller
494d3f9002
Skip 'icc.patch' in var/spack/repos/builtin/packages/py-gevent/package.py for py-gevent@23.7.0+ (#41568) 2023-12-19 12:44:29 -06:00
Harmen Stoppels
4f8b856145
e4s: add julia (#41768) 2023-12-19 18:17:54 +01:00
Massimiliano Culpo
0eca79e7e4
Add an audit to prevent virtual packages with variants specified (#41747)
Currently, a virtual spec is composed of just a name and a version. When a virtual spec contains other components, such as variants, Spack won't emit warnings or errors but will silently drop them - which is unexpected by users.
2023-12-19 18:05:33 +01:00
Ben Wibking
f245bde772
adios2: fix build failure in 2.7.1 (#41753) 2023-12-19 17:58:05 +01:00
Mikael Simberg
4aee067bb0
umpire: backport -fcompare-debug-second flag removal (#41506) 2023-12-19 17:24:52 +01:00
Martin Aumüller
cc25a0e561
ffmpeg: mostly build fixes (#41050) 2023-12-19 17:23:23 +01:00
Aiden Grossman
3f063153f0
openblas: add patches to build with clang (#39138) 2023-12-19 17:22:29 +01:00
Dr Marco Claudio De La Pierre
aa350a4ed1
removing deprecated: recipes tower-agent and tower-cli, as nf- prefixed recipes available (#41576)
Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@seqera.io>
2023-12-19 17:16:26 +01:00
Brian Van Essen
e36bee41a0
lbann: relax the requirement on protobuf (#41591) 2023-12-19 17:16:04 +01:00
dependabot[bot]
138d0c7a13
build(deps): bump black from 23.11.0 to 23.12.0 in /lib/spack/docs (#41615)
Bumps [black](https://github.com/psf/black) from 23.11.0 to 23.12.0.
- [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/23.11.0...23.12.0)

---
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>
2023-12-19 17:14:05 +01:00
Thomas-Ulrich
a688479564
easi: specify better the impalajit dependency (#41637) 2023-12-19 17:08:22 +01:00
Wouter Deconinck
5ead4c2d56
pcre: ensure consistency between autotools and cmake builds (#41644)
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-12-19 16:57:59 +01:00
Richard Berger
2e18fbbdeb
legion: do not set HIP_PATH env variable (#41660)
* legion: do not set HIP_PATH env variable

* flecsi: workaround Legion CMake for +rocm
2023-12-19 16:14:19 +01:00
Howard Pritchard
02eafeee03
openmpi: allow external libevent in general case (#41686)
add a internal-libevent variant to add an out.

related to #41549

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-12-19 14:54:25 +01:00
wspear
812a43621b
tau : v2.33.1 and later requires otf2 v3 (#41691) 2023-12-19 12:20:47 +01:00
Richard Berger
0fe338b526
legion: inject correct mpicc to embedded GASnet slingshot11 config (#41701) 2023-12-19 12:20:05 +01:00
Tom Payerle
3dc02e55e6
ufs-weather-model: add build dependency (#41724) 2023-12-19 04:18:48 -07:00
Adam J. Stewart
7023edb37c
PyTorch: update ecosystem (#41713) 2023-12-19 12:18:25 +01:00
James Beal
f1fdaca345
samtools: add v1.19 (#41634)
Co-authored-by: James Beal <jb23@sanger.ac.uk>
2023-12-19 12:13:57 +01:00
Mikael Simberg
d4454e54dc
ut: add v2.0.0 and v2.0.1 (#41771) 2023-12-19 04:13:33 -07:00
Paul Kuberry
969718d176
xyce: remove CMake test for all compilers (#41679) 2023-12-19 12:10:16 +01:00
Jack Morrison
0a9179fddb
intel-mpi-benchmarks: add v2021.7, v2021.6, v2021.5, v2021.4 (#41730) 2023-12-19 11:42:13 +01:00
Pramod Kumbhar
b5b0a76991
creduce: fix build of @develop (#41258) 2023-12-19 11:30:42 +01:00
Christopher Christofi
59b39f3eba
uthash: add new package (#41732) 2023-12-19 11:26:13 +01:00
Wouter Deconinck
7a0c4e8017
acts: new versions 31.* (#41733)
This adds three new versions in the 31.* series. Release notes of 31.0.0 at https://github.com/acts-project/acts/releases/tag/v31.0.0. No changes to the CMakeLists.txt files that need addressing in the package recipe.

The only new feature I'm a bit concerned about is https://github.com/acts-project/acts/pull/2626, which replaces testing for C++20 concepts support by the feature-testing macro `__cpp_concepts`, which is also a C++20 feature. So technically we now should require `cxxstd=20` even though Acts itself still allows (and defaults to) 17. Judging by https://en.cppreference.com/w/cpp/compiler_support/20, the support for feature-testing macros was added very early by most compilers.
2023-12-19 11:13:07 +01:00
Thomas Madlener
1ddf4ee6ba
whizard: fix support for building with hepmc output (#41538) 2023-12-19 11:12:27 +01:00
dependabot[bot]
12d0507cb7
build(deps): bump black in /.github/workflows/style (#41616)
Bumps [black](https://github.com/psf/black) from 23.11.0 to 23.12.0.
- [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/23.11.0...23.12.0)

---
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>
2023-12-19 10:47:57 +01:00
Wouter Deconinck
cf99912352
flexiblas: explicitly set SYSCONFDIR (#41748)
As of CMake 3.4, [GNUInstallDirs](https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html) treats `SYSCONFDIR` differently for a prefix that starts with `/opt`, then "the SYSCONFDIR value etc becomes /etc/opt/...." In the case of flexiblas, that results in failing attempts to write files to a system directory.

Since [flexiblas version 1](0f2d2c7659 (diff-1e7de1ae2d059d21e1dd75d5812d5a34b0222cef273b7c3a2af62eb747f9d20aR16)), we can override SYSCONFDIR with our own defines.
2023-12-19 10:47:16 +01:00
snehring
9723fe88f5
rebayes: add v1.2.2 (#41749) 2023-12-19 10:44:16 +01:00
Christopher Christofi
2439ff56a5
kalign: add v3.4.0 (#41758)
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
2023-12-19 10:35:23 +01:00
Massimiliano Culpo
2ef8d09fc7
spack config get/blame: with no args, show entire config
This PR changes the default behavior of `spack config get` and `spack config blame`
to print a flattened version of the entire spack configuration, including any active 
environment, if the commands are invoked with no section arguments.

The new behavior is used in Gitlab CI to help debug CI configuration, but it can also
be useful when asking for more information in issues, or when simply debugging Spack.
2023-12-19 01:26:53 -08:00
Mosè Giordano
e5e767b300
julia: set compatibility with suite-sparse (#41754) 2023-12-19 10:17:06 +01:00
Rocco Meli
1c6b38f36d
gnina: add version 1.1 (#41762) 2023-12-19 09:39:46 +01:00
Arne Becker
091cd47caa
tnftp: new package (#41763) 2023-12-19 09:38:42 +01:00
John W. Parent
1ebf1a0c6c
libxml2: correct improper use of base builder meta (#41760) 2023-12-19 09:34:59 +01:00
Greg Becker
56761649a2
environment modifications for externals (#41723)
* allow externals to configure environment modifications

* docs for external env modification

---------

Co-authored-by: becker33 <becker33@users.noreply.github.com>
2023-12-18 22:24:15 -06:00
dependabot[bot]
6a19cf1b42
build(deps): bump docker/metadata-action from 5.3.0 to 5.4.0 (#41764)
Bumps [docker/metadata-action](https://github.com/docker/metadata-action) from 5.3.0 to 5.4.0.
- [Release notes](https://github.com/docker/metadata-action/releases)
- [Commits](31cebacef4...9dc751fe24)

---
updated-dependencies:
- dependency-name: docker/metadata-action
  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>
2023-12-18 16:31:02 -08:00
Thomas Madlener
ef4274ed2e
podio: Add latest tag 0.17.4 (#41735) 2023-12-18 22:37:00 +01:00
dependabot[bot]
88b8fc63ef
build(deps): bump isort in /.github/workflows/style (#41650)
Bumps [isort](https://github.com/pycqa/isort) from 5.12.0 to 5.13.2.
- [Release notes](https://github.com/pycqa/isort/releases)
- [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pycqa/isort/compare/5.12.0...5.13.2)

---
updated-dependencies:
- dependency-name: isort
  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>
2023-12-18 10:23:51 -08:00
dependabot[bot]
639a6a6897
build(deps): bump isort from 5.12.0 to 5.13.2 in /lib/spack/docs (#41651)
Bumps [isort](https://github.com/pycqa/isort) from 5.12.0 to 5.13.2.
- [Release notes](https://github.com/pycqa/isort/releases)
- [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pycqa/isort/compare/5.12.0...5.13.2)

---
updated-dependencies:
- dependency-name: isort
  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>
2023-12-18 10:23:18 -08:00
Massimiliano Culpo
af96fef1da
spack.config: cleanup and add type hints (#41741) 2023-12-18 17:05:36 +01:00
Michael Kuhn
7550a41660
gcc: fix run environment variables not being exported in environments (#41729)
Since views use symlinks, all compiler binaries were skipped in this
case. Instead, only skip them if their target does not exist.
2023-12-18 16:19:38 +01:00
Mikael Simberg
ffd2a34d9e
pika-algorithms: Add upper bound for pika version (#41736) 2023-12-18 15:12:36 +01:00
Michael Kuhn
6a74a82e19
glib: add v2.78.3 (#41697) 2023-12-18 10:06:23 +01:00
Harmen Stoppels
ebb7c5ac8f
asp.py: remove "CLI" reference (#41718)
Can also be an environment root, or programatically
`Spec("x").concretized()`.
2023-12-18 09:52:12 +01:00
Peter Scheibel
14c7bfe9ce
spack develop: convert to config (#35273)
Convert the 'develop' section of an environment to a dedicated configuration section.
This means for example that instead of having to define `develop` specs in the
`spack.yaml`, the environment can `include:` another `develop.yaml` configuration
which specifies which specs should be developed in the environment.

This change is not expected to be disruptive given that existing environment `spack.yaml`
files will conform to the new schema.

(Update 11/28/2023) I have implemented the `develop`/`undevelop` commands in terms
of more-generic modification functions added to the `config` module: `change_or_add`
and `update_all`. It is assumed that the semantics added here (described in 11/18 update)
would be desirable to extend to other config update actions (e.g. adding compilers, 
changing package requirements, adding mirrors).

(Update 11/18/2023) I have updated this such that `spack develop`, and
`spack undevelop` to potentially modify all writable scopes, like 
https://github.com/spack/spack/pull/41147. https://github.com/spack/spack/pull/35307
will be useful for modifying included scopes, but generally speaking specifying a 
`--scope` will not be required for `spack develop`: `spack develop` will add new 
develop specs to whatever scope already has develop specs defined, or to the
highest-priority writable scope (which should be the env scope).

TODOs:

- [x] If you `spack undevelop` a package which is mentioned at multiple layers of
      configuration, then currently this would only modify one of them. That's not
      technically a new issue (has always existed for configuration modification), but
      may be confusing to users when presented via an interface other than `spack config set`
- [x] Need to add (or confirm) the ability to modify individual config files by providing
      a path (rather than using a scope identifier as a key to retrieve associated config).
- [x] `spack develop` adds new develop specs to the scope that defines them
      (potentially skipping higher priority scopes to e.g. augment included scope files)

---------

Co-authored-by: scheibelp <scheibelp@users.noreply.github.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2023-12-18 00:47:53 -08:00
Christopher Christofi
ed52b505d4
py-plum-dispatch: add new package (#41536)
* py-plum-dispatch: add new package

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-12-17 12:18:02 -06:00
Wouter Deconinck
b111064e22
py-htgettoken: use os.environ, avoid AttributeError (#41717)
* py-htgettoken: use os.environ, avoid AttributeError

This avoids the following error:
```
Warning: could not load runtime environment due to AttributeError: 'EnvironmentModifications' object has no attribute 'get'
```

* py-htgettoken: allow for undefined variables

* py-htgettoken: use dict get()

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-12-17 12:17:23 -06:00
Wouter Deconinck
17d47accf9
qt: apply patch for apple-clang@15: (#41695) 2023-12-17 07:35:46 -05:00
Christopher Christofi
d7fb298a6b
py-pyopenssl: add version 18.0.0 (#41709) 2023-12-17 01:05:38 -06:00