Commit graph

29556 commits

Author SHA1 Message Date
Glenn Johnson
3ed219578b
py-xxhash: fix xxhash dependency (#34971)
* py-xxhash: fix xxhash dependency

The dependency should be xxhash@0.8.0:.

* Add version 3.2.0
2023-01-16 23:58:10 -06:00
Loïc Pottier
0040236cc6
rabbitmq-c: added RabbitMQ C interface (#34892)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2023-01-16 19:02:42 -08:00
Glenn Johnson
0629c8e5fa
itk: add version 5.3.0 (#34967)
* Add depends_on("mpi") to fix missing <mpi.h>
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2023-01-17 03:52:10 +01:00
Glenn Johnson
6f19eb5e67
hisat2: add version 2.2.1 and sra variant (#34966)
- add python dependency
- add perl dependency
- set python and perl interpreters in scripts
2023-01-17 03:31:00 +01:00
Glenn Johnson
b7e416046f
sra-tools: add version 3.0.3 and fix build (#34965) 2023-01-17 03:29:52 +01:00
Glenn Johnson
b2cc36109f
stringtie: add version 2.2.1 and fix build (#34973)
- stringtie uses internal samtools so remove dependency on samtools
- add dependency for zlib
- use make release target to get correct flags
2023-01-17 02:55:06 +01:00
Sergey Kosukhin
1262dcfb9f
intel-oneapi-mpi: fix setup_dependent_build_environment (#34956) 2023-01-16 23:11:43 +01:00
Benjamin Meyers
c3dc7a8349
py-fastfold add py-numpy upper bound (#34962) 2023-01-16 14:07:36 -08:00
iarspider
84d2c8a693
Add checksum for hwloc 2.9.0 (#34919) 2023-01-16 13:12:38 -08:00
Sebastian Ehlert
37b1bc9c26
Add package file for xtb and py-xtb (#34857)
* Add package file for xtb and py-xtb

* Retain maintainers from PythonPackage

* Update package files

- use extends("python") instead of tampering with PYTHONPATH
- use PyPI for downloading sdist of py-xtb
- add simple-dftd3 0.7.0
- add dftd4 3.5.0
- remove --wrap-mode=nodownload from toml-f

* Remove logic for download URL
2023-01-16 13:07:21 -08:00
Harmen Stoppels
3489cc0a9b
Refer to mirrors by name, path, or url (#34891)
With this change we get the invariant that `mirror.fetch_url` and
`mirror.push_url` return valid URLs, even when the backing config
file is actually using (relative) paths with potentially `$spack` and
`$env` like variables.

Secondly it avoids expanding mirror path / URLs too early,
so if I say `spack mirror add name ./path`, it stays `./path` in my
config. When it's retrieved through MirrorCollection() we
exand it to say `file://<env dir>/path` if `./path` was set in an
environment scope.

Thirdly, the interface is simplified for the relevant buildcache
commands, so it's more like `git push`:

```
spack buildcache create [mirror] [specs...]
```

`mirror` is either a mirror name, a path, or a URL.

Resolving the relevant mirror goes as follows:
    
- If it contains either / or \ it is used as an anonymous mirror with
   path or url.
- Otherwise, it's interpreted as a named mirror, which must exist.

This helps to guard against typos, e.g. typing `my-mirror` when there
is no such named mirror now errors with:

```
$ spack -e . buildcache create my-mirror
==> Error: no mirror named "my-mirror". Did you mean ./my-mirror?
```

instead of creating a directory in the current working directory. I
think this is reasonable, as the alternative (requiring that a local dir
exists) feels a bit pendantic in the general case -- spack is happy to
create the build cache dir when needed, saving a `mkdir`.

The old (now deprecated) format will still be available in Spack 0.20,
but is scheduled to be removed in 0.21:

```
spack buildcache create (--directory | --mirror-url | --mirror-name) [specs...]
```

This PR also touches `tmp_scope` in tests, because it didn't really
work for me, since spack fixes the possible --scope values once and
for all across tests, so tests failed when run out of order.
2023-01-16 10:14:41 -08:00
Auriane R
9a25e21da8
Add target propagation for pika package (#34924) 2023-01-16 17:57:50 +01:00
Alec Scott
d156e2ee91
Add py-python-lsp-server v1.7.0 (#34946) 2023-01-16 10:54:19 -06:00
Harmen Stoppels
891a63cae6
Revert "4th chunk of nf-core deps from update/nextflow-tools (#34564)" (#34960)
This reverts commit 4e63d92bc9.
2023-01-16 17:00:33 +01:00
eugeneswalker
886ea7c490
e4s: add py-h5py (#34914) 2023-01-16 15:52:24 +00:00
Glenn Johnson
fcf9c639ee
Make docbook-xml work across all entity versions (#34733)
Packages that use docbook-xml may specify a specific entity version.
When this is specified as a version constraint in the package recipe it
will cause problems when using `unify = True` in a Spack environment, as
there could be multiple versions of docbook-xml in the spec. In
practice, any entity version should work with any other version and
everything should work with the latest version. This PR maps all Spack
docbook-xml entity versions to the docbook-xml version in the spec.
Ideally, the version in the spec would be the latest version. With this
PR, even if a package specifies an older entity version, it will map
to the entity version (latest) in the spec. This means that there can be one
docbook-xml version in a Spack environment spec and packages requesting
older entity versions will still work.

To help facilitate this, docbook-xml version constraints for packages
that have them have been removed. Those packages are dbus and gtk-doc.
2023-01-16 16:03:03 +01:00
Marco De La Pierre
4e63d92bc9
4th chunk of nf-core deps from update/nextflow-tools (#34564) 2023-01-16 08:01:24 -07:00
Gilles Gouaillardet
17a67b9a56
fix libtool filter for Fujitsu compilers (#34916)
Since legit regular expressions are matched, do not pass string=True
to the filter

Refs #34897
2023-01-16 15:56:13 +01:00
Wouter Deconinck
904eefc930
harfbuzz: new version 5.3.1, 6.0.0 (fixes aarch64) (#34908)
A few new versions of harbuzz, but just jumping to the last non-6 version as preferred.

No build system changes:
- within 5 series: https://github.com/harfbuzz/harfbuzz/compare/5.1.0...5.3.1
- from 5 to 6: https://github.com/harfbuzz/harfbuzz/compare/5.3.1...6.0.0

The 5 series fixes a build issue for aarch64, https://github.com/harfbuzz/harfbuzz/issues/3768.
2023-01-16 15:55:03 +01:00
Jack Morrison
add8022490
Fix incorrect configuration file name in docs (#34925) 2023-01-16 14:52:08 +01:00
Glenn Johnson
645faad379
cp2k: add v2022.2, update CUDA settings (#34757) 2023-01-16 14:13:40 +01:00
Adam J. Stewart
d0866e4d02
Qt: patch additional config file (#34682) 2023-01-16 07:42:01 -05:00
Dan Bonachea
1095958cac
GASNet 2022.9.2 package update (#34942)
This allows client packages like UPC++ to display more precise version
information when their GASNet dependency was fetched from git.
2023-01-16 12:48:22 +01:00
Alec Scott
911e9edf07
Add Go v1.19.5, v1.18.10, and remove deprecated versions (#34594) 2023-01-16 12:46:20 +01:00
AMD Toolchain Support
b9048dbee9
AMD Optimized CPU Libraries: add v4.0 (#34681)
What's in AOCL 4.0:
1. amdblis
        LPGEMM variants with post-ops support
        AMD "Zen4" support for BLIS

2. amdlibflame
        Upgrade to LAPACK 3.10.1 specification
        Improvements in a few more variants of SVD and Eigen Value routines
        Multithread support enabled for selected APIs

3. amdfftw
        AVX-512 enablement of DFT kernels
        AVX-512 optimization of copy and transpose routines

5. amdlibm
        Black & Scholes support (logf, expf, erff, both scalar and vector)
        AVX-512 variants of vector functions

6. aocl-sparse
        New Iterative Solver APIs
        AVX-512 support for SPMV API

7. amdscalapack
        Upgrade to Netlib ScaLAPACK 2.2.0

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-01-16 12:05:31 +01:00
Cory Bloor
55f71e41d5
rocsolver: expand version compatibility with fmt (#34941) 2023-01-16 11:14:13 +01:00
Alec Scott
07ee8e99ca
restic: add v0.15.0 (#34945) 2023-01-16 11:03:07 +01:00
Alec Scott
307a8f8565
rclone: add v1.61.1 and deprecate old versions due to CVE-2020-28924 (#34944) 2023-01-16 10:59:04 +01:00
Alec Scott
1ca7da4831
Add v0.109.0 and deprecate versions < v0.79.1 due to a CVE (#34943) 2023-01-16 10:57:55 +01:00
eugeneswalker
b9a16a599a
e4s ci: py-libensemble: activate variants (#34915) 2023-01-16 10:57:28 +01:00
Jonathan R. Madsen
590adf57d2
omnitrace: add new versions (#34955)
- v1.5.0
- v1.6.0
- v1.7.0
- v1.7.1
- v1.7.2
- v1.7.3
- v1.7.4
2023-01-16 10:47:10 +01:00
dependabot[bot]
d45c228401
build(deps): bump actions/setup-python from 4.4.0 to 4.5.0 (#34939)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.4.0 to 4.5.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](5ccb29d877...d27e3f3d7c)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-01-16 10:33:12 +01:00
Adam J. Stewart
d0cb5efa3b
py-segmentation-models-pytorch: add v0.3.2 (#34853) 2023-01-16 10:10:40 +01:00
Adam J. Stewart
5f4b736006
Drop Python 3.6 again (#34442) 2023-01-16 10:09:40 +01:00
Auriane R
c7d1746064
Fix version number for fmt dependency of pika package (#34922) 2023-01-16 01:07:08 -08:00
SXS Bot
a1889440d7
spectre: add v2023.01.13 (#34929)
Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
2023-01-14 23:21:59 -08:00
Christopher Christofi
f521c31657
py-annoy: new package with version 1.17.1 (#34911)
* py-annoy: add 1.17.1

* add version specifier on dependency package
2023-01-14 17:21:56 -08:00
Todd Gamblin
d4e714bb2e
spack list: add --count option (#34950)
Sometimes I just want to know how many packages of a certain type there are.

- [x] add `--count` option to `spack list` that output the number of packages that
      *would* be listed.

```console
> spack list --count
6864
> spack list --count py-
2040
> spack list --count r-
1162
```
2023-01-14 16:08:40 -08:00
John W. Parent
ff38ff25cb
Support windows paths in a spec (#34405)
Refactor Spack's spec syntax parsing to handle Windows style paths
Amend unit tests to reflect this updated behavior.
2023-01-14 07:52:37 +01:00
Dominik Thoennes
6e95417c98
trilinos: enable mumps solver in amesos2 if variant is set (#34927)
* enable mumps solver in amesos2 if variant is set for trilinos
* fix formatting
2023-01-13 21:08:22 -08:00
Cyrus Harrison
4727a9b976
add conduit 0.8.6 release (#34894) 2023-01-13 20:53:21 -08:00
John W. Parent
44c69cadf4
Proper scons executable on Windows (#34934) 2023-01-13 19:28:29 -08:00
Dr. Christian Tacke
1034b23320
slurm: Add Version 22-05-7-1 (#34902) 2023-01-13 19:23:26 -08:00
Paul R. C. Kent
ef9049feac
Add 15.0.7 (#34912) 2023-01-13 19:18:24 -08:00
Sam Grayson
f6006445da
Add parsl-monitoring (#34769)
* Add packages

* Style

* Respond to comments

* Change conflct dep type

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-13 17:07:39 -06:00
eugeneswalker
2c87f59d36
py-gevent%oneapi@2023.0.0: -Wno-error=incompatible-function-pointer-types (#34901) 2023-01-13 17:06:16 -06:00
kwryankrattiger
229ee7cad9
Paraview rocm (#34790)
* paraview: add `rocm` variant

This conflicts with CUDA and requires at least ParaView 5.11.0. More
dependencies are also needed.

* E4S: Add ParaView for ROCm and CUDA stacks

* DAV SDK: Update ParaView version and GPU variants

* Verify using hipcc vs amdclang++ for newer hip

Co-authored-by: Ben Boeckel <ben.boeckel@kitware.com>
2023-01-13 12:41:57 -06:00
Marco De La Pierre
85e2fb0c4d
Adding py-strawberryfields from Xanadu, and its deps (#34849)
* adding 1st version of py-strawberryfields

* py-strawberryfields: minor edit

* added backbone for 4x new SF dependencies

* edits to SF and its 4x new deps

* added all deps for SF

* added one version to py-lark-parser

* py-quantum-xir with tarball from github

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

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

* updated version for py-quantum-xir : pypy fixed

* py-pennylane: added pythonpackage.maintainers, too

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-01-13 10:39:29 -08:00
Todd Gamblin
88a604e7f4
config: make path replacements lazy (#34758)
Currently, all of the replacements in `spack.util.path.replacements()` get evaluated for
each replacement. This makes it easy to get bootstrap issues, because config is used
very early on in Spack.

Right now, if I run `test_autotools_gnuconfig_replacement_no_gnuconfig` on my M1 mac, I
get the circular reference error below. This fixes the issue by making all of the path
replacements lazy lambdas.

As a bonus, this cleans up the way we do substitution for `$env` -- it's consistent with
other substitutions now.

- [x] make all path `replacements()` lazy
- [x] clean up handling of `$env`

```console
> spack unit-test -k test_autotools_gnuconfig_replacement_no_gnuconfig

...

==> [2022-12-31-15:44:21.771459] Error: AttributeError:

The 'autotools-config-replacement' package cannot find an attribute while trying to build from sources. This might be due to a change in Spack's package format to support multiple build-systems for a single package. You can fix this by updating the build recipe, and you can also report the issue as a bug. More information at https://spack.readthedocs.io/en/latest/packaging_guide.html#installation-procedure

/Users/gamblin2/src/spack/lib/spack/spack/package_base.py:1332, in prefix:
       1330    @property
       1331    def prefix(self):
  >>   1332        """Get the prefix into which this package should be installed."""
       1333        return self.spec.prefix

Traceback (most recent call last):
  File "/Users/gamblin2/src/spack/lib/spack/spack/build_environment.py", line 1030, in _setup_pkg_and_run
    kwargs["env_modifications"] = setup_package(
                                  ^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/build_environment.py", line 757, in setup_package
    set_module_variables_for_package(pkg)
  File "/Users/gamblin2/src/spack/lib/spack/spack/build_environment.py", line 596, in set_module_variables_for_package
    m.std_cmake_args = spack.build_systems.cmake.CMakeBuilder.std_args(pkg)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/build_systems/cmake.py", line 241, in std_args
    define("CMAKE_INSTALL_PREFIX", pkg.prefix),
                                   ^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/package_base.py", line 1333, in prefix
    return self.spec.prefix
           ^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/spec.py", line 1710, in prefix
    self.prefix = spack.store.layout.path_for_spec(self)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/directory_layout.py", line 336, in path_for_spec
    path = self.relative_path_for_spec(spec)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/directory_layout.py", line 106, in relative_path_for_spec
    projection = spack.projections.get_projection(self.projections, spec)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/projections.py", line 13, in get_projection
    if spec.satisfies(spec_like, strict=True):
       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/spec.py", line 3642, in satisfies
    if not self.virtual and other.virtual:
           ^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/spec.py", line 1622, in virtual
    return spack.repo.path.is_virtual(self.name)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 890, in is_virtual
    return have_name and pkg_name in self.provider_index
                                     ^^^^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 770, in provider_index
    self._provider_index.merge(repo.provider_index)
                               ^^^^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 1096, in provider_index
    return self.index["providers"]
           ~~~~~~~~~~^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 592, in __getitem__
    self._build_all_indexes()
  File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 607, in _build_all_indexes
    self.indexes[name] = self._build_index(name, indexer)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 616, in _build_index
    index_mtime = self.cache.mtime(cache_filename)
                  ^^^^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/llnl/util/lang.py", line 826, in __getattr__
    return getattr(self.instance, name)
                   ^^^^^^^^^^^^^
  File "/Users/gamblin2/src/spack/lib/spack/llnl/util/lang.py", line 825, in __getattr__
    raise AttributeError()
AttributeError
```
2023-01-13 10:27:07 -08:00
Seth R. Johnson
33859d3d5f
Celeritas: new versions 0.1.4 and 0.2.0 (#34883) 2023-01-13 09:44:29 -08:00