Commit graph

30259 commits

Author SHA1 Message Date
snehring
8e8d6e5adb
mothur: add v1.48.0 and variants (#33326) 2022-10-18 08:54:23 -06:00
dependabot[bot]
b21e54dffa
build(deps): bump docker/setup-buildx-action from 2.1.0 to 2.2.0 (#33384)
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.1.0 to 2.2.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](95cb08cb26...c74574e6c8)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-action
  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>
2022-10-18 10:22:30 +02:00
Massimiliano Culpo
fe2656f182
intel-oneapi-compilers: fix Python 2.7 compliance (#33383) 2022-10-18 07:19:25 +02:00
Adam J. Stewart
0b014ff9cd
py-fiona: add v1.8.22 (#33372) 2022-10-17 22:33:50 -06:00
eugeneswalker
dd003f66a8
e4s ci stack: add trilinos +rocm (#31601) 2022-10-17 21:04:31 +00:00
Michael Kuhn
9d11b96e4b
lz4: add 1.9.4 (#33334) 2022-10-17 14:42:03 -06:00
Brian Van Essen
47bfc60845
Bugfix HIP and aluminum rocm build (#33344)
* Fixed two bugs in the HIP package recipe.  The first is that the
HIP_PATH was being set to the actual spec, and not the spec prefix.

The second bug is that HIP is expected to be in /opt/rocm-x.y.z/hip
but it's libraries can exist at both /opt/rocm-x.y.z/hip/lib and
/opt/rocm-x.y.z/lib.  This means that the external detection logic may
find it in either and it turns out that some modules only expose one
of those two locations.  Logic is added to ensure that the internal
HIP_PATH and associated ROCM_PATH are correctly set in both cases.

* Added support for Aluminum to use the libfabric plugin with either
RCCL or NCCL.
2022-10-17 13:07:27 -07:00
Mosè Giordano
9b87b4c8cd
grid: reference fftw-api instead of fftw (#33374)
This makes it possible to compile with, e.g., `cray-fftw`, not just `fftw`.
2022-10-17 14:06:15 -06:00
snehring
c0361168a5
New packages: libbigwig, methyldackel (#33273)
* libbigwig: adding new package libbigwig
* methyldackel: adding new package methyldackel
* libbigwig: tighten up curl variant
2022-10-17 12:40:01 -07:00
Robert Underwood
da6aeaad44
Initial contribution of LibPressio ecosystem (#32630)
* Add libpressio and dependencies; some of these packages are
  maintained as forks of the original repositories and in those
  cases the docstring mentions this.
* Add optional dependency in adios2 on libpressio
* cub package: set CUB_DIR environment variable for dependent
  installations
* Clear R_HOME/R_ENVIRON before Spack installation (avoid sources
  outside of Spack from affecting the installation in Spack)
* Rename dlib to dorian3d-dlib and update dependents; add new dlib
  implementation. Pending an official policy on how to handle
  packages with short names, reviewer unilaterally decided that
  the rename was acceptable given that the new Spack dlib package
  is referenced more widely (by orders of magnitude) than the
  original

Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com>
2022-10-17 13:30:54 -06:00
Luke Diorio-Toth
fb090a69f4
py-xopen: version bump to 1.6.0 (#33231)
* version bump to 1.6.0

* added py-isal, updated URL
2022-10-17 19:16:09 +00:00
Stephen Sachs
2e55812417
Classic Intel compilers do not support gcc-toolchain (#33281)
* Classic Intel compilers do not support gcc-toolchain

This fix removes `--gcc-toolchain=` from the ~.fcg` files for the classic Intel
compilers. AFAIK this option is only supported for Clang based compilers.

This lead to an issue when installing cmake. Reproducer:
```
spack install cmake@3.24.2%intel@2021.7.0~doc+ncurses+ownlibs~qt
build_type=Release arch=linux-amzn2-skylake_avx512
```

Tagging maintainer @rscohn2

* Add `-gcc-name` for icc

.. and `-gxx-name` for icpc.

AFAIK this is used for modern C++ support, so we can ignore `ifort`.

Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-10-17 10:46:11 -06:00
Harmen Stoppels
e7b14dd491
database: don't warn adding missing build deps (#33361)
When installing an individual spec `spack --only=package --cache-only /xyz`
from a buildcache, Spack currently issues tons of warnings about
missing build deps (and their deps) in the database.

This PR disables these warnings, since it's fine to have a spec without
its build deps in the db (they are just "missing").
2022-10-17 18:30:19 +02:00
Adam J. Stewart
839cf48352
py-horovod: add v0.26 (#33311)
* py-horovod: add v0.26

* py-petastorm: add v0.12.0
2022-10-17 09:14:55 -07:00
Harmen Stoppels
39105a3a6f
installer.py: traverse_dependencies has local deptype (#33367)
Currently `traverse_dependencies` fixes deptypes to traverse once and
for all in the recursion, but this is incorrect, since deptypes depend
on the node (e.g. if it's a dependency and cache-only, don't follow
build type edges, even if the parent is build from sources and needs
build deps.)
2022-10-17 16:14:12 +00:00
Massimiliano Culpo
9081871966
GnuPG: add v2.3.8 and update stack (#33368) 2022-10-17 10:13:52 -06:00
iarspider
ad430a7504
Add checksum for py-ipykernel 6.15.2 (#33360) 2022-10-17 10:59:21 -05:00
iarspider
db342d8727
Add checksum for py-secretstorage 3.3.3 (#33366) 2022-10-17 10:54:31 -05:00
Carlos Bederián
32761cdb7b
python: add 3.10.7, 3.9.14, 3.8.14, 3.7.14 (#32623) 2022-10-17 17:47:10 +02:00
Scott Wittenburg
29df7e9be3
Support spackbot rebuilding all specs from source (#32596)
Support spackbot rebuilding all specs from source when asked (with "rebuild everything")

- Allow overriding --prune-dag cli opt with env var
- Use job variable to optionally prevent rebuild jobs early exit behavior
- ci rebuild: Use new install argument to insist deps are always installed from binary, but
package is only installed from source.
- gitlab: fix bug w/ untouched pruning
- ci rebuild: install from hash rather than json file
- When doing a "rebuild everything" pipeline, make sure that each install job only consumes
binary dependencies from the mirror being populated by the current pipeline.  This avoids
using, e.g. binaries from develop, when rebuilding everything on a PR.
- When running a pipeline to rebuild everything, do not die because we generated a hash on
the broken specs list.  Instead only warn in that case.
- bugfix: Replace broken no-args tty.die() with sys.exit(1)
2022-10-17 09:45:09 -06:00
Harmen Stoppels
ea80113d0f
Github Discussions can be used for Q&A (#33364) 2022-10-17 08:38:25 -07:00
Rui Peng Li
4fe53061a8
hypre 2.26.0 (#33299) 2022-10-17 08:31:28 -07:00
iarspider
bfe49222d5
Add checksum for py-prompt-toolkit 3.0.31 (#33362) 2022-10-17 09:02:19 -06:00
iarspider
42a27f3075
Add checksum for py-grpcio-tools 1.48.1 (#33358) 2022-10-17 10:01:22 -05:00
Harmen Stoppels
e882583b01
installer.py: fix/test get_deptypes (#33363)
Fixing an oversight in https://github.com/spack/spack/pull/32537

`get_deptypes` should depend on new `package/dependencies_cache_only`
props.
2022-10-17 08:57:58 -06:00
Scott Wittenburg
1be6506e29
gitlab ci: Do not force protected build jobs to run on aws runners (#33314) 2022-10-17 07:29:56 -07:00
iarspider
25e35c936b
Add checksum for py-astroid 2.12.7, py-astroid 2.12.10, py-setuptools 62.6.0, py-wrapt 1.14.1, py-pylint 2.15.0 (#32976)
* Add checksum for py-astroid 2.12.7, py-setuptools 62.6.0

* Also add checksum for py-wrapt

* Update package.py

* Update package.py (#57)

* Update package.py

* Update package.py

* Update package.py
2022-10-17 08:09:52 -06:00
Harmen Stoppels
2c802c12a5
installer.py: show timers for binary install (#33305)
Print a message of the form
```
Fetch mm:ss.  Build: mm:ss.  Total: mm:ss
```
when installing from buildcache. 

Previously this only happened for source builds.
2022-10-17 15:54:40 +02:00
iarspider
f3523d8655
py-jupyterlab-pygments: install from wheel to avoid cyclic dependency (#33278)
* py-jupyterlab-pygments: avoid cyclic dependency

* Fix style

* Update package.py

* Update package.py

* [@spackbot] updating style on behalf of iarspider

* Update package.py

* Flake-8

* fix

Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-17 07:42:01 -06:00
Adam J. Stewart
84fbccd682
py-numpy: add v1.23.4 (#33260) 2022-10-17 15:23:08 +02:00
iarspider
8dc2d37447
Add checksum for py-sniffio 1.3.0 (#32975) 2022-10-17 05:19:40 -06:00
Harmen Stoppels
9933a9046a
py-tensorflow-hub: zlib, again. (#33359) 2022-10-17 12:39:16 +02:00
Michael Kuhn
f3ebe237e5
mariadb-c-client: add 3.3.2, 3.2.7, 3.1.18, 3.0.10 (#33335) 2022-10-17 09:53:07 +02:00
Wouter Deconinck
7993d10e54
sdl2: add v2.0.22 and v2.24.1 (#33351) 2022-10-17 09:37:34 +02:00
Diego Alvarez
574ab3e40a
nextflow: add v20.10.0 (#33354) 2022-10-17 09:35:45 +02:00
Mosè Giordano
1338dbca56
libblastrampoline: Add versions 5.1.1, 5.2.0 (#33352) 2022-10-17 09:23:51 +02:00
Adam J. Stewart
02fb32bc1e
py-setuptools: add v65.5.0 (#33353) 2022-10-17 09:17:10 +02:00
Adam J. Stewart
25e4d48227
py-sphinx: add v5.3 and v5.2 (#33356) 2022-10-16 22:45:07 +02:00
Hans Fangohr
7547f1c414
octopus: upgrade to 12.1 (#33343) 2022-10-16 18:19:01 +02:00
Miroslav Stoyanov
0c505e459b
tasmanian: disable openmp by default (#33345) 2022-10-16 18:17:44 +02:00
Adam J. Stewart
23fe981c41
py-meson-python: add new versions (#33294) 2022-10-16 18:00:24 +02:00
Harmen Stoppels
f7f11fc881
py-tensorflow: fix zlib (#33349)
* py-tensorflow: fix zlib

* [@spackbot] updating style on behalf of haampie

Co-authored-by: haampie <haampie@users.noreply.github.com>
2022-10-16 05:09:56 -06:00
Adam J. Stewart
496f4193a6
meson: update OneAPI compiler support patch (#33293) 2022-10-16 11:53:54 +02:00
Jonathon Anderson
10491e98a8
CI: allow multiple matches to combine tags (#32290)
Currently "spack ci generate" chooses the first matching entry in
gitlab-ci:mappings to fill attributes for a generated build-job,
requiring that the entire configuration matrix is listed out
explicitly. This unfortunately causes significant problems in
environments with large configuration spaces, for example the
environment in #31598 (spack.yaml) supports 5 operating systems,
3 architectures and 130 packages with explicit size requirements,
resulting in 1300 lines of configuration YAML.

This patch adds a configuraiton option to the gitlab-ci schema called
"match_behavior"; when it is set to "merge", all matching entries
are applied in order to the final build-job, allowing a few entries
to cover an entire matrix of configurations.

The default for "match_behavior" is "first", which behaves as before
this commit (only the runner attributes of the first match are used).

In addition, match entries may now include a "remove-attributes"
configuration, which allows matches to remove tags that have been
aggregated by prior matches. This only makes sense to use with
"match_behavior:merge". You can combine "runner-attributes" with
"remove-attributes" to effectively override prior tags.
2022-10-15 17:29:53 +00:00
iarspider
898c0b45fb
Add checksum for py-seaborn 0.12.0 (#33145)
* Add checksum for py-seaborn 0.12.0

* Update package.py

* Update package.py

* [@spackbot] updating style on behalf of iarspider

* Update package.py

Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-15 10:34:30 -05:00
Michael Kuhn
b2d7782b00
rocksdb: add 7.7.3 (#33341) 2022-10-14 22:34:17 -06:00
Harmen Stoppels
2f6a56a43b
depfile: update docs (#33279) 2022-10-15 06:10:05 +02:00
Michael Kuhn
31cda96181
glib: add 2.74.0 and 2.72.4 (#33332) 2022-10-14 21:27:08 -06:00
WuK
19226ecc49
gptl: new version 8.1.1; use the correct mpi fortran compiler (#33235)
* gptl: new version 8.1.1; use the correct `mpifc`
* add `F90` and `$F77`
2022-10-14 15:54:41 -07:00
Greg Sjaardema
2a166a5cc4
seacas: update to latest release (#33330)
Add checksum for latest tag/release
2022-10-14 15:49:06 -07:00