Commit graph

31615 commits

Author SHA1 Message Date
Andrew Wood
344e8d142a
Restrict a patch of rhash to versions >=1.3.6 (#34310) 2022-12-22 08:02:15 -07:00
Harmen Stoppels
161fbfadf4
Fix combine_phase_logs text encoding issues (#34657)
Avoid text decoding and encoding when combining log files, instead
combine in binary mode.

Also do a buffered copy which is sometimes faster for large log files.
2022-12-22 15:32:48 +01:00
Wladimir Arturo Garces Carrillo
3304312b26
neve: add new package (#34596)
Co-authored-by: WladIMirG <WladIMirG@users.noreply.github.com>
2022-12-22 07:27:07 -07:00
Alec Scott
3279ee7068
Add --fresh to docs to actually upgrade spack environments (#34433) 2022-12-22 11:19:24 +00:00
Todd Gamblin
8f3f838763
docs: show module documentation before submodules (#34258)
Currently, the Spack docs show documentation for submodules *before* documentation for
submodules on package doc pages. This means that if you put docs in `__init__.py` in
some package, the docs in there will be shown *after* the docs for all submodules of the
package instead of at the top as an intro to the package. See, e.g.,
[the lockfile docs](https://spack.readthedocs.io/en/latest/spack.environment.html#module-spack.environment),
which should be at the
[top of that page](https://spack.readthedocs.io/en/latest/spack.environment.html).

- [x] add the `--module-first` option to sphinx so that it generates module docs at top of page.
2022-12-22 11:50:48 +01:00
Todd Gamblin
09864d00c5
docs: remove monitors and analyzers (#34358)
These experimental features were removed in #31130, but the docs were not.

- [x] remove the `spack monitor` and `spack analyze` docs
2022-12-22 11:47:13 +01:00
Benjamin S. Kirk
0f7fa27327
librsvg: add 2.40.21, which does not require rust (#34585)
* librsvg: add 2.40.21, which does not require rust and has some security backports

https://download.gnome.org/sources/librsvg/2.40/librsvg-2.40.21.news

* librsvg: prevent finding broken gtkdoc binaries when ~doc is selected.

On my CentOS7 hosts, ./configure finds e.g. /bin/gtkdoc-rebase even when
~doc is selected.  These tools use Python2, and fail with an error:
"ImportError: No module named site"

So prevent ./configure from finding these broken tools when not building
the +doc variant.
2022-12-22 11:28:30 +01:00
Rocco Meli
a27139c081
openbabel: add 3.1.0 and 3.1.1 (#34631) 2022-12-22 03:17:50 -07:00
Vasileios Karakasis
4d4338db16
reframe: rework recipe, add v4.0.0-dev4 (#34584) 2022-12-22 09:53:42 +01:00
Annop Wongwathanarat
6d64ffdd1a
quantum-espresso: enable linking with armpl-gcc and acfl for BLAS and FFT (#34416) 2022-12-22 09:50:51 +01:00
Harmen Stoppels
e9ea9e2316
index.json.hash, no fatal error if key cannot be fetched (#34643) 2022-12-22 09:48:05 +01:00
Benjamin Fovet
2a5509ea90
kokkos: add v3.7.01 (#34645)
Co-authored-by: Benjamin Fovet <benjamin.fovet@cea.fr>
2022-12-22 09:45:13 +01:00
Adam J. Stewart
b9d027f0cc
py-pytorch-lightning: add v1.8.6 (#34647) 2022-12-22 09:43:57 +01:00
Christopher Christofi
6d54dc2a44
perl-config-simple: add 4.58 (#34649) 2022-12-22 09:43:41 +01:00
renjithravindrankannath
6cd9cbf578
Using corresponding commit ids of hiprand for each releases (#34545) 2022-12-22 09:36:14 +01:00
Alex Richert
72e81796d1
bacio: patch for v2.4.1 (#34575) 2022-12-22 09:12:29 +01:00
Andre Merzky
f116e6762a
add py-psij-python and py-pystache packages (#34357)
* add psij package and deps

* update hashes, URLs

* linting

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

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

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

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

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

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

* Update package.py

apply suggested change

* Update package.py

apply suggested change

* Update package.py

ensure maintainer inheritance

* add psij to exaworks meta-package

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-12-21 20:07:35 -07:00
Howard Pritchard
c74bbc6723
paraview: patch catalyst etc. to build with oneapi (#33562)
without this patch, build of paraview has a meltdown when reaching 3rd party catalyst and other packages
with these types of errors:

   335    /tmp/foo/spack-stage/spack-stage-paraview-5.10.1-gscoqxhhakjyyfirdefuhmi2bzw4scho/spack-src/VTK/ThirdParty/fmt/vtkfmt/vtkfmt/format.h:1732:11: error: cannot capture a bi
            t-field by reference
   336          if (sign) *it++ = static_cast<Char>(data::signs[sign]);
   337              ^

Signed-off-by: Howard Pritchard <howardp@lanl.gov>

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2022-12-21 17:07:24 -07:00
Harmen Stoppels
492a603d5e
json: remove python 2 only code (#34615) 2022-12-21 14:18:12 -07:00
Adam J. Stewart
dab68687bd
py-cartopy: older versions don't support Python 3.10 (#34626) 2022-12-21 21:23:22 +01:00
Thomas Madlener
1a32cea114
podio: add v0.16.2 (#34606) 2022-12-21 12:52:47 -07:00
Hector Martinez-Seara
aaec76652b
relion: add v4.0.0 (#34600) 2022-12-21 20:41:13 +01:00
Michael Kuhn
f748911ea0
glib: add 2.74.3 (#34603) 2022-12-21 20:40:04 +01:00
Cory Bloor
e60e74694f
rocm: make amdgpu_target sticky (#34591)
The sticky property will prevent clingo from changing the amdgpu_target
to work around conflicts. This is the same behaviour as was adopted for
cuda_arch in 055c9d125d.
2022-12-21 20:21:20 +01:00
Sergey Kosukhin
2ef026b8c6
eckit: skip broken test (#34610) 2022-12-21 20:20:05 +01:00
Mark W. Krentel
a6c2569b18
hpctoolkit: replace filter_file with upstream patch (#34604)
Replace the filter_file for older configure with rocm 5.3 with an
upstream patch.  Further, the patch is no longer needed for develop or
later releases.
2022-12-21 20:18:58 +01:00
shanedsnyder
5483b5ff99
dashan-runtime,darshan-util,py-darshan: update package versions for darshan-3.4.2 (#34583) 2022-12-21 20:18:27 +01:00
louisespellacy-arm
2b78a7099d
arm-forge: add 22.1.2 (#34569) 2022-12-21 20:09:42 +01:00
lpoirel
34cdc6f52b
starpu: add conflict for ~blocking +simgrid (#34616)
see 1f5a911d43
2022-12-21 20:09:23 +01:00
Adam J. Stewart
3aafdb06c9
py-pyproj: add new versions (#34633) 2022-12-21 20:00:53 +01:00
Harmen Stoppels
4a22c1c699
urlopen: handle timeout in opener (#34639) 2022-12-21 19:40:26 +01:00
Andrey Perestoronin
f021479ef0
feat: 🎸 Add new 2023.0.0 oneVPL package (#34642) 2022-12-21 11:07:41 -07:00
Manuela Kuhn
3f374fb62f
py-vcrpy: add 4.2.1 (#34636) 2022-12-21 11:02:55 -07:00
Niclas Jansson
949be42f32
neko: add v0.5.0 (#34640) 2022-12-21 11:02:37 -07:00
Rob Falgout
e5abd5abc1
hypre: add v2.27.0 (#34625) 2022-12-21 11:02:23 -07:00
Harmen Stoppels
4473d5d811
etags for index.json invalidation, test coverage (#34641)
Implement an alternative strategy to do index.json invalidation.

The current approach of pairs of index.json / index.json.hash is
problematic because it leads to races.

The standard solution for cache invalidation is etags, which are
supported by both http and s3 protocols, which allows one to do
conditional fetches.

This PR implements that for the http/https schemes. It should also work
for s3 schemes, but that requires other prs to be merged.

Also it improves unit tests for index.json fetches.
2022-12-21 18:41:59 +01:00
Mikael Simberg
c3e61664cf
Add patch for pika on macOS (#34619) 2022-12-21 13:41:49 +01:00
Manuela Kuhn
c3217775c3
py-scikit-image: add 0.19.3 (#34618)
* py-scikit-image: add 0.19.3

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-20 12:59:48 -06:00
kwryankrattiger
58a7e11db9
DAV: VTK-m needs to install examples for smoke test (#34611)
SDK deployment targets being able to validate and run VTK-m via spack
deployments, so examples should be installed.
2022-12-20 09:56:50 -08:00
Andrey Perestoronin
ac570bb5c4
2023.0.0 oneAPI release promotion (#34617) 2022-12-20 08:47:08 -07:00
Massimiliano Culpo
b2c806f6fc
archspec: add support for zen4 (#34609)
Also add:
- Upper bound for Xeon Phi compiler support
- Better detection for a64fx
2022-12-20 11:22:50 +01:00
Nicholas Knoblauch
bd613b3124
Remove dep on jupyter meta-package (#34573) 2022-12-19 17:22:34 -06:00
Manuela Kuhn
f1b85bc653
py-nipype: add 1.8.5 and py-looseversion: add new package (#34608) 2022-12-19 13:25:22 -06:00
Hector Martinez-Seara
e1fab4dd51
Gromacs: added version 2022.4 (#34599) 2022-12-19 15:30:20 +01:00
Anton Kozhevnikov
a924079f66
[ELPA] add sha256 for elpa-2022.11.001.rc2.tar.gz (#33439) 2022-12-19 04:12:02 -07:00
Adam J. Stewart
c5aff1d412
py-horovod: patch no longer applies (#34593) 2022-12-19 11:49:02 +01:00
Adam J. Stewart
6c9602ee64
aws-sdk-cpp: add v1.10.32 (#34592) 2022-12-19 11:48:31 +01:00
Adam J. Stewart
64327bfef0
py-pyvista: add v0.37.0 (#34590) 2022-12-19 11:48:01 +01:00
Adam J. Stewart
05c3cb7cc9
netcdf-cxx: add patch to fix macOS build (#34588) 2022-12-19 11:46:33 +01:00
Adam J. Stewart
c87b251639
XNNPACK: fix build on macOS, update deps (#34555) 2022-12-19 11:44:56 +01:00