Commit graph

32099 commits

Author SHA1 Message Date
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
Adam J. Stewart
f2332a17d3
Node.js: new versions, newer Python support, macOS fixes (#34478) 2022-12-19 11:40:31 +01:00
Adam J. Stewart
c7f24a132e
py-numpy: add v1.24.0 (#34602) 2022-12-18 17:17:06 -07:00
Alec Scott
96a7af1dd2
Add py-docstring-to-markdown v0.11 (#34595) 2022-12-18 14:59:47 -06:00
eugeneswalker
db1caa9e92
intel-oneapi-dpl: add v2022.0.0 (#34601) 2022-12-18 13:44:23 -05:00
iarspider
237d26460d
LLVM: replace libelf dependency with elf (#34265)
* LLVM: replace libelf dependency with elf

I didn't test this extensively, but in CMS LLVM builds just fine with elfutils.

* [@spackbot] updating style on behalf of iarspider

Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-12-17 14:44:27 -08:00
Harmen Stoppels
1020b65297
fix != -> == typo (#34568) 2022-12-17 20:15:15 +01:00
Adam J. Stewart
dceb4c9d65
Update PyTorch ecosystem (#34582) 2022-12-17 11:51:59 -07:00
Alex Richert
50570ea334
Add static-only option for ESMF (#34576) 2022-12-17 04:27:22 -07:00
eugeneswalker
7e836b925d
e4s: disable mac stack due to binary relocation issue#32571 (#34560) 2022-12-17 10:53:15 +00:00
Benjamin S. Kirk
cec3da61d2
Add gimp & dependent packages (#34558)
* exiv2: add new versions

* babl: new package required to build GIMP

* gegl: new package required to build GIMP

* gexiv2: new package required to build GIMP

* libmypaint: new package required to build GIMP

* mypaint-brushes: new package required to build GIMP

* vala: new package required to build GIMP

* GIMP: new package definition for building GIMP-2.10 from source

* libjxl: update for 0.7.0

* libwmf: a library for reading vector images in Windows Metafile Format (WMF)

* libde265: an open source implementation of the h.265 video codec

* libwebp: add new versions

* GIMP: additional variants for building GIMP-2.10 from source

* libde265: remove boilerplate

* fixes for style precheck

* updates based on feedback

* fixes for style precheck
2022-12-17 03:52:56 -07:00
Mikhail Titov
7ed53cf083
Update package versions: RADICAL-Cybertools (RE, RG, RP, RS, RU) (#34572)
* rct: update packages (RE, RG, RP, RS, RU) with new versions

* re: fixed radical-pilot requirement for radical-entk
2022-12-16 22:24:00 -07:00
eugeneswalker
bdc3ab5b54
intel-oneapi-compilers: add v2023.0.0 (#34571) 2022-12-16 21:38:51 -07:00
Jack Morrison
5a985e33ea
Add --enable-orterun-prefix-by-default configure option for OpenMPI (#34469) 2022-12-16 17:59:24 -07:00
Bernhard Kaindl
9817593c1c
Automake requires Thread::Queue, but it is only provided with in perl+threads. (#34076)
Update the depends_on("perl") to depends_on("perl+threads").

This and #34074 is needed to properly handle e.g. the perl-Thread-Queue
rpm package:

It may not be installed on RedHat-based hosts, which can lead to automake
build failures when `spack external find perl` or `spack external find --all`
was used to use the system-provided perl install.
2022-12-16 16:11:11 -08:00
Rémi Lacroix
1cc78dac38
octopus: Ensure MPI is used consistently (#33969)
Some variants have MPI dependencies, make sure they can be used only when the `mpi` variable is enabled.
2022-12-16 15:17:37 -08:00
Marco De La Pierre
e2c5fe4aa3
adding 2nd bunch of nf-core deps from update/nextflow-tools (#34562)
* adding 2nd bunch of nf-core deps from update/nextflow-tools

* Update var/spack/repos/builtin/packages/py-a2wsgi/package.py

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-16 15:18:49 -07:00