Commit graph

30259 commits

Author SHA1 Message Date
Ben Darwin
9b6b1a277d
minc-toolkit: add MINC_TOOLKIT environment variable at runtime (#32331)
This variable is used by some programs both internal and external to the
toolkit itself to discover shared objects, data, etc.
2022-08-23 11:03:12 -07:00
Toyohisa Kameyama
a08d6e790d
py-scipy: Fortran compiler specify code is change to setup.cfg for Fujitsu compiler (#32142)
* py-numpy: Change Fortran detect order for Fujitsu Compiler.

* create setup.cfg instead of command line.
2022-08-23 10:06:49 -07:00
Jen Herting
00feccde34
New package: py-loguru (#32074)
* [py-loguru] New package

* [py-loguru] Removed commented out line

* [py-loguru] Added types removed extra dependencies

* [py-loguru] missing windows dependency. listing windows as a conflict for now

* [py-loguru] depends on py-colorama when platform=windows

* [py-loguru] flake8

* [py-loguru] Import update

* [py-loguru]

- python is a runtime dependency
- setuptools is a build dependency

* [@spackbot] updating style on behalf of qwertos

Co-authored-by: James A Zilberman <jazrc@rit.edu>
Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-08-23 10:00:25 -07:00
Jen Herting
2c567edc1d
New package: py-python-javabridge (#32075)
* [py-python-javabridge] New package

* [py-python-javabridge] Added dependencies

* [py-python-javabridge] Added types

* [py-python-javabridge] py-setuptools and java are dependencies

* [py-python-javabridge] Import update

* [@spackbot] updating style on behalf of qwertos

Co-authored-by: James A Zilberman <jazrc@rit.edu>
Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-08-23 09:59:09 -07:00
Martin Pokorny
51293f3750
libfabric: new versions (#32083)
* libfabric: add new versions

1.15.0, 1.15.1, main (previously named master)

* Add OPX fabric option, with conflict for versions before v1.15.0

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-23 10:33:49 -06:00
kwryankrattiger
b7024010d3
SDK: Quick fix to allow SDK to build with HIP (#32321) 2022-08-23 07:09:56 -07:00
Simon Pintarelli
44258a7cce
meson: create unique names for build directory (#32062)
Taken from CMakePackage
2022-08-23 13:24:32 +02:00
Seth R. Johnson
0f25d3b219
Add cxxstd flag to googletest and default mock to true (#32171) 2022-08-23 13:05:03 +02:00
Seth R. Johnson
79a462c084
Geant4: update cmake defines and add support for nvhpc (#32185)
* geant4: use define function

* geant4: Change new feature from conflicts to when

* geant4: add support/conflicts for nvhpc

* fixup! geant4: add support/conflicts for nvhpc
2022-08-23 12:57:00 +02:00
Zhilin Zheng
b307d6e766
remove compiler optimize level limit of O2 for GCC (#32303)
gfortran can make it with O3, it might be better to remove this limitation.
2022-08-23 12:13:47 +02:00
Wouter Deconinck
abdecd2a9b
acts: add new dependency on vecmem and autodiff (#26790)
Co-authored-by: Hadrien G. <knights_of_ni@gmx.com>
2022-08-23 11:31:33 +02:00
Tamara Dahlgren
3c3b18d858
spack ci: add support for running stand-alone tests (#27877)
This support requires adding the '--tests' option to 'spack ci rebuild'.
Packages whose stand-alone tests are broken (in the CI environment) can
be configured in gitlab-ci to be skipped by adding them to
broken-tests-packages.

Highlights include:
- Restructured 'spack ci' help to provide better subcommand summaries;
- Ensured only one InstallError (i.e., installer's) rather than allowing
  build_environment to have its own; and
- Refactored CI and CDash reporting to keep CDash-related properties and
  behavior in a separate class.

This allows stand-alone tests from `spack ci` to run when the `--tests`
option is used.  With `--tests`, stand-alone tests are run **after** a
**successful** (re)build of the package.  Test results are collected
and report(able) using CDash.

This PR adds the following features:
- Adds `-t` and `--tests` to `spack ci rebuild` to run stand-alone tests;
- Adds `--fail-fast` to stop stand-alone tests after the first failure;
- Ensures a *single* `InstallError` across packages
    (i.e., removes second class from build environment);
- Captures skipping tests for externals and uninstalled packages
    (for CDash reporting);
- Copies test logs and outputs to the CI artifacts directory to facilitate
    debugging;
- Parses stand-alone test results to report outputs from each `run_test` as
    separate test parts (CDash reporting);
- Logs a test completion message to allow capture of timing of the last
    `run_test` part;
- Adds the runner description to the CDash site to better distinguish entries
    in CDash tables;
- Adds `gitlab-ci` `broken-tests-packages` to CI configuration to skip
    stand-alone testing for packages with known issues;
- Changes `spack ci --help` so description of each subcommand is a single line;
- Changes `spack ci <subcommand> --help` to provide the full description of
    each command (versus no description); and
- Ensures `junit` test log file ends in an `.xml` extension (versus default where
    it does not).

Tasks:

- [x] Include the equivalent of the architecture information, or at least the host target, in the CDash output
- [x] Upload stand-alone test results files as  `test` artifacts
- [x] Confirm tests are run in GitLab
- [x] Ensure CDash results are uploaded as artifacts
- [x] Resolve issues with CDash build-and test results appearing on same row of the table 
- [x] Add unit tests  as needed
- [x] Investigate why some (dependency) packages don't have test results (e.g., related from other pipelines)
- [x] Ensure proper parsing and reporting of skipped tests (as `not run`) .. post- #28701 merge
- [x] Restore the proper CDash URLand or mirror ONCE out-of-band testing completed
2022-08-23 00:52:48 -07:00
Mikael Simberg
8b49790784
Constrain __skip_rocmclang workaround in pika package (#32208) 2022-08-23 01:41:54 -06:00
robgics
abad24265e
ampl: Add new version and add variants for more install control. (#32317) 2022-08-23 09:40:53 +02:00
Daryl W. Grunau
4095666013
eospac: support intel-classic@2021 (#32323)
Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2022-08-23 09:14:22 +02:00
Ryan Marcellino
877393e019
py-jupytext: add v1.14.1 (#32313) 2022-08-23 09:12:54 +02:00
kwryankrattiger
0d29bc00ec
Kokkos: ROCm and CUDA are not compatible in Kokkos (#32181) 2022-08-23 08:24:56 +02:00
Ryan Marcellino
b203418720
New package: py-mergedeep (#32322) 2022-08-23 00:45:30 -05:00
Ryan Marcellino
3e3e387a45
New package: py-pymdown-extensions (#32324) 2022-08-23 00:44:39 -05:00
Vanessasaurus
04339fbe9a
Automated deployment to update package flux-core 2022-08-23 (#32320)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2022-08-22 20:33:42 -06:00
Dom Heinzeller
560b6432cc
Update ESMF from JCSDA/NOAA-EMC spack fork (esmf@8.3.0 with external parallelio) (#32222)
* Update ESMF package from JCSDA/NOAA-EMC spack fork

* Update var/spack/repos/builtin/packages/esmf/package.py

Fix url_for_version

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

* [@spackbot] updating style on behalf of climbfuji

Co-authored-by: Jim Edwards <jedwards@ucar.edu>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: climbfuji <climbfuji@users.noreply.github.com>
2022-08-22 17:36:07 -07:00
Cody Balos
bea8936e02
sundials: add v6.3.0 and logging-mpi variant (#32315) 2022-08-22 15:37:59 -06:00
Ryan Marcellino
95e8c4a615
New package: py-ghp-import (#32316) 2022-08-22 14:29:16 -07:00
Wouter Deconinck
c92db8a22a
gaudi: consistent test dependencies when +examples (#32134)
* gaudi: consistent test dependencies when +examples

Gaudi requires testing to be enabled for examples to be built, so all
test dependencies are also there for `+examples`. This PR fixes a
missing pytest dependency when `+examples` is used but no testing is
enabled. The construct with the loop is to ensure the identical
dependencies are always used, even as version ranges my start to differ.

Testing with gaudi_add_tests was added in v35r0. Some nosetests and
QMtests were in the tree before, but not accessible it seems. The
effective dependency since 35.0 is also applied for pytest, extending
the range that was there before disentangling `optional`, at
9d67d1e034/var/spack/repos/builtin/packages/gaudi/package.py

* gaudi: version 36.7 in other PR...
2022-08-22 14:24:36 -07:00
Valentin Volkl
afecd70bc8
dd4hep: add version 1.22 (#32209) 2022-08-22 15:21:50 -06:00
Adam J. Stewart
9296a76658
py-shapely: add v1.8.3 (#32218) 2022-08-22 14:09:38 -07:00
Ryan Marcellino
e6e569e07c
New package: py-py-f90nml (#32314) 2022-08-22 19:03:42 +00:00
Eric Brugger
ca9b2fe6ad
VisIt: Add patch to include jpeg library in install. (#32245) 2022-08-22 11:59:07 -07:00
Mark Abraham
70f0a725cc
hwloc: fix build with +onepai-level-zero (#31622)
Flags to configure were erroneously managed to configure twice. 

Removed the one that was wrong so that a configure warning is no longer issued.
2022-08-22 12:45:58 -06:00
Barry Rountree
fd80e34037
teckit: Fixes missing xmlparse.h issue. (#32295)
The "release" tarball provided by github lacks several files in
the SFconv/expat/xmlparse directory, including xmlparse.  Using
tarballs based off of version tags solves the problem.

o Changes version() to use commits associated with version tags.
o Adds several additional versions.
o Adds myself as maintainer.
o Adds hook to execute autogen.sh.
o Adds autotools &ct dependences.
o Removes expat dependence.
2022-08-22 18:39:28 +00:00
Paul Romano
7fc78b8b0f
OpenMC: add v0.13.1 (#32263)
* openmc: add v0.13.1

* Add @paulromano as maintainer of openmc and py-openmc

* Address review comments from @adamjstewart

* Add back MPI variant in openmc package
2022-08-22 18:09:37 +00:00
Adam J. Stewart
1039caabed
crunch: add new package (#31980) 2022-08-22 18:05:06 +00:00
Ryan Mast
5edb0fe96a
helics: update v3 options and add missing versions (#32121)
* helics: update v3 options and add missing versions

* helics: allow using openssl 3.x for encryption support

* helics: fix style errors

* helics: Apply suggestion from code review

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

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-22 17:49:57 +00:00
iarspider
2860f2f70a
Add checksum for py-requests 2.27.1, 2.28.0, 2.28.1 (#31896)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-08-22 11:46:01 -06:00
Jean-Paul Pelteret
85b8a41ccb
deal.II 9.4: Fix issues due to override of CMake FIND_PACKAGE macro (#32079) 2022-08-22 11:37:52 -06:00
Harmen Stoppels
6e5d6ebf99
openmpi: fix patches for %nvhpc (#32308) 2022-08-22 10:57:51 -06:00
Adam J. Stewart
177e2e2672
xgboost: GCC 8+ required (#32282) 2022-08-22 08:48:18 -07:00
Arjun Guha
72b133a875
racket: fix spec (#32304) 2022-08-22 14:50:11 +00:00
Adam J. Stewart
dc0836804f
py-rasterio: add v1.3.2 (#32277) 2022-08-22 16:15:33 +02:00
kwryankrattiger
a38beeaed2
HPX: ROCm and Cuda conflict needed (#32178)
Discovered this missing conflict when building the e4s enviroment with
unify:when_possible. #31940
2022-08-22 16:13:59 +02:00
Kelly (KT) Thompson
1c61f0420a
Provide patches provided by consumers of draco. (#32281) 2022-08-22 16:04:58 +02:00
Robert Cohn
00b244853e
enable packages that use numpy for oneapi e4s stack (#32293)
* enable geopm oneapi

* enable packages that depend on py-numpy

* disable nan warnings

* undo geopm enable

* undo geopm, it has multiple compile issues
2022-08-22 07:02:22 -07:00
Kendra Long!
1a030aa417
draco: add v7_14_0 (#32267) 2022-08-22 16:02:11 +02:00
Eric Brugger
c28f1c0b42
VisIt: add conduit and mfem variants (#32255) 2022-08-22 15:59:29 +02:00
Olivier Cessenat
a20c9b2d8e
keepassxc: option autotype with pcsclite (#32288) 2022-08-22 15:50:41 +02:00
Jonas Thies
88a58abcf8
openfoam-org: add v9 and v10 (#32274) 2022-08-22 15:33:40 +02:00
Rémi Lacroix
e16f0b9f12
Molden: update URLs. (#32207) 2022-08-22 14:48:44 +02:00
Valentin Volkl
4d0612abfc
baurmc: correct compile flag (#31305) 2022-08-22 14:28:20 +02:00
Valentin Volkl
408076adf0
prophecy4f: add hep tag, install to share (#31308) 2022-08-22 14:27:54 +02:00
Cory Bloor
dde6d00ab9
hip@4.5.2: fix installation (#31416)
In a fast-moving project with as many forks as LLVM, it's difficult to
accurately determine if a function exists just by checking the version
number. The existing version check fails, for example, with llvm-amdgpu
from ROCm 4.5. It is more robust to directly check if the function
exists.
2022-08-22 12:39:09 +02:00