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2022-08-23Relative paths in default prefix_inspections start with ./ (#31867)Harmen Stoppels2-11/+12
2022-08-23`spack -e x config --scope=y add z` add to scope (#31746)Harmen Stoppels2-1/+9
* `spack -e x config --scope=y add z` add to scope instead of to the environment file.
2022-08-23cpu-features: fix fetch failure (#32325)iarspider1-1/+2
* cpu-features: fix fetch failure `master` branch was renamed to `main` * Update var/spack/repos/builtin/packages/cpu-features/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-08-23intel-oneapi-compilers-classic: fix paths (#32305)Robert Cohn1-1/+7
* Fix intel-oneapi-compilers-classic bin path * Update package.py * intel-oneapi-compilers-classic fix path Co-authored-by: OfirGan <offirgan@gmail.com>
2022-08-23minc-toolkit: add MINC_TOOLKIT environment variable at runtime (#32331)Ben Darwin1-0/+3
This variable is used by some programs both internal and external to the toolkit itself to discover shared objects, data, etc.
2022-08-23py-scipy: Fortran compiler specify code is change to setup.cfg for Fujitsu ↵Toyohisa Kameyama1-6/+7
compiler (#32142) * py-numpy: Change Fortran detect order for Fujitsu Compiler. * create setup.cfg instead of command line.
2022-08-23New package: py-loguru (#32074)Jen Herting1-0/+25
* [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>
2022-08-23New package: py-python-javabridge (#32075)Jen Herting1-0/+21
* [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>
2022-08-23libfabric: new versions (#32083)Martin Pokorny1-1/+5
* 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>
2022-08-23SDK: Quick fix to allow SDK to build with HIP (#32321)kwryankrattiger1-1/+5
2022-08-23meson: create unique names for build directory (#32062)Simon Pintarelli1-1/+9
Taken from CMakePackage
2022-08-23Add cxxstd flag to googletest and default mock to true (#32171)Seth R. Johnson2-17/+23
2022-08-23Geant4: update cmake defines and add support for nvhpc (#32185)Seth R. Johnson1-17/+27
* 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
2022-08-23remove compiler optimize level limit of O2 for GCC (#32303)Zhilin Zheng1-5/+0
gfortran can make it with O3, it might be better to remove this limitation.
2022-08-23acts: add new dependency on vecmem and autodiff (#26790)Wouter Deconinck1-3/+9
Co-authored-by: Hadrien G. <knights_of_ni@gmx.com>
2022-08-23spack ci: add support for running stand-alone tests (#27877)Tamara Dahlgren26-448/+1722
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
2022-08-23Constrain `__skip_rocmclang` workaround in pika package (#32208)Mikael Simberg1-1/+1
2022-08-23ampl: Add new version and add variants for more install control. (#32317)robgics1-6/+37
2022-08-23eospac: support intel-classic@2021 (#32323)Daryl W. Grunau5-0/+76
Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2022-08-23py-jupytext: add v1.14.1 (#32313)Ryan Marcellino1-1/+3
2022-08-23Kokkos: ROCm and CUDA are not compatible in Kokkos (#32181)kwryankrattiger1-0/+1
2022-08-23New package: py-mergedeep (#32322)Ryan Marcellino1-0/+19
2022-08-23New package: py-pymdown-extensions (#32324)Ryan Marcellino1-0/+20
2022-08-22Automated deployment to update package flux-core 2022-08-23 (#32320)Vanessasaurus1-1/+2
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2022-08-22Update ESMF from JCSDA/NOAA-EMC spack fork (esmf@8.3.0 with external ↵Dom Heinzeller1-33/+74
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>
2022-08-22sundials: add v6.3.0 and logging-mpi variant (#32315)Cody Balos1-0/+10
2022-08-22New package: py-ghp-import (#32316)Ryan Marcellino1-0/+19
2022-08-22gaudi: consistent test dependencies when +examples (#32134)Wouter Deconinck1-1/+11
* 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 https://github.com/spack/spack/blob/9d67d1e0346203a20b7ba44940061da855d405ca/var/spack/repos/builtin/packages/gaudi/package.py * gaudi: version 36.7 in other PR...
2022-08-22dd4hep: add version 1.22 (#32209)Valentin Volkl1-0/+1
2022-08-22py-shapely: add v1.8.3 (#32218)Adam J. Stewart1-7/+9
2022-08-22New package: py-py-f90nml (#32314)Ryan Marcellino1-0/+20
2022-08-22VisIt: Add patch to include jpeg library in install. (#32245)Eric Brugger3-0/+87
2022-08-22hwloc: fix build with +onepai-level-zero (#31622)Mark Abraham1-2/+1
Flags to configure were erroneously managed to configure twice. Removed the one that was wrong so that a configure warning is no longer issued.
2022-08-22teckit: Fixes missing xmlparse.h issue. (#32295)Barry Rountree1-3/+17
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.
2022-08-22OpenMC: add v0.13.1 (#32263)Paul Romano2-14/+14
* 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
2022-08-22crunch: add new package (#31980)Adam J. Stewart2-3/+26
2022-08-22helics: update v3 options and add missing versions (#32121)Ryan Mast1-11/+46
* 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>
2022-08-22Add checksum for py-requests 2.27.1, 2.28.0, 2.28.1 (#31896)iarspider1-1/+5
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-08-22deal.II 9.4: Fix issues due to override of CMake FIND_PACKAGE macro (#32079)Jean-Paul Pelteret1-0/+13
2022-08-22openmpi: fix patches for %nvhpc (#32308)Harmen Stoppels3-155/+0
2022-08-22xgboost: GCC 8+ required (#32282)Adam J. Stewart1-0/+2
2022-08-22racket: fix spec (#32304)Arjun Guha1-0/+2
2022-08-22py-rasterio: add v1.3.2 (#32277)Adam J. Stewart1-0/+1
2022-08-22HPX: ROCm and Cuda conflict needed (#32178)kwryankrattiger1-0/+3
Discovered this missing conflict when building the e4s enviroment with unify:when_possible. #31940
2022-08-22Provide patches provided by consumers of draco. (#32281)Kelly (KT) Thompson5-0/+183
2022-08-22enable packages that use numpy for oneapi e4s stack (#32293)Robert Cohn1-3/+3
* enable geopm oneapi * enable packages that depend on py-numpy * disable nan warnings * undo geopm enable * undo geopm, it has multiple compile issues
2022-08-22draco: add v7_14_0 (#32267)Kendra Long!1-0/+1
2022-08-22VisIt: add conduit and mfem variants (#32255)Eric Brugger1-0/+30
2022-08-22keepassxc: option autotype with pcsclite (#32288)Olivier Cessenat1-0/+4
2022-08-22openfoam-org: add v9 and v10 (#32274)Jonas Thies1-0/+10