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2022-07-31black: reformat entire repository with blackTodd Gamblin6756-134773/+150194
2022-07-31black: fix style check package and flake8 formatting for blackTodd Gamblin2-41/+52
Black will automatically fix a lot of the exceptions we previously allowed for directives, so we don't need them in our custom `flake8_formatter` anymore. - [x] remove `E501` (long line) exceptions for directives from `flake8_formatter`, as they won't help us now. - [x] Refine exceptions for long URLs in the `flake8_formatter`. - [x] Adjust the mock `flake8-package` to exhibit the exceptions we still allow. - [x] Update style tests for new `flake8-package`. - [x] Blacken style test.
2022-07-31black: clean up noqa comments from most of the codeTodd Gamblin16-37/+72
Many noqa's in the code are no longer necessary now that the column limit is 99 characters. Others can easily be eliminated, and still more can just be made more specific if they do not have to do with line length. The only E501's still in the code are in the tests for `spack.util.path` and the tests for `spack style`.
2022-07-31black: break up long strings that black cannot fixTodd Gamblin34-48/+272
2022-07-31black: configurationTodd Gamblin1-2/+9
This adds necessary configuration for flake8 and black to work together. This also sets the line length to 99, per the data here: * https://github.com/spack/spack/pull/24718#issuecomment-876933636 Given the data and the spirit of black's 88-character limit, we set the limit to 99 characters for all of Spack, because: * 99 is one less than 100, a nice round number, and all lines will fit in a 100-character wide terminal (even when the text editor puts a \ at EOL). * 99 is just past the knee the file size curve for packages, and it means that packages remain readable and not significantly longer than they are now. * It doesn't seem to hurt core -- files in core might change length by a few percent but seem like they'll be mostly the same as before -- just a bit more roomy. - [x] set line length to 99 - [x] remove most exceptions from `.flake8` and add the ones black cares about - [x] add `[tool.black]` to `pyproject.toml` - [x] make `black` run if available in `spack style --fix` Co-Authored-By: Tom Scogland <tscogland@llnl.gov>
2022-07-29cabana: new version 0.5 (#31807)Sam Reeve1-10/+11
2022-07-29py-segmentation-models-pytorch: add v0.3.0 (#31806)Adam J. Stewart1-2/+7
2022-07-29Add checksum for numba 0.55.2 and 0.56, py-llvmlite 0.39.0 (#31802)iarspider2-2/+7
* Add checksum for numba 0.55.2 and 0.56 * Add checksum for py-llvmlite 0.39.0 * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-07-29OpenGL restructure (#31748)Chuck Atkins19-323/+414
* OpenGL: Restructures the OpenGL packages This provides concrete glx and osmesa packages which delegate to virtual libglx and libosmesa packages provided by mesa. This was necessary because GLX and OSMesa both provide gl implementations but with mesa providing the girtual gl package there was no way to properly distinguish which of the two opengl implementations was beiing requested when querying the spec['gl'] dependency. This additional level of indirection allows for that. * OpenGL: Adjust downstream dependents of OpenGL for the restructure This implements the necessary fixes in the packages that depend on OpenGL to work with the restructuring. This also attempts to create a consistent variant for specifying glx or osmesa.
2022-07-29vdt: add missing python dependency (#31795)Seth R. Johnson1-4/+8
* vdt: add missing python dependency * vdt: fix dependency and add explicit exe path
2022-07-29gaudi: new version 36.6 (#31799)Wouter Deconinck1-2/+3
No build system changes. Changelog at https://gitlab.cern.ch/gaudi/Gaudi/-/tags/v36r6, comparison at https://gitlab.cern.ch/gaudi/Gaudi/-/compare/v36r5...v36r6
2022-07-29iwyu: new version 0.18 (#31798)Seth R. Johnson1-0/+2
2022-07-28Deprecate visit 3.3.0 because it is broken (#31790)Scott Wittenburg1-1/+1
2022-07-28Dyninst: add version 12.2.0 (#31789)Tim Haines1-0/+1
2022-07-28new package: r-signac (#31703)Glenn Johnson2-0/+69
Also includes new package depdendency for r-rcpproll.
2022-07-28New package: trexio (#31769)Evgeny Posenitskiy1-0/+46
* [WIP] first working Spack spec for TREXIO * add patch to prepend -lhdf5_hl to LIBS * Fix spack stype issues * trexio: Fix hashes and hdf5 variant build * trexio: Remove import from Spack * trexio: Fix the isort error * Apply suggestions from code review By @tldahlgren Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-07-28sentieon-genomics: update version to 202112.05 (#31788)snehring1-0/+1
2022-07-28Cabana: add test variants (#31776)Sam Reeve1-20/+16
* Simplify Cabana build flags * Add unit tests, examples, and performance options
2022-07-28py-rsatoolbox: add 0.0.4 (#31785)Manuela Kuhn2-0/+24
2022-07-28New version of Arbor package (#31660)Brent Huisman1-50/+76
2022-07-28gcc: fix unstable patch urls (#31784)Harmen Stoppels5-6/+514
the patch urls dynamically generate a diff, which includes metadata about the git version used, meaning they are not content-addressable. instead ship the patches with spack.
2022-07-28Adding NVIDIA HPC SDK 22.7 (#31770)Filippo Spiga1-0/+4
2022-07-28mpitrampoline: New version 5.0.1 (#31772)Erik Schnetter1-0/+2
2022-07-27Adding Flamemaster product (#31126)AMD Toolchain Support1-0/+281
* Adding Flamemaster product About FlameMaster: Flamemaster is an open source C++ program package for 0D combustion and 1D laminar flame calculations. * Addressed review comments and style tests errors * Addressed style tests errors * Incorporated spack style of coding * Fixed following spack style error [E228] missing whitespace around modulo operator * Update package.py addressing style issues * Update package.py * Changes to maintainers entry
2022-07-27c-blosc2: New version 2.2.0 (#31577)Erik Schnetter1-0/+3
2022-07-27New ExaCA package (#31777)Sam Reeve1-0/+43
2022-07-27Add Caliper v2.8.0 and rocm support (#31632)David Boehme1-18/+23
* Add Caliper v2.8.0 * Add conflict for +rocm+cuda
2022-07-27lcio, podio, edm4hep: Add latest versions (#31749)Thomas Madlener3-0/+4
* lcio: add latest version * edm4hep: Add latest versions * podio: Add latest versions
2022-07-27ZSH: add lmod and local etc variants (#29651)Andrew-Dunning-NNL1-4/+32
* zsh: add lmod and local etc support * zsh: fix indentation
2022-07-27VisIt: Update to VisIt 3.3.0. (#31654)Eric Brugger2-2/+24
2022-07-27WarpX: Add sensei insitu variant (#31542)kwryankrattiger1-5/+13
2022-07-27dd4hep: add v1.21 (#31705)Valentin Volkl1-0/+1
2022-07-27herwig3, thepeg: correct lhapdfsets dependency, specify boost libs (#31744)Valentin Volkl2-13/+3
* herwig3: change lhapdfsets dependency type to build These data sets are needed for a check during build, but due to the difficulty of versioning the datasets it is preferred not to keep the them in the run environment. * herwig3: explicitly state needed boost libs * thepeg: explicitly state needed boost libs * style * stylestyle
2022-07-27py-scipy: -fPIC appending trouble with gcc@10: (#31698)Pitamila1-0/+2
`-fPIC` mandatory option squeezed by error, the NPY_DISTUTILS_APPEND_FLAGS appears handy Co-authored-by: duperrayp <duperrayp@u-un00s16835>
2022-07-27Tau must get GCC path from environment on Cray (#31751)wspear1-0/+6
* Tau must get GCC path from environment on Cray self.compiler doesn't provide the path to the gcc compiler when using cray cc and the spack internal compiler overrides the location in PATH. If possible get the location from the GCC_PATH variable instead. * Fix flake8 issues * Update package.py
2022-07-27Update omnitrace package with v1.3.0 (#31754)Jonathan R. Madsen1-5/+9
2022-07-27py-sphinx: add v5.1.1 (#31756)Adam J. Stewart1-0/+1
2022-07-27tixi: new versions (#31761)Melven Roehrig-Zoellner1-0/+3
2022-07-27valgrind: new version (#31762)Melven Roehrig-Zoellner1-0/+1
2022-07-27itensor: new version, restrict hdf5 to :1.10 (#31764)Melven Roehrig-Zoellner1-1/+2
2022-07-26curl: 7.84.0 (#31725)Harmen Stoppels1-0/+1
2022-07-26cabana: add cajita variant (#31753)eugeneswalker1-0/+5
* cabana: add cajita variant * Update var/spack/repos/builtin/packages/cabana/package.py Co-authored-by: Sam Reeve <6740307+streeve@users.noreply.github.com> * cabana: cannot build +cajita ~mpi Co-authored-by: Sam Reeve <6740307+streeve@users.noreply.github.com>
2022-07-26e4s ci stack: add spec: hdf5-vol-async (#31747)eugeneswalker1-0/+2
* e4s ci stack: add spec: hdf5-vol-async * hdf5-vol-async: add e4s tag
2022-07-26mpich@4.0.2 %oneapi: patch config.rpath (#31740)eugeneswalker2-0/+33
2022-07-26openmpi: +pmi implies schedulers=slurm (#31722)Harmen Stoppels1-2/+2
2022-07-26libjwt: new versions, missing dep, disable examples (#31723)Harmen Stoppels1-0/+6
2022-07-26jansson: new version, disable docs (#31724)Harmen Stoppels1-4/+6
We don't have the build deps for the docs, so disable for now.
2022-07-26json-c: 0.16 (#31726)Harmen Stoppels1-0/+1
2022-07-26munge: 0.5.15 (#31727)Harmen Stoppels1-0/+1
2022-07-26libgcrypt: bump (#31728)Harmen Stoppels1-0/+2