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2022-08-03QTLTools: add new package (#31881)dunatotatos1-0/+30
2022-08-03libspng: add new package (#31878)Jen Herting1-0/+17
Co-authored-by: James A Zilberman <jazrc@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-08-03Make parmmg dependent on mmg and metis (#31838)Yang Zongze3-0/+17
1. copy source of mmg to its install tree for parmmg's build 2. add cmake args for parmmg 3. add '+mmg' when '+parmmg' for petsc
2022-08-03py-pytorch-lightning: add v1.7.0 (#31871)Adam J. Stewart1-1/+5
2022-08-03mpich: fix hwloc config option for version >= 4.0 (#31874)Ken Raffenetti1-4/+13
In MPICH 4.0, the config option for external hwloc changed from --with-hwloc-prefix to --with-hwloc
2022-08-02black: fix bootstrap for Python 3.6 (#31872)Chris Green1-0/+11
* py-platformdirs: sanitize UTF-8 setup.cfg on Python 3.6 * py-platformdirs: black compliance * Minimal fix per @adamjstewart
2022-08-02libedit: Make sure libedit linkes to the correct terminfo lib from spack ↵Chuck Atkins1-0/+10
(#31870)
2022-08-02ca-certificates-mozilla: add v2022-07-19 and v2022-04-26(#31863)Harmen Stoppels1-0/+10
2022-08-02butterflypack %oneapi: patch CMakeLists to solve issue #31818 (#31848)eugeneswalker2-0/+15
* butterflypack %oneapi: patch CMakeLists to solve issue #31818 * uncomment builds affected by failing butterflypack Co-authored-by: e <e>
2022-08-02new package: py-alphafold (#27849)Andrew W Elble14-2/+380
* new package: alphafold and related dependencies, depends on #27138 * [@spackbot] updating style on behalf of aweits * fix Co-authored-by: aweits <aweits@users.noreply.github.com>
2022-08-02Allow building with camp@0.2.3 for raja@0.14.0 and umpire@6.0.0 (#31853)Peter Scheibel2-2/+2
2022-08-02py-pre-commit 2.20.0Harmen Stoppels1-0/+2
2022-08-02gdb: add v12.1 (#31765)Melven Roehrig-Zoellner1-0/+1
2022-08-02Add mctc-lib v0.3.1 and toml-f v0.3.0 (#31847)Sebastian Ehlert2-0/+2
2022-08-02Add meson Python build backend (#31809)Adam J. Stewart3-0/+66
2022-08-02py-flake8: add v5.0 (#31854)Adam J. Stewart4-45/+62
2022-08-01kokkos: set CMAKE_CXX_STANDARD instead of Kokkos_CXX_STANDARD (#31841)eugeneswalker1-1/+1
* kokkos@develop: set CMAKE_CXX_STANDARD instead of Kokkos_CXX_STANDARD * use CMAKE_CXX_STANDARD regardless of kokkos version
2022-08-01lerc: add libs property (#31684)Adam J. Stewart1-0/+4
2022-08-01mxnet: prefer stable release (#31821)Adam J. Stewart1-1/+5
2022-08-01amrex: add v22.08 (#31844)Weiqun Zhang1-1/+2
2022-08-01arm-forge: add v22.0.4. (#31835)RichardABunt1-0/+9
2022-08-01python: fix clingo bootstrapping on Apple M1/M2 (#31792)Adam J. Stewart2-7/+10
2022-08-01celeritas: new package (#31834)Seth R. Johnson2-0/+91
ROOT also needs updating for downstream macOS packages
2022-08-01py-breathe: fix version constraints to avoid concretizing old breathe (#31828)Seth R. Johnson1-1/+2
2022-08-01gperftools: make the "libunwind" variant conditional (#31673)Erik Schnetter1-1/+3
libunwind is supported on Linux only
2022-07-31wi4mpi: New version 3.6.0 (#31681)Erik Schnetter1-0/+1
* wi4mpi: New version 3.6.0
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