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2024-06-03hugo: add v0.126.3 (#44530)Owen Solberg1-0/+1
Co-authored-by: Owen Solberg <owen.solberg@sana.com>
2024-06-03seqfu: new package (#44445)Diego Alvarez S2-0/+45
* Add seqfu --------- Co-authored-by: dialvarezs <dialvarezs@users.noreply.github.com>
2024-06-03hip@6.1: fix reference to hsa-rocr-dev so it works when externally defined ↵eugeneswalker1-1/+1
(#44528)
2024-06-03Consolidate concretization output for environments (#44489)Todd Gamblin6-87/+161
When Spack concretizes environments, it prints every (newly concretized) root spec individually with all of its dependencies. For most reasonably sized environments, this is too much output. This is true for three commands: * `spack concretize` when concretizing an environment with newly added specs * `spack install` when installing an environment with newly added specs * `spack spec` with no arguments in an environment The output dates back to before we had unified environments or nicer spec traversal routines, and we can improve it. This PR makes environment concretization output analogous to what we do for regular specs. Just like `spack spec` for a single spec, we show all root specs with no indentation, so you can easily see the specs you explicitly requested. Dependencies are shown: 1. With indentation according to their depth in a breadth-first traversal starting at the roots; 2. Only once if they appear on paths from multiple roots So, the default is now consistent with `spack spec` for one spec--it's `--cover=nodes`. i.e., if there are 100 specs in your environment, you'll get 100 lines of output. If you want to see more details, you can do that with `spack spec` using the arguments you're already familiar with. For example, if you wanted to see dependency types and *all* dependencies, you could use `spack spec -l --cover=edges`. Or you could add deptypes and namespaces with, e.g. `spack spec -ltN`. With no arguments in an environment, `spack spec` concretizes (if necessary) and shows the concretized environment. If you run `spack concretize` *first*, inspecting the environment repeatedly with `spack spec` will be fast, as everything is already in the `spack.lock` file. - [x] factor most logic of `Spec.tree()` out of `Spec` class into `spack.spec.tree()`, which can take multiple specs as roots. - [x] make `Spec.tree()` call `spack.spec.tree()` - [x] `spack.environment.display_specs()` now uses `spack.spec.tree()` - [x] Update `spack concretize` - [x] Update `spack install` - [x] Update `spack spec` to call `spack.spec.tree()` for environments. - [x] Continue to output specs individually for `spack spec` when using `--yaml` or `--json`
2024-06-03nb: new package (#44456)James Taliaferro1-0/+45
* new package: nb * only one filter_file, install completions * completions now implicit, merged by the view
2024-06-03rdkit (#44476)Rocco Meli1-0/+1
2024-06-03pflogger: add version 1.15.0 (#44467)Matt Thompson1-0/+1
2024-06-03Slate version 2024 05 31 (#44529)G-Ragghianti3-0/+11
* updating version for slate, blaspp, and lapackpp * verified new hashes
2024-06-03`seacas`: protect against known mixed-toolchain problem (#44378)Chris Marsh1-0/+11
* Protected against a known problem with mixed gcc/apple-clang toolchains. Fixes #44330 --------- Co-authored-by: Chrismarsh <Chrismarsh@users.noreply.github.com>
2024-06-03Apply patch to allow vtk to compile with %gcc 13 and 14. (#44332)Chris Marsh1-0/+8
* Apply patch from upstream to allow vtk compilation with %gcc 12 and 14. * Fixes #44331 * fix soec usage * fix compiler version range * Finalize version range, switch to .diff file --------- Co-authored-by: Chrismarsh <Chrismarsh@users.noreply.github.com>
2024-06-02upcxx: update to latest gasnet and fix some bitrot (#44488)Dan Bonachea2-8/+42
* Now need to explicitly depend on libfabric for Cray EX * Ensure build uses the selected CUDA and ROCm versions * Correct spelling on `configure --with-ldflags` * Patch a defect regarding `configure --with-ldflags` * Default to Spack's copy of GASNet-EX, which is newer than embedded
2024-06-01gasnet: add v2024.5.0 (#44478)Dan Bonachea1-7/+17
* Add GASNet v 2024.5.0 * cosmetic fix to info output * Add a missing dependency * Ensure GASNet detects the provided ROCm/CUDA dependency * [@spackbot] updating style on behalf of bonachea --------- Co-authored-by: bonachea <bonachea@users.noreply.github.com>
2024-06-01py-fortls: add v3.1.0 (#44477)Rocco Meli1-1/+4
* Spglib: add version 2.4.0 * DLA-Future: fix +test option * update * [@spackbot] updating style on behalf of RMeli * Apply suggestions from code review Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> --------- Co-authored-by: RMeli <RMeli@users.noreply.github.com> Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2024-06-01gmsh: add v4.11.1, master (#41320)Filippo Spiga1-0/+3
* Adding gmsh 4.11.1 * Becoming a maintainer --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2024-06-01py-griddataformats: add v1.0.2 (#44475)Rocco Meli1-2/+5
* update * Apply suggestions from code review Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2024-06-01apptainer: adding version 1.3.1 (#44104)snehring5-1/+80
e2fsprogs: adding version 1.47.0 and fuse2fs variant fuse-overlayfs: adding version 1.13 squashfuse: adding version 0.5.1 and 0.5.2 e2fsprogs: fixing audit errors apptainer: expanding deps to cover more versions, fix binary_path logic. apptainer: add go version deps, fix e2fsprogs patch sums, rework dep paths fuse-overlayfs: tightening up the libfuse dep Signed-off-by: Shane Nehring <snehring@iastate.edu>
2024-05-31mapl: add 2.46.2, 2.40.5 (#44466)Matt Thompson1-0/+2
2024-05-31pass: new package (#44454)James Taliaferro1-0/+63
* New package: password-store * add bash completion as variant * also patch the cygwin platform snippet * update description and maintainers * make completions implicit and don't overwrite the completions package * remove completion option * formatting * clean up file filter syntax * remove reference to completion variant * remove dependency on bash-completion * clarify comments * bashcompdir is already the default * add optional dependency on xclip * fix formatting
2024-05-31ruby: adding version 3.3.2 (#44447)snehring1-0/+1
Signed-off-by: Shane Nehring <snehring@iastate.edu>
2024-05-31tamaas: adding new versions and python install fix (#44469)Lucas Frérot2-1/+75
* tamaas: install python extension with explicit pip call * tamaas: patching compilation issues with recent compilers * tamaas: added versions 2.7.0 and 2.7.1
2024-05-31add in the latest versions of FMS (#44471)Ryan Mulhall1-0/+8
Co-authored-by: rem1776 <rem1776@github.com>
2024-05-31dla-future: Add 0.5.0 (#44463)Raffaele Solcà1-2/+20
* add dla-future@0.5.0 * [@spackbot] updating style on behalf of rasolca * fix typo * review suggestions --------- Co-authored-by: rasolca <rasolca@users.noreply.github.com>
2024-05-31Updated version (#44461)potter-s1-0/+1
Co-authored-by: Simon Potter <sp39@sanger.ac.uk>
2024-05-31util-macros: ensure url_for_version works for older versions (#44421)Wouter Deconinck1-5/+5
* util-macros: ensure url_for_version only used for older versions * util-macros: use url.substitute_version after xz -> bz2 * util-macros: mv url_for_version down the file
2024-05-31py-junit2html: new package, version '31.0.2' (#44399)Lydéric Debusschère1-0/+23
* py-junit2html: new package, version '31.0.2' * py-junit2html: install from sources instead of from wheel
2024-05-31Bump-up rocm-opencl with 6.1.0 & 6.1.1 and adding hsa library path in ↵renjithravindrankannath2-4/+22
LD_LIBRARY_PATH (#44171) * Adding hsa library path in LD_LIBRARY_PATH * Prepending instead of setting LD_LIBRARY_PATH to hsa-rocr-dev/lib * adding rocm-opencl 6.1.0 & 6.1.1 updates
2024-05-31Updates meep to latest release 1.29.0 (#44468)Matt Schramm1-0/+1
2024-05-31Adding HPX v1.10.0 to package (#44470)Hartmut Kaiser1-0/+1
2024-05-31Changes for NVIDIA HPC SDK 24.5 (#44354)jmuddnv1-0/+10
2024-05-31fujitsu-mpi: point MPI compiler wrappers to Spack compiler wrappers (#44457)jdomke1-0/+6
Using OMPI_ environment variables, like openmpi does.
2024-05-31traverse: pass key correctly (#44460)Harmen Stoppels2-2/+25
Fixes a bug where custom keys to identify nodes were not passed correctly.
2024-05-31py-numexpr: add v2.8.8, v2.9.0 (#44451)Wouter Deconinck1-0/+3
2024-05-31petsc4py: fix typo with version (#44452)Satish Balay1-1/+1
2024-05-31protobuf: fix 3.4:3.21 patch checksum (#44443)Tom Bradford1-2/+2
2024-05-31dla-future-fortran: fix +test option (#44458)Rocco Meli1-1/+5
* Spglib: add version 2.4.0 * DLA-Future: fix +test option
2024-05-30paraview: update cuda_arch management (#44243)Alberto Invernizzi1-35/+53
* refactor logic to switch to cmake for cuda management
2024-05-30corrected the vmd 1.9.3 tarball checksum (#44433)Tom Bradford1-1/+1
2024-05-30Bootstrapping: don't use Mac OS binaries on Windows (#44193)John W. Parent1-2/+5
`BuildcacheBootstrapper` uses `Spec.intersects` to match specs needed for bootstrapping against the binary cache. The specs were not sufficiently-detailed to prevent matching e.g. cached binaries for Mac OS on Windows; this commit adds the platform to each requested bootstrap spec to prevent that.
2024-05-30unmaintained pkgs: bump versions 2024-05-20 (#44274)Alec Scott72-98/+166
* unmaintained pkgs: bump versions 2024-05-20 * seqkit: revert changes * msgpack-c: add dependency on boost * msgpack-c: revert to test neovim * revert: parallel, openblas, and re2c due to conflicts * gmsh: revert changing version * trilinos: limit version of suite-sparse to fix build * gtkorvo-atl: deprecate develop before remove * msgpack-c: deprecate v1.4.1 * msgpack-c: fix style --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2024-05-30Package/gettext: Old version issues (#44440)Teague Sterling1-6/+9
gcc@:5 hits https://savannah.gnu.org/bugs/index.php?65811 in gettext@0.22: also fix patch of configure script Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2024-05-30Bump-up the version for RoCm-6.1.1 release (#44178)Sreenivasa Murthy Kolam55-103/+628
* initial commit for RoCm-6.1.1 release * fix style issues * update the version for rocmlir and rocm-cmake * restrict the patch for 6.0.0 release * fix build failure for hipsolver-6.1.1 release * update the hipblaslt for rocm-6.1.1 release * add the patch for hipsparselt for 6.1.1 rel
2024-05-30petsc, py-petsc4py: add v3.21.2 (#44439)Satish Balay2-0/+2
2024-05-30remove platform=cray (#43796)Massimiliano Culpo107-1359/+104
Remove support for `cray` as a separate platform. Any platform previously detected as `cray` is now detected as `linux`. Users who still need platform=cray have to stick to Spack 0.22
2024-05-30rocm-validation-suite: custom patch update for lib and lib64 yaml library ↵renjithravindrankannath2-20/+32
path (#44287)
2024-05-30conmon: add v2.1.12 (#44389)Wouter Deconinck1-0/+1
2024-05-30tests: use fewer default paths (#44432)Harmen Stoppels5-69/+60
Set config:install_tree:root and modules:default:roots to something sensible.
2024-05-30concretizer: enforce host compat when reuse only (#44428)Harmen Stoppels3-4/+35
Fixes a bug in the concretizer where specs depending on a host incompatible libc would be used. This bug triggers when nothing is built. In the case where everything is reused, there is no libc provider from the perspective of the solver, there is only compatible_libc. This commit ensures that we require a host compatible libc on any reused spec, additionally to requiring compat with the chosen libc provider. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-05-29nim: add v2.0.4 (#44375)Diego Alvarez S1-3/+5
* Add nim 2.0.4 * Use install instead of copy --------- Co-authored-by: dialvarezs <dialvarezs@users.noreply.github.com>
2024-05-29Patch to add hsa prefix/include path (#44334)renjithravindrankannath3-15/+17
* Patch to add hsa prefix/include path:wq * Style check error fix * The patch need to be applied to 2024.01.stable. ROCm 6.0 requires hpctoolkit 2024.01.1 or later * Fixing style chec error
2024-05-29Update py-pyspark and py-py4j (#44263)Teague Sterling10-22/+151
* Adding a py4j variant that requires Java via spack to avoid situations where a system doesn't have Java and py4j expects it * Adding new versions of py-pyspark * Adding a new variant to require java (via py4j) and clean up dependency handling * Adding myself as a maintainer for py-pyspark and py-py4j * Fix overlooked version bump in py4j * Version bump to meet py-spark expectations * Version bump to add latest compatibile version with pyspark * Matching py-grpcio bump * Adding variants and dependents for pyspark * Adding runtime deps * Changing default java requirement. I'm not sure this is the right call * Changing py4j with java dependency handling * Fix style * Update package.py fix unnecessary f-strinh * Make +java the default for both * Fix nested deps * Revert styles after default change * Added new versions and GCC 14 compatbility conflicts * Added new versions and compatibility conflicts for gcc 14 * Added new versions paired to arrow (for gcc14 compat) * Update py-protobuf compiler conflict * Update depends to match See https://github.com/grpc/grpc/blob/master/src/python/grpcio_status/setup.py * Updating dependencies and conflicts for py-googleapis-common-protos. Added new version to avoid future issues * Remove upper bound version on py-protobuf and add default_args * Adding new versions and updating dependencies back to versions 1.35.0 * Updating oldest numpy deps * Fixing merge * bit more cleaniness for var/spack/repos/builtin/packages/py-googleapis-common-protos/package.py * Adding latest matching version of py-grpcio and py-grpcio-status * Update package.py https://github.com/spack/spack/pull/44263#discussion_r1612317943 * Update dependencies * Adding additional versions for dependent packages. Deprecated two versions: 1.16 is old, built for python ~3.6, and does not build for 3.8. 1.52.0 was removed from pypi * Revert py-grpcio-tools changes. Will include in separate PR * Adding patches and constraints to get 1.48 to build as it's a dependency that is called out for some other packages * Updating to account for yanked packages for dependencies * Fix style * Update sha256 for py-grpcio v0.16.0 to reflect change --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
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