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2023-04-19coreutils: New version 9.3 (#37021)Erik Schnetter1-0/+1
2023-04-19make version(...) kwargs explicit (#36998)Harmen Stoppels308-580/+661
- [x] Replace `version(ver, checksum=None, **kwargs)` signature with `version(ver, checksum=None, *, sha256=..., ...)` explicitly listing all arguments. - [x] Fix various issues in packages: - `tags` instead of `tag` - `default` instead of `preferred` - `sha26` instead of `sha256` - etc Also, use `sha256=...` consistently. Note: setting `sha256` currently doesn't validate the checksum length, so you could do `sha256="a"*32` and it would get checked as `md5`... but that's something for another PR.
2023-04-19py-torch: define property cmake_prefix_paths (#37012)Wouter Deconinck1-0/+7
* py-torch: define property cmake_prefix_paths `py-torch` installs `libtorch` and a cmake config in a non-standard location. This points downstream code to the relevant locations. From there it should pick up the correctly library and include paths for C++ projects. * py-torch: python_platlib suggestion Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * [@spackbot] updating style on behalf of wdconinc * py-torch: back to self.spec["python"].package.platlib * [@spackbot] updating style on behalf of wdconinc --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-04-19Add mfem v4.5.2 and related updates/tweaks in other packages (#36154)Veselin Dobrev10-51/+115
* Add mfem v4.5.2 and related updates/tweaks in other packages * [mfem] Add the release source link for MFEM v4.5.2 * [mfem] Remove 'goxberry' (his request) from MFEM's maintainers list
2023-04-19Extract depfile logic from cli command into a core module (#36995)Harmen Stoppels3-156/+317
2023-04-19installer.py: drop build edges of installed packages by default (#36707)Alec Scott2-1/+52
This means that `spack install` will now build the minimal set of packages required to install the root(s). To opt out of build edge pruning, use `spack install --include-build-deps`. Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-04-19apachetop: add v0.23.2 (#37017)Alec Scott1-0/+1
2023-04-19r-rcpptoml: add v0.2.2 (#36886)Alec Scott1-0/+1
2023-04-18editing: add higher-precedence `SPACK_EDITOR` environment variableTodd Gamblin4-4/+57
Other tools like git support `GIT_EDITOR` which takes higher precedence than the standard `VISUAL` or `EDITOR` variables. This adds similar support for Spack, in the `SPACK_EDITOR` env var. - [x] consolidate editor code from hooks into `spack.util.editor` - [x] add more editor tests - [x] add support for `SPACK_EDITOR` - [x] add a documentation section for controlling the editor and reference it
2023-04-18refactor: unify use of spack.util.editorTodd Gamblin3-59/+107
Code from `spack.util.editor` was duplicated into our licensing hook in #11968. We really only want one place where editor search logic is implemented. This consolidates the logic into `spack.util.editor`, including a special case to run `gvim` with `-f`. - [x] consolidate editor search logic in spack.util.editor - [x] add tests for licensing case, where `Executable` is used instead of `os.execv` - [x] make `_exec_func` argument of `editor()` into public `exec_fn` arg - [x] add type annotations
2023-04-18Fix compilation on Cray (target: any) (#37011)Massimiliano Culpo2-0/+29
fixes #36628 Fix using compilers that declare "target: any" in their configuration. This should happen only on Cray with the module based programming environment.
2023-04-18Update and fix py-dgl+cuda (#36823)Benjamin Meyers1-8/+32
* Update and fix py-dgl+cuda * [@spackbot] updating style on behalf of meyersbs * Update py-dgl
2023-04-18lammps: backport fix for `+rocm+kokkos+kspace` (#36850)Jonathon Anderson1-0/+15
* lammps: backport hipfft fix for ROCm-based builds * lammps: Mark incompatibility with Kokkos 4.x for old versions
2023-04-18spack ci: preserve custom attributes in build jobs (#36651)Jonathon Anderson3-96/+79
* Simplify test/cmd/ci.py::test_ci_generate_with_custom_scripts * Rearrange the build-job logic in generate_gitlab_ci_yaml * Preserve all unknown attributes in build jobs * Slip tests for custom attributes in the tests for other job types * Support custom artifacts * [@spackbot] updating style on behalf of blue42u * Don't bother sorting needs --------- Co-authored-by: blue42u <blue42u@users.noreply.github.com>
2023-04-18r-httpuv: add v1.6.9 (#36951)Alec Scott1-0/+1
2023-04-18r-git2r: add v0.31.0 (#36864)Alec Scott1-0/+2
2023-04-18r-highr: add v0.10 (#36867)Alec Scott1-0/+2
2023-04-18DaV SDK: Enable ParaView raytracing with in SDK (#36844)kwryankrattiger3-3/+10
* DaV SDK: Enable ParaView raytracing with in SDK * CI: Drop swr testing from Data Vis SDK * ISPC: extend LLVM requirement to main * DaV SDK: Disallow concretizing develop unifyfs No longer needed after mochi-margo patch
2023-04-18New packages: py-ogb, py-outdated, py-littleutils (#36824)Benjamin Meyers3-0/+76
* New packages: py-ogb, py-outdated, py-littleutils * Update var/spack/repos/builtin/packages/py-outdated/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-04-18py-scipy: link with OpenMP version of armpl-gcc when requested (#37002)Annop Wongwathanarat1-4/+10
2023-04-18fix typo (#36997)Harmen Stoppels1-1/+1
2023-04-18Revert addition of SPACK_EDITOR pending review.Todd Gamblin5-160/+62
This reverts commit d8a26905ee0fc9e72a05a87bf7ced7e7fc2d4900. This reverts commit 1ee049ccc3d4d4bf1e8dafad0247f3cef01dda58. These were spuriously pushed to `develop`.
2023-04-18editing: add higher-precedence `SPACK_EDITOR` environment variableTodd Gamblin4-4/+57
Other tools like git support `GIT_EDITOR` which takes higher precedence than the standard `VISUAL` or `EDITOR` variables. This adds similar support for Spack, in the `SPACK_EDITOR` env var. - [x] consolidate editor code from hooks into `spack.util.editor` - [x] add more editor tests - [x] add support for `SPACK_EDITOR` - [x] add a documentation section for controlling the editor and reference it
2023-04-18refactor: unify use of spack.util.editorTodd Gamblin3-59/+104
Code from `spack.util.editor` was duplicated into our licensing hook in #11968. We really only want one place where editor search logic is implemented. This consolidates the logic into `spack.util.editor`, including a special case to run `gvim` with `-f`. - [x] consolidate editor search logic in spack.util.editor - [x] add tests for licensing case, where `Executable` is used instead of `os.execv` - [x] make `_exec_func` argument of `editor()` into public `exec_fn` arg - [x] add type annotations
2023-04-17Allow users to remove items from hierarchy per-path (#31351)Greg Becker4-2/+34
* lmod modules: allow users to remove items from hierarchy per-spec This allows MPI wrappers that depend on MPI to be removed from the MPI portion of the hierarchy and be made available when the appropriate compiler is loaded. module load gcc module load mpi-wrapper # implicitly loads mpi module load hdf5 This allows users to treat an mpi wrapper like an mpi program
2023-04-17py-html5lib, madgraph5amc: correct hashes of empty files (#36979)Wouter Deconinck2-6/+1
* py-html5lib: correct hashes of empty files Going through and fixing hashes that are due to empty string. ```console $ grep -Ir $(echo -n | sha256sum | awk '{print$1}') $SPACK_ROOT/var/spack/repos/builtin /home/wdconinc/git/spack/var/spack/repos/builtin/packages/madgraph5amc/package.py: sha256="e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", /home/wdconinc/git/spack/var/spack/repos/builtin/packages/py-html5lib/package.py: version("0.99", sha256="e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855") ``` ```console $ spack checksum py-html5lib 0.99 ==> Found 1 version of py-html5lib: 0.99 https://files.pythonhosted.org/packages/source/h/html5lib/html5lib-0.99.tar.gz ==> Fetching https://files.pythonhosted.org/packages/source/h/html5lib/html5lib-0.99.tar.gz version("0.99", sha256="aff6fd3031c563883197e5a04b7df324086ff5f358278a0386808c463a077e59") ``` * madgraph5: remove incorrectly hashed version
2023-04-17qt: new version 5.15.9 (#36709)Wouter Deconinck1-0/+1
This adds the new LTS version of Qt5. No build system changes needed. The bundled libjpeg and sqlite versions were updated, but it is unclear if these are actual build requirements, and we have not been tracking these specific versions in the version dependencies (likely due to exactly this lack of clarity). Compare: https://github.com/qt/qtbase/compare/v5.15.8-lts-lgpl...v5.15.9-lts-lgpl
2023-04-17Revert "move depfile logic into its own module, separate traversal logic ↵Harmen Stoppels2-264/+147
from model (#36911)" (#36985) This reverts commit a676f706a8783e9d517e95e8cd2b6997e527fc3c.
2023-04-17xyce: patch issue affecting MPICH (#36826)Paul Kuberry2-0/+41
2023-04-17Add NetCDF95 package. (#36959)Rémi Lacroix1-0/+20
* Add NetCDF95 package. NetCDF95 is an alternative Fortran interface to the NetCDF library which uses Fortran 2003 features. * [@spackbot] updating style on behalf of RemiLacroix-IDRIS --------- Co-authored-by: RemiLacroix-IDRIS <RemiLacroix-IDRIS@users.noreply.github.com>
2023-04-17Boost: add version 1.82.0 (#36924)Tim Haines1-0/+8
2023-04-17netcdf-c: major refactoring, new variants and versions (#36485)Sergey Kosukhin4-232/+310
2023-04-17CI: update Linux images in ML pipelines (#36766)Adam J. Stewart5-12/+23
Add missing openssl/curl/pkgconfig deps to py-tokenizers Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-04-17r-rstantools: add v2.3.1 (#36890)Alec Scott1-0/+1
2023-04-17r-r-utils: add v2.12.2 (#36884)Alec Scott1-0/+1
2023-04-17move depfile logic into its own module, separate traversal logic from model ↵Harmen Stoppels2-147/+264
(#36911)
2023-04-17cgl: add v0.60.7 (#36940)Alec Scott1-0/+1
2023-04-17masurca: add v4.1.0 (#36942)Alec Scott1-0/+1
2023-04-17spot: add v2.11.4 (#36943)Alec Scott1-0/+1
2023-04-17glab: add v1.28.0 (#36946)Alec Scott1-0/+3
2023-04-17plumed: add 2.8.2, 2.7.6 and their supported gromacs combinations (#36929)Carlos Bederián2-28/+36
* plumed: Add 2.8.2, 2.7.6 * gromacs: add plumed 2.8.2 and 2.7.6 support
2023-04-17slang: add v2.3.3 (#36952)Alec Scott1-0/+1
2023-04-17transdecoder: add v5.7.0 (#36953)Alec Scott1-0/+1
2023-04-17Add "build" stage to many Go packages (#36795)Alec Scott6-6/+45
2023-04-17py-lightly: py-torch+distributed required (#36955)Adam J. Stewart1-1/+9
2023-04-17py-sphinx: add new versions (#36938)Adam J. Stewart1-0/+6
2023-04-17ruby-rake: add v13.0.6 (#36945)Alec Scott1-0/+1
2023-04-17hepmc3: add v3.2.6 (#36941)Alec Scott1-0/+1
2023-04-17Add umpire support to SIRIUS (#36958)Taillefumier Mathieu1-0/+7
2023-04-17Add dependency changes to R packages (#36937)Glenn Johnson9-11/+22
This PR adds dependency changes that were missed with some recent merges of R package updates.
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