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2024-02-16bigdft-futile: new versions 1.9.3, 1.9.4 (#42646)Martin Lang1-0/+2
2024-02-16py-black: add v24.2.0 (#42639)Adam J. Stewart1-0/+1
2024-02-16py-jsonargparse: add v4.27.5 (#42640)Adam J. Stewart2-1/+2
2024-02-16openmpi: add ucc to fabrics (#41889)Carlos Bederián1-0/+9
2024-02-16Update maintainers for Kokkos and add Kokkos 4.2.1 (#42690)Nicolas Morales1-1/+2
* update kokkos spack package maintainers * add Kokkos 4.2.01 * Update var/spack/repos/builtin/packages/kokkos/package.py Co-authored-by: Luc Berger <lberge@sandia.gov> --------- Co-authored-by: Alec Scott <alec@bcs.sh> Co-authored-by: Luc Berger <lberge@sandia.gov>
2024-02-16nfft: new versions 3.5.1, 3.5.2, 3.5.3 (#42645)Martin Lang1-0/+3
2024-02-16dftbplus: new versions 22.2, 23.1 (#42647)Martin Lang1-0/+2
2024-02-16Update package.py for hypre release 2.31.0 (#42689)Rob Falgout1-0/+1
2024-02-16Add aocc support to ESMF (#42708)Alex Richert1-0/+4
* Add aocc support to ESMF * Update package.py
2024-02-16add new CUTLASS versions (#42715)WuK1-0/+2
2024-02-16perl-datetime-format-iso8601: New package (#42719)Arne Becker1-0/+34
Adds DateTime::Format::ISO8601
2024-02-16clingo: add version 5.7.0 (#42707)Todd Gamblin1-0/+1
5.7.0 was just released. It includes a number of changes requested and/or upstreamed by Spack developers, e.g.: * API for accessing optimization priorities: https://github.com/potassco/clingo/pull/406 * Hash optimization: https://github.com/potassco/clingo/pull/441 * Contributing Guide: https://github.com/potassco/clingo/pull/465 * Hiding more ELF symbols: * https://github.com/potassco/clingo/pull/447 * https://github.com/potassco/clingo/pull/449
2024-02-16dlb: add v3.4 (#42722)Victor Lopez Herrero1-0/+1
2024-02-16Add support for clang with OpenMP and other minor changes to oneapi build ↵Mikael Simberg1-0/+10
system (#42717) * Add support for clang in oneapi packages with OpenMP * Add fallback search for libomp in OneApi package with OpenMP threading * Add requires for the compiler when using threads=openmp in intel-oneapi-mkl * Cosmetic changes to messages in oneapi.py * Update error message in oneapi.py Co-authored-by: Robert Cohn <rscohn2@gmail.com> * Update another error message in oneapi.py Co-authored-by: Robert Cohn <rscohn2@gmail.com> * Inline helper error function in oneapi.py * Update one more error message in oneapi.py * Wrap long line in oneapi.py --------- Co-authored-by: Robert Cohn <rscohn2@gmail.com>
2024-02-16[intel-oneapi-mkl] provide omp lib for threads=openmp (#42653)Robert Cohn1-0/+2
2024-02-15SST: only run autoreconf for versions from Git branches (#42712)Eric Berquist3-13/+19
2024-02-15celeritas: new version 0.4.2 (#42702)Seth R. Johnson1-3/+5
2024-02-14elpa: fix checksum (#42674)Harmen Stoppels1-1/+1
2024-02-14veclibfort: explicitly add platform=darwin as requirement (#42664)Henrik Stooss1-0/+2
2024-02-14VTK: limit patches to v8 (#42505)John W. Parent1-3/+3
* VTK: limit patches to v8 * Finer scrope on patch version applicability
2024-02-14Deprecate ROCm 5.1.0 till 5.2.3 (#41794)Sreenivasa Murthy Kolam50-248/+294
2024-02-13Remove boost as dependency for trilinos+stk (#39556)Jon Rood2-13/+2
* Remove boost as dependency for trilinos+stk. * Formatting. * Put bounds on STK requirement of Boost.
2024-02-13boost: Add patch to workaround mpl compiler error with gcc 8.3 and c++17. ↵Victor Brunini2-0/+64
(#39144) Works around this issue: https://github.com/boostorg/mpl/issues/44 Co-authored-by: psakievich <psakiev@sandia.gov>
2024-02-13ELPA package: add patched version from Nov 2023 (#42539)Nichols A. Romero1-0/+5
2024-02-13pdt: add aocc support (#42634)Alex Richert1-1/+1
2024-02-13py-py-tes: add new package (#42531)Maciej Wójcik1-0/+24
* py-py-tes: add new package * py-py-tes: add constraint on Python
2024-02-13khmer: new package @2.1.1 (#42450)George Young1-0/+32
* khmer: new package @2.1.1 * rationalising patch * adding dep, modifying patch * Update var/spack/repos/builtin/packages/khmer/package.py Indeed! Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13possvm: new package @1.2 (#42516)George Young3-0/+79
* possvm: new package @1.2 * black! * appeasing flake8 * Updating commit ID * Adding graphing dep * Update var/spack/repos/builtin/packages/py-markov-clustering/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13py-pysftp: add new package (#42525)Maciej Wójcik1-0/+18
* py-pysftp: add new package * py-pysftp: correct version Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13Adds the spack recipe for building the pynpm python package (#42582)Jeremy Fix1-0/+22
* Adds the spack recipe for building the pynpm python package * fix license header * Update var/spack/repos/builtin/packages/py-pynpm/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13cellpose: new package @2.2.3 (#42403)George Young5-0/+152
* py-fastremap: new package @1.14.1 * py-pyqtgraph: new package @0.13.3 * py-roifile: new package @2024.1.10 * py-superqt: new package @0.6.1 * cellpose: new package @2.2.3 * Appeasing black ... * Dropping the cuda variant * Update var/spack/repos/builtin/packages/py-fastremap/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Adding python version dependency * Update var/spack/repos/builtin/packages/py-pyqtgraph/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqtgraph/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-roifile/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-superqt/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Adding missing dep & conflict * Appeasing black * Adding missing py- prefix for dep * Switching over to py-pyqt6 * Switching over to py-pyqt6 --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13py-biobb-structure-checking: new package (#42580)Dani1-0/+26
* new builtin package: py-biobb-structure-checking * Update var/spack/repos/builtin/packages/py-biobb-structure-checking/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * dependencies are also build dependencies --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13new builtin package: py-biobb-io (#42451)Dani1-0/+23
* new builtin package: py-biobb-io * Update var/spack/repos/builtin/packages/py-biobb-io/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13py-biobb-gromacs: add new package (#42579)Dani1-0/+24
* new builtin package: py-biobb-gromacs * Update var/spack/repos/builtin/packages/py-biobb-gromacs/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * added setuptools dependency --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2024-02-13squashfuse: add versions (#42589)Jordan Ogas1-4/+11
2024-02-13clfft: workaround compiler error (#42519)Henri Menke1-0/+6
2024-02-12psipred: new package @4.02 (#42529)George Young1-0/+71
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2024-02-12ROCm packages and dependents: add 6.0.2 release (#42544)Sreenivasa Murthy Kolam54-87/+187
* Bump up the version for rocm-6.0.2 release * extend the patches that were created for apps for rocm-6.0.0 and rocm-6.0.2 releases (but apply hipfft patch for only 6.0.0)
2024-02-12Adds latest releases of eccodes/eckit/metkit (#42618)Victoria Cherkas3-0/+3
2024-02-12Fix multiple issues with Python in views (#42601)Harmen Stoppels1-32/+40
This fixes bugs, performance issues, and removes no longer necessary code. Short version: 1. Creating views from Python extensions would error if the Spack `opt` dir itself was in some symlinked directory. Use of `realpath` would expand those, and keying into `merge_map` would fail. 2. Creating views from Python extensions (and Python itself, potentially) could fail if the `bin/` dir contains symlinks pointing outside the package prefix -- Spack keyed into `merge_map[target_of_symlink]` incorrectly. 3. In the `python` package the `remove_files_from_view` function was broken after a breaking API change two years ago (#24355). However, the entire function body was redundant anyways, so solved it by removing it. 4. Notions of "global view" (i.e. python extensions being linked into Python's own prefix instead of into a view) are completely outdated, and removed. It used to be supported but was removed years ago. 5. Views for Python extension would _always_ copy non-symlinks in `./bin/*`, which is a big mistake, since all we care about is rewriting shebangs of scripts; we don't want to copy binaries. Now we first check if the file is executable, and then read two bytes to check if it has a shebang, and only if so, copy the entire file and patch up shebangs. The bug fixes for (1) and (2) basically consist of getting rid of `realpath` entirely, and instead simply keep track of file identifiers of files that are copied/modified in the view. Only after patching up regular files do we iterate over symlinks and check if they target one of those. If so, retarget it to the modified file in the view.
2024-02-12h5hut: fix to work with latest hdf5 (H5_USE_110_API) (#42607)John Biddiscombe1-1/+17
2024-02-12caliper: allow newer papi to be used (#42501)Richard Berger1-1/+1
2024-02-12pdc: add v0.4 (#42508)Jean Luca Bez1-6/+23
2024-02-12nco: add v5.1.9 (#42512)Brian Vanderwende1-0/+3
2024-02-12bdw-gc: add v8.2.6 (#42524)Ivan Maidanski1-1/+2
2024-02-12lcio: add v2.21 (#42514)Thomas Madlener1-0/+1
2024-02-12podio: add 0.99 pre-release version and deprecate all older versions (#42526)Thomas Madlener1-6/+31
2024-02-12samtools: add v1.19.2 (#42550)James Beal2-0/+3
Co-authored-by: James Beal <jb23@sanger.ac.uk>
2024-02-12edm4hep: add v0.10.5, deprecate broken v0.10.4 (#42561)Thomas Madlener1-1/+6
2024-02-12litestream: add new package (#42565)Caetano Melone1-0/+25
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