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2023-01-17Forward lookup of "test_log_file" and "test_failures" (#34882)Massimiliano Culpo1-2/+4
* Forward lookup of "test_log_file" and "test_failures" refers #34531 closes #34487 fixes #34440 * Add unit test * py-libensemble: fix tests * Support stand-alone tests with cached files as install-time tests Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2023-01-17cp2k: enable linking with armpl-gcc for BLAS and FFT (#34981)Annop Wongwathanarat1-0/+4
2023-01-17python: 3.11.1, use -flto=thin when clang (#34951)Harmen Stoppels1-1/+6
2023-01-17Bump gnupg & libksba, (CVE) (#34976)Harmen Stoppels2-6/+34
* gnupg: 2.4.0 * libksba: 1.6.3 (CVE-2022-47629)
2023-01-17faiss: fixed error when importing faiss python package (#34672)Loïc Pottier1-1/+7
This is only a work-around for the actual problem that Python is used to install libraries instead of CMake, so we end up with BUILD_RPATH not INSTALL_RPATHs. Signed-off-by: Loïc Pottier <pottier1@llnl.gov> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-01-17bubblewrap: 0.7.0 (#34975)Harmen Stoppels1-0/+1
2023-01-17perl-file-temp: add 0.2311 (#34866)Christopher Christofi1-0/+15
2023-01-17libcroco: Get the `doc` variant working (#34735)Glenn Johnson1-7/+29
2023-01-17mvapich: add new package in preparation for v3.0 (#34276)MatthewLieber1-0/+293
* Add new file for MVAPICH 3.0a release Creating this as a new package since it requires some new configuration options and because we are moving to the name "MVAPICH" and droping the 2 (following a similar move by MPICH). Co-authored-by: Nat Shineman <shineman.5@osu.edu> Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
2023-01-17flexiblas: add versions up to v3.3.0 (#34874)Ashwin Kumar1-0/+4
2023-01-17New version for openCARP packages, v12.0 (#34710)Marie Houillon3-2/+12
Co-authored-by: openCARP consortium <info@opencarp.org>
2023-01-17mfem: support pumi w/zoltan and parmetis (#34864)Cameron Smith1-1/+14
2023-01-17crtm: overhaul package, add crtm-fix (#34715)Dom Heinzeller2-2/+125
Update crtm from JCSDA-EMC spack fork, add crtm-fix
2023-01-17ncview: bypass compiler check against netcdf-c compiler (#34580)Dom Heinzeller1-9/+10
2023-01-17OpenCV: checksum for 4.5.5, make contrib optional (#34313)iarspider1-5/+11
* OpenCV: checksum for 4.5.5, make contrib optional * [@spackbot] updating style on behalf of iarspider * Add conflicts for contrib modules * Fix typo * Implement changes from review * Update var/spack/repos/builtin/packages/opencv/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: iarspider <iarspider@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-17gcc: add patch for noexcept declarations (#34964)Glenn Johnson1-0/+7
There are some declarations that need to be declared noexcept for valarray. This affects gcc 9.5:11.2.
2023-01-16Re adding 4th chunk of nf-tools deps (#34974)Marco De La Pierre19-0/+417
* Revert "Revert "4th chunk of nf-core deps from update/nextflow-tools (#34564)" (#34960)" This reverts commit 891a63cae616dbc92acdad0e0eb626edbd0862a0. * fix to py-python-multipart, as per PR review
2023-01-17py-macs2: add version 2.2.7.1 and support python@3.10: (#34970)Glenn Johnson1-3/+21
* py-macs2: add version 2.2.7.1 and support python@3.10: The tarball from PyPi includes the Cythonized C files. The tarball from github does not. Remove the Cythonized C files from the source so that they are rebuilt with the Spack Python/Cython combination. This is necessary for python-3.10 but make sense for other combinations as well. * Edits based on review - set python version constraint on version 2.2.4 - removed all python-2 versions and related constraints.
2023-01-16py-xxhash: fix xxhash dependency (#34971)Glenn Johnson1-1/+4
* py-xxhash: fix xxhash dependency The dependency should be xxhash@0.8.0:. * Add version 3.2.0
2023-01-16rabbitmq-c: added RabbitMQ C interface (#34892)Loïc Pottier1-0/+39
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2023-01-17itk: add version 5.3.0 (#34967)Glenn Johnson1-0/+2
* Add depends_on("mpi") to fix missing <mpi.h> Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2023-01-17hisat2: add version 2.2.1 and sra variant (#34966)Glenn Johnson2-4/+77
- add python dependency - add perl dependency - set python and perl interpreters in scripts
2023-01-17sra-tools: add version 3.0.3 and fix build (#34965)Glenn Johnson2-0/+21
2023-01-17stringtie: add version 2.2.1 and fix build (#34973)Glenn Johnson1-1/+5
- stringtie uses internal samtools so remove dependency on samtools - add dependency for zlib - use make release target to get correct flags
2023-01-16intel-oneapi-mpi: fix setup_dependent_build_environment (#34956)Sergey Kosukhin1-5/+5
2023-01-16py-fastfold add py-numpy upper bound (#34962)Benjamin Meyers1-0/+2
2023-01-16Add checksum for hwloc 2.9.0 (#34919)iarspider1-0/+1
2023-01-16Add package file for xtb and py-xtb (#34857)Sebastian Ehlert6-11/+74
* Add package file for xtb and py-xtb * Retain maintainers from PythonPackage * Update package files - use extends("python") instead of tampering with PYTHONPATH - use PyPI for downloading sdist of py-xtb - add simple-dftd3 0.7.0 - add dftd4 3.5.0 - remove --wrap-mode=nodownload from toml-f * Remove logic for download URL
2023-01-16Add target propagation for pika package (#34924)Auriane R1-0/+17
2023-01-16Add py-python-lsp-server v1.7.0 (#34946)Alec Scott1-0/+1
2023-01-16Revert "4th chunk of nf-core deps from update/nextflow-tools (#34564)" (#34960)Harmen Stoppels19-418/+0
This reverts commit 4e63d92bc927aeb5380bdc48500abda4cda4b5bd.
2023-01-16Make docbook-xml work across all entity versions (#34733)Glenn Johnson4-4/+57
Packages that use docbook-xml may specify a specific entity version. When this is specified as a version constraint in the package recipe it will cause problems when using `unify = True` in a Spack environment, as there could be multiple versions of docbook-xml in the spec. In practice, any entity version should work with any other version and everything should work with the latest version. This PR maps all Spack docbook-xml entity versions to the docbook-xml version in the spec. Ideally, the version in the spec would be the latest version. With this PR, even if a package specifies an older entity version, it will map to the entity version (latest) in the spec. This means that there can be one docbook-xml version in a Spack environment spec and packages requesting older entity versions will still work. To help facilitate this, docbook-xml version constraints for packages that have them have been removed. Those packages are dbus and gtk-doc.
2023-01-164th chunk of nf-core deps from update/nextflow-tools (#34564)Marco De La Pierre19-0/+418
2023-01-16harfbuzz: new version 5.3.1, 6.0.0 (fixes aarch64) (#34908)Wouter Deconinck1-1/+7
A few new versions of harbuzz, but just jumping to the last non-6 version as preferred. No build system changes: - within 5 series: https://github.com/harfbuzz/harfbuzz/compare/5.1.0...5.3.1 - from 5 to 6: https://github.com/harfbuzz/harfbuzz/compare/5.3.1...6.0.0 The 5 series fixes a build issue for aarch64, https://github.com/harfbuzz/harfbuzz/issues/3768.
2023-01-16cp2k: add v2022.2, update CUDA settings (#34757)Glenn Johnson1-4/+25
2023-01-16Qt: patch additional config file (#34682)Adam J. Stewart1-89/+102
2023-01-16GASNet 2022.9.2 package update (#34942)Dan Bonachea1-0/+7
This allows client packages like UPC++ to display more precise version information when their GASNet dependency was fetched from git.
2023-01-16Add Go v1.19.5, v1.18.10, and remove deprecated versions (#34594)Alec Scott3-109/+14
2023-01-16AMD Optimized CPU Libraries: add v4.0 (#34681)AMD Toolchain Support7-36/+94
What's in AOCL 4.0: 1. amdblis LPGEMM variants with post-ops support AMD "Zen4" support for BLIS 2. amdlibflame Upgrade to LAPACK 3.10.1 specification Improvements in a few more variants of SVD and Eigen Value routines Multithread support enabled for selected APIs 3. amdfftw AVX-512 enablement of DFT kernels AVX-512 optimization of copy and transpose routines 5. amdlibm Black & Scholes support (logf, expf, erff, both scalar and vector) AVX-512 variants of vector functions 6. aocl-sparse New Iterative Solver APIs AVX-512 support for SPMV API 7. amdscalapack Upgrade to Netlib ScaLAPACK 2.2.0 Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-01-16rocsolver: expand version compatibility with fmt (#34941)Cory Bloor3-1/+161
2023-01-16restic: add v0.15.0 (#34945)Alec Scott1-0/+1
2023-01-16rclone: add v1.61.1 and deprecate old versions due to CVE-2020-28924 (#34944)Alec Scott1-7/+38
2023-01-16Add v0.109.0 and deprecate versions < v0.79.1 due to a CVE (#34943)Alec Scott1-3/+18
2023-01-16e4s ci: py-libensemble: activate variants (#34915)eugeneswalker1-1/+1
2023-01-16omnitrace: add new versions (#34955)Jonathan R. Madsen1-0/+7
- v1.5.0 - v1.6.0 - v1.7.0 - v1.7.1 - v1.7.2 - v1.7.3 - v1.7.4
2023-01-16py-segmentation-models-pytorch: add v0.3.2 (#34853)Adam J. Stewart2-4/+10
2023-01-16Drop Python 3.6 again (#34442)Adam J. Stewart2-8/+5
2023-01-16Fix version number for fmt dependency of pika package (#34922)Auriane R1-1/+1
2023-01-14spectre: add v2023.01.13 (#34929)SXS Bot1-0/+3
Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
2023-01-14py-annoy: new package with version 1.17.1 (#34911)Christopher Christofi1-0/+21
* py-annoy: add 1.17.1 * add version specifier on dependency package
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