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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
2023-01-13trilinos: enable mumps solver in amesos2 if variant is set (#34927)Dominik Thoennes1-0/+1
* enable mumps solver in amesos2 if variant is set for trilinos * fix formatting
2023-01-13add conduit 0.8.6 release (#34894)Cyrus Harrison1-0/+1
2023-01-13Proper scons executable on Windows (#34934)John W. Parent1-1/+7
2023-01-13slurm: Add Version 22-05-7-1 (#34902)Dr. Christian Tacke1-0/+1
2023-01-13Add 15.0.7 (#34912)Paul R. C. Kent1-0/+1
2023-01-13Add parsl-monitoring (#34769)Sam Grayson2-0/+44
* Add packages * Style * Respond to comments * Change conflct dep type Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-13py-gevent%oneapi@2023.0.0: -Wno-error=incompatible-function-pointer-types ↵eugeneswalker1-0/+6
(#34901)
2023-01-13Paraview rocm (#34790)kwryankrattiger2-14/+25
* paraview: add `rocm` variant This conflicts with CUDA and requires at least ParaView 5.11.0. More dependencies are also needed. * E4S: Add ParaView for ROCm and CUDA stacks * DAV SDK: Update ParaView version and GPU variants * Verify using hipcc vs amdclang++ for newer hip Co-authored-by: Ben Boeckel <ben.boeckel@kitware.com>
2023-01-13Adding py-strawberryfields from Xanadu, and its deps (#34849)Marco De La Pierre9-1/+142
* adding 1st version of py-strawberryfields * py-strawberryfields: minor edit * added backbone for 4x new SF dependencies * edits to SF and its 4x new deps * added all deps for SF * added one version to py-lark-parser * py-quantum-xir with tarball from github * Update var/spack/repos/builtin/packages/py-strawberryfields/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * updated version for py-quantum-xir : pypy fixed * py-pennylane: added pythonpackage.maintainers, too Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-01-13Celeritas: new versions 0.1.4 and 0.2.0 (#34883)Seth R. Johnson1-0/+2
2023-01-12libfabric can now find external installation (#33796)Brian Van Essen1-1/+52
* Added support for libfabric to find an external installation and identify variants supported. * Change the fabrics definition to only include CXI when on a cray system with a libfabric-based slingshot network. * Added a conflict when trying to build the CXI fabric value since it is only available as closed source at this time.
2023-01-12Ninja package: resolve circular dependency (#34887)John W. Parent1-1/+5
#33128 Introduces a dependency on re2c into the Ninja build recipe. This is problematic on Windows as we use CMake to build re2c, and Ninja to drive the CMake build. This PR resolves this issue by adding a variant to toggle the use of re2c with ninja.
2023-01-12py-matplotlib: add v3.6.3 (#34903)Adam J. Stewart1-0/+1
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