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2023-06-11py-mypy: add 1.3.0 (#38286)Manuela Kuhn1-0/+2
* py-mypy: add 1.3.0 * Remove redundant py-typed-ast dependency * Read python@3.7 dep
2023-06-11py-deeptools: add 3.5.2, update dependency versions (#38287)George Young1-5/+7
* py-deeptools: add 3.5.2, update dependency versions * Update var/spack/repos/builtin/packages/py-deeptools/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * Update var/spack/repos/builtin/packages/py-deeptools/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * Rearranging dependencies to match setup.py --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-06-11py-jedi: add 0.18.2 (#38177)Manuela Kuhn1-13/+7
* py-jedi: add 0.18.2 * Add setuptools as run dependency
2023-06-11py-multidict: add 6.0.4 (#38284)Manuela Kuhn1-4/+4
2023-06-11py-mne: add 1.4.2 (#38228)Manuela Kuhn1-0/+1
2023-06-11Gxsview new version 2023.05.29 (#38310)Olivier Cessenat1-0/+3
* netpbm: new version 10.73.43 * gxsview: new version 2023.05.29
2023-06-11[py-spacy-legacy] New package (#38276)Jen Herting1-0/+18
2023-06-11[py-spacy-loggers] new package (#38275)Jen Herting1-0/+18
2023-06-11[py-langcodes] new package (#38273)Jen Herting1-0/+18
2023-06-11py-nbclassic: add 1.0.0 and py-notebook-shim: add 0.2.3 (#38289)Manuela Kuhn2-4/+5
2023-06-11New version for openCARP packages, v13.0 (#37940)Marie Houillon4-16/+36
* New version for openCARP packages * Update carputils dependencies * Update types of openCARP dependencies * Add type "run" to setuptools dependency Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add package py-common as carputils dependency * Add setuptools dependency for py-common * Remove spaces on blank line * Restrict type of dependency setuptools to "build" Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: openCARP consortium <info@opencarp.org> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-11py-pybktree: new package (#38209)George Young1-0/+17
* py-pykbtree: new package * py-pybktree: new package --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-11py-pandas: exchange import_modules with skip_modules (#38227)Manuela Kuhn1-11/+1
2023-06-11py-more-itertools: add 9.1.0 (#38229)Manuela Kuhn1-7/+4
2023-06-10slurm: add new version(23.02.2, 22.05.9) (#38285)kjrstory1-0/+2
2023-06-10Automated deployment to update package flux-core 2023-06-10 (#38308)Vanessasaurus1-0/+1
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-06-10Add new Podman package versions and fix patch (#38234)Carson Woods1-2/+4
* Add new podman versions and correct the versions which patch is applied to * Replace the existing maintainer with alecbcs at maintainers request
2023-06-09correct SHA for ABINIT 9.8.3 and add ABINIT 9.8.4 (#38283)Fabien Bruneval1-1/+2
2023-06-09[py-typer] new package (#38270)Jen Herting1-0/+21
* [py-typer] new package * [py-typer] added version 0.7.0
2023-06-09[py-catalogue] added version 2.0.8 (#38266)Jen Herting1-1/+4
2023-06-09comgr: enable testing (#35605)afzpatel1-0/+4
2023-06-09[gromacs] Fix intel (classic) libstdc++ path (#37822)Stephen Sachs1-3/+27
* [gromacs] Fix intel (classic) libstdc++ path Gromacs's `cmake` run will look for `--gcc-toolchain` (e.g. LLVM, icpx) or `--gcc-name` (e.g. icpc) in `CMAKE_CXX_FLAGS`. Only if it does not find a good g++ candidate there it will look for `GMX_GPLUSPLUS_PATH`: https://github.com/gromacs/gromacs/blob/cb6b311c39fc726a72170c4593b754c8d0a492ac/cmake/FindLibStdCpp.cmake#L97 Spack installed intel compilers already define a g++ for std libs. But in `icp{c,x}.cfg` instead of the compile line. If we use the pre-defined g++ we not only have less chance of mixing g++ versions, but also don't need to explicitly add `gcc` as dependency to `gromacs`. * Fix format * Use a variant As there is no way to check if a file exists at depends_on stage * Fix format * New name and fail if variant is used with other compiler * Line too long.
2023-06-09BLT package: add version 0.5.3 (#38247)Chris White1-0/+1
2023-06-08glab: add new versions (#38236)Martin Pokorny1-0/+1
* glab: add new versions * Update var/spack/repos/builtin/packages/glab/package.py Co-authored-by: Alec Scott <alec@bcs.sh> --------- Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-08py-mako: add 1.2.4 (#38194)Manuela Kuhn1-3/+3
2023-06-08py-lxml: add 4.9.2 (#38191)Manuela Kuhn1-1/+2
2023-06-08py-looseversion: add 1.2.0 (#38190)Manuela Kuhn1-1/+3
2023-06-08py-msgpack: add 1.0.5 (#38230)Manuela Kuhn1-0/+1
2023-06-08py-mistune: add 2.0.5 (#38214)Manuela Kuhn1-0/+1
2023-06-08py-llvmlite: add 0.40.0, update llvm dependency information (#38171)George Young1-2/+6
* py-llvmlite: add 0.40.0, update llvm dependency information * Update var/spack/repos/builtin/packages/py-llvmlite/package.py Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * Update var/spack/repos/builtin/packages/py-llvmlite/package.py Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * Update var/spack/repos/builtin/packages/py-llvmlite/package.py Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * Update var/spack/repos/builtin/packages/py-llvmlite/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-08gatk: add 4.4, update to java@17 (#38211)George Young1-1/+3
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08bowtie2: add 2.5.1 (#38201)George Young1-0/+2
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08trimgalore: add 0.6.10, adding variants (#38206)George Young1-0/+8
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08seqtk: add 1.4 (#38193)George Young1-0/+1
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08py-markupsafe: add 2.1.3 (#38198)Manuela Kuhn1-3/+1
2023-06-08New packages: eprosima-fastdds and dependencies (#38079)Daniele Cesarini3-0/+58
2023-06-08ocaml: don't use the spack compiler (#38251)Juan Miguel Carceller1-1/+1
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-06-08py-lightning: add v2.0.3 (#38260)Adam J. Stewart2-3/+14
2023-06-08bedtools2: patching to build with gcc@13 (#38254)George Young2-0/+27
* bedtools2: patching to build with gcc@13 * bedtools2: patching to build with gcc@13 * Update var/spack/repos/builtin/packages/bedtools2/package.py Yep, sure. Makes sense. Co-authored-by: Alec Scott <alec@bcs.sh> --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-08Mold: 1.11.0 (#38235)Axel Huebl1-3/+12
* Mold: 1.11.0 Add the latest release of the `mold` linker. * SHA for 1.7.1: zip to tar
2023-06-08py-lightly: add v1.4.7 (#38259)Adam J. Stewart1-2/+7
2023-06-08bdw-gc: add v8.2.4 (#37969)Ivan Maidanski1-3/+12
* bdw-gc: add v8.2.4 * bdw-gc: Fix download URL for old package versions --------- Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2023-06-08(r-rcpp)ensmallen: new package (#38249)Wouter Deconinck2-0/+51
* ensmallen: new package ensmallen is a high-quality C++ library for non-linear numerical optimization. * r-rcppensmallen: new package --------- Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-06-08junit4: add v4.13.2 (#38122)Alec Scott1-0/+1
2023-06-08(r-rcpp)armadillo: new version 12.4.0 (#38246)Wouter Deconinck2-0/+4
* armadillo: new version 12.4.0 No build system changes necessary, https://gitlab.com/conradsnicta/armadillo-code/-/compare/12.2.x...12.4.x * r-rcpparmadillo: new version 0.12.4.0.0
2023-06-08bismark: add 0.24.1, add HISAT2 dependency (#38210)George Young1-0/+2
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08quantum-espresso: add 7.2 (#38223)Carlos Bederián1-0/+1
2023-06-08trilinos: drop preferred version (#38086)Seth R. Johnson1-5/+1
2023-06-08cni-plugins: add v1.3.0 (#38064)Alec Scott1-0/+1
2023-06-07py-keyring: add 23.13.1 (#38183)Manuela Kuhn1-5/+9
* py-keyring: add 23.13.1 * [@spackbot] updating style on behalf of manuelakuhn
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