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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
2023-06-07`py-nvidia-dali`: update versions up to v1.26.0 (#38022)Thomas Bouvier1-5/+120
* `py-nvidia-dali`: update versions up to v1.26.0 * Add proper `cuda` dependency version
2023-06-07`py-horovod`: add versions v0.27.0 and v0.28.0 (#38016)Thomas Bouvier1-2/+4
* `py-horovod`: add versions v0.27.0 and v0.28.0 * fix: typo * Add upper version bound for `py-pyarrow`
2023-06-07py-json5: add 0.9.14 (#38178)Manuela Kuhn1-1/+2
2023-06-07py-jaraco-classes: add 3.2.3 (#38167)Manuela Kuhn1-2/+1
2023-06-07py-jupyter-client: add 8.2.0 (#38180)Manuela Kuhn1-0/+1
2023-06-07chemfiles: add v0.10.4 (#38063)Alec Scott1-0/+1
2023-06-07casacore: add v3.5.0 (#37806)Martin Pokorny1-20/+22
2023-06-07OpenFAST: add v3.3.0, v3.4.0 and v3.4.1 (#37407)Nate deVelder1-0/+3
2023-06-07Guard for define in netcdf 4.9.0 and later. (#37853)Dan Lipsa2-0/+16
* Guard for define in netcdf 4.9.0 and later. This code is already available in ParaView 5.11.0 so no patching needed there. * Add latest needed version (even if not in spack). --------- Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
2023-06-07llvm: add new versions and set default for libomptarget according to os (#38092)Sajid Ali1-0/+5
* llvm: add new versions and set default for libomptarget according to os modified: var/spack/repos/builtin/packages/llvm/package.py * Incorporate reviewer suggestions Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com> --------- Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
2023-06-07nwchem: remove -mtune=native flags (#37892)Carlos Bederián1-0/+4
Co-authored-by: Edoardo Aprà <edoardo.apra@gmail.com>
2023-06-06julia: Update patch for llvm 14 without binary files (#37959)Mosè Giordano1-2/+2
2023-06-06openssl: add versions 1.1.1u, 3.0.9, 3.1.1 (#38023)Erik Schnetter1-3/+18
2023-06-06Add nextflow 23.04.1 (#38166)Diego Alvarez S1-0/+13
2023-06-06perl: convert to new stand-alone test process (#37727)Tamara Dahlgren1-11/+14
2023-06-06tests/ginkgo: converted to new stand-alone test process (#35730)Tamara Dahlgren1-55/+52
* Ginkgo: converted to new stand-alone test process * ginkgo: update string formatting, compiler setting
2023-06-06tests/darshan-util: convert to new stand-alone test process (#37836)Tamara Dahlgren1-24/+11
2023-06-06tests/oommf: convert to new stand-alone test process (#38009)Tamara Dahlgren1-77/+46
* oommf: convert to new stand-alone test process * oommf: Switch build-time tests to documented approach
2023-06-06tests/mfem: convert to new stand-alone test process (#38011)Tamara Dahlgren1-19/+11
* mfem: convert to new stand-alone test process * Restore make target, use config_mk property
2023-06-06@develop+stokhos: do not set Stokhos_ENABLE_PCE_Scalar_Type=False (#38187)eugeneswalker1-3/+0
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