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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
2023-06-07Add documentation about package signing model (#30939)Christopher Kotfila2-0/+485
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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>
2023-06-06E4S Cray CI Stack (#37837)eugeneswalker7-2/+503
* e4s cray ci stack * e4s ci: add cray * add zen4 tag * WIP: new defintions just for cray * updates * remove ci signing job overrride, not necessary * echo $PATH and show modules loaded * add mirror * add external def for cray-libsci * comment out quantum-espresso * use /etc/protected-runner as key path * cray ci stack: do not remove tags: [spack, public] * make cray stack composable * generate job should run on public tagged runner, override default config:install_tree:root * CI: Use relative path in default script * CI: Use relative includes paths for shell runners * Use concrete_env_dir for relpath * ml-darwin-aarch64-mps: jax has bazel codesign issue --------- Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com> Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
2023-06-06CachedCMakePackage: fix bug where CMAKE_CUDA_ARCHITECTURES=none is set (#38169)Mikael Simberg1-2/+2
#37592 updated cached cmake packages to set CMAKE_CUDA_ARCHITECTURES. The condition `if archs != "none"` lead to `CMAKE_CUDA_ARCHITECTURES=none` when cuda_arch=none (incorrect check on the value of a multi-valued variant), i.e. CMAKE_CUDA_ARCHITECTURES is always set. This PR udpates the condition to if archs[0] != "none" to ensure CMAKE_CUDA_ARCHITECTURES is only set if cuda_arch is not none (which seems to be the pattern used in other packages). This does the same for HIP (although in general ROCmPackage disallows amdgpu_target=none when +rocm).
2023-06-06julia: Update patch for llvm 14 without binary files (#37959)Mosè Giordano1-2/+2
2023-06-06containers: don't install epel-release on Fedora (#37766)Jonathon Anderson9-44/+54
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
2023-06-06Don't build rocky:9 images for ppc64le (#38202)Massimiliano Culpo1-1/+1
See https://docs.rockylinux.org/release_notes/9_2/
2023-06-06@develop+stokhos: do not set Stokhos_ENABLE_PCE_Scalar_Type=False (#38187)eugeneswalker1-3/+0
2023-06-06eigenexa: convert to new stand-alone test process (#35745)Tamara Dahlgren1-19/+16
2023-06-05`libraqm`: add missing `fribidi` dependency (#36125)Thomas Bouvier2-0/+28
* `libraqm`: add missing `fribidi` dependency * `libraqm`: add `sheenbidi` variant * [@spackbot] updating style on behalf of thomas-bouvier --------- Co-authored-by: thomas-bouvier <thomas-bouvier@users.noreply.github.com>
2023-06-05Rename fpic variant to pic for fms (#38101)Alex Richert1-2/+2
2023-06-05Add MADIS package (#38097)Alex Richert1-0/+75
* Add MADIS package * madis update * [@spackbot] updating style on behalf of AlexanderRichert-NOAA * allow arg mismatch for gcc@10: for madis
2023-06-05ninja-phylogeny: adding new package ninja-phylogeny (#38182)snehring1-0/+28
2023-06-05asdcplib: add v2_10_38 (#37971)Alec Scott1-0/+1
2023-06-05fjcontrib: add v1.052 (#38116)Alec Scott1-0/+1
2023-06-05py-jupyterlab: add 4.0.1 incl. new dependencies (#38102)Manuela Kuhn15-55/+312
2023-06-05seal: add v4.1.1 (#38155)Alec Scott1-0/+1
2023-06-05ncbi-rmblastn: adding new version 2.14.0 (#38173)snehring1-1/+13
* ncbi-rmblastn: adding new version 2.14.0 * ncbi-rmblastn: add maintainer
2023-06-05azcopy: add v10.19.0 (#38106)Alec Scott1-0/+1
2023-06-05hssp: add v3.1.5 (#38107)Alec Scott1-0/+1
2023-06-05diamond: add v2.1.7 (#38115)Alec Scott1-0/+1
2023-06-05optional-lite: add v3.5.0 (#38148)Alec Scott1-0/+1
2023-06-05nccmp: add v1.9.1.0 (#38142)Alec Scott1-0/+1
2023-06-05starpu: add release 1.3.11 (#38172)Nathalie Furmento1-0/+1
2023-06-05Update RtD and Sphinx configuration (#38046)Massimiliano Culpo5-43/+41
2023-06-05Update package.py require HDF5 1.14+ (#38026)Houjun Tang1-8/+1
2023-06-05fastqc: add 0.12.1, update patch files (#37934)George Young3-3/+40
* fastqc: add 0.12.1 * fastqc: add 0.12.1 * Update var/spack/repos/builtin/packages/fastqc/package.py Yeah, had considered doing the same, I'd just opted to maintain the status quo. All good. Co-authored-by: Alec Scott <alec@bcs.sh> * Update package.py Style fiddles to make the bot contented. --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-05amrex: add version 23.06 (#38056)Weiqun Zhang1-0/+1
2023-06-05iozone: add v3_506 (#38118)Alec Scott1-0/+1
2023-06-05iqtree2: add v2.2.2 (#38119)Alec Scott1-0/+1
2023-06-05jimtcl: add v0.82 (#38120)Alec Scott1-0/+1
2023-06-05jline3: add v3.22.0 (#38121)Alec Scott1-0/+1
2023-06-05kubernetes: add v1.27.2 (#38123)Alec Scott1-0/+1
2023-06-05simde: add v0.7.6 (#38157)Alec Scott1-0/+1
2023-06-05leptonica: add v1.83.1 (#38125)Alec Scott1-0/+1
2023-06-05libcint: add v5.3.0 (#38127)Alec Scott1-0/+1
2023-06-05libeatmydata: add v131 (#38128)Alec Scott1-0/+1
2023-06-05libibumad: add v46.0 (#38130)Alec Scott1-0/+1
2023-06-05librdkafka: add v2.1.1 (#38131)Alec Scott1-0/+1
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