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2023-06-27Revert "Updates to symlinking for Windows (#34701)" (#38578)Harmen Stoppels13-817/+191
This reverts commit 66f75407d136c0c06ed01774d5815728afba35ca.
2023-06-26CachedCMakePackage: set build type (#38502)Brian Van Essen2-8/+1
Fixed the cached CMake package so that the build_type field is saved in the cached configuration file.
2023-06-26py-numpy: add v1.24.4 (#38555)Adam J. Stewart1-0/+1
2023-06-26Updates to symlinking for Windows (#34701)David Alexander13-191/+817
* Support hardlinks/junctions on Windows systems without developer mode enabled * Generally, use of llnl.util.symlink.symlink is preferred over os.symlink since it handles this automatically * Generally an error is now reported if a user attempts to create a symlink to a file that does not exist (this was previously allowed on Linux/Mac). * One exception to this: when Spack installs files from the source into their final prefix, dangling symlinks are allowed (on Linux/Mac - Windows does not allow this in any circumstance). The intent behind this is to avoid generating failures for installations on Linux/Mac that were succeeding before. * Because Windows is strict about forbidding dangling symlinks, `traverse_tree` has been updated to skip creating symlinks if they would point to a file that is ignored. This check is not transitive (i.e., a symlink to a symlink to an ignored file would not be caught appropriately) * Relocate function: resolve_link_target_relative_to_the_link (this is not otherwise modified) Co-authored-by: jamessmillie <smillie@txcorp.com>
2023-06-26krb5: add missing findutils dependency (#38440)Manuela Kuhn1-0/+1
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-26modules: ignore more Modules variables in from_sourcing_file (#38455)Xavier Delaruelle3-6/+51
Update list of excluded variables in `from_sourcing_file` function to cover all variables specific to Environment Modules or Lmod. Add specifically variables relative to the definition of `module()`, `ml()` and `_module_raw()` Bash functions. Fixes #13504
2023-06-26Adds new Qthreads package version (#38421)Carson Woods1-2/+16
* Add new versions of Qthreads * Add version URLs explicitly as it has recently changed * Use function to extrapolate version URL for older versions * Fix url formatter
2023-06-26Openfoam: replace two boolean variants with multi-valued variant for ↵kjrstory1-6/+11
precision option (#37736)
2023-06-26llvm: fix build against libstdc++ 13 (#38329)Martin Aumüller1-0/+7
llvm @13-15 is required for ispc, but fails to build with GCC 13. 14.0.6 and 15.0.7 built successfully with upstream patch, 13.0.1 still fails. Thus upstream patch is applied to 14 and 15 only.
2023-06-26ufs-utils: update urls, versions, and dependencies (#37255)Alex Richert1-4/+9
2023-06-26tests/heffte/tasmanian: convert to new stand-alone test process (#35750)Tamara Dahlgren2-119/+37
2023-06-26cromwell: add v85 (#38427)George Young1-3/+8
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-26netcdf-c: apply patches (#38324)Sergey Kosukhin1-0/+19
* netcdf-c: fix building on macOS * netcdf-c: add patch fixing multi-threaded HDF5 calls * netcdf-c: update patch url
2023-06-26mmseqs2: patching to support building with %gcc@13: (#38296)George Young1-0/+8
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-26scotch: add new variants + bison version min. (#37958)Cameron Book1-3/+5
2023-06-26ginkgo: add version 1.6.0 (#38439)Terry Cojean1-4/+3
2023-06-26acfl: remove version 23.04 (#38363)Annop Wongwathanarat1-34/+0
2023-06-26armpl-gcc: remove version 23.04 (#38362)Annop Wongwathanarat1-52/+1
2023-06-26py-python-lzo: add 1.15 (#38418)George Young1-1/+2
* py-python-lzo: add 1.15 * Update package.py --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-26demuxlet: add new package (#38425)snehring1-0/+35
2023-06-26spectre: add v2023.06.19 (#38474)SXS Bot1-0/+3
Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
2023-06-26tests/*mpi*: convert to new stand-alone test process (#35802)Tamara Dahlgren3-135/+99
2023-06-26Add raw attribute to env.set command (#38465)Xavier Delaruelle5-9/+58
Update `env.set` command and underlying `SetEnv` object to add the `raw` boolean attribute. `raw` is optional and set to False by default. When set to True, value format is skipped for object when generating environment modifications. With this change it is now possible to define environment variable whose value contains variable reference syntax (like `{foo}` or `{}`) that should be set as-is. Fixes #29578
2023-06-26acts: ensure Python_EXECUTABLE uses ^python when +python (#38540)Wouter Deconinck1-0/+4
By default, `find_package(Python)` searches from highest version to lowest version, identifying the highest version that satisfies the requirements. This means that `/usr/bin/python3.11` will be found before `$(spack location -i python)/bin/python3.10`, even when other packages have been built with the `python` in spack. This ensures that the `python` dependency is explicitly the `python` version that is used.
2023-06-26py-scipy: add v1.11.0 (#38546)Adam J. Stewart3-10/+25
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-06-26MOLGW: add new package (#37878)Fabien Bruneval1-0/+112
2023-06-26bzip2: add pkg-config file (#38355)is-a-gamer1-0/+19
Co-authored-by: HongZhi He <a13041902330@outlook.com>
2023-06-25libxml2: convert to new stand-alone test process (#37694)Tamara Dahlgren1-35/+82
2023-06-24ascent: add optional occa dep (#38426)Cyrus Harrison1-0/+13
Co-authored-by: cyrush <cyrush@users.noreply.github.com>
2023-06-24gmap-gsnap: updating to 2023-06-01 (#38428)George Young1-0/+6
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-24circe2: add new package (#38491)Thomas Madlener1-0/+42
2023-06-24apptainer: add squashfuse dep (#38499)snehring1-0/+1
2023-06-24etsf-io: convert to new stand-alone test process (#35746)Tamara Dahlgren1-19/+6
2023-06-24gaudi: new versions 36.[11-14] (#38498)Wouter Deconinck1-0/+4
2023-06-24hpctoolkit: convert to new stand-alone test process (#35752)Tamara Dahlgren1-15/+20
2023-06-24clp and osi depend on pkgconfig (#31505)miheer vaidya2-0/+2
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-06-24GSI-ncdiag: add v1.1.0 and v1.1.1. (#38196)David Huber1-1/+3
Co-authored-by: [David Huber] <[david.huber@noaa.gov]>
2023-06-24Fix syntax to set default target in aws-pcluster pipelines (#38048)Stephen Sachs5-5/+5
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-24libzmq: Fix static assertion failure with gcc-13 (#38391)Dennis Klein1-0/+9
2023-06-24pfunit: fix the max_array_rank variant definition (#38528)Matthew Thompson1-2/+2
2023-06-24DMTCP: add v3.0.0. (#38307)Kapil Arya1-1/+3
2023-06-24lammps: new verisons (#38532)Richard Berger1-4/+6
2023-06-24Fixes openmpi configure args for multinode execution on slurm (#38403)Gurkirat Singh1-5/+15
Remove `--enable-mca-no-build=btl-uct` check for ucx spec as it is already fixed in the openmpi open-mpi/ompi#6666
2023-06-24range-v3: remove overbroad boost dependence (#38539)Chris Green1-8/+10
Co-authored-by: greenc-FNAL <greenc-FNAL@users.noreply.github.com>
2023-06-23libEnsemble: add v0.10.0 (#37954)Stephen Hudson1-4/+6
* libEnsemble: add v0.10.0 * Make new deps required * Fixes to deps * Update var/spack/repos/builtin/packages/py-libensemble/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Fix build, run * Reorder required deps --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-23py-pytest: add 7.3.2 (#38522)Manuela Kuhn1-8/+8
* py-pytest: add 7.3.2 * [@spackbot] updating style on behalf of manuelakuhn * Swap py-importlib-metadata dependency order * Restrict python version for older versions
2023-06-23Add recipe for iterative-stats (#38039)mschouler1-0/+35
* Add recipe for iterative-stats * Fix branch name and remove comment * Add git link * Add package maintainer * Enforce multiple requested changes * Update var/spack/repos/builtin/packages/py-iterative-stats/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update checksum * Fix openturns dependency specification * Add python variant spec to openturns --------- Co-authored-by: Marc Schouler <marc.schouler@inria.fr> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-23Added version 0.33 (#38534)julian-zeidler1-0/+1
2023-06-23fix version dependency logic (#38535)G-Ragghianti1-1/+1
2023-06-23zlib-ng: add latest, default to drop in replacement of zlib (#37370)Harmen Stoppels1-6/+25
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