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2022-08-18hiredis: set install_name on macos, ccache: optional hiredis (#32219)Axel Huebl2-2/+15
* hiredis: set install_name on macos * ccache: make hiredis optional Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-08-17Update busco to 5.4.3 (#32221)snehring3-4/+90
* metaeuk: new package * sepp: new package * busco: adding version 5.4.3 * busco: adding maintainers * metauk: more accurate cmake dep * sepp: adding missing dep and accurate python dep * sepp: remove install_tree * sepp: extend python
2022-08-18py-pytorch-lightning: add v1.7.2 (#32226)Adam J. Stewart1-0/+1
2022-08-17mpich: add patch fixing MPI_MIN for unsigned integers (#32188)Sergey Kosukhin1-0/+8
2022-08-17bugfix: use cmake version from dependency (#31739)Tom Scogland10-7/+42
Ensure that build tools with module-level commands in spack use the version built as part of their build graph if one exists. This is now also required for mesa, scons, cmake and ctest, out of graph versions of these tools in path will not be found unless added as an external. This bug appeared because a new version of rocprim needs cmake 3.16, while I have 3.14 in my path I had added an external for cmake 3.20 to the dag, but 3.14 was still used to configure rocprim causing it to fail. As far as I can tell, all the build tools added in build_environment.py had this problem, despite the fact that they should have been resolving these tools by name with a path search and find the one in the dag that way. I'm still investigating why the path searching and Executable logic didn't do it, but this makes three of the build systems much more explicit, and leaves only gmake and ninja as dependencies from out in the system while ensuring the version in the dag is used if there is one. The additional sqlite version is to perturb the hash of python to work around a relocation bug which will be fixed in a subsequent PR.
2022-08-17LLVM: add @15.0.0-rc1 (#31945)牟展佑1-1/+2
2022-08-17rct: update packages (RE, RG, RP, RS, RU) with new versions (#32216)Mikhail Titov5-5/+20
2022-08-17e4s mac ci: try lambda, the new mac studio runner (#32169)eugeneswalker2-7/+9
2022-08-17Add HDF5 version 1.13.2. (#32202)Larry Knox1-2/+1
* Add HDF5 version 1.13.2. Remove HDF5 versions 1.13.0 and 1.13.1. * Correct formatting.
2022-08-17Add riscv-gnu-toolchain package. (#32047)wanlinwang1-0/+66
Create a package for riscv-gnu-toolchain, a cross-compilation tool.
2022-08-17clingo: fix bootstrapping on M1/monterey with command line toolsTodd Gamblin1-1/+6
The Python that comes with XCode command line tools is a bit weird. This fixes two issues that were preventing it from bootstrapping: - [x] CommandLineTools python does not come with a `python-config` executable. If you don't have one of these, CMake's FindPython will, for some reason, assume that you want Python 2, so you need to set `CLINGO_PYTHON_VERSION` to ensure that clingo tells `find_package(Python <VERSION>)` the right thing. - [x] We weren't setting `PYTHONHOME` correctly in Python's `package.py`. We were setting it to the `prefix` from Python `sysconfig`, but `prefix` tells you where the executable lives. CommandLineTools python reports its prefix as /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8 but that doesn't exist. It looks like Apple builds the full python and just copies pieces of it into command line tools. PYTHONHOME is supposed to tell you where the default python library location is. So you have to look at the `base`, which `sysconfig` reports as /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8 On most systems this is probably the same as `prefix`, but not with CommandLineTools, which has its system library in a different place. The second change here was cherry-picked to 0d981a012d before merging and doesn't show up here. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-08-17python: simplify `libs()` and `headers()` methods in `python/package.py`Adam J. Stewart1-28/+46
- [x] Rework `headers` to search a sequence of directories and to display all searched locations on error, as opposed to handling each directory with a variable - [x] Make `headers` and `libs` do the same type of search and raise the same sort of errors. Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2022-08-17New package: py-bitshuffle (#31876)Jen Herting1-0/+26
* [py-bitshuffle] New package * [py-bitshuffle] compiling against spack hdf5 * [py-bitshuffle] flake8 * [py-bitshuffle] update import ine * [@spackbot] updating style on behalf of qwertos Co-authored-by: James A Zilberman <jazrc@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-08-17ncbi-toolkit: adding new version (#32098)snehring1-9/+8
2022-08-17Add omnitrace version 1.4.0 (#32160)Jonathan R. Madsen1-5/+9
* Add version 1.4.0 - override build variant with explicit variant instead of __init__ workaround * Update package.py
2022-08-17fasta-36.3.8h_2020-05-04 (#32180)Mike Renfro1-0/+5
* Adding 36.3.8h_2020-05-04 * [@spackbot] updating style on behalf of mikerenfro Co-authored-by: mikerenfro <mikerenfro@users.noreply.github.com>
2022-08-17rclone: add v1.59.1 (#32011)Erik Schnetter1-0/+1
2022-08-17acts: new versions 19.7.0, 20.0.0 (#32177)Wouter Deconinck1-2/+4
2022-08-17amr-wind: remove propagation of shared and openmp variant to dependencies. ↵Jon Rood1-5/+1
(#32182)
2022-08-17kokkos: set CMAKE_CXX_STANDARD instead of Kokkos_CXX_STANDARD (#31841)eugeneswalker1-1/+1
* kokkos@develop: set CMAKE_CXX_STANDARD instead of Kokkos_CXX_STANDARD * use CMAKE_CXX_STANDARD regardless of kokkos version
2022-08-17Add c++14 support flag for xl compiler (#31826)Peter Scheibel1-0/+8
2022-08-17lerc: add libs property (#31684)Adam J. Stewart1-0/+4
2022-08-17mxnet: prefer stable release (#31821)Adam J. Stewart1-1/+5
2022-08-17amrex: add v22.08 (#31844)Weiqun Zhang1-1/+2
2022-08-17e4s oneapi stack: remove notes for now-fixed builds (#31839)eugeneswalker1-3/+1
2022-08-17arm-forge: add v22.0.4. (#31835)RichardABunt1-0/+9
2022-08-17CI: reduce the amount of tests run in the original concretizer (#32179)Massimiliano Culpo2-3/+4
* CI: reduce the amount of tests run in the original concretizer * Don't test Python 3.6 on the original concretizer
2022-08-16kokkos: fix conflict for deprecated `sycl` namespaceTodd Gamblin1-1/+2
We're seeing errors pop up with older versions of Kokkos and newer versions of `oneapi`, specifically: error: no member named 'ONEAPI' in namespace 'sycl' This hapens because `sycl::ONEAPI` is `sycl::ext::oneapi` since oneapi `2022.0.0`. `kokkos@3.6:` uses the new namespace. A conflict was present for this, but it was too specific -- both to `dpcpp` and to the `2022.0.0` version. - [x] Expand version ranges in `kokkos` conflict - [x] Add conflict for `oneapi` in addition to `dpcpp`
2022-08-16filesystem: in recursive mtime, check only files that exist (#32175)Wouter Deconinck1-1/+1
* filesystem: use lstat in recursive mtime When a `develop` path contains a dead symlink, the `os.stat` in the recursive `mtime` determination trips up over it. Closes #32165.
2022-08-16bugfix: silence `clingo` warning about `requirement_policy/3`Todd Gamblin1-0/+1
`requirement_policy/3` is generated and may not be in Spack's inputs to Clingo. Currently this is causing warnings like: ``` $ spack spec zlib /global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:510:3-43: info: atom does not occur in any rule head: requirement_policy(Package,X,"one_of") /global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:517:3-43: info: atom does not occur in any rule head: requirement_policy(Package,X,"one_of") /global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:523:3-43: info: atom does not occur in any rule head: requirement_policy(Package,X,"any_of") /global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:534:3-43: info: atom does not occur in any rule head: requirement_policy(Package,X,"any_of") Input spec -------------------------------- zlib Concretized -------------------------------- zlib@1.2.11%gcc@7.5.0+optimize+pic+shared arch=cray-sles15-haswell ``` - [x] Silence warning with `#defined requirement_policy/3`
2022-08-16Add variant to install jellyfish in krakenuniq. (#32174)dunatotatos1-1/+7
2022-08-16Configuration: allow users to enforce hard spec constraints (#27987)Peter Scheibel7-75/+545
Spack doesn't have an easy way to say something like "If I build package X, then I *need* version Y": * If you specify something on the command line, then you ensure that the constraints are applied, but the package is always built * Likewise if you `spack add X...`` to your environment, the constraints are guaranteed to hold, but the environment always builds the package * You can add preferences to packages.yaml, but these are not guaranteed to hold (Spack can choose other settings) This commit adds a 'require' subsection to packages.yaml: the specs added there are guaranteed to hold. The commit includes documentation for the feature. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-08-16python: use base instead of prefix in `python/package.py`Todd Gamblin1-1/+1
2022-08-16Python: remove ensurepip variantAdam J. Stewart1-18/+1
2022-08-16celeritas: update checksum for git describe difference (#32000)Seth R. Johnson1-2/+2
* celeritas: update checksum for git describe difference Using `$Format:%h$` and the export-subst gitattribute property mean that the release checksum can change post release... ``` $ diff -ru spack-stage-celeritas-0.1.0-hv7ewpjouekqws2y5iaql2cnp6tn76iz/ spack-stage-celeritas-0.1.0.wtf-ynyck3df2a7kkgkqrpwapgz3l2i62omz/ diff -ru spack-stage-celeritas-0.1.0-hv7ewpjouekqws2y5iaql2cnp6tn76iz/spack-src/cmake/CgvFindVersion.cmake spack-stage-celeritas-0.1.0.wtf-ynyck3df2a7kkgkqrpwapgz3l2i62omz/spack-src/cmake/CgvFindVersion.cmake --- spack-stage-celeritas-0.1.0-hv7ewpjouekqws2y5iaql2cnp6tn76iz/spack-src/cmake/CgvFindVersion.cmake 2022-07-31 19:45:03.000000000 -0400 +++ spack-stage-celeritas-0.1.0.wtf-ynyck3df2a7kkgkqrpwapgz3l2i62omz/spack-src/cmake/CgvFindVersion.cmake 2022-07-31 19:45:03.000000000 -0400 @@ -75,7 +75,7 @@ # Get a possible Git version generated using git-archive (see the # .gitattributes file) - set(_ARCHIVE_TAG "HEAD -> master, tag: v0.1.0") + set(_ARCHIVE_TAG "tag: v0.1.0") set(_ARCHIVE_HASH "04fe945d9") set(_TAG_REGEX "v([0-9.]+)(-dev[0-9.]+)?") Binary files spack-stage-celeritas-0.1.0-hv7ewpjouekqws2y5iaql2cnp6tn76iz/v0.1.0.tar.gz and spack-stage-celeritas-0.1.0.wtf-ynyck3df2a7kkgkqrpwapgz3l2i62omz/v0.1.0.tar.gz differ ``` * celeritas: Use exported and re-uploaded tar.gz for reproducibility
2022-08-16e4s: add flecsi +cuda (#32158)eugeneswalker1-0/+1
2022-08-16e4s: add ascent +cuda (#32153)eugeneswalker1-0/+1
2022-08-16e4s: add amrex +cuda (#32152)eugeneswalker1-1/+2
2022-08-16podio, edm4hep: start to deprecate old versions (#32143)Thomas Madlener2-17/+85
2022-08-16direnv: add v2.32.1 (#32094)Alberto Invernizzi1-0/+1
2022-08-16e4s: add papi +rocm (#32150)eugeneswalker1-0/+1
2022-08-16e4s: add caliper +rocm (#32149)eugeneswalker1-0/+1
2022-08-15nlohmann-json: add v3.11.2 and make 'multiple_headers' the default (#31865)Florian Albrechtskirchinger1-1/+6
* nlohmann-json: add v3.11.2 * nlohmann-json: variant multiple_headers should be the default
2022-08-15CI/documentation: constrain pygments to avoid latest version (2.13.0) (#32163)Peter Scheibel1-0/+1
All PRs are failing the docs build on account of an error with pygments. These errors coincide with a new release of pygments (2.13.0) and restricting to < 2.13 allows the doc tests to pass, so this commit enforces that constraint for the docs build. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-08-15Check that no reserved names are overridden by package recipes (#32092)Massimiliano Culpo1-0/+40
A few attribute in packages are meant to be reserved for Spack internal use. This audit checks packages to ensure none of these attributes are overridden. - [x] add additional audit check
2022-08-15llvm: fix ncurses/terminfo builds (#32028)Andrew W Elble1-1/+6
* llvm: fix ncurses/terminfo builds * use suggestion * formatting
2022-08-15tophat: fixing build issue with newer automakes (#32082)snehring1-0/+4
2022-08-15netpbm: new super stable version 10.73.40 (#32087)Olivier Cessenat1-0/+1
2022-08-15MFEM: Add an exceptions variant. (#32096)Eric Brugger1-0/+2
2022-08-15bridger: adding ncurses dep (#32103)snehring1-0/+1