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2024-05-13gaudi: upstream patch when @38.1 for missing #include <list> (#44121)Wouter Deconinck1-0/+5
* gaudi: upstream patch when @38.1 for missing #include <list> * gaudi: apply list patch for all versions
2024-05-13spack uninstall: improve error message for dependent environment (#44149)Greg Becker1-0/+2
2024-05-13whip: Add 0.3.0 (#44146)Mikael Simberg1-0/+1
Co-authored-by: Mikael Simberg <simbergm@cscs.ch>
2024-05-13spack checksum: do not add expand=False to wheels (#44118)Adam J. Stewart1-11/+1
2024-05-12llvm: add 18.1.5, 18.1.4 (#44123)Paul R. C. Kent1-0/+2
2024-05-12R: common package updates for 4.4.0 (#44088)bk6-2/+25
* r-ggplot2: v3.5.1, r-haven: v2.5.4, r-jsonlite: v1.8.8, r-pkgload: v1.3.4, r-vctrs: v0.6.5 * r-scales: v1.3.0
2024-05-12Add applications to aws-pcluster-* stacks (#43901)Stephen Sachs5-38/+73
* Add openfoam to aws-pcluster-neoverse_v1 stack * Add more apps to aws-pcluster-x86_64_v4 stack * Remove WRF while hdf5 cannot build in buildcache at the moment * Update comment * Add more apps for aws-pcluster-neoverse_v1 stack * Remove apps that currently do not build * Disable those packages that won't build * Modify syntax such that correct cflags are used * Changing syntax again to what works with other packages * Fix overriding packages.yaml entry for gettext * Use new `prefer` and `require:when` clauses to clarify intent * Use newer spack version to install intel compiler This removes the need for patches and makes sure the `prefer` directives in `package.yaml` are understood. * `prefer` not strong enough, need to set compilers * Revert "Use newer spack version to install intel compiler" This reverts commit ecb25a192cc430ca946415108847d637b4000795. Cannot update the spack version to install intel compiler as this changes the compiler hash but not the version. This leads to incompatible compiler paths. If we update this spack version in the future make sure the compiler version also updates. Tested-by: Stephen Sachs <stesachs@amazon.com> * Remove `prefer` clause as it is not strong enough for our needs This way we can safely go back to installing the intel compiler with an older spack version. * Prefer gcc or oneapi to build gettext * Pin gettext version compatible with system glibc-headers * relax gettext version requirement to enable later versions * oneapi cannot build older gettext version
2024-05-12whizard: Add version 3.1.4 (#43045)Juan Miguel Carceller1-1/+3
* whizard: Add a patch to fix builds with pythia8 >= 8.310 * Add whizard 3.1.4 and update accordingly --------- Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2024-05-12octave: use pcre2 for @8: (#42636)Alex Richert1-1/+6
* octave: use pcre2 for @8: * Add 'pcre2' variant to octave to control pcre vs. pcre2 * Update var/spack/repos/builtin/packages/octave/package.py Co-authored-by: Alec Scott <hi@alecbcs.com> --------- Co-authored-by: Alex Richert <alexander.richert@noaa.gov> Co-authored-by: Alec Scott <hi@alecbcs.com>
2024-05-12fastjet: Add a cxxstd variant (#44072)Juan Miguel Carceller1-0/+13
* fastjet: Add a cxxstd variant * Use f-strings * Add multi=False --------- Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2024-05-12clang: support cxx20_flag and cxx23_flag (#43438)Wouter Deconinck2-1/+33
* clang: support cxx20_flag and cxx23_flag * clang: coverage test cxx{}_flag and c{}_flag additions
2024-05-11Bump version on `develop` to v0.23dev0 (#44137)Todd Gamblin1-1/+1
2024-05-11changelog: add changes form 0.21.1 and 0.21.2 (#44136)Todd Gamblin1-0/+45
These changes were added to the release branch but did not make it onto `develop`.
2024-05-11oci: improve default_retry (#44132)Harmen Stoppels1-3/+12
Apparently urllib can throw a range of different exceptions: 1. HTTPError 2. URLError with e.reason set to the actual exception 3. TimeoutError from getresponse, which is not wrapped
2024-05-10qpdf: new package (#44066)James Taliaferro1-0/+45
* New package: qpdf * Update var/spack/repos/builtin/packages/qpdf/package.py Co-authored-by: Alec Scott <hi@alecbcs.com> * Fix format of cmake_args --------- Co-authored-by: Alec Scott <hi@alecbcs.com>
2024-05-10New package: py-nuitka (#44079)James Smillie1-0/+24
2024-05-10Buildcache/ensure symlinks proper prefix (#43851)John W. Parent7-13/+29
* archive: relative links only Ensure all links written into tarfiles generated from Spack prefixes do not contain symlinks pointing outside the prefix * binary_distribution: limit extraction to prefix Ensure files extracted from spackballs are not links pointing outside of the prefix * Ensure rpaths are properly set on Windows * hard error on extraction of absolute links * refactor for non link-modifying approach * Restore tarball extraction to original impl * use custom readlink * cleanup symlink module * make lstrip
2024-05-10Windows: Non config changes to support Gitlab CI (#43965)John W. Parent9-119/+119
* Quote python for shlex * Remove python path quoting patch * spack env: Allow `C` "protocol" for config_path When running spack on windows, a path beginning with `C://...` is a valid path. * Remove makefile from ci rebuild * GPG use llnl.util.filesystem.getuid * Cleanup process_command * Remove unused lines * Fix tyop in encode_path * Double quote arguments * Cleanup process_command * Pass cdash args with = * Escape parens in CMD script * escape parens doesn't only apply to paths * Install deps * sfn prefix * use sfn with libxml2 * Add hash to dep install * WIP * REview * Changes missed in prior review commit * Style * Ensure we handle Windows paths with config scopes * clarify docstring * No more MAKE_COMMAND * syntax cleanup * Actually correct is_path_url * Correct call * raise on other errors * url2path behaves differently on unix * Ensure proper quoting * actually prepend slash in slash_hash --------- Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com> Co-authored-by: Mike VanDenburgh <michael.vandenburgh@kitware.com>
2024-05-10dd4hep: cleanup recipe, remove deprecated versions and patches (#44110)Juan Miguel Carceller3-123/+1
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2024-05-10edm4hep: cleanup recipe, remove deprecated versions and patches (#44113)Juan Miguel Carceller2-86/+3
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2024-05-10libtheora: Remove unneeded autoreconf section (#44063)Chris Marsh1-6/+0
* Remove autoreconf section that was causing issues with libtool mismatch. Fixes issue #43498
2024-05-10dla-future: Add 0.4.1 (#44115)Mikael Simberg1-0/+3
* dla-future: Add 0.4.1 * Use ninja as generator in dla-future
2024-05-10pika: Add 0.25.0 (#44114)Mikael Simberg1-0/+2
2024-05-10libhugetlbfs: Fix the build with an update to 2.24 (#44059)Stephen Sachs1-5/+15
Co-authored-by: Stephen Sachs <stesachs@amazon.com> Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2024-05-10PythonExtension: fix issue where package does not extend python (#44109)Harmen Stoppels1-8/+12
2024-05-09flux-sched: set the version if the ver file is missing (#44068)Tom Scogland1-0/+4
* flux-sched: set the version if the ver file is missing problem: flux-sched needs a version, it normally gets this from a release tarball or from git tags, but if using a source archive or a git clone without tags the version is missing solution: set the version through cmake based on the version spack sees when the version file is missing * Update var/spack/repos/builtin/packages/flux-sched/package.py Co-authored-by: Alec Scott <hi@alecbcs.com> --------- Co-authored-by: Alec Scott <hi@alecbcs.com>
2024-05-09miniforge3: add new versions with mamba installation (#43995)Christopher Christofi1-39/+52
* miniforge3: add new version with mamba installation * fix styling * update maintainers * Fix variant directive ordering
2024-05-09Fix filtering external specs (#44093)Massimiliano Culpo4-0/+64
When an include filter on externals is present, implicitly include libcs. Also, do not penalize deprecated versions if they come from externals.
2024-05-09pythia8: add a cxxstd variant (#44077)Juan Miguel Carceller1-0/+14
* pythia8: add a cxxstd variant * Add multi=False, fix regexp --------- Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2024-05-09kokkos-nvcc-wrapper: add missing versions (#44089)Richard Berger1-0/+4
2024-05-09mmg: Build & install shared libraries, add 5.7.2 & 5.7.3(#43749)Julien Cortial1-0/+3
2024-05-09Universal Ctags: Add version 6.1.20240505.0 (#44058)Rémi Lacroix1-0/+3
2024-05-09CI/Update macOS runners: macos-latest switched to macos-14 (#44094)Massimiliano Culpo1-1/+1
macos-latest switched to macos-14, so now we are running two identical jobs.
2024-05-09package: libsodium update URL to GitHub (#44090)Vanessasaurus1-10/+6
Problem: the libsodium download endpoints are not reliable, they fail multiple times a day for several of our automated pipelines. Solution: use the GitHub releases and branches. Signed-off-by: vsoch <vsoch@users.noreply.github.com>
2024-05-09Kokkos: adding new release 4.3.01 (#44086)Luc Berger2-0/+3
2024-05-09Octopus 14.1 : Add new version hash (#44083)Ashwin Kumar Karnad1-0/+6
* octopus: add hash for new version * octopus: add --enable-silent-deprecation flag when @14.1:
2024-05-09amr-wind: add missing variants (#44078)Jon Rood1-16/+33
* amr-wind: add missing variants * Fix copy and paste. * waves2amr is only available on amr-wind@2.0 * Style. * Use satisfies.
2024-05-08Orca (standalone) 5.0.4 (#44011)alvaro-sch1-1/+2
* orca: added latest version 5.0.4 * Fixed openmpi versions
2024-05-08mpich: Add license (#43821)Ken Raffenetti1-1/+1
2024-05-08hipsparselt: new package (#44080)Sreenivasa Murthy Kolam2-0/+169
* Initial commit for adding hipsparselt recipe * correct the style errors * remove master version
2024-05-08gcc: use -idirafter for libc headers (#44081)Harmen Stoppels1-1/+1
GCC C++ headers like cstdlib use `#include_next <stdlib.h>` to wrap libc headers. We're using `-isystem` for libc, which puts those headers too early in the search path. `-idirafter` fixes this so `include_next` works.
2024-05-08JAX: add v0.4.27, NCCL variant (#44071)Adam J. Stewart2-113/+131
2024-05-08add flag to turn off building tests and examples (#44075)Jake Koester1-0/+6
2024-05-08py-jsonargparse: add v4.28.0 (#44074)Adam J. Stewart1-0/+1
2024-05-08hypre: add cublas and rocblas variants (#44038)Jon Rood1-1/+12
* Add cublas and roblas variants to hypre. * Fix mistakes. * Remove newline. * Address suggestions.
2024-05-08Bump up the version for ROCm-6.1.0 (#43843)renjithravindrankannath58-66/+1054
* Bump up the version for ROCm-6.1.0 * Style check error correction and patch files * Update for rocm-openmp-extras 6.1 * updating rocm-openmp-extras and math libraries with 6.1 * Style check error correcion * updating hipcub, hipfort & miopen-hip for 6.1 * Rocm-openmp-extras and some mathlib updates * iAudit error correction and rocmlir update * Updating dependency on suite-sparse and adding path * Style check error corection * hip-tensor 6.1.0 update * rdc 6.1 needs grpc 1.59.1 * rvs 6.1 updates and patch
2024-05-08build(deps): bump actions/checkout from 4.1.4 to 4.1.5 (#44045)dependabot[bot]8-19/+19
Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.4 to 4.1.5. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/0ad4b8fadaa221de15dcec353f45205ec38ea70b...44c2b7a8a4ea60a981eaca3cf939b5f4305c123b) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2024-05-08darshan-runtime,darshan-util,py-darshan: add darshan-3.4.5 packages (#43989)shanedsnyder3-3/+10
* add darshan-3.4.5 packages, update URLs * py-setuptools version switches for py-darshan * more py-darshan test dependencies * try a conditional importlib_resources dependency
2024-05-08iq-tree: add new version delete duplicate package (#44043)snehring4-45/+5
* iq-tree: add new version delete duplicate package * Replace iqtree2 dependency orthofinder: replace iqtree2 with iq-tree@2 py-phylophlan: replace iqtree2 with iq-tree@2
2024-05-08gitlab ci: tutorial: add `julia` and `vim` (#44073)Harmen Stoppels2-2/+2
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