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Merge from upstream including buildcache fix https://github.com/spack/spack/pull/46074 #436
Merge from upstream including buildcache fix https://github.com/spack/spack/pull/46074 #436
Commits on Aug 22, 2024
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VTK package: patch to fix NetCDFC - HDF5 interface (spack#43087)
Patch from Windows is also needed on Linux
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llvm-amdgpu: Conflict with MacOS (spack#45633)
Currently, the llvm-amdgpu package doesn't compile on MacOS, but it is also not marked as a conflict. This causes problems because it seems that Spack is very happy to pull in llvm-amdgpu as the default package to satisfy any virtual libllvm dependency, which can cause dependent specs to fail to install on MacOS. This commit marks a conflict between this llvm package and the Darwin platform.
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Add a new audit to find missing package.py files (spack#45868)
* Add a new audit to find missing package.py files * Remove directory without package.py
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Commits on Aug 23, 2024
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removing -Ofast with aocc (spack#45880)
Co-authored-by: shbhaska <shbhaska@amd.com>
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poppler: change the URL of the test repository (spack#45857)
* poppler: change the URL of the test repository
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py-ipykernel: add version 6.29.5 (spack#45876)
* py-ipykernel: add version 6.29.5 * add maintainers for spack package
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xrootd: change urls to xrootd.web.cern.ch (spack#45895)
* xrootd: change urls to xrootd.web.cern.ch * xrootd: change homepage
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Add missing MultiMethodMeta metaclass in builders (spack#45879)
* Add missing MultiMethodMeta metaclass in builders and remove the Python 2 fallback option in favor of hard errors to catch similar issues going forward. The fallback option can cause about 10K stat calls due to use of `realpath` in the inspect module, depending on how deep Spack itself is nested in the file system, which is ... undesirable. * code shuffling to avoid circular import * more reshuffling * move reserved variant names into variants module
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acts: add v36.0.0, v36.1.0 and fixes (spack#45874)
* acts: add v36.0.0, v36.1.0 and fixes This commit makes several changes to the Acts repository, namely: 1. It adds versions 36.0.0 and 36.1.0. 2. It adds the traccc plugin and related dependencies. 3. It updates the version requirements of some dependencies. 4. It adds the Geant4 module of GeoModel. 5. It updates the C++ standard requirement. 6. It adds a new variant determining the scalar type to use. This commit supercedes spack#45851. Thanks @jmcarcell for the version updates; I have added you as co-author. Co-authored-by: Juan Miguel Carceller <22276694+jmcarcell@users.noreply.github.com> * Updates * alphabetic cmake args --------- Co-authored-by: Juan Miguel Carceller <22276694+jmcarcell@users.noreply.github.com>
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py-autograd: mark numpy 2 compatibility (spack#45942)
* py-autograd: mark numpy 2 compatibility * Fix syntax error
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ddt: add v23.0.4 -> v24.0.3 (spack#45861)
* ddt: add v23.0.4 -> v24.0.3 * ddt: fix url_for_version for 22.1.3 --------- Co-authored-by: Lydéric Debusschère <lyderic.de@gmail.com>
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davix: add versions 0.8.2-0.8.7 and dependencies (spack#45853)
* davix: add versions 0.8.2-0.8.7 and dependencies This commit adds new versions 0.8.2-0.8.7 of the davix package, and it also improves the handling of embedded packages. Davix will try to build libcurl from its own embedded version of that code, which doesn't mesh well with Spack's design philosophy, so I've changed the CMake configuration to disallow the builtin libcurl and use a Spack dependency instead. Up to version 0.8.7, RapidJSON was also builtin, but version 0.8.7 allows users to specify that they want to use a pre-installed version of RapidJSON, so this commit also adds that as a dependency for versions 0.8.7:. * Fix old versions
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VTK-m: Point to github mirror for source tarball (spack#45893)
* VTK-m: Point to github mirror for source tarball The gitlab.kitware.com source location seems to have intermittent network issues. Switching the to mirror hosted at Github may alleviate some of the timeouts. * Update sha256 for GitHub tarballs --------- Co-authored-by: Zack Galbreath <zack.galbreath@kitware.com>
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Commits on Aug 24, 2024
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mirror: fetch by digest (spack#45809)
Source mirrors store entries by digest and add a human readable alias of the form 'name-version'. If no digest is available, the alias is used as the primary storage location. Spack erroneously fetches by alias when the digest path does not exist. This is problematic if `version(..., sha256=...)` changes in package.py, and the mirror is populated with the old shasum. That would result in an error when a digest is available, but in case of git versions with a modified commit sha, the wrong sources would be fetched without error. With this PR, only the digest path is used, not the alias, in case a digest is available. This is also a small performance optimization, as the number of request is halved for mirrors that don't contain the sources. Further, for git sources the tag was used as a digest, but this is a moving target. Only commit sha is used now. Also whenever the alias already existed, Spack used to keep it in place when updating the mirror cache, which means that aliases would always point to outdated mirror entries whenever digests are modified. With this PR the alias is moved in place. Lastly, fix a recent regression where `Stage.disable_mirrors` disabled mirrors but not the local download cache, which was the intention.
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Commits on Aug 26, 2024
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Python: add v3.12.5, default to latest version (spack#45712)
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
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netfilter pkgs: avoid 3rd party urls, add latest official version (sp…
…ack#46027) Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
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R: external detection (spack#46023)
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
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ci generate
: don't warn when no cdash config (spack#46004)Right now if you run `spack ci generate` you get a warning about CDash credentials even if there's no CDash configuration specified. We should only warn if there was actually a CDash config. Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
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gaudi: remove redundant dependency on cppgsl (spack#46029)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
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kokkos: add v4.4.00 (spack#45758)
Co-authored-by: Patrick Diehl <diehlpk@lanl.gov>
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fastjson: add v1.2.83, v2.0.52 (spack#45733)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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parallel-hashmap: add v1.3.12 (spack#46017)
Co-authored-by: pranav-sivaraman <pranav-sivaraman@users.noreply.github.com>
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sundials: new test API (spack#45373)
* sundials: new test API --------- Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
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Commits on Aug 27, 2024
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acts: add version 36.2.0 (spack#46052)
This commit adds version 36.2.0 of ACTS. As far as I can tell, there are no dependency changes.
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detray: add version 0.73.0 (spack#46053)
This commit adds version 0.73.0 of the detray package. As this version drops support for pre-C++20 standards, I had to update the `cxxstd` variant logic.
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Remove "prevent_cray_detection" context manager (spack#46060)
This context manager was used to prevent detecting a platform as "cray". Since now Cray machines are detected as linux, we can remove the context manager.
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Commits on Aug 28, 2024
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Spec.from_detection now accounts for external prefix (spack#46063)
Change the signature of Spec.from_detection to set the external prefix, and the external modules, if they are present. Delete "spack.package_prefs.spec_externals" since it is unused.
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gromacs: add conflict between NVSHMEM and cuFFTMp (spack#46065)
* Add conflict between NVSHMEM and cuFFTMp for GROMACS package These don't work in the same build configuration. * [@spackbot] updating style on behalf of mabraham * Update package.py Also constrain NVSHMEM appropriately * Update var/spack/repos/builtin/packages/gromacs/package.py Co-authored-by: Andrey Alekseenko <al42and@gmail.com> * Update package.py * [@spackbot] updating style on behalf of mabraham * Update package.py * Update package.py * Update package.py * [@spackbot] updating style on behalf of mabraham --------- Co-authored-by: mabraham <mabraham@users.noreply.github.com> Co-authored-by: Christoph Junghans <christoph.junghans@gmail.com> Co-authored-by: Andrey Alekseenko <al42and@gmail.com>
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Drop now redundant use of inspect (spack#46057)
inspect.isclass -> isinstance(..., type) inspect.getmro -> cls.__mro__
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boost: install
BoostConfig.cmake
even when header-only (spack#46062)* Install BoostConfig.cmake even when header-only * boost: Only use --without-libraries when --with-libraries would have an empty list
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mfem, pflotran, alquimia: remove old versions with xsdk string (in ve…
…rsion) that were used in old/removed xsdk releases (spack#45837)
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Don't check checksums on spack-develop packages (spack#46076)
Fix regression introduced in spack 0.22.1 where Spack would ask about checksums on spack-develop packages.
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py-numcodecs rename git branch to match upstream (spack#46085)
* py-numcodecs rename git branch to match upstream
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pmix: add v5.0.3 and fix variants (spack#45621)
* Add pmix v5.0.3 and fix variants * Update pmix homepage link * pmix: Simplify/update hwloc dependency * pmix: Update versions for --disable-sphinx configure option * pmix: Add munge variant * pmix: Add zlib dependency * pmix: Fix dependency py-sphinx@5
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perl-compress-bzip2: new package (spack#46055)
* perl-compress-bzip2: new package Adds Compress::Bzip2 * Use bzip2 from Spack, not system
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Commits on Aug 29, 2024
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Remove "get_compiler_duplicates" (spack#46077)
This function is used only in tests.
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tau: fix (cray) compiler names/paths (spack#46104)
fixes a build issue on cray ci
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paraview: add cdi support (spack#44222)
* add basic CDI package * add CDI variant to paraview * [@spackbot] updating style on behalf of albestro --------- Co-authored-by: albestro <albestro@users.noreply.github.com>
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linaro-forge: added 24.0.4 version (spack#46112)
Updated platform.machine() to only match "aarch64". "arm64" not supported by "spack arch"
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CMakePackage: Set policy CMP0042 NEW on macos (spack#46114)
so linking to shared libraries works well at runtime on darwin for all packages with cmake_minimum_required < 3.
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conduit package: Honor compiler extra_rpaths + extras (spack#46046)
- Honor compiler extra_rpaths (this build bypasses spack wrappers, so the RPATHs are added explicitly as CMake options) - Use root_cmakelists_dir instead of adding it to the command line - Add BLT as a dependency, allowing different versions outside of what is in the tarball - Put a copy of host-config in the stage directory: this allows examination of the host-config when a build fails (before, the host-config was just stored in the install directory, which is deleted by default on a failed build)
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Commits on Aug 30, 2024
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cray: allow failure due to broken blas (spack#46111)
1. libsci_cray.so is broken, as it fails to list `libdl.so` in DT_NEEDED. 2. cray compilers fail to build a different blas
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Remove
DetectedPackage
class (spack#46071)This PR simplifies the code doing external spec detection by removing the `DetectedPackage` class. Now, functions accepting or returning lists of `DetectedPackage`, will accept or return list of specs. Performance doesn't seem to change if we use `Spec.__reduce__` instead of `DetectionPackage.__reduce__`.
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Put some more constraint on a few mpi providers (spack#46132)
This should help not selecting, by default, some niche implementation that are supposed to be externals. Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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windows-vis: fix failing pipeline (spack#46135)
* seacas: fix gnu parallel dep * add vtk@9.0 platform=windows conflict
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unzip: use more generic strip flag for cce (spack#46087)
* Use more generic strip flag for cce * [@spackbot] updating style on behalf of etiennemlb * Apply always
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Commits on Aug 31, 2024
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build(deps): bump actions/upload-artifact from 4.3.6 to 4.4.0 (spack#…
…46149) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4.3.6 to 4.4.0. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@834a144...5076954) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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sfcio: add v1.4.2 (spack#46146)
* sfcio: add v1.4.2 * [@spackbot] updating style on behalf of AlexanderRichert-NOAA
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build(deps): bump actions/setup-python from 5.1.1 to 5.2.0 (spack#46129)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.1.1 to 5.2.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@39cd149...f677139) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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New package: py-ops (spack#46122)
* New package: py-ops * [py-ops] - added version 2.16.0 - ran black - updated copyright - added license() --------- Co-authored-by: vehrc <vehrc@rit.edu>
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New package: py-jsonlines (spack#46124)
* py-jsonlines: new package * py-jsonlines: fix dependency --------- Co-authored-by: Alex C Leute <acl2809@rit.edu>
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podio: apply patch for gcc 14 builds (spack#45854)
* podio: apply patch for gcc 14 builds Podio versions after 0.17.0 but before 1.0.0 are broken when using gcc 14 because of a missing include, which is addressed in the podio pull request at AIDASoft/podio#600. This commit patches pre-1.0.0 versions of Podio so they can be compiled with gcc 14, which is important for building Acts. * Style * Style 2 * Fixes * Add comment: * Add sha256
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whizard: add a patch when using hepmc3 3.3.0 or newer (spack#45862)
* whizard: add a patch when using hepmc3 3.3.0 or newer * whizard: comment with patch origin --------- Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com> Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
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Commits on Sep 1, 2024
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dd4hep: mark conflict with root@6.31.1: (spack#45855)
dd4hep versions up to and including 1.27 had a conflict with root versions starting from 6.31.1, as shown in AIDASoft/DD4hep#1210. This PR explicitly adds that conflict to the spec.
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Commits on Sep 2, 2024
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package cln 1.3.7 feelpp#2 (spack#46162)
* package cln 1.3.7 feelpp#2 * add myself as maintainer * fix style issue, rm blankline
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docs: update conditional definition arch (spack#46139)
Signed-off-by: Georgia Stuart <gstuart@umass.edu> Co-authored-by: Jordan Galby <67924449+Jordan474@users.noreply.github.com>
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cuda: add v12.6.1 (spack#46143)
Update build system conflict between CUDA 12.6 and Clang 18
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[neovim] add utf8proc dependency (spack#46064)
I believe utf8proc was added as a neovim dependency in neovim/neovim#26165 and is only in the master branch.
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podio: Add the new datasource variant once it is available (spack#46078)
* podio: Add the new datasource variant once it is available * Make sure to require a suitable minimal root version
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py-sympy: add version 1.13.0 (spack#46163)
* sympy: add version 1.13.0 * sympy: update deps
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py-cellprofiler: add 4.2.6 new package (spack#44824)
* py-cellprofiler: add 4.2.6 new package * py-mysqlclient: Limit pkg-config patch to @1.4: Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
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Commits on Sep 3, 2024
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* nvpl-blas: add new version 0.3.0 * nvpl-lapack: add new version 0.2.3.1
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solver: minor cleanup and optimization (spack#46176)
Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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root: fix X11 and OpenGL-related issues on macOS (spack#45632)
* root: Add dependency on libglx We have been trying to build the Acts package on MacOS, and in this process we have been running into problems with the ROOT spec on that operating system; the primary issue we are encountering is that the compiler is unable to find the `GL/glx.h` header, which is part of glx. It seems, therefore, that ROOT depends on libglx, but this is not currently encoded in the spec. This commit ensures that ROOT depends on the virtual libglx package when both the OpenCL and X11 variants are enabled. * Enable builtin glew on MacOS * Allow `root+opengl+aqua~x` on macOS
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root: fix @loader_path on macOS (spack#44826)
* root: fix @loader_path on macOS * root: use loader patch from upstream Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * add missing comma * root: rm unused patch * root: conflict on macos 12 for @:6.27 when +python --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
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Commits on Sep 4, 2024
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Add conflict between llvm-amdgpu until version 5 and ninja since vers…
…ion 1.12.0 (spack#45788) * Add conflict between llvm-amdgpu and ninja since version 1.12.0 * Update llvm-amdgpu and ninja conflict to extend to 6.0
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trilinos: update @[master,develop] dependency on kokkos (spack#46182)
==> Error: InstallError: For Trilinos@[master,develop], ^kokkos version in spec must match version in Trilinos source code. Specify ^kokkos@4.4.00 for trilinos@[master,develop] instead of ^kokkos@4.3.01.
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texlive: clean up recipe (spack#45863)
* texlive: clean up recipe * Update the poppler dependency * Fix typo --------- Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
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py-rasterio: add v1.3.11 (spack#46195)
* py-rasterio: add v1.3.11 * Use default_args
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rocm-openmp-extras: Avoiding registration of duplicate check-targets …
…and fix for the failure in hostexec (spack#45658) * Adding addtional check for omptarget library for amdgpu in nvidia environment * Avoiding registration of duplicate when built on cuda * Adding hsa library path in LD_LIBRARY_PATH * Correction in hsa prefix library path in LD_LIBRARY_PATH
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py-trieregex: new package (spack#46154)
* py-trieregex: new package
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Merge remote-tracking branch 'upstream/develop' into maintenance/merg…
…e-from-upstream-2024-09-04
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Commits on Sep 5, 2024
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py-schema: add v0.7.7 (spack#46210)
* py-schema: add v0.7.7 * py-schema: fix when spec Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
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seacas: require +metis and +mpi instead of +parmetis (spack#46205)
This change aligns the build condition for parmetis with the depends_on condition. The current build condition of parmetis looks for "+parmetis" in the spec which is not added by the depends_on as that adds "^parmetis" instead.
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libfabric: Add CUDA variant (spack#46203)
Signed-off-by: Jack Morrison <jack.morrison@cornelisnetworks.com>
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Replace
if ... in spec
withspec.satisfies
in d* and e* packages (s……pack#46126) * Replace if ... in spec with spec.satisfies in d* and e* packages * Use virtuals for different mpi implementations in esmf * esmf: ^[virtuals=mpi] mpt * extrae: ^[virtuals=mpi] intel-oneapi-mpi --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
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Remove
test_external_package_module
(spack#46218)This test was possibly meant for the Cray platform, and currently is a no-op. Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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Pass Database layout in constructor (spack#46219)
Ensures that Database instances do not reference a global `spack.store.STORE.layout`. Simplify Database.{add,reindex} signature.
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pika: Add 0.28.0 (spack#46207)
* pika: Add 0.28.0 * Add conflict between pika 0.28.0 and dla-future
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reindex: ensure database is empty before reindex (spack#46199)
fixes two tests that did not clear the in-memory bits of a database before calling reindex.
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gaudi: Specify boost dependencies explicitly and cleanup package (spa…
…ck#46194) * gaudi: Specify boost components and add +fiber for v39 * gaudi: Limit fmt version to allow building master branch * Make boost dependencies a bit more readable * Remove patches for no longer existing versions
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Merge remote-tracking branch 'upstream/develop' into maintenance/merg…
…e-from-upstream-2024-09-04 Updated merge with fixes to previously-faulty conflict resolution on: * `var/spack/repos/builtin/packages/perl-bioperl/package.py` * `var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py`
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