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2024-09-12codespaces: add ubuntu22.04 (#46100)Wouter Deconinck2-0/+6
2024-09-12py-zope-*: add new versions (#46338)Wouter Deconinck2-5/+19
2024-09-12mdspan: fix typo in satisfies condition (#46340)Wouter Deconinck1-1/+1
2024-09-12re2: add versions through 2024-07-02; add variant icu (#46337)Wouter Deconinck1-2/+36
2024-09-12pcre2: add v10.44 (#46341)Wouter Deconinck1-2/+3
2024-09-12pika: Add conflict between HIP and GCC (libstdc++) >= 13 (#46291)Mikael Simberg1-0/+2
2024-09-11acts: further simplify `cxxstd` handling (#46333)Todd Gamblin1-8/+3
See https://github.com/spack/spack/pull/46314#discussion_r1752940332. This further simplifies `cxxstd` variant handling in `acts` by removing superfluous version constraints from dependencies for `geant4` and `root`. The version constraints in the loop are redundant with the conditional variant values here: ```python _cxxstd_values = ( conditional("14", when="@:0.8.1"), conditional("17", when="@:35"), conditional("20", when="@24:"), ) _cxxstd_common = { "values": _cxxstd_values, "multi": False, "description": "Use the specified C++ standard when building.", } variant("cxxstd", default="17", when="@:35", **_cxxstd_common) variant("cxxstd", default="20", when="@36:", **_cxxstd_common) ``` So we can simplify the dependencies in the loop to: ```python for _cxxstd in _cxxstd_values: for _v in _cxxstd: depends_on(f"geant4 cxxstd={_v.value}", when=f"cxxstd={_v.value} +geant4") depends_on(f"geant4 cxxstd={_v.value}", when=f"cxxstd={_v.value} +fatras_geant4") depends_on(f"root cxxstd={_v.value}", when=f"cxxstd={_v.value} +tgeo") ``` And avoid the potential for impossible variant expressions. Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
2024-09-11bugfix: unit test broken everywhere by package change(#46344)Peter Scheibel1-1/+0
Openmpi provider statements were changed in #46102. The package change was fine in and of itself, but apparently one of our tests depends on the precise constraints used in those statements. I updated the test to remove the checks for constraints that were removed.
2024-09-11boost: add v1.86.0 (#46321)Stephen Nicholas Swatman1-0/+1
This commit adds Boost v1.86.0.
2024-09-11acts: add v36.3.0 (#46320)Stephen Nicholas Swatman1-0/+3
This commit adds v36.3.0 of ACTS, and also marks a previously missing conflict with Boost 1.85.0
2024-09-11hep tag: new versions as of 2024/09/11 (#46322)Stephen Nicholas Swatman5-0/+7
This commit updates acts-algebra-plugins to v0.25.0, actsvg to v0.4.47, detray to v0.74.2, geomodel to v6.5.0, and vecmem to v1.7.0.
2024-09-11scnlib: new package (#46313)Pranav Sivaraman1-0/+61
2024-09-11py-scikit-learn: add v1.5.2 (#46327)Adam J. Stewart1-2/+3
2024-09-11py-xgboost: add v2.1.1 (#46260)Adam J. Stewart2-61/+59
* py-xgboost: add v2.1.1 * setuptools no longer needed * Better comment
2024-09-11New packages: py-regionmask and py-pyogrio (#46209)Dom Heinzeller3-8/+81
* Add py-geopandas versions 1.0.0 and 1.0.1, update dependencies * New package py-pyogrio - dependency of newer py-geopandas * New package py-regionmask - needs py-geopandas
2024-09-11Fix variant expressions that will never match (#46314)Todd Gamblin13-36/+9
In #44425, we add stricter variant audits that catch expressions that can never match. This fixes 13 packages that had this type of issue. Most packages had lingering spec expressions from before conditional variants with `when=` statements were added. For example: * Given `conflicts("+a", when="~b")`, if the package has since added `variant("a", when="+b")`, the conflict is no longer needed, because `a` and `b` will never exist together. * Similarly, two packages that depended on `py-torch` depended on `py-torch~cuda~cudnn`, which can't match because the `cudnn` variant doesn't exist when `cuda` is disabled. Note that neither `+foo` or `~foo` match (intentionally) if the `foo` variant doesn't exist. * Some packages referred to impossible version/variant combinations, e.g., `ceed@1.0.0+mfem~petsc` when the `petsc` variant only exist at version `2` or higher. Some of these correct real issues (e.g. the `py-torch` dependencies would have never worked). Others simply declutter old code in packages by making all constraints consistent with version and variant updates. The only one of these that I think is not all that useful is the one for `acts`, where looping over `cxxstd` versions and package versions ends up adding some constraints that are impossible. The additional dependencies could never have happened and the code is more complicated with the needed extra constriant. I think *probably* the best thing to do in `acts` is to just not to use a loop and to write out the constraints explicitly, but maybe the code is easier to maintain as written. Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
2024-09-11openmpi: update dependency wrt mpi standard versions (#46102)Satish Balay1-3/+4
* openmpi: update mpi version dependency * Use "disjoint sets" for version ranges
2024-09-11Update FMS: apply patch for fms@2023.03, add variant shared and patch for ↵Dom Heinzeller1-0/+17
fms@2024.02 (#46238) * Update var/spack/repos/builtin/packages/fms/package.py: apply patch for fms@2023.03 to fix compiler options bug in cmake config, add variant shared and corresponding patch for fms@2024.02 * Fix fms package audit: use https://github.com/NOAA-GFDL/FMS/commit/c9bba516ba1115d4a7660fba92f9d67cf3fd32ad.patch?full_index=1 instead of https://github.com/NOAA-GFDL/FMS/pull/1418/commits/c9bba516ba1115d4a7660fba92f9d67cf3fd32ad.patch?full_index=1 * Update checksum of patch for fms@2023.03
2024-09-11fixesproto: add xextproto dep (#46325)Harmen Stoppels1-0/+1
needed according to pc file
2024-09-11py-fluidfft and co: add new packages (#46236)Pierre Augier7-0/+214
* Add new packages: py-fluidfft and co * py-fluidfft: add few contrains (version dependencies)
2024-09-11CUDA: support Grace Hopper 9.0a compute capability (#45540)Adam J. Stewart7-27/+49
* CUDA: support Grace Hopper 9.0a compute capability * Fix other packages * Add type annotations * Support ancient Python versions * isort * spec -> self.spec Co-authored-by: Andrew W Elble <aweits@rit.edu> * [@spackbot] updating style on behalf of adamjstewart --------- Co-authored-by: Andrew W Elble <aweits@rit.edu> Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2024-09-11CDO: add patch for missing algorithm header (#45692)Jannek Squar3-0/+59
* add cdo patch for missing algorithm header * add patch for 2.2.2:2.3.0 Signed-off-by: Jannek <squar@informatik.uni-hamburg.de> * Add conflict of old cdo with new gcc * Update var/spack/repos/builtin/packages/cdo/add_algorithm_header_222.patch Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * Adjust patch hash * Update var/spack/repos/builtin/packages/cdo/package.py fix copy-paste-error on hash Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> --------- Signed-off-by: Jannek <squar@informatik.uni-hamburg.de> Co-authored-by: Jannek <squar@informatik.uni-hamburg.de> Co-authored-by: Try2Code <stark.dreamdetective@gmail.com> Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2024-09-11OpenCV: add v4.8-4.10 (#46223)Adam J. Stewart1-4/+10
2024-09-11cp2k: add v2024.3 (#46297)Rocco Meli1-0/+1
2024-09-11nvhpc: add 'compiler' tag to the override (#46301)Massimiliano Culpo1-1/+1
fixes #46295 A proper solution would be a tag directive that accumulates tags with the ones defined in base classes. For the time being, rewrite them explicitly. Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-09-11boost package: fix Windows build (#43732)James Smillie2-26/+75
* Boost:Adjust bootstrapping/b2 options as needed for Windows (the bootstrapping phase sufficiently differs between Windows/Unix that it is handled entirely within its own branch). * Boost: Paths in user-config.jam should be POSIX, including on Windows * Python: `.libs` for the Python package should return link libraries on Windows. The libraries are also stored in a different directory.
2024-09-10Bump up the version for ROCm-6.2.0 (#45701)afzpatel58-100/+544
* initial update for rocm 6.2 * fix typo in rocprofiler-register * update rocm-device-libs * add patch to use clang 18 for roctracer-dev * add updates for rocm-opencl and rocm-validation-suite * add hipify-clang patch * update remaining packages to 6.2 * update hipblaslt mivisionx patches * update rocm-tensile to 6.2.0 * add hipsparselt changes for 6.2 * add rocm-openmp-extras patch * add build-time test for rocprofiler-register * update flang-legacy support for 6.2 * simplify version range * update boost dependency in rpp --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2024-09-10SIRIUS: add v7.6.1 (#46296)Taillefumier Mathieu1-0/+1
bug fix update for sirius
2024-09-10Deprecate `config:install_missing_compilers` (#46237)Massimiliano Culpo11-391/+19
The option config:install_missing_compilers is currently buggy, and has been for a while. Remove it, since it won't be needed when compilers are treated as dependencies. Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-09-10perl-bio-ensembl-io: new package (#44509)Teague Sterling1-0/+47
* Adding the perl-bio-db-bigfile package * Adding perl-bio-ensembl-io package * Update package.py * Update package.py * Update package.py * Update package.py * Updating dependent package handling Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Updating dependent package handling Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Reverting variants Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Rename package.py to package.py * Update package.py * Update package.py * Removing unneeded dependencies Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Updated from testing by @ebiarnie Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Updated from testing by @ebiarnie Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Fixing depends Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Fix styles Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Update package.py --------- Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
2024-09-10fast-float: new package (#46137)Pranav Sivaraman1-0/+36
* fast-float: new package * fast-float: add test dependency * fast-float: fix doctest dependency type * fast-float: convert deps to tuple * fast-float: add v6.1.5 and v6.1.6 * fast-float: patch older versions to use find_package(doctest)
2024-09-10py-your: Changed software pull location (#46201)Tony Weaver1-3/+5
* py-your: new package Spack package recipe for YOUR, Your Unified Reader. YOUR processes pulsar data in different formats. Output below from spack install py-your spack install py-your ==> Installing py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x [83/83] ==> No binary for py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x found: installing from source ==> Fetching https://github.com/thepetabyteproject/your/archive/refs/tags/0.6.7.tar.gz ==> No patches needed for py-your ==> py-your: Executing phase: 'install' ==> py-your: Successfully installed py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x Stage: 1.43s. Install: 0.99s. Post-install: 0.12s. Total: 3.12s * Removed setup_run_environment After some testing, both spack load and module load for the package will include the bin directory generated by py-your as well as the path to the version of python the package was built with, without the need for the setup_run_environment function. I removed that function (Although, like Tamara I thought it would be necessary based on other package setups I used as a basis for this package). Note: I also updated the required version of py-astropy from py-astropy@4.0: to @py-astropy@6.1.0: In my test builds, the install was picking up version py-astropy@4.0.1.post1 and numpy1.26. However when I tried to run some of the code I was getting errors about py-astropy making numpy calls that are now removed. The newer version of py-astropy corrects these. Ideally this would be handled in the py-astropy package to make sure numpy isn't too new * Changed software pull location The original package pulled a tagged release version from GitHub. That tagged version was created in 2022 and has not been updated since. It no longer runs because newer versions of numpy have removed deprecation warnings for several of their calls. The main branch for this repository has addressed these numpy issues as well as some other important fixes but no new release has been generated. Because of this and the apparent minimal development that now appears to be going on, it is probably best to always pull from the main branch * [@spackbot] updating style on behalf of aweaver1fandm * py-your: Changed software pull location 1. Restored original URL and version (0.6.7) as requested 2. Updated py-numpy dependency versions to be constrained based on the version of your. Because of numpy deprecations related to your version 0.6.7 need to ensure that the numpy version used is not 1.24 or greater because the depracations were removed starting with that version
2024-09-10Add additional cuda-toolkit location variable used by py-torch (#46245)Robert Underwood1-0/+1
superceds #46128 Co-authored-by: Robert Underwood <runderwood@anl.gov>
2024-09-10perl-bioperl: add v1.6.924, v1.7.8, deprecate v1.007002, refactor ↵Teague Sterling1-71/+65
dependeicies, update url (#46213) * perl-bioperl: add v1.6.924 Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * fix style Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * perl-bioperl: add v1.6.924, v1.7.2, deprecate v1.007002, refactor dependencies Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * perl-bioperl: add v1.7.8 Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * perl-bioperl: update url Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * perl-bioperl: cleanup version urls Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * remove v1.7.2 --------- Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
2024-09-10r: do not create dir in setup_dependent_package (#46282)Harmen Stoppels2-19/+10
2024-09-10spec.py: dedent format logic (#46279)Harmen Stoppels1-36/+33
2024-09-10bugfix: `elfutils` has no bzip2 or xz variants (#46294)Todd Gamblin1-1/+1
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
2024-09-10boost: Refactor header-only install and add missing compiled libraries (#46281)Mikael Simberg1-31/+23
2024-09-10cmake: remove last occurrences of std_cmake_args globals (#46288)Harmen Stoppels4-4/+12
2024-09-09gptune: new test API (#45383)AcriusWinter2-68/+132
* gptune: new test API * gptune: cleanup; finish API changes; separate unrelated test parts * gptune: standalone test cleanup with timeout constraints * gptune: ensure stand-alone test bash failures terminate; enable in CI * gptune: add directory to terminate_bash_failures * gptune/stand-alone tests: use satisifes for checking variants --------- Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2024-09-09makedepf90: new package (#45816)Philipp Edelmann1-0/+24
* makedepf90: new package * reorder versions and dependencies
2024-09-09numactl: Add versions 2.0.16-2.0.18 (#46150)David Collins3-1/+31
* Add numactl 2.0.16-2.0.18 * Create link-with-latomic-if-needed-v2.0.16.patch Add a link to libatomic, if needed, for numactl v2.0.16. * Add some missing patches to v2.0.16 * Create numactl-2.0.18-syscall-NR-ppc64.patch In short, we need numactl to set __NR_set_mempolicy_home_node on ppc64, if it's not already defined. * Apply a necessary patch for v2.0.18 on PPC64 * Add libatomic patch for v2.0.16
2024-09-09py-poxy: add new package (#46214)Pranav Sivaraman1-0/+35
* py-poxy: add new package * py-poxy: depends on misk >= 0.8.1
2024-09-09Revert "Set module variables for all packages before running ↵Harmen Stoppels2-30/+1
setup_dependent_…" (#46283) This reverts commit 6f08db463149efdea126abf8fdc770f684b4199d.
2024-09-09darshan-runtime: fix JOBID determination (#46148)Kevin Kuriakose1-4/+4
2024-09-09reindex: do not assume fixed layout (#46170)Harmen Stoppels6-152/+274
`spack reindex` relies on projections from configuration to locate installed specs and prefixes. This is problematic because config can change over time, and we have reasons to do so when turning compilers into depedencies (removing `{compiler.name}-{compiler.version}` from projections) This commit makes reindex recursively search for .spack/ metadirs.
2024-09-09Add new package py-fluiddyn (#46235)Pierre Augier1-0/+42
2024-09-09pika: Add conflict with fmt 11 and newer (#46280)Mikael Simberg1-0/+2
2024-09-09perl-graphviz: add graphviz dependency (#46268)Teague Sterling1-0/+1
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
2024-09-09Fix regression in spec format string for indiviual variants (#46206)Jordan Galby2-2/+19
Fix a regression in {variants.X} and {variants.X.value} spec format strings.