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* Automated deployment to update package flux-sched 2024-09-05
* flux-sched: add back check for run environment
* flux-sched: add conflict for gcc and clang above 0.37.0
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Co-authored-by: github-actions <github-actions@users.noreply.github.com>
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Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
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* provide dlaff libs
* fix incompatibility with ntpoly
* add cuda conflicts
* [@spackbot] updating style on behalf of RMeli
* Update var/spack/repos/builtin/packages/elsi/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* move pexsi conflict to context
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Co-authored-by: RMeli <RMeli@users.noreply.github.com>
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
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autotools packages with a configure script should generate the libtool
executable, there's no point in `depends_on("libtool", type="build")`.
the libtool executable in `<libtool prefix>/bin/libtool` is configured
for the wrong toolchain (libtools %compiler instead of the package's
%compiler).
Some package link to `libltdl.so`, which is fine, but had a wrong
dependency type.
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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>
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This commit adds Boost v1.86.0.
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This commit adds v36.3.0 of ACTS, and also marks a previously missing
conflict with Boost 1.85.0
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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.
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* py-xgboost: add v2.1.1
* setuptools no longer needed
* Better comment
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* 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
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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>
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* openmpi: update mpi version dependency
* Use "disjoint sets" for version ranges
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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
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needed according to pc file
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* Add new packages: py-fluidfft and co
* py-fluidfft: add few contrains (version dependencies)
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* 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
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Co-authored-by: Andrew W Elble <aweits@rit.edu>
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
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* 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>
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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>
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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>
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* 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.
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* 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
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Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
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bug fix update for sirius
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* 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
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Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
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* 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)
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* 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
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superceds #46128
Co-authored-by: Robert Underwood <runderwood@anl.gov>
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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
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Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
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* 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
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Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
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* makedepf90: new package
* reorder versions and dependencies
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* 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
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* py-poxy: add new package
* py-poxy: depends on misk >= 0.8.1
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