* Add patches for building clingo with MSVC
* Help python find clingo DLL
* If an executable is located in "C:\Program Files", Executable was
running into issues with the extra space. This quotes the exe
to ensure that it is treated as a single value.
Signed-off-by: Kiruya Momochi <65301509+KiruyaMomochi@users.noreply.github.com>
This commit extends the DSL that can be used in packages
to allow declaring that a package uses different build-systems
under different conditions.
It requires each spec to have a `build_system` single valued
variant. The variant can be used in many context to query, manipulate
or select the build system associated with a concrete spec.
The knowledge to build a package has been moved out of the
PackageBase hierarchy, into a new Builder hierarchy. Customization
of the default behavior for a given builder can be obtained by
coding a new derived builder in package.py.
The "run_after" and "run_before" decorators are now applied to
methods on the builder. They can also incorporate a "when="
argument to specify that a method is run only when certain
conditions apply.
For packages that do not define their own builder, forwarding logic
is added between the builder and package (methods not found in one
will be retrieved from the other); this PR is expected to be fully
backwards compatible with unmodified packages that use a single
build system.
* Updating package file for osu-micro-benchmarks for the 6.2 release
* updating sha hash for 6.2 tarball
Co-authored-by: natshineman <shineman.5@osu.edu>
* Add netcdf-c 4.9.0 and netcdf-fortran 4.6.0
With v4.9.0 netcdf-c introduces zstandard compression option which is added as a variant.
* Fix when= in dependency
* Turn on variant zstd by default
Co-authored-by: kgerheiser <kgerheiser@icloud.com>
* alquimia, pflotran, plasma, py-mpi4py, strumpack - add in new versions
* Fix hip CI failure
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
* udunits: Update download URL
* udunits: Deprecate older versions
Unidata now only provides the latest version of each X.Y branch. Older 2.2 versions have been deprecated accordingly but are still available in the build cache.
Co-authored-by: RemiLacroix-IDRIS <RemiLacroix-IDRIS@users.noreply.github.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Update wgrib2 from JCSDA/NOAA-EMC fork
* var/spack/repos/builtin/packages/wgrib2/package.py: fix typo in comment, add conflict for variants netcdf3, netcdf4
* wget hdf5/netcdf4 internal dependencies for wgrib2
* Black-format var/spack/repos/builtin/packages/wgrib2/package.py
* More format changes in var/spack/repos/builtin/packages/wgrib2/package.py
* Update py-sphinxcontrib-mermaid
* Add py-myst-parser
* Fix py-mdit-py-plugins and py-myst-parser dependencies
* Add py-exhale package
* Update var/spack/repos/builtin/packages/py-mdit-py-plugins/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-myst-parser/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-myst-parser/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-myst-parser/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update py-exhale and py-myst-parser dependencies
* Add @svenevs as py-exhale maintainer
* Update var/spack/repos/builtin/packages/py-mdit-py-plugins/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Scan the text files for relocatable prefixes *before* creating a tarball,
to reduce the amount of work to be done during install from binary
cache.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
* py-drep: new package
* fixed file extension
* added darwin conflict
* py-checkm-genome and py-pysam: bumped version and updated deps (#10)
added checkm and pysam deps
* added dep documentation and fixed style
* changed checkm and pysam back to dev version for upstreaming
* added url and perl run dep
* fixed style
* acts: new versions
In the 20.x release line, these are the changes, https://github.com/acts-project/acts/compare/v20.0.0...v20.2.0
- `option(ACTS_SETUP_ACTSVG "Build ActSVG display plugin" OFF)` introduced in v20.1.0
- `option(ACTS_USE_SYSTEM_ACTSVG "Use the ActSVG system library" OFF)` introduced in v20.1.0
- `option(ACTS_BUILD_PLUGIN_ACTSVG "Build SVG display plugin" OFF)` introduced in v20.1.0
- `option(ACTS_USE_EXAMPLES_TBB "Use Threading Building Blocks library in examples" ON)` introduced in v20.1.0
- `option(ACTS_EXATRKX_ENABLE_ONNX "Build the Onnx backend for the exatrkx plugin" OFF)` introduced in v20.2.0
- `option(ACTS_EXATRKX_ENABLE_TORCH "Build the torchscript backend for the exatrkx plugin" ON)` introduced in v20.2.0
In the 19.x release line, these are the changes: https://github.com/acts-project/acts/compare/v19.7.0...v19.9.0
- `option(ACTS_USE_EXAMPLES_TBB "Use Threading Building Blocks library in examples" ON)` introduced in v19.8.0
The new build options have not been implemented in this commit but will be implemented next.
* acts: new variant svg
* actsvg: new package
* actsvg: style fixes
* acts: new versions 20.3.0 and 19.10.0
* astsvg: depends_on boost googletest
* actsvg: new version 0.4.26 (and style fix)
Includes fix to build issue when +examples, https://github.com/acts-project/actsvg/pull/23
* acts: new variant tbb when +examples @19.8:19 @20.1:
* acts: set ACTS_USE_EXAMPLES_TBB
* acts: no need for ACTS_SETUP_ACTSVG
* acts: move tbb variant to examples block
* acts: ACTS_USE_SYSTEM_ACTSDD4HEP removed in 20.3
* acts: use new ACTS_USE_SYSTEM_LIBS
* acts-dd4hep: new version 1.0.1, maintainer handle fixed
* acts: simplify variant tbb condition
* updated python version requirements
* updated sha256
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-checkm-genome and py-pysam: bumped version and updated deps
* updated setuptools dep type
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* axom@0.7.0: require cmake@3.21:
* Update var/spack/repos/builtin/packages/axom/package.py
Co-authored-by: Chris White <white238@llnl.gov>
Co-authored-by: Chris White <white238@llnl.gov>
* fixed version numbers to python 2 and old biopython
* changed shortbred pacakge to pypi, removed python 2 version
* added package description
* re-added shortbred package with depreciated flag
* fixed style and removed unnecessary python dep (it can't build with python 2 anyway)
* removed whitespace and readded the python2.7.9+ dep
* fixed style
Without this patch one hits this error trying to compiler papi with Intel OneAPI:
icx: error: Note that use of '-g' without any optimization-level option will turn off most compiler optimizations similar to use of '-O0' [-Werror,-Wdebug-disables-optimization]
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* Fixed two bugs in the HIP package recipe. The first is that the
HIP_PATH was being set to the actual spec, and not the spec prefix.
The second bug is that HIP is expected to be in /opt/rocm-x.y.z/hip
but it's libraries can exist at both /opt/rocm-x.y.z/hip/lib and
/opt/rocm-x.y.z/lib. This means that the external detection logic may
find it in either and it turns out that some modules only expose one
of those two locations. Logic is added to ensure that the internal
HIP_PATH and associated ROCM_PATH are correctly set in both cases.
* Added support for Aluminum to use the libfabric plugin with either
RCCL or NCCL.
* Add libpressio and dependencies; some of these packages are
maintained as forks of the original repositories and in those
cases the docstring mentions this.
* Add optional dependency in adios2 on libpressio
* cub package: set CUB_DIR environment variable for dependent
installations
* Clear R_HOME/R_ENVIRON before Spack installation (avoid sources
outside of Spack from affecting the installation in Spack)
* Rename dlib to dorian3d-dlib and update dependents; add new dlib
implementation. Pending an official policy on how to handle
packages with short names, reviewer unilaterally decided that
the rename was acceptable given that the new Spack dlib package
is referenced more widely (by orders of magnitude) than the
original
Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com>
* Classic Intel compilers do not support gcc-toolchain
This fix removes `--gcc-toolchain=` from the ~.fcg` files for the classic Intel
compilers. AFAIK this option is only supported for Clang based compilers.
This lead to an issue when installing cmake. Reproducer:
```
spack install cmake@3.24.2%intel@2021.7.0~doc+ncurses+ownlibs~qt
build_type=Release arch=linux-amzn2-skylake_avx512
```
Tagging maintainer @rscohn2
* Add `-gcc-name` for icc
.. and `-gxx-name` for icpc.
AFAIK this is used for modern C++ support, so we can ignore `ifort`.
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
* petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0
* workaround for dealii build failure [with petsc version check]
* pism: add compatibility fix to for petsc@3.18
* add in hipsolver dependency
* Add checksum for py-gitpython 3.1.27
* Update package.py
* Update var/spack/repos/builtin/packages/py-gitpython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new package + deps
* Update var/spack/repos/builtin/packages/py-about-time/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-alive-progress/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* removed unnecessary python version dep
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add new lua releases
* split install phase and move it into a build phase, remove hardcoded standard flag
* revert back to the original hardcoded std flag, guard patch against versions above 5.4
* py-pyopenssl: add version 22.1.0
* Update var/spack/repos/builtin/packages/py-pyopenssl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add checksum for py-regex 2022.8.17
* Update var/spack/repos/builtin/packages/py-regex/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add checksum for py-async-lru 1.0.3
* [@spackbot] updating style on behalf of iarspider
* Update var/spack/repos/builtin/packages/py-async-lru/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
Co-authored-by: iarspider <iarspider@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add bioc attribute to r-do-db
* add version 1.38.1 to bioconductor package r-annotationforge
* add version 1.30.4 to bioconductor package r-biocparallel
* add version 2.64.1 to bioconductor package r-biostrings
* add version 4.4.4 to bioconductor package r-clusterprofiler
* add version 2.12.1 to bioconductor package r-complexheatmap
* add version 1.18.1 to bioconductor package r-delayedmatrixstats
* add version 3.22.1 to bioconductor package r-dose
* add version 3.38.4 to bioconductor package r-edger
* add version 1.16.2 to bioconductor package r-enrichplot
* add version 2.20.2 to bioconductor package r-ensembldb
* add version 1.32.4 to bioconductor package r-genomeinfodb
* add version 1.32.1 to bioconductor package r-genomicalignments
* add version 1.48.4 to bioconductor package r-genomicfeatures
* add version 1.44.1 to bioconductor package r-ggbio
* add version 3.4.4 to bioconductor package r-ggtree
* add version 1.24.2 to bioconductor package r-hdf5array
* add version 2.30.1 to bioconductor package r-iranges
* add version 1.36.3 to bioconductor package r-keggrest
* add version 3.52.4 to bioconductor package r-limma
* add version 1.8.1 to bioconductor package r-matrixgenerics
* update r-org-hs-eg-db
* add version 1.38.1 to bioconductor package r-organismdbi
* add version 1.36.1 to bioconductor package r-pathview
* add version 1.56.1 to bioconductor package r-rtracklayer
* add version 1.4.1 to bioconductor package r-scaledmatrix
* add version 1.24.1 to bioconductor package r-scran
* add version 1.6.3 to bioconductor package r-scuttle
* add version 1.18.1 to bioconductor package r-singlecellexperiment
* add version 1.20.2 to bioconductor package r-treeio
* Revert "Add bioc attribute to r-do-db"
This reverts commit 36be5c6072.
* Fix quotes on versions
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
For older versions of intel-oneapi-compilers, running the compiler in
preprocessor / compilation mode would trigger warnings that
`-Wl,-rpath,...` flags were unused.
This in turn caused certain configure scripts to fail as they did not
expect output from the compiler (it's treated as an error). Notably
cmake's bootstrap phase failed to detect c++ features of the compiler.
As a workaround, add this flag to silence the warning, since I don't
think we can scope the flags to compile+link mode.
* bump version for libvterm, required by neovim
* bump version for neovim and add related dep constraints
see release note:
d367ed9b23
in particular:
'deps: Bump required libvterm to v0.3'
https://github.com/neovim/neovim/pull/20222
* spack.compiler.Compiler: introduce prefix property
We currently don't really have something that gives the GCC install
path, which is used by many LLVM-based compilers (llvm, llvm-amdgpu,
nvhpc, ...) to fix the GCC toolchain once and for all.
This `prefix` property is dynamic in the sense that it queries the
compiler itself. This is necessary because it's not easy to deduce the
install path from the `cc` property (might be a symlink, might be a
filename like `gcc` which works by having the compiler load a module
that sets the PATH variable, might be a generic compiler wrapper based
on environment variables like on cray...).
With this property introduced, we can clean up some recipes that have
the logic repeated for GCC.
* intel-oneapi-compilers: set --gcc-sysroot to %gcc prefix
* hpctoolkit: add version 2022.10.01
1. add version 2022.10.01
2. remove version for master branch, develop is now the main branch
3. add CPATH and LD_LIBRARY_PATH to module run environment,
this is for apps that want to use the start/stop interface
4. cleanup style in variants, depends and conflicts
5. remove all-static variant, nothing uses it
6. deprecate more old versions
* [@spackbot] updating style on behalf of mwkrentel
* Add when(+level_zero) to the gtpin variant.
* Test commit to see if this passes E4S.
* Another test commit to see if E4S succeeds.
* Add temporary hack to ignore +mpi for version 2022.10.01 and issue a
warning instead.
Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
* Add checksum for py-msgpack 1.0.4
* Update var/spack/repos/builtin/packages/py-msgpack/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add checksum for py-virtualenv 20.16.4
* Add checksum for py-werkzeug 2.2.2
* Restore py-virtualenv/package.py
* Update var/spack/repos/builtin/packages/py-werkzeug/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add checksum for py-skl2onnx 1.12
* Update var/spack/repos/builtin/packages/py-skl2onnx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add checksum for py-tables 3.7.0
* Update package.py
* Update var/spack/repos/builtin/packages/py-tables/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
ROOT has a webgui which is available with the `+root7` variant. This is a fairly large part of a ROOT install (275MB out of 732MB on my system) which is not necessarily useful in all use cases (e.g. inside containers on network-restricted HPC/HTC compute nodes). This new variant adds the option to retain the ROOT7 functionality but not necessarily include the `webgui` aspects.
`__unused__` defined in `general.h` conflict with the one defined by libc headers,
so change it to `__attribute__unused__` according to s.zharkoff:
https://bugs.gentoo.org/828550#c11
cmd:
`grep -rl "__unused__" . | xargs -n1 sed -i -e 's/\b__unused__\b/__attribute__unused__/g' -e 's/(unused)/(__unused__)/g'`
* Add checksum for py-scikit-build 0.15.0 and use sources from pypi
* Update var/spack/repos/builtin/packages/py-scikit-build/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add checksum for py-terminado 0.15.0
* Update var/spack/repos/builtin/packages/py-terminado/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* added metaphlan v4, cleaned up phylophlan
* added iqtree2
* fixed phylophlan, builds now
* changed config.yaml to default
* fixed style
* py-jsonschema: add 4.16.0 and new package py-hatch-fancy-pypi-readme (#32929)
* acfl: add v22.1 (#32915)
Co-authored-by: Annop Wongwathanarat <annop.wongwathanarat@arm.com>
* Fixup errors introduced by Clingo Pr: (#32905)
* re2c depends on cmake on Windows
* Winbison properly added to bootstrap package search list
* Set CMAKE_HIP_ARCHITECTURES with the value of amdgpu_target (#32901)
* libtiff: default to +zlib+jpeg (#32945)
* octave: add version 7.2.0 (#32943)
* simgrid new releases (#32920)
* [rocksdb] Added rtti variant (#32918)
* rvs binary path updated for 5.2 rocm release (#32892)
* Add checksum for py-pytest-runner 6.0.0 (#32957)
* py-einops: add v0.5.0 (#32959)
* Replace repo with the NVIDIA one (#32951)
* Add checksum for py-tomli 2.0.1 (#32949)
* QMCPACK: add @3.15.0 (#32931)
* Tidied up configure arguments to use special spack autotools features. (#32930)
* casper: old domain fell off, adding github repo (#32928)
* unifyfs: pin mercury version; add boost variant (#32911)
Mercury has a new version (v2.2) releasing soon that UnifyFS does not build with and hasn't been tested with. This pins UnifyFS to the last version of Mercury used/tested.
Add a variant to avoid building/using boost
Append -std=gnu99 to cflags if building with gcc@4. Needed for mochi-margo to compile
* trilinos: constrain superlu-dist version (#32889)
* trilinos: constrain superlu-dist version for 13.x
* syntax
* FEniCSx: Updates for 0.5.1 (#32665)
* Updates for DOLFINx 0.5.1 and associated packages
* xtensor needed on anything less than main
* Switch back to Python 3.7 minimum.
* Might be good to point out in our README how to fix Python version?
* Fix basix, xtensor dep
* Add numba feature
* Fix checksum
* Make slepc optional
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* simgrid: add variant and remove flag (#32797)
* simgrid: remove std c++11 flag
* simgrid: add msg variant
* Axom: bring in changes from axom repo (#32643)
* bring in changes from axom repo
Co-authored-by: white238 <white238@users.noreply.github.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Add checksum for py-pyparsing 3.0.9 (#32952)
* rdma-core: fix syntax for external discoverability (#32962)
* Add checksum for py-flatbuffers 2.0.7 (#32955)
* amrex: add v22.10 (#32966)
* Remove CMakePackage.define alias from most packages (#32950)
* Bug fix for `ca-certificates-mozilla/package.py` to enable `spack install --source` (#32953)
* made suggested changes to iqtree2, py-dendropy, py-metaphlan, and py-pkgconfig. Poetry install still broken
* reverted py-pkgconfig deps to poetry-core
* made iqtree2 less dedundant, changes to py-dendropy and py-pkgconfig deps
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
Co-authored-by: Annop Wongwathanarat <annop.wongwathanarat@gmail.com>
Co-authored-by: Annop Wongwathanarat <annop.wongwathanarat@arm.com>
Co-authored-by: John W. Parent <45471568+johnwparent@users.noreply.github.com>
Co-authored-by: Auriane R <48684432+aurianer@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Kai Torben Ohlhus <k.ohlhus@gmail.com>
Co-authored-by: Vinícius <viniciusvgp@gmail.com>
Co-authored-by: Matthieu Dorier <mdorier@anl.gov>
Co-authored-by: renjithravindrankannath <94420380+renjithravindrankannath@users.noreply.github.com>
Co-authored-by: iarspider <iarspider@gmail.com>
Co-authored-by: Paul R. C. Kent <kentpr@ornl.gov>
Co-authored-by: Brian Van Essen <vanessen1@llnl.gov>
Co-authored-by: snehring <7978778+snehring@users.noreply.github.com>
Co-authored-by: Cameron Stanavige <stanavige1@llnl.gov>
Co-authored-by: Cody Balos <balos1@llnl.gov>
Co-authored-by: Jack S. Hale <mail@jackhale.co.uk>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Lucas Nesi <lucas31nesi@hotmail.com>
Co-authored-by: Chris White <white238@llnl.gov>
Co-authored-by: white238 <white238@users.noreply.github.com>
Co-authored-by: Martin Pokorny <mpokorny@caltech.edu>
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
