* elpa: port to microarch
* flake8
* Update package.py
* Update var/spack/repos/builtin/packages/elpa/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Adding libid3tag package for supporting feh
* Adding libexif package for supporting feh
* Adding imlib2 package for supporting feh
* Adding the feh package
* Rewording the cleanup function for libid3tag
* Fixing some flake8 issues for imlib2 and libid3tag
* Adding sources for the patches and swapping rm for os.remove
* Flake8 fixes
* swapping md5sums for sha256sums
* CUDA HeaderList: Unit Test
* Spec Header Dirs: Only first include/
Avoid matching recurringly nested include paths that usually
refer to internally shipped libraries in packages.
Example in CUDA Toolkit, shipping a libc++ fork internally
with libcu++ since 10.2.89:
`<prefix>/include/cuda/some/more/details/include/` or
`<prefix>/include/cuda/std/detail/libcxx/include`
regex: non-greedy first match of include
Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* CUDA: Re-Enable 10.2.89 as Default
* ibm-java: add version 8.0.6.0
Add version 8.0.6.0 and remove 8.0.5.30. IBM is fairly aggressive
about removing old versions, and 8.0.5.30 is no longer available from
their download site.
* Restore version 8.0.5.30, although it is no longer available for
download from IBM.
* Addition of repository branches to maestrowf.
* Addition of 1.1.5dev pre-release.
* Correction of a merge conflict.
* Addition of Maestro release 1.1.5
* Addition of Maestro release 1.1.6 (removal of 1.1.5)
* Sets 1.1.6 to the preferred version.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Tweak to the url to point to latest.
* Fix Apex and OTF2 support
- Comment out apex as a dependncy: it is bundled with HPX.
- Apply a patch to v1.3.0 to correctly build with APEX.
- Add otf2 as a dependency when APEX is enabled.
* Remove depends_on('apex')
* augustus: Set compile commands for each compiler and Fix for using 'boost' on Spack
* fix for flake8
* delete 'string' args
* Fix args of filter_file func
* Fix args of other filter_file func
* Add patch to fix issue building current llvm develop master on power9
* Conform to proper block commenting
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add tensorflow
Change-Id: Id778c68d148cc42f0b478a9d10a8f937cb54cdc6
* make bazel and tensorflow build
Change-Id: Iae9005e8f4dcc8f1ed36ea9337d2430aeebb291f
* fix flake8
Change-Id: Ib05529dd796eab4a8855a5d7775cc4efea8e479d
* 2nd flake8 attempt
Change-Id: I46224be3a374b2a65793048b0c5178ea64adbd78
* replace md5 sums with sha256
* add version 1.13.2
* bazel() -> bazel('build',...
* specify versions of bazel dependency
* build with CUDA
* add TODOs
* add more todo"s
* improve enum34 dependency
* py-future is a dependency as of v1.14
* Update var/spack/repos/builtin/packages/tensorflow/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/tensorflow/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/tensorflow/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/tensorflow/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* enable nccl, cuda by default
* explain patches
* add todo
* remove unnecessary copt_flag
* use join
* join argument must be an iterable
* split long line; use same opts for non-cuda build
* without opt flags, configure hangs
* introduce build phases; re-arrange
* undo mistake
* restore unset tmp_path
* as of v1.14, nccl_install_path is parsed correctly, hence change ...prefix.lib to ...prefix
* now, version 1.14 compiles successfully with cuda
* add version 2.1.0
* specify bazel dependency for version 2.1.0-rc0
* account for deprecated bazel opts for v2.1.0-rc0
* disable mkldnn contraction kernel
* Flake8 fixes
* md5 -> sha256
* Fix TF and TF-estimator version deps
* Don't just comment out patch
* Add myself as a maintainer
* Patch py-astor to support newer py-setuptools
* Add more versions and bazel version constraints
* Add a build phase
* Add note about configure interactivity
* dev-build -> build-env
* Disable iOS build
* Use correct optimization flags
* Add variants for all possible features
* nccl isn't always a dependency
* Specify correct dependency versions for each release
* Libs may not be in lib or lib64
* Add py-opt-einsum package
* Add newer version of py-protobuf
* Add newer version of py-wrapt
* Fix Python 2.6 syntax error
* Code review
* Set more env vars for older versions
* Add more env vars, fix bazel versions, add conflicts
* Fix config options
* Specify version that support --config args
* Add py-future dependency for Python 2
* Fix cuda config flag and compute capabilities
* Fix installation on macOS, add unit tests
* Override cuda variant default to True on non-macOS
* Rename tensorflow to py-tensorflow
* Has to extend something
* Fix os.symlink call
* convert cuda_arc values to capabilities
* restore nccl prefix path for v1.13.1
* Revert to v2
* Remove extraneous period
* Add new version of jdk/openjdk
* More stable cuda_arch formatting
* Fix bazel unit tests
* Fix symlinking
* Fix unit tests
* +gcp by default until build error figured out
* apply strict constraint checks for patches, otherwise Spack may incorrectly treat a version range constraint as satisfied when mixing x.y and x.y.z versions
* add mixed version checks to version comparison tests
* package for Simmetrix SimModSuite
* simmodsuite: passes flake8
* simmetrix: add version, set cmake prefix path
A given install will either use the libs built on rhel7 or rhel6.
For now, I'm sticking with the non-spack install convention of
placing the libraries into sub-directories named according to their
build process (os + compiler).
* simmetrix: add older version
* simmetrix: set build env paths
easier to build pumi using CMAKE_PREFIX_PATH
* simmetrix: address review comments
* simmetrix: add new version and remove old one
* simmetrix: flake8 fixes
* simmodsuite: oslib var is in self
* simmodsuite: update version and checksum
* simodsuite: set LD_LIBRARY_PATH for cad kernels
* update license
* update setup_environment calls
* increase indentation for flake8
* python3.8 flake8 fixes
* use spack consistent naming
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* sha256 required, update versions and hashes
* Added build dependency on gawk
* Use virtual depdendency
* Added patch to prepare libgpg-error for use with gawk@5
* Added reasoning with link for need for patch
* Add a transaction around repeated calls to `spec.prefix` in the activation process
* cache the computation of home in the python package to speed up setting deps
* ensure that module-scope variables are only set *once* per module
* amber: Improved package.py and added version 18
- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()
* dealii: Added 'threads' variant that controls the TBB dependency (#13931)
* dealii: Added 'threads' variant that controls the DEAL_II_WITH_THREADS cmake option and the dependency on Intel TBB
* Update var/spack/repos/builtin/packages/dealii/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* amber: Improved package.py and added version 18
- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()
* amber: Adding missing flex and bison dependencies
* Removed cray variant; flex and bison now build only
* amber: Improved package.py and added version 18
- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()
* amber: Adding missing flex and bison dependencies
* Removed cray variant; flex and bison now build only
* dealii: Fixed flake8 issues
* amber: corrected typo
* amber: Removed unused variant python
* dealii: Added 'threads' variant that controls the DEAL_II_WITH_THREADS cmake option and the dependency on Intel TBB
* Update var/spack/repos/builtin/packages/dealii/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Created an initial recipe for Sensei
* Cleanup syntax
* Small fixes for the Sensei recipe
* Cosmetic fixes to comply with PEP8
* More cosmetic fixes before PR
* Added more documentation before PR
* Fixed flake8 errors
* Fixes following PR review
* Fixes to pass Flake8 passes
* Some changes following PR review and support for SENSEI 3
* Update var/spack/repos/builtin/packages/sensei/package.py
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Fixed Flake8 errors
Commit 78724357 added versions 2019.5 to 2019.8 but failed to update
the patches for these versions.
1. gcc_generic-pedantic patch -- include this up through 2019.5. This
was fixed in the TBB source tree in 2019.6.
2. tbb_cmakeConfig patch -- this needs to be modified (different file)
for 2019.5 and later.
3. tbb_gcc_rtm_key patch -- replace this with filter_file. This is
simpler and eliminates the need to update the patch whenever the
surrounding context changes.
* dont add perl bin directory to PATH when setting up env (this is already handled by spack core in a way that omits system dirs); also consolidate repeated logic between build/run env setup.
* the bin/ dir of each dependency is already added to PATH in Spack core, so there is no need to do this in the Perl package
* BLD: enforce C++11 std for boost + xl_r
* the spack `cxxstd` variant is not sufficient to enforce
`-std=c++11` usage in boost compile lines when `xl_r` compiler
spec is in use; while it would be nice if this were fixed
in a boost config file somewhere, for now this patch
allows boost to build on POWER9 with
an %xl_r compiler spec if the user specifies i.e.,:
`spack install boost@1.70.0+mpi cxxstd=11 %xl_r@16.1.1.5`
* Update var/spack/repos/builtin/packages/boost/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
The documentation states that Spack builds R without the recommmened
packages, with Spack handling the build of those packages to satisfy
dependencies. From the docs:
> Spack explicitly adds the --without-recommended-packages flag to
> prevent the installation of these packages. Due to the way Spack
> handles package activation (symlinking packages to the R installation
> directory), pre-existing recommended packages will cause conflicts for
> already-existing files. We could either not include these recommended
> packages in Spack and require them to be installed through
> --with-recommended-packages, or we could not install them with R and
> let users choose the version of the package they want to install. We
> chose the latter.
However, this is not what Spack is actually doing. The
`--without-recommended` configure option is not passed to R and
therefore those packages are built. This prevents R extension activation
from working as files in the recommended packages installed with R will
block linking of file from the respective `r-` packages.
This PR adds the `--without-recommended` flag to the configure options
of the R package. This will then have the Spack R build match what is
documented.
* Replace git-based Bioconductor R packages
The current collection of bioconductor packages tend to have scattered
dependencies and missing versions. This commit replaces git-based
packages with tool-generated Spack package recipes with correct
dependencies and descriptions in place.
* Fix some broken package names, add periods to title docstrings
* r-clue: new package at 0.3-57
* r-genomeinfodbdata: add 1.2.1
* r-gofuncr: new package at 1.4.0
* r-pfam-db: add 3.8.2
* Add missed package r-genelendatabase
* update r-goseq package
* update r-glimma package
* update r-rots package
* r-org-hs-eg-db: add 3.8.2
* r-vgam: fix incorrect R version
* r-rnaseqmap: new package at 2.42.0
* r-rhdf5lib: new package at 1.6.0
* r-scrime: new package at 1.3.5
* r-delayedmatrixstats: new package at 1.6.0
* r-hdf5array: new package at 1.12.1
* r-biocfilecache: new package at 1.8.0
* r-ctc: add new versions, dependencies
* r-genemeta: new package at 1.56.0
* r-scrime: fix flake8
* r-ensembldb: add missing dependencies
* Added missing dependencies to packages with certain DESCRIPTIONS
* r-mapplots: new package at 1.5.1
* r-beachmat: new package at 2.0.0
* r-beeswarm: new package at 0.2.3
* r-biocneighbors: new package at 1.2.0
* r-biocsingular: new package at 1.0.0
* r-ecp: new package at 3.1.1
* r-enrichplot: new package at 1.4.0
* r-europepmc: new package at 0.3
* r-ggbeeswarm: new package at 0.6.0
* r-ggplotify: new package at 0.0.3
* r-ggraph: new package at 1.0.2
* r-gridgraphics: new package at 0.4-1
* r-rcppannoy: new package at 0.0.12
* r-rcpphnsw: new package at 0.1.0
* r-rsvd: new package at 1.0.1
* r-scater: new package at 1.12.2
* r-singlecellexperiment: new package at 1.6.0
* r-tximport: new package at 1.12.3
* r-upsetr: new package at 1.4.0
* r-vioplot: new package at 0.3.2
* r-readr: add 1.3.1
* r-matrixstats: add 0.54.0
* r-ecp: flake8 fix
* r-biocmanager: new package at 1.30.4
* update bioconductor packages requiring BiocManager, new versions
* r-lambda-r: add 1.2.3
* r-vegan: add 2.5-5
* r-cner, r-rcppannoy, r-reportingtools, r-rsvd: add missing newlines at EOF
* r-chemometrics: flake8 fixes
* r-vgam: flake8 fixes
* CRAN packages: use cloud.r-project.org
* Use DESCRIPTION for R version constraints over bioconductor releases
* Update missed packages ABAData, acde, affydata
* Update remaining missed packages
* bio: Drop 'when' clause from first checksummed versions
* bio: improve package description generation logic
* r-genomeinfodbdata: use explicit sha256 sums
* r-pfam-db: update dependencies, add 3.10.0
* update r-org-hs-eg-db
* r-dirichletmultinomial: re-add gsl
* r-polyclip: new package at 1.10-0
* r-farver: new package at 1.1.0
* r-tweenr: new package at 1.0.1
* r-ggforce: new package at 0.3.1
* r-ggforce: remove redundant dep
* r-ggraph: add missing deps
* r-rcpphnsw: remove redundant depends_on
* r-reportingtools: re-add r-r-utils dep
* r-rhdf5: add gmake dep
* r-rhtslib: add system dependencies
* r-rsamtools: add gmake dep
* r-farver: remove redundant dep
* r-tweenr: remove redundant dep
* r-variantannotation: add gmake dep
* r-rgraphviz: add graphviz dep
* r-vsn: correct r-hexbin constraint
* r-scater: fix obsolete deps
* r-variantannotation: fix gmake dep type
* r-scater: tighten R version constraints
* r-rsamtools: fix gmake dep type
* r-rhtslib: fix gmake dep type
* r-rhtslib: use xz over lzma
* r-rhdf5: fix gmake dep type
* r-farver: replace with newer recipe for 2.0.1
* r-mzr: remove old dependency
* r-reportingtools: remove builtin dependency
* r-mzr: add gmake dep
* r-rhtslib: make system libraries link deps
* r-genomeinfodbdata: fix R version constraints
* r-geoquery: remove old deps from new versions
* r-genomicfeatures: tighten r-rmysql dep
* r-ensembldb: tighten r-annotationhub dep
* r-complexheatmap: fix r-dendextend dep
* r-cner: fix utils dep name
* r-clusterprofiler: fix r-gosemsim version req
* r-biostrings: fix r-iranges version reqs
* r-rhdf5lib: add gmake dep
* r-oligoclasses: fix r-biocinstaller dep range
* r-organismdbi: fix r-biocinstaller dep range
* r-hdf5array: add gmake dep
* r-gtrellis: tighten r-circlize version req
* r-gostats: fix r-graph version req
* r-glimma: fix old dependency ranges
* r-biostrings: syntax fix
* r-organismdbi: syntax fix
* r-dose: fix r-igraph dep
* r-dose: fix r-scales, r-rvcheck deps
* r-affy: fix r-biocinstaller dep
* r-ampliqueso: fix homepage
* r-aneufinder: fix r-biocgenerics dep
* r-beachmat: fix changed deps
* r-biocneighbors: fix old R constraint
* r-biocmanager: rewrite recipe for 1.30.10
* Update var/spack/repos/builtin/packages/r-biocinstaller/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/r-oligoclasses/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update cartopy version and fix recipe
Cartopy 0.17.0 works fine with proj 6
* Update cartopy version and fix recipe
Cartopy 0.17.0 works fine with proj 6
* Set ACCEPT_USE_OF_DEPRECATED_PROJ_API_H flag when building extension
* Add variants to py-cartopy recipe as suggested
* Fix proj dependency
* Split dependency
* Fix PEP-8; remove extra dependency
* Bump up QE version number to 6.4.1.
* Fix QMCPACK conflicts.
* HDF5 dependencies where over specified which could cause unnecessary installs of HDF5.
* Update QMCPACK testing option.
* Remove support for serial QE 6.4.1 converter. Add support for parallel QE 6.4.1. converter with serial HDF5.
* Switch to setup_run_environment.
* Fix setup_run_environment call arguements.
* Fix typo.
* switch run_env to env
* package py-cheroot
* package py-cheroot
* autopep8, docutils cleanup
* Update var/spack/repos/builtin/packages/py-cheroot/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* missing deps
* flake8
* license bits
* Update var/spack/repos/builtin/packages/py-cheroot/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-cheroot/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-cheroot/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-cheroot/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* python dep
* flake8
Note to spack people: these are expected to be end of line releases for both the 3.1.5 an 3.0.5 releases
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* metabat: add versions 2.14 and 2.13
* update build environment
* Update var/spack/repos/builtin/packages/metabat/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/metabat/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* update py-nbconvert
* add setuptools dependency, like all the other jupyter packages
it seems to be using setuptools for some commands all the time
but requires it for the newest version
* added dependencies, not necessarily only needed for the latest one
* depends on new packages (defusedxml, pandocfilters, testpath)
* should also be moved to pypi sources?
* '@5:@5:' is a valid spec -> intended?
* make dependencies optional
* Update dependencies and add description
* relax py-mistune dependency restriction
* Update var/spack/repos/builtin/packages/py-nbconvert/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* new package: py-arrow
* actually use dependencies from 0.14.7 not from current HEAD
* drop dependencies that dont appear in the source
* readd sphinx as doc dependency
* update dependencies
* drop doc-only dependencies
* add new package : busybox@1.31.1
* 1. add some other version for busybox
2. change Busybox class to MakefilePackage
3. move make('defconfig') and make() to build() function
4. change install_tree('', prefix) to install_tree('.', prefix)
* add variant for enabling testing
* enable tests and clean up other options
* add numbered versions
* updates to avoid enable_tests variant; correct versioning
* fixes for style
* appropriate partitioners are enabled if 'all' is specified - so no need to check in spec
* define url so spack knows how to fetch the tar.gz files for different versions
* Add SOLLVE package with Shintaro's help on rebasing.
Co-authored-by: Vivek Kale <vivek.lkale@gmail.com>
* sollve: reflect suggestions by @adamjstewart
* sollve: update target detection
Copied from llvm/package.py.
* sollve: fix a few things
- url -> git
- remove git in version()
- explicit cmake options in else clauses
- add newlines for better readability
* Added new package libmmtf-cpp required by py-pymol
* Added SPDX-License-Identifier to MIT
* Updated py-pymol to version 2.3.0
* py-pymol: Added mising py-pmw dependency
* py-pymol: flake8 minor change
* py-pymol: Added patch for apbstools_tcltk8.6
This patch is borrowed from archlinux
https://bugs.archlinux.org/task/39526
* libmmtf-cpp: flake8 compliance
* libmmtf-cpp: flake8 compliance
* libmmtf-cpp: change license to (Apache-2.0 OR MIT) when refering to the MIT license
* libmmtf-cpp: Added header text about license as in examples
* py-pymol: removed unnecesary dependency mesa-glu
* py-pymol: removed unnecesary patch
* py-pymol: Removed empty line at the end of the file to comply with flake8.
* Add the py-coloredlogs package
* Remove extraneous line.
* Remove dashed line.
* Add version for humanfriendly dep and build to type.
* Change source url to use pypi.
* Improved library access for lm-sensors and implemented use in papi.
* Fixed comment formatting
* Removed explicit "None" from return of libs().
* Added two new software release versions.
* fix runtime error involving py-pycairo and PDF
* Update var/spack/repos/builtin/packages/py-python-mapnik/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* fix env setup
* Add the py-importlib_re package
* Rename package to conform with spack naming convention.
* Rename package to py-importlib-resources
Add python depend modules for previous python versions and depends_on python.
* Add whitespaces.
* use bazel commit in #13112, and add version 0.24.1, and corresponding cc_env patch
* undo preferred java version by dodo47
* patch for v0.26
* Update install steps
* Add patches for more versions
* Add unit tests
* Update patches for new Spack env vars
* env is already defined, use spackEnv
This makes several installs from the same download cache impossible once
the hash of the used perl-install changes.
Fixes: #13824
Change-Id: I5f10d9d54ae999d0ca7e4171f989dfca2e6a7169
* Add py-wub, with supporting fixes
- add py-wub
- add py-pycmd because py-wub needs it
- update py-statsmodels, which needs at least v0.9.0 to work with
python3.7 because cython.
* Update based on Adam's comments
* Fix dependency types for py-six in py-wub
* statsmodels tests fail, update comment w/ Issue #
The statsmodels tests weren't run in the previous version of the
package. If I enable them, the fail.
Update the package comment with the statsmodels issue I opened to
track the problem:
https://github.com/statsmodels/statsmodels/issues/6263
* Update dependency types in py-wub/package.py
* flake8 cleanups
* Make statsmodels tests work
- need to use patsy@0.5.1:
- need to run the tests from within the build/lib* dir
* Add mg, a gnu-emacs like fork of microemacs
* Use Package, since not really an Autotools package
Switch from AutotoolsPackage to Package. Even though mg has a
configure script, it's not really an Autotools package.
* Need to also provide --prefix to configure
* Make relative binaries relocate text files properly
* rb strings aren't valid in python 2
* move perl to new interface for setup_environment family methods
