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2019-12-06Add h5sh python package (#14001)Seth R. Johnson1-0/+25
* Add h5sh package * Fix requirements and update version
2019-12-05hpcviewer: add version 2019.09 (#14004)Mark W. Krentel1-7/+10
Add version 2019.09. Adjust the iteration through versions to eliminate the need for version_list.
2019-12-05Add new TensorFlow package (#13112)Dominik Dold19-43/+978
* 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
2019-12-05paraview: Adjust python version constraints (#13999)Chuck Atkins1-2/+2
py-matplotlib: No constraint necessary for py3 but py2 has an upper bound py-numpy: No constraint necessary for py3 but py2 has an upper bound
2019-12-05Added go 1.13.5 and 1.12.14 (#13997)Paul1-0/+2
2019-12-05py-pillow: allow older versions to build with python 3.4 (#14000)Chuck Atkins1-1/+2
2019-12-05eospac: fix url (#13998)Christoph Junghans1-8/+8
2019-12-05New package: swipl (#13978)Alexander Knieps1-0/+71
* New package: swipl * Removed boilerplate, added maintainer * Fixed python 2 incompatibility * Update var/spack/repos/builtin/packages/swipl/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * swipl: Added conflict with intel compiler
2019-12-04patching: do strict version range checking (#13989)Peter Scheibel2-0/+4
* 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
2019-12-05Add py-matplotlib 3.1.2 (#13994)Adam J. Stewart1-1/+2
2019-12-04CUDA: Keep 10.1.243 As Preferred (#13983)Axel Huebl1-1/+2
Keep CUDA 10.1.243 as the preferred version until the issue of including implementation details of libcu++ is addressed.
2019-12-04Update libensemble to v0.6.0 (#13987)Stephen Hudson1-1/+2
2019-12-04Add latest version of py-scikit-learn (#13979)Adam J. Stewart1-1/+2
2019-12-04Add Elfutils 0.178 (#13976)Tim Haines1-1/+7
* Add elfutils-0.178 * Disable debuginfod server * Fix flake8
2019-12-04Use correct range check for the version (#13977)Tim Haines1-1/+1
Update to #13893
2019-12-03Release a new version v2.1.8.0 for SZ (#13974)Sheng Di1-1/+4
* Release a new version v2.1.8.0 for SZ * add maintainer * add parallel = False to avoid potential compile issue
2019-12-03mpich: update build requirements (#13966)Rob Latham1-0/+6
To build from git, MPICH will need newer autoconf, automake, and libtool than typically available on many systems.
2019-12-03argobots: consistently use 'master' (#13965)Rob Latham1-4/+4
Commit 71cd91e4 changed "latest from git" to 'master' from former 'develop'. Build dependencies still pointed to @develop, though
2019-12-03new package: Simmetrix SimModSuite (#8730)Cameron Smith1-0/+242
* 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
2019-12-03kaldi: Change process of version analysis when using Fujitsu compiler. (#13960)t-karatsu2-0/+14
2019-12-03fix_cantera_installation (#13962)asmaahassan901-2/+2
For a successful cantera installation, googletest has to be installed with gmock on, and sundials has to be of version less than 3.2
2019-12-03bump libfabric to 1.9.0 (#13964)Phil Carns1-0/+6
2019-12-03Update MrBayes to 3.2.7a and correct MPI variants (#13929)Yuanqi Wang1-13/+10
* Update MrBayes and correct MPI variant * Use tarballs and remove autotools dependencies * MrBayes: remove ISA variants
2019-12-03Update package libgpg error (#13697)Jannek Squar3-0/+201
* 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
2019-12-02Add missing metis include to superlu-dist (#13956)Chris White1-1/+3
* Add missing metis include to superlu-dist * Fix PEP-8 line length * Fix PEP-8 indent
2019-12-02add more versions (#13957)Sinan1-3/+10
2019-12-02Speedup environment activation (#13557)Massimiliano Culpo1-2/+8
* 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
2019-12-02amber: Improved package.py and added version 18 (#13945)Hector Martinez-Seara2-50/+159
* 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
2019-12-02Fix conflict with respect to openssl and qt3 built for openspeedshop. (#13946)Jim Galarowicz1-1/+1
* Fix conflict with respect to openssl and qt3 built for openspeedshop. * Another fix because the first was incorrect.
2019-12-02eq-r: Fix use of Executable.__call__() (#13952)Justin M Wozniak1-1/+1
2019-12-01dealii: Added 'threads' variant that controls the TBB dependency (#13931)Alexander Knieps1-3/+10
* 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>
2019-12-01Package/sensei: PR request for SENSEI (in situ analysis tool) recipe (#12973)Sergei Shudler1-0/+134
* 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
2019-11-30Add VTK version 8.2.0 (#13941)Benjamin Fovet1-0/+1
2019-11-30New python packages (#9974)jwallior5-0/+98
* New package: add py-jellyfish * New package: add py-us * New package: add py-xlwt * New package: add py-svgpathtools * New package: add py-svgwrite * Change checksums to sha256 * Fix Copyright year. * Add missing dependencies.
2019-11-30Add package opencascade (#13938)Benjamin Fovet1-0/+67
* Add new package : opencascade * Remove boilerplate comment * Fix flake8 errors * Explicitly disable 3rd parties
2019-11-30cbtf: add rpcsvc-proto and libtirpc dependency. (#13798)Toyohisa Kameyama1-0/+6
2019-11-30Mark py-argparse dependency everywhere with ^python@:2.6 (#13928)iarspider8-8/+8
* Mark py-argparse dependency everywhere with ^python@:2.6 * Update package.py * Update package.py
2019-11-30add new package : lshw (#13933)darmac1-0/+28
* add new package : lshw * update lshw package * remove build methord
2019-11-29Update Geant4 version and recipe (#13840)iarspider1-1/+2
* Update Geant4 version and recipe According to the Geant4 developers, Geant4 supports Qt5 since at least 10.00. * Update to new API
2019-11-29Mass conversion of setup_(dependent_)?environment (#13924)Adam J. Stewart185-818/+806
* Mass conversion of setup_(dependent_)?environment * prefix -> self.prefix
2019-11-29intel-tbb: fix and update patches for latest versions (#13932)Mark W. Krentel4-48/+33
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.
2019-11-29add new package : pipework (#13934)darmac1-0/+21
2019-11-29add new package : qperf (#13935)darmac1-0/+28
2019-11-29Handle external perl (#13903)Peter Scheibel1-27/+8
* 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
2019-11-28Loosen restriction on setuptools version of ↵iarspider1-1/+1
py-backports-shutil-get-terminal-size: the bug seems to be fixed at least in setuptools 41.0.0 (#13927)
2019-11-27BLD: enforce C++11 std for boost + xl_r (#13829)Tyler Reddy1-0/+6
* 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>
2019-11-27Build R without recommended packages (#12015)Glenn Johnson1-0/+1
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.
2019-11-27Replace git-based Bioconductor R packages (#12005)Justin S186-1326/+3320
* 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>
2019-11-27Add version 2.1.0 to 'aspect' package (#13830)Rene Gassmoeller1-3/+4
2019-11-27Update cartopy version and fix recipe (#13898)iarspider1-7/+19
* 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
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2025-03-26 18:35:16 +0000