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2020-06-30[py-mdanalysis] new version and added dependencies (#16819)Jen Herting1-10/+36
* [py-mdanalysis] new version and added dependencies Original commit message: Author: Andrew Elble <aweits@rit.edu> Date: Thu Nov 14 08:35:14 2019 -0500 mdanalysis * [py-mdanalysis] python is type build/run * [py-mdanalysis] updated numpy version requirement for all listed versions of py-mdanalysis * [py-mdanalysis] updated biopython version requirement for all listed versions of py-mdanalysis * [py-mdanalysis] updated py-griddataformats version requirement for all listed versions of py-mdanalysis * [py-mdanalysis] gsd only required after version 1.17.0 and requires gsd@1.4.0 * [py-mdanalysis] only requires mmtf-python after version 0.16.0 and requires version 1.0.0 * [py-mdanalysis] has required py-joblib since version 0.16 * [py-mdanalysis] updated py-scipy version requirement for all listed versions of py-mdanalysis * [py-mdanalysis] updated py-matplotlib version requirement for all listed versions of py-mdanalysis * [py-mdanalysis] has required py-mock since version 0.18.0 * [py-mdanalysis] py-scikit-learn only required after version 0.16.0 and only for +analysis variant * [py-mdanalysis] Reordered and reformatted for readability * [py-mdanalysis] flake8 fixes * [py-mdanalysis] proactively adding version 1.0.0 while I'm here since major release * [py-mdanalysis] fixing some forgotten colons
2020-06-30[py-crossmap] added version 0.3.9 (#17233)Jen Herting1-2/+2
* [py-crossmap] added version 0.3.9 * [py-crossmap] py-numpy not required * [py-crossmap] py-cython must be >= 0.17
2020-06-30[ruby] fixing path to gcc such that users can use gem to install nati… ↵Jen Herting1-0/+11
(#17141) * [ruby] fixing path to gcc such that users can use gem to install native gems to their home directory * [ruby] working on making flake8 happier * [ruby] Line can't really be split cleanly. Enhancing flake8's calm. ya learn something new every day... * [ruby] line break where requested * [ruby] make raw string * [ruby] only running for x86_64-linux everything else is untested * [ruby] finding rbconfig.rb in a cross platform manner
2020-06-30New package/graphblast (#17289)Sinan1-0/+42
* new package: GraphBlast * polish * add cuda_arch setup * flake8 * the package requires cuda variant and dependency * add comments * define cuda_arch * implement multiple and custom cuda arches * tidy up, improve * flake8 * improve style * add variant description * use patch method, add new version for latest commit building since master now fails * remove gcc conflict, tidy up * also indicate build range for boost Co-authored-by: Sinan81 <sbulut@3vgeomatics.com> Co-authored-by: Sinan81 <Sinan81@github>
2020-06-30dssp: new package at v3.1.4 (#17188)Harsh Bhatia2-5/+42
Renamed xspp to hspp
2020-06-30postgis: added package at v3.0.1 (#12635)Sinan1-0/+81
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Sinan81 <Sinan81@github>
2020-06-29py-mpi4py: Implement headers Property (#17295)Sebastian Gottfried1-0/+5
py-mpi4py installs its header files at a difficult-to-predict location: $prefix/lib/python-x.y/site-packages/mpi4py/include With the new `headers` properties, dependent packages have now an easy way to obtain this location: spec['py-mpi4py'].headers.directories[0]
2020-06-29New package: hepmcanalysis (#17296)iarspider2-0/+105
* [WIP] Add hepmcanalysis package * Implement install() for hepmcanalysis * Flake-8 Co-authored-by: iarspider <iarpsider@gmail.com>
2020-06-29R: new versions (#17297)Amjad Kotobi1-0/+2
2020-06-29GDAL: add v3.1.1 (#17302)Adam J. Stewart1-1/+2
2020-06-29Some files could not be created due to errors, which have been fixed. (#17250)h-denpo6-20/+368
added support for Fujitsu compiler.
2020-06-29cp2k: variant tuning `lmax` was broken (#17266)Fabien Bruneval1-1/+1
* cp2k: variant tuning `lmax` was broken - `spack install cp2k lmax=6` now works * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-29New package py-networkit (6.1, 7.0) (#17195)Fabian Brandt1-0/+42
2020-06-29New package: coin3d (#17251)iarspider1-0/+51
* New package: coin3d * Update package.py * Flake-8 * Update var/spack/repos/builtin/packages/coin3d/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add link-time dependencies * Add configure flags for boost; remove version 4.0.0 (doesn't compile) Co-authored-by: iarspider <iarpsider@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-29nfs-utils: fix compile error on debian (#17292)darmac1-0/+1
use pkgconfig to detect libtirpc
2020-06-29New package: fjcontrib + new variants for fastjet (#17255)iarspider2-0/+95
* New package: fjcontrib + new variants for fastjet * Flake-8 * Flake-8 once more * Update package.py * Allow choosing which plugins to build Build all plugins by default. * Flake-8 * Always build all plugins * Update package.py Co-authored-by: iarspider <iarpsider@gmail.com>
2020-06-29codar-cheetah: added v1.1.0 and v1.0.0 (#17286)Kshitij Mehta1-1/+3
2020-06-29geant4: depends on "qt@5: +opengl" when +qt (#17264)Wouter Deconinck1-1/+1
The Geant4 cmake check requires Qt5OpenGL_FOUND, so we must require the Qt5 +opengl variant. If not, the cmake phase fall through to Qt4 and fails due to a missing Qt4::QtGui target. In Geant4InterfaceOptions.cmake: ``` if(Qt5Core_FOUND AND Qt5Gui_FOUND AND Qt5Widgets_FOUND AND Qt5OpenGL_FOUND AND Qt5PrintSupport_FOUND) ``` Ref: https://github.com/Geant4/geant4/blob/master/cmake/Modules/Geant4InterfaceOptions.cmake#L90 (5baee230e93612916bcea11ebf822756cfa7282c, Import Geant4 10.6.0 source tree)
2020-06-29fujitsu-mpi: added "headers" and "libs" methods (#17253)Tomoki, Karatsu1-0/+19
2020-06-28Prevent libffi 3.3 from adding contradictory tuning flags (#17285)Seth R. Johnson1-0/+8
Fixes #17187
2020-06-28package/qgis: add new versions (#17284)Sinan1-1/+7
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-06-28intel: added new versions (#17287)Amjad Kotobi1-0/+2
2020-06-28vmc: New Package (#17282)Dr. Christian Tacke2-0/+79
"""The Virtual Monte Carlo (VMC) library"""
2020-06-28redis: add config file from source code (#17225)darmac1-0/+5
* redis: add config file from source code * Update var/spack/repos/builtin/packages/redis/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-28WarpX: Development Branch (#17163)Axel Huebl1-2/+2
* WarpX: Development Branch Update the name of our development branch. * WarpX version: develop keyword development is not a "newest"-like keyword, but `master`/`develop`/`dev` are. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Renamed: develop version Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-27make gcc build on aarch64 (#17280)Greg Becker1-6/+8
2020-06-27CUDA: CUDAHOSTCXX Env (#16869)Axel Huebl1-0/+2
This is a general CMake CUDA language hint to use the CXX compiler has host compiler for NVCC. Seems like a good default since we do not express the CUDA compiler in Spack otherwise yet (e.g. no `self.compiler.cuda` or `self.compiler.cudahostcxx`).
2020-06-27perl-date-manip: New Package Date::Manip (#17259)Dr. Christian Tacke1-0/+22
2020-06-27[gaudi] new version, cleanup (#17268)vvolkl1-14/+6
2020-06-27Patch needed also for version 7.0 (#17269)Fabian Brandt1-1/+1
2020-06-27LIBXSMM 1.16.1 (#17274)Hans Pabst1-1/+2
2020-06-27migrate to git and update commit (#17276)albestro1-2/+2
2020-06-27superlu-mt: add pic and int64 variants (#11361)David Gardner1-2/+20
* add pic and int64 variants * update to Language-specific PIC flags
2020-06-26Fix super invocation in Intel packages (#17248)Adam J. Stewart2-2/+2
2020-06-25py-azureml-sdk: add new package (and deps) (#17261)Adam J. Stewart45-9/+917
2020-06-25Ascent & Conduit: ~python default (#17230)Axel Huebl2-4/+4
* Ascent: ~python default Packages that build optional python bindings do not build them by default in Spack: https://spack.readthedocs.io/en/latest/packaging_guide.html#variant-names This reduces long dependency trees and build times, e.g. for apps just using C/C++/Fortran bindings of a library. * Conduit: ~python default Packages that build optional python bindings do not build them by default in Spack: https://spack.readthedocs.io/en/latest/packaging_guide.html#variant-names This reduces long dependency trees and build times, e.g. for apps just using C/C++/Fortran bindings of a library.
2020-06-25munge: Update homepage URL (#17257)Dr. Christian Tacke1-1/+1
2020-06-25add new package: datatransferkit (#17158)Ge Wenjun1-0/+46
* add new package: datatransferkit * fix style * remove the build type;add~dtk;'shared' variant;homepage * add maintainer
2020-06-25add sra-toolkit@2.10.7 (#16947)manifest1-0/+3
* sra-tools * sra-tools style fix * sratoolkit version update
2020-06-25libtirpc: Add 1.2.6 (#17209)Michael Kuhn1-0/+2
Earlier versions do not compile with gcc@10:.
2020-06-25Update ArborX for new Kokkos (#17213)Andrey Prokopenko1-19/+40
* Update ArborX for new Kokkos * Set maintainer
2020-06-25prevent multiple version sigils in the same spec (#17246)Greg Becker4-7/+7
* prevent multiple version sigils in the same spec * fix packages with malformed versions
2020-06-25mpich: Allow building with external hwloc library (#15305)Erik Schnetter1-1/+20
This is in principle supported already, but requires a patch to avoid build errors. Closes #15302 Co-authored-by: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
2020-06-25Separate Apple Clang from LLVM Clang (#17110)Massimiliano Culpo62-94/+136
* Separate Apple Clang from LLVM Clang Apple Clang is a compiler of its own. All places referring to "-apple" suffix have been updated. * Hack to use a dash in 'apple-clang' To be able to use autodoc from Sphinx we need a valid Python name for the module that contains Apple's Clang code. * Updated packages to account for the existence of apple-clang Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Added unit test for XCode related functions Co-authored-by: Gregory Becker <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-25msmc2: added package at v2.1.2 (#17170)manifest1-0/+43
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-24Update the version of Cereal. (#17244)Brian Van Essen1-0/+1
2020-06-24chill: Patch to include gmp, isl, and libquadmath (#16996)John Jolly4-1/+150
The rose library uses the `strtoflt128` and `quadmath_snprintf` functions. In order to successfully link the rose library, chill must also link the GCC libquadmath library to resolve the two functions. This patch changes the chill build to include this library. Chill will also not compile unless headers from the gmp and isl libraries are found in the includes path. Two patches - one each for gmp and isl - modify the chill build process to add options to specify those paths. These options follow the similar pattern as seen with BOOSTHOME and ROSEHOME options which already exist in the chill build process. Because of the addition of GMPHOME and ISLHOME options, build requirements for gmp and isl are also added.
2020-06-24vtk: Add patch for finding Fujitsu-MPI wrapper commands. (#17069)Tomoki, Karatsu2-0/+21
2020-06-24mvapich2: Fix build with gcc@10: (#17114)Michael Kuhn1-0/+10
2020-06-24openjdk and jdk: extend the list of provided versions of java (#17151)Sergey Kosukhin2-1/+4
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