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2020-07-02glusterfs: add pkgconfig dependency (#17343)darmac1-0/+1
2020-07-02jmol: add version 14.31.0 (#17351)g-mathias1-2/+14
Also: * Add url_for_version function * Add Java to PATH for run environment * Update `install` method to handle old and new version Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
2020-07-02Random123: add versions 1.10, 1.13.2 (#17361)Kelly (KT) Thompson1-2/+6
2020-07-02quicksilver: add v1.0Christoph Junghans1-1/+2
2020-07-02py-tensorflow: Fix for tensorflow issue #40688 (#17324)takanori-ihara1-2/+3
* py-tensorflow: Fix for #40688 * py-tensorflow: Fix for tensorflow issue #40688
2020-07-02FrontISTR: add version 5.1 (#17349)Michio Ogawa1-0/+1
2020-07-02keepalived: openssl is a link and build dependency (#17346)darmac1-1/+1
2020-07-02openmpi: add singularity variant (#17288)Amjad Kotobi1-0/+10
2020-07-02New packages: heputils and mcutils (#17330)iarspider2-0/+70
heputils is a (conditional) dependency of mcutils
2020-07-02cpprestsdk: add version 2.10.16 (#17331)Harmen Stoppels1-1/+10
Also * Patch is only needed for 2.9.1 * Add openssl dependency * Build with -DWERROR:BOOL=Off
2020-07-02mapnik: add version 3.0.23, update boost dependency (#17338)Sinan1-2/+3
2020-07-02examl + (#17265)manifest1-0/+50
* examl + * examl style fix * examl flake8 fix * Update var/spack/repos/builtin/packages/examl/package.py using `working_dir` Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-02py-fortran-language-server: new package at v1.11.1 (#17318)Andrew Gaspar1-0/+23
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-02py-shroud: added v0.12.1 (#17332)Michael Kuhn1-1/+2
py-setuptools is also needed at runtime, otherwise we get errors: ``` ModuleNotFoundError: No module named 'pkg_resources' ```
2020-07-02autotools: Fix config.guess detection, take two (#17333)Michael Kuhn1-5/+3
The previous fix from #17149 contained a thinko that produced errors for packages that overwrite configure_directory.
2020-07-02py-opt-einsum: added v3.2.1, v3.2.0 and v2.3.2 (#17339)Sinan1-1/+5
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-07-02py-sphinxcontrib-bibtex: added v1.0.0 (#17336)Paul R. C. Kent1-0/+1
2020-07-02amrex: added v20.07 (#17337)mic841-1/+31
Also added support for hdf5, petsc and hypre
2020-07-02biobloom: use the correct standard library for Fujitsu compilers (#17327)ketsubouchi1-0/+6
2020-07-01Moved flake8, shell and documentation tests to Github Action (#17328)Massimiliano Culpo6-125/+100
* Move flake8 tests on Github Actions * Move shell test to Github Actions * Moved documentation build to Github Action * Don't run coverage on Python 2.6 Since we get connection errors consistently on Travis when trying to upload coverage results for Python 2.6, avoid computing coverage entirely to speed-up tests.
2020-07-01Fix hashlib function capitalization (#17323)Adam J. Stewart1-1/+1
2020-07-01Documentation update for container example (#17321)Glenn Johnson1-2/+2
This updates the documentation to reflect #17316.
2020-07-01Use apple-clang for MacOS nightly tests (#17320)Greg Becker1-6/+6
2020-06-30hbase: refine url , java and version (#17306)darmac1-9/+12
* hbase: refine url , java and version * Update var/spack/repos/builtin/packages/hbase/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-30Merge branch 'releases/v0.15' into developGregory Becker4-9/+108
2020-06-30changelog for v0.15.0v0.15.0Gregory Becker1-2/+96
2020-06-30bump version numberGregory Becker3-7/+12
2020-06-30Activate environment in container file (#17316)Glenn Johnson2-2/+4
* Activate environment in container file This PR will ensure that the container recipes will build the spack environment by first activating the environment. * Deactivate environment before environment collection For Singularity, the environment must be deactivated before running the command to collect the environment variables. This is because the environment collection uses `spack env activate`.
2020-06-30run github workflows on release branches (#17317)Greg Becker4-0/+4
2020-06-30Don't detect "classic" on Cray to avoid a compiler bug (#17314)Massimiliano Culpo4-2/+16
* Don't detect "classic" on Cray to avoid a compiler bug * add tests Co-authored-by: Gregory Becker <becker33@llnl.gov>
2020-06-30Add fish shell support (#9279)Johannes Blaschke10-6/+1171
* share/spack/setup-env.fish file to setup environment in fish shell * setup-env.fish testing script * Update share/spack/setup-env.fish Co-Authored-By: Elsa Gonsiorowski, PhD <gonsie@me.com> * Update share/spack/qa/setup-env-test.fish Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * updates completions using `spack commands --update-completion` * added stderr-nocaret warning * added fish shell tests to CI system Co-authored-by: becker33 <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Elsa Gonsiorowski, PhD <gonsie@me.com>
2020-06-30Cray compiler: fix implicit rpaths for classic versions (#17310)Greg Becker4-14/+41
* check link dirs for existence
2020-06-30cmake v3.17.3 (#17313)Andrew Gaspar1-0/+1
2020-06-30half: fix __F16C__ include of immintrin.h (#17272)Andrew W Elble2-0/+25
Small fix so that immintrin.h gets included properly when the compiler sets __F16C__. Upstream has been notified.
2020-06-30filebench:remove autoreconf() (#17305)darmac1-8/+0
2020-06-30add constrain for hpx 1.4.* and boost 1.73.0 (#17307)albestro1-0/+4
https://github.com/STEllAR-GROUP/hpx/issues/4728#issuecomment-640685308
2020-06-30cleverleaf: Add C++ link flags for Fujitsu. (#17308)Tomoki, Karatsu2-0/+14
2020-06-30Add OpenFOAM 2006 (2020-06) release (#17309)Mark Olesen1-0/+1
Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
2020-06-30Catch2 v2.12.3 (#17312)Andrew Gaspar1-1/+7
Added master branch, too
2020-06-30[whizard] Fix Runtime Compiler Paths (#17300)vvolkl1-0/+12
* [whizard] fix runtime compilers fix * [whizard] flake8 * [whizard] add master branch
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
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