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2019-10-28Update URL parsing regexes and tests (#13411)Adam J. Stewart236-740/+581
* Update URL parsing regexes and tests * Get rid of no longer used README * Merge py-udunits and py-cf-units * netcdf -> netcdf-c * setup_environment -> setup_*_environment * Fix doc tests * Few last minute fixes * Simplify prefix removal copypasta
2019-10-28Update the module files for cbtf-krell and openspeedshop (#13400)Jim Galarowicz5-86/+97
* Update the module files for cbtf-krell and openspeedshop adding man paths and needed papi and libmonitor paths. * Update module files for new API. * Use the same python for both develop and release branches.
2019-10-28new Package/scs (#13454)Sinan2-0/+55
* new package: SCS * make flake8 happy * add missing patch, improve style * fix typo * Update var/spack/repos/builtin/packages/scs/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * move filefilter to edit phase
2019-10-28update conduit for 0.5.0 release (#13455)Cyrus Harrison2-25/+92
* add support for static (via ~shared) and use vtk-m 1.2 * updating vtkh package to output cmake configure file and pinning it to vtkm 1.2 * trying a different cmake for vtkh * removing problematic b * making conduit respect ~python * fixing ascent python logic * update ascent package * consistant cmake usage * conditionally add tbb in ascent if vtkh * applying becker fix * adding vtkh tag * fixing vtkh tagged version * updating ascent and conduit for static builds * enabling openmp * reverting files that should not have been changed * ascent updates * more robust handling of variants * fixing ascent package typo * ascent: add optional support for mfem * enable mfem conduit support for ascent * add optional adios dep to conduit * remove ver req from conduit * ascent: remove confusing comment * tweaks to conduit and ascent pkg recipes * fix typo in conduit package * pref conduit master * fixing mfem typo for ascent * reverting files * adding mirror for bzip * changing mfem to depend on conduit@master to get updated relay * restore use of conduit 0.3.1 or greater for mfem * set master as prefered conduit version * allow mfem to use conduit master * adding rover package and editing ascent * updating vtkm cmake dep * updates from axom * guard ascent python support on +shared * removing rover to simply ascent package * add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified * fix fortran compiler check so it can work on cray systems * working towards cuda fix for vtkm lagrange filter * update ascent package with more variants, and patch to avoid nvcc issue * hdf5 flags fix for BGQ * flake8 * extra guards for cuda patch * conduit and ascent fortran fix * fix patch for non cuda case * add test variant to conduit, tweak ascent pkg * change min ver of cmake used for ascent * h5z-zfp package: unset FC when ~fortran * conform to expected upstream solution * pinning vtkm * going back to vtkm master * add back vtk-m variant for shared libs * update ascent and vtkh packages * wire up option to run tests during install * add post install test * add testing to ascent * tweak for blueos xl * add ctest output on error for run_tests * enable ctest output on error for run_tests * add testing of the using-with-make example * update using-with-make examples * typo in ascent using-with-cmake test * fix ascent using test exe names * more fixes, less sleep * more fixes, less sleep ... * remove unwired up version * improvments suggested on review * adding new cmake * Update package.py * Update package.py * changes post cori os update * fix cray hack * Update package.py Fixing 'fix'. Inconsistent variable names in conduit package * type in spack recipes * add zfp support to conduit * fix indent error in conduit pkg * move to use build phases, add sphinx rtd as dep, fix ex names in tests * add conduit 0.5.0 release * flake8 * remove old cray hack * incorp feedback from review * fix to use proper build env sig
2019-10-28Fix gcc recipe for RHEL7. (#13460)Kelly (KT) Thompson1-5/+5
* Fix gcc recipe for RHEL7. + It appears that macOS related changes to the gcc recipe broke gcc on RHEL7. This bug manifests as `libstdc++.so: undefined reference to libiconv` when gcc is used. + Fixes #13452 by moving `--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix)` into the darwin OS section of the configuration. + Change qualification of `depends_on(libiconv)` to limit dependency to macOS. * Replace deprecated 'setup_environment' with 'setup_run_environment'. * Fix cut and paste error. * Rename 'run_env' to just 'env'.
2019-10-28Paraview package: add version 5.7.0 and update environment setup (#13255)Jon Rood1-16/+17
Replace setup_environment/setup_dependent_environment with setup__dependent_build_environment and setup_run_environment according to 9ddc98e
2019-10-28Packages: Add cuDNN versions; update LBANN dependencies (#13412)Brian Van Essen2-1/+7
* Add cuDNN version 7.6.3-10.1 (for x86_64 and ppc64le) * Add py-pytest and py-protobuf depenencies to LBANN
2019-10-28Go package: add versions (including 1.13.3) and update environment setup ↵Paul1-9/+18
(#13254) * Add versinos 1.13.3, 1.13.2, 1.12.12, and 1.12.11 * Replace setup_environment/setup_dependent_environment with setup_build_environment and setup_dependent_{build, run}_environment according to 9ddc98e
2019-10-28Fix PyTorch build with Intel MKL (#13464)Adam J. Stewart1-0/+5
2019-10-28Update emacs to version 26.3 (#13469)Glenn Johnson1-0/+1
2019-10-28scotch: added version 6.0.8 (#13467)Mark Olesen1-0/+1
2019-10-27Add dependency and patch for perl-dbfile (#13261)wenlibin021-0/+5
* Add dependency and patch perl-dbfile There are two problems for the building of `perl-dbfile`: 1) this package depends on the package `berkeley-db` 2) fix the building using a patch, which locates the position of `berkeley-db` and modify the configuration file for the building * Update and reformat the script package.py * Simplify the patch * Update package.py * Update package.py
2019-10-27QE Update Oct 2019 (#13406)Nichols A. Romero1-31/+18
* This filter_file was difficult to maintain and is no longer needed. * Clarify lack of support for HDF5 in serial QE. * Update QE and HDF5 conflicts based on user feedback.
2019-10-27Add Lizard (LZ5) (#13456)Axel Huebl3-8/+109
* Add Lizard (LZ5) Add a new package for Lizard, formerly LZ5, a very fast compressor and decompressor library. * c-blosc2: use external lizard Use an external Lizard (LZ5) dependency and add missing "when="s for other compressor dependents.
2019-10-27Libbeagle fixes (#13463)Glenn Johnson2-8/+9
* Fixes for libbeagle This PR fixes a couple of issues with the libbeagle package. - Use args.append('--with-cuda=%s' % self.spec['cuda'].prefix) - Disable the default of compiling with -march=native as Spack now inserts architecture specific flags - Set BEAST_LIB in the beast1 package not in libbeagle. * Use new setup_run_environment method
2019-10-27new package: py-pandocfilters (#13418)Andreas Baumbach1-0/+15
dependency of py-nbconvert
2019-10-27LLVM code-signing on OSX: link to the offical documentation (#13428)Andreas Baumbach1-7/+8
* LLVM code-signing on OSX: link to the offical documentation * LLVM: update setup_environment method
2019-10-27mariadb: Fix openssl dependencies (#13443)Michael Kuhn1-0/+2
2019-10-27mariadb-c-client: Add 3.1.4 (#13447)Michael Kuhn1-0/+1
2019-10-27new package: ecos (#13453)Sinan1-0/+30
2019-10-27Update PyTorch variable name (#13461)Adam J. Stewart1-1/+1
2019-10-26MPICH: Fix Slurm Find Issue (#13263)Axel Huebl1-0/+9
Set include and library path to slurm explicitly.
2019-10-26Add latest version of py-fiscalyear (#13451)Adam J. Stewart1-2/+4
2019-10-25Add py-twine package (#13449)Adam J. Stewart1-0/+22
2019-10-25Add py-pkginfo package (#13448)Adam J. Stewart1-0/+19
2019-10-25Add latest version of py-tqdm (#13446)Adam J. Stewart1-2/+7
2019-10-25Add latest version of py-requests-toolbelt (#13445)Adam J. Stewart1-2/+3
2019-10-25Add latest version of py-readme-renderer (#13444)Adam J. Stewart1-3/+5
2019-10-25New package: gpu-burn (#13108)Glenn Johnson2-0/+73
2019-10-25py-nbformat package: add version 4.4.0 (#13421)Andreas Baumbach1-0/+1
2019-10-25New package: py-defusedxml (#13419)Andreas Baumbach1-0/+17
2019-10-25New package: OSQP (#13432)Sinan1-0/+22
2019-10-25LIBXSMM package: add version 1.14 (#13436)Hans Pabst1-1/+2
2019-10-25lmdb package: add version 0.9.24 (#13437)Michael Kuhn1-0/+1
2019-10-25sqlite package: add version 3.30.1 (#13438)Michael Kuhn1-0/+1
2019-10-25py-gensim: new package at 3.8.0 (#13136)Justin S1-0/+28
* py-gensim: new package at 3.8.0 * py-gensim: add 3.8.1
2019-10-24Views: fix python in views when python prefix is under a symlink (#12575)Greg Becker1-1/+12
* Fix python in views when python prefix is under a symlink * Add todo for future generalization
2019-10-24Add latest version of NetCDF libraries (#13416)Adam J. Stewart3-5/+9
2019-10-24Extend HPX package (#13219)Mikael Simberg1-6/+24
* Add master branch as version to HPX package * Remove C++98 option from HPX package * Add option to turn off examples in HPX package * Add MPI variant to HPX package
2019-10-24New package: py-cdsapi (#13363)Jannek Squar1-0/+19
* New package py-cdsapi to access Climate Data Store for downloading climate and weather reanalysis data * Improvements
2019-10-24mfem: add version 4.0 (without cuda) (#11880)Geoffrey Oxberry2-7/+84
* mfem: add version 4.0.0 (without cuda, raja, etc) * mfem@4.0.0: add occa variant * mfem@4.0.0: add raja variant * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py
2019-10-23blast-legacy: fix build issues (#13370)Eric Martin1-1/+2
2019-10-23subread: add version 2.0.0 (#13368)Eric Martin1-0/+1
2019-10-23sundials: add version 5.0.0 and new variant (#13375)Cody Balos1-66/+106
* sundials: add version 5.0.0 and new variant plus some cleanup * sundiaks: fix formatting * sundials: fix dependencies
2019-10-23vt: add version 0.5772 (#13367)Eric Martin1-0/+1
2019-10-23add `spack dev-build` command; deprecate `spack diy` (#13374)Greg Becker1-0/+27
Rename the `spack diy` command to `spack dev-build` to make the use case clearer. The `spack diy` command has some useful functionality for developers using Spack to build their dependencies and configure/build/install the code they are developing. Developers do not notice it, partly because of the obscure name. The `spack dev-build` command has a `-u/--until PHASE` option to stop after a given phase of the build. This can be used to configure your project, run cmake on your project, or similarly stop after any stage of the build the user wants. These options are analogous to the existing `spack configure` and `spack build` commands, but for developer builds. To unify the syntax, we have deprecated the `spack configure` and `spack build` commands, and added a `-u/--until PHASE` option to the `spack install` command as well. The functionality in `spack dev-build` (specifically `spack dev-build -u cmake`) may be able to supersede the `spack setup` command, but this PR does not deprecate that command as that will require slightly more thought.
2019-10-23bison: Fix parallel build (#13402)Michael Kuhn2-4/+88
2019-10-23mysql: Use correct python command (#13393)Michael Kuhn1-9/+10
* mysql: Use correct python command python~pythoncmd does not provide a python symlink for python3, so make sure we pick the right command. * mysql: Adapt to build env changes
2019-10-23hypre: Add new variants to expose existing features. (#13373)Sarah Osborn1-5/+36
* hypre: Add new variants to expost existing features. * hypre: Add new variants to expose existing features. * hypre: Shorten description line. * hypre: Add an explicit else clause to disable some features.
2019-10-23Add latest version of py-pbr (#13380)Adam J. Stewart1-7/+23
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