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2018-10-22sundials: update to version 3.2.1 (#9603)Satish Balay1-1/+2
2018-10-22PLASMA: add version 18.9.0 (w/CMake) (#9489)Piotr Luszczek2-55/+49
* Add version 18.9.0 (w/CMake) * Add version dependent install methods to handle transition from Make-based package (17.1) to CMake-based package, using the NEST package as an example * Remove unnecessary build_targets method for older Make-based version * Don't retrieve just the C/Fortran interfaces for netlib-lapack - blas/lapack libs are now handled the same for all implementations * Remove netlib-lapack detection patch
2018-10-22license: exclude ignored files from the license check (#9578)Todd Gamblin1-1/+1
Previously, if you built the docs, you'd get license errors for generated .rst files. This removes them from the list of licensed files.
2018-10-22Update STRUMPACK package: (#9580)Pieter Ghysels1-40/+26
* add new version 3.1.0 * add conflict for parmetis without mpi * strumpack >= 3.1.0 uses -DTPL_ENABLE_<package> instead of -DSTRUMPACK_USE_<package> * require cmake at least 3.2
2018-10-22py-gtk needs to build with python@2.7 and also requires atk, so the atk ↵Peter Scheibel1-5/+0
python dependency cannot be unconditionally constrained to @3: (#9596)
2018-10-19PMIX: replace md5 hash with sha256 for recent versions (#9585)Daniel Topa1-10/+6
2018-10-19plumed: libmatheval support (#9586)Ricardo Silva3-1/+10
* plumed: add libmatheval dependency (used by the 'function' module) * guile: add variant to build with threads interface * libmatheval: add flex dependency
2018-10-19new package: trimal (starting at 1.4.1) (#9592)Justin Stanley1-0/+25
2018-10-19new package: lastz (starting at 1.04.00) (#9593)Justin Stanley1-0/+18
2018-10-19bcftools: add version 1.9 (#9595)Justin Stanley1-0/+2
2018-10-19New package: DFT-FE (#9197)Ricardo Silva1-0/+65
2018-10-19new package: dbcsr (#9491)Denis Davydov2-0/+55
Also add its dependency, py-fypp
2018-10-19jdk: added version 11.0.1 (#9583)Justin Stanley1-0/+3
2018-10-19warpx: new package (#9584)Dave1-0/+78
2018-10-18r-biom-utils: changed MD5 to SHA, added list_url (#9539)Dan Han1-1/+2
2018-10-18binutils: add older version 2.25.1 (#9579)sknigh1-0/+1
Added version available in RHEL/Centos 7
2018-10-18blaze package: add versions 3.3 and 3.4 (#9546)Jordan Moxon1-1/+3
2018-10-18r-matr and r-callr: add new versions, list_urls (#9562)Dan Han2-1/+5
2018-10-18qt4: Patch configure to allow webkit with recent gcc (#9264)Neil Flood2-0/+26
2018-10-18llvm: rename "trunk" version to "develop" (#9320)Geoffrey Oxberry1-2/+2
2018-10-18Update samrai 2.4.4 (#9311)David Wells1-16/+22
* Add support for samrai+silo. * Add patch for SAMRAI 2.4.4
2018-10-18r-rmarkdown: add r-catools dependency (#9470)Justin Stanley1-0/+1
2018-10-18parquet: add -fPIC option (#9367)Matthias Wolf1-0/+8
This adds a pic variant and also exports all compiler flags as CMake arguments
2018-10-18qt: addversion 5.11.2 (#9555)Michael Kuhn1-0/+1
2018-10-18Allow setting language of compiler messages (#9486)Michael Kuhn3-0/+16
* Add a build_language config.yaml option which controls the language of compiler messages * build_language defaults to "C", in which case the compiler messages will be in English. This allows Spack log parsing to detect and highlight error messages (since the regular expressions to find error messages are in English) * The user can use the default language in their environment by setting the build_language config variable to null or ''
2018-10-18spark: set JAVA_HOME for hadoop CLASSPATH fetching (#9439)Matt Belhorn1-0/+1
Sets the `JAVA_HOME` in the `hadoop` subprocess called during `spark.setup_environment`.
2018-10-18new package: trinotate (starting at 3.1.1) (#9471)Justin Stanley1-0/+42
2018-10-18byobu: add new version 5.127 (#9529)Matthias Diener1-0/+1
2018-10-18ranimation: added list_url (#9538)Dan Han1-0/+1
2018-10-18freetype: Add version 2.9.1 (#9551)Michael Kuhn1-0/+1
2018-10-18braker: add missing deps (#9573)Levi Baber0-0/+0
2018-10-18add pumi version docstring (#9577)Cameron Smith1-0/+6
2018-10-18py-seaborn: add version 0.9.0 (#9553)Matthias Wolf1-0/+1
2018-10-18py-hdfs: new package (#9575)Matthias Wolf1-0/+19
2018-10-18lbann: add aluminum dependency (#9523)Brian Van Essen5-16/+107
* Added support for the Aluminum library to LBANN and Hydrogen. Also fixed several bugs in the grouping of dependencies of both packages. * Updated the conduit package to have the proper dependency on the python variant. * Added new versions for NCCL * Fixed a bug in how Hydrogen set the path for OpenBLAS. * Added support for conduit in LBANN.
2018-10-18vtk: add support for Xdmf IO. (#9510)Ruben Di Battista4-8/+87
* vtk: add variants for Xdmf IO support, ffmpeg support, and MPI * vtk: depends on boost when Xdmf support is enabled * vtk: add backported patch for python3.7 * vtk: New policy only for cmake >= 3.12 * mesa: add py-argparse dependency (for build) * lz4: use MOREFLAGS instead of LIBS to add -lrt
2018-10-18Add new python package: hepdata-validator (#9547)Javier Cervantes1-0/+22
* Add new python package: hepdata-validator * Update to new license header
2018-10-17Revert "py-hdfs: new package (#9421)" (#9572)Levi Baber1-38/+0
This reverts commit 5a7d0c458b1034de22a7055276b2398167f5e3da.
2018-10-18py-numpy: update to version 1.15.2 (#9535)Leonhard Reichenbach1-0/+1
2018-10-18scalasca: add 2.4 (#9556)Michael Kuhn1-2/+10
scalasca actually requires cubew, not the full cube bundle. However, cubew@4.4 causes the build of previous versions to fail because there is no cube-config script anymore.
2018-10-17py-hdfs: new package (#9421)Matthias Wolf1-0/+38
2018-10-17relicense: remove outdated blurb in README.mdTodd Gamblin1-5/+0
- all of Spack is Apache-2.0/MIT - no packages are LGPL-2.1
2018-10-17relicense: update COPYRIGHT, LICENSE-*, README, CONTRIBUTING, and NOTICETodd Gamblin7-536/+344
This updates Spack's top-level metadata files to reflect the new Apache-2.0 and MIT licenses.
2018-10-17relicense: add `spack license` commandTodd Gamblin3-0/+228
- `spack license list-files`: list all files that should have license headers - `spack license list-lgpl`: list files still under LGPL-2.1 - `spack license verify`: check that license headers are correct - Added `spack license verify` to style tests
2018-10-17relicense: add Apache2/MIT header to `spack create`Todd Gamblin1-4/+12
2018-10-17relicense: replace LGPL headers with Apache-2.0/MIT SPDX headersTodd Gamblin3359-76151/+13518
- remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-17relicense: remove LGPL-2.1-only farmhash packageTodd Gamblin2-64/+0
- we did not get consent for this package
2018-10-17relicense: remove significant contributions from peetsvTodd Gamblin17-711/+0
- This is bundled into one commit to make it easy to revert if we do get consent from peetsv's company to relicense these contributions. - Revert "dialign-tx adding patch for gcc@5.4.0 (#6413)" - This reverts commit 09eeb991a2ac0d749ffdbfe2f1cc415dd5d5dc85. - Remove the following LGPL-2.1 packages because we have not gotten consent to relicense them: - fast-gbs - igv - metasv - perl-xml-libxml - py-cnvkit - py-crossmap - py-pybedtools - py-pyfaidx - py-pyvcf - py-vmd-python - r-cghflasso - r-dismo - r-proc - r-spatial - r-utf8
2018-10-17omega-h: fix dependencies (#9552)Dan Ibanez1-11/+5
* omega-h: fix dependencies 1. Remove Gmodel altogether. Omega_h doesn't actually call Gmodel for anything, it was more or less just doing additional unit testing for Gmodel 2. Make Trilinos off by default. Most codes do not need the ParameterList interface, and Kokkos through Trilinos is not well explored in Spack 3. Use modern CMake style to choose the zlib dependency
2018-10-17omega-h: update to versions 9.19.0, 9.19.1 (#9548)Satish Balay1-0/+5
* omega-h: update to versions 9.19.0, 9.19.1 * omega-h: add build conflict for gcc-8
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