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2019-05-15New package: py-spatialist (#11427)Sinan1-0/+27
2019-05-15New package: py-tblib (#11425)Sinan1-0/+18
2019-05-15New package: py-scoop (#11423)Sinan1-0/+22
2019-05-15New package: py-progressbar2 (#11421)Sinan1-0/+20
2019-05-15New package: py-python-utils (#11422)Sinan1-0/+19
2019-05-14nut: add v0.1.1 (#11444)Christoph Junghans1-2/+3
2019-05-14r-construct: new package at 1.0.3 (#11452)Justin S1-0/+29
2019-05-14r-rstan: add 2.18.2 (#11447)Justin S1-0/+7
2019-05-14r-loo: new package at 2.1.0 (#11448)Justin S1-0/+21
2019-05-15LBANN: add support for new python front end (#11395)Brian Van Essen12-17/+177
* LBANN: add python dependency and required python library dependencies * LBANN: add version 0.99 as alias for develop branch * LBANN: build Conduit library by default * LBANN: CUB is included with Hydrogen for later versions * New package: py-graphviz (dependency for LBANN) * New package: py-texttable (dependency for LBANN) * New package: py-onnx (dependency for LBANN) * New package: py-typing-extensions (dependency for py-onnx) * Conduit: add version 0.4.0 * NCCL: Add versions 2.4.6-1 and 2.4.2-1 * Protobuf: Add versions 3.7.1 and 3.7.0 * py-protobuf: add version 3.7.1 * py-typing: add version 3.6.4 * cuDNN: add versions. The source differs depending on the architecture, so the versions include a suffix to encode this. For example this adds 7.5.1-10.1-x86_64 as well as 7.5.1-10.1-ppc64le * cuDNN: Newer versions require newer versions of CUDA * Hydrogen: add configure options for CUB and Aluminum
2019-05-14gmap-gsnap: add 2019-05-12 (#11453)Justin S1-0/+1
2019-05-14r-rstantools: new package at 1.5.1 (#11451)Justin S1-0/+16
2019-05-14r-caroline: new package at 0.7.6 (#11450)Justin S1-0/+19
2019-05-14r-stanheaders: add 2.18.1 (#11446)Justin S1-0/+1
2019-05-14r-withr: add 2.1.2 (#11445)Justin S1-0/+1
2019-05-14repeatmasker: add 4.0.9, refactor interactive config (#11385)Justin S1-10/+23
2019-05-15PNetCDF package: enable option required by NetCDF (#11420)Jon Rood1-0/+3
The --enable-relax-coord-bound option was added in 1.8.0. NetCDF 4.6.3 enabled relax coords by default and required it from PNetCDF. PNetCDF 1.10.0 enabled it by default but for versions between 1.8.0 and 1.10.0 it should be enabled explicitly.
2019-05-15CUDA package: exclude compat libs (#11449)Peter Scheibel1-0/+21
CUDA 10.0 provides Compatability libraries for running newer versions of CUDA with older drivers. These do not work with newer drivers.
2019-05-14megadock: new package at 4.0.3 (#10537)Justin S1-0/+77
* megadock: new package at 4.0.3 * megadock: remove CudaPackage redundancies * megadock: move env vars to build targets, use cuda_arch variant * megadock: flake8 fixes, more flexible mathlib
2019-05-15Fix py-yt for Python 2 by requesting older py-ipython version (#11416)Jon Rood2-0/+3
* Fix py-yt for Python 2 by requesting older py-ipython version. * Add conflicts statement to py-ipython because version 7: is not compatible with python@2.7
2019-05-15New Package: NTPoly (#11412)william-dawson1-0/+29
2019-05-14Remove vestigial print statement in module logic (#11438)Greg Becker1-1/+0
Remove a vestigial print statement introduced in #8570
2019-05-14Add new versions of metaphysicl and change masa to use branch instead of ↵Jon Rood2-2/+4
tag. (#11436)
2019-05-14r-bh: add 1.69.0-1 (#11435)Justin S1-0/+2
2019-05-14rename py-pauvr to py-pauvre (#11437)Levi Baber1-2/+2
* rename py-pauvr to py-pauvre
2019-05-14m4 package: fix OS version check (#11290)George Zagaris1-1/+1
f242f5f removed spec.architecture.platform_os, which was used to test an option in the 'm4' package. The attribute is now accessed as 'spec.architecture.os'.
2019-05-13Add master branch of leveldb (#11405)Adam J. Stewart1-0/+2
2019-05-11tests: stop testing Python 3.4Todd Gamblin1-5/+0
2019-05-11tests: require Python 2.6 tests to passTodd Gamblin1-2/+0
2019-05-10bugfix: Do not run spack spec in the test environment for Python 2.6Todd Gamblin1-1/+3
- Trying to get our Python 2.6 tests working again. - This seems to crash travis in the 2.6 environment, for whatever reason.
2019-05-10enable coverage for python 2.6 unit testsTodd Gamblin1-1/+1
2019-05-11New package: py-pycares (starting at 3.0.0) (#11340)Shane R. Spencer1-0/+20
2019-05-10mesa: Add 19.0.4 (#11415)Chuck Atkins1-2/+4
2019-05-10LIBXSMM 1.12 (#11414)Hans Pabst1-1/+2
2019-05-10Add new version of PGI compiler. (#11417)Jon Rood1-0/+1
2019-05-11sqlite: add versions; restore old versions; variant resolves security ↵Chris Green3-4/+116
issues. (#11336) * Add versions 3.27.{0,1,2} and 3.28.0 * Add url_for_version: the URL format includes the year so this function maps version ranges to years * Restore patches for versions removed in 84c547c: this commit removed versions before 3.26.0 due to a security issue with FTS support. Add a +fts variant (default true) that enables FTS support along with a conflict for +fts with earlier versions.
2019-05-11coverage: only run coverage for subset of unit testsTodd Gamblin2-7/+8
- Codecov cannot handle as many coverage reports as we are generating - as a result, our PR coverage pages have been broken for a while, and it's hard to tell people where to enhance their testing in PR reviews. - Scale back to only running coverage for 3.7 and 2.7 unit tests - This is *probably* better. We run the build tests for good measure, but we do not need to evaluate them for coverage. The coverage reports are about unit tests.
2019-05-10paraview: Fix OpenGL search to ignore glvnd (#11400)Chuck Atkins1-0/+1
2019-05-10py-pauvr:new package (#11292)xfzhao1-0/+21
* py-pauvr:new package * py-pauvr: using url and Releases * py-pauvr: remove extra comments
2019-05-10permissions: preserve suid and sgid bits (#10727)Greg Becker2-0/+46
* Don't overwrite suid/sgid bits when setting permissions * add tests for permission setting
2019-05-10Intel packages: multiple installs and optional scalapack libs (#11384)Glenn Johnson1-1/+5
Add fixes to support multiple installs and dependents using a subset of IntelPackage functionality. * Update IntelPackage to only return scalapack libraries if the root spec depends on MPI: scalapack requires MPI to be mentioned as a dependency in the DAG. Package builds using intel-mkl for its blas/lapack implementations but not for scalapack were failing to build. Ideally it would be possible to ask if any of the packages in the DAG are actually requesting the scalapack functionality provided by the IntelPackage and only return scalapack libs in that case, but that is not easily done at this time. Fixes #11314 Fixes #11289 * set HOME when the intel silent installer is run. This prevents the installer from using the ~/intel directory (which can cause conflicts for multiple installs of the same IntelPackage) Fixes #9713
2019-05-09modules: use new `module` function instead of `get_module_cmd` (#8570)Greg Becker8-248/+118
Use new `module` function instead of `get_module_cmd` Previously, Spack relied on either examining the bash `module()` function or using the `which` command to find the underlying executable for modules. More complicated module systems do not allow for the sort of simple analysis we were doing (see #6451). Spack now uses the `module` function directly and copies environment changes from the resulting subprocess back into Spack. This should provide a future-proof implementation for changes to the logic underlying the module system on various HPC systems.
2019-05-10make license check more-strictPeter Josef Scheibel2-39/+93
The license text is now expected to match almost exactly (not accounting for formatting in different file types (e.g. rst vs. bash script vs. python)
2019-05-10update aom package licensePeter Josef Scheibel1-2/+10
2019-05-10update license date range for simgridPeter Josef Scheibel1-1/+1
2019-05-10dyninst: update cmake args and boost dependency (#11378)Mark W. Krentel1-8/+18
* Starting with the upcoming 10.1 release, Dyninst changed the names of some cmake args to camel case: LIBELF_* to LibElf_* and LIBDWARF_* to LibDwarf_*. This change is needed now for @develop and will be used for 10.1 when it is released. * New versions of Dyninst now requires cmake version 3.4.0 or later. * Restrict boost dependency version to < 1.70.0 to avoid build error
2019-05-09update to texlive 2019 (#11365)David Gardner1-2/+2
2019-05-10elpa: override headers prop for common include-dir localizationTiziano Müller4-19/+24
... and apply this in SIRIUS, CP2K & QE. Thanks to @scheibelp for the idea.
2019-05-10packages/cp2k: require libxsmm 1.11+Tiziano Müller1-1/+2
2019-05-10packages/cp2k: build with -ggdb with GNU for backtracesTiziano Müller1-1/+5