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2017-06-22New package augustus (#4586)Audrey Thoma1-0/+70
* augustus: adding augustus * augustus: fixing flake8 things * augustus: simplifying verbose
2017-06-22Add latest version of libtiff (#4574)Adam J. Stewart1-1/+2
2017-06-22Add latest version of libmng (#4575)Adam J. Stewart1-2/+8
2017-06-22created py-tomopy package and fixed its dependencies (#4576)Stas Sergienko14-15/+140
* added py-tomopy package * fixed dependencies and added import_modules * edited deps for tomopy with import_modules and added py-olefile pkg * changed module name * changed dependency to python because it will not build with setuptools * fixed dependency list for py-tomopy and py-dxchange * added py-nose dependency * fixed tests * commented out dependency py-counter * fixed dependency py-pybtex-docutils * removed nose as a dependency * fixed flake8 errors * fixed import_modules * fixed import_modules indent * fixed various issues in tomopy and deps files
2017-06-22New package albert (#4568)Audrey Thoma1-0/+41
* albert: adding new package albert * albert: fixing dependency type and build process
2017-06-22gmap-gsnap: adding gmap-gsnap package (#4570)Audrey Thoma1-0/+36
2017-06-22Update for paraview 5.4.0 (#4582)Mark Olesen1-0/+8
- paraview 5.2.1 -> 5.4.0 supports both Qt4 and Qt5, but the assumed default version changes between versions. So explicitly define which QT major version is being used.
2017-06-21fix issue #4577 (#4579)becker331-1/+1
2017-06-21Module cmd fix (#3250)becker337-70/+346
* Parse modules in a way that works for both lmod and tcl * added test and made method more robust * refactoring for pythonic clarity * Improved detection of 'module' shell function + refactored module utilities into spack.util.module_cmd * Improved regex to reject nested parentheses we are not prepared to handle * make tests backwards compatible with python 2.6 * Improved regex to account for sh being aliased to bash and used in bash module definition on some systems * Improve test compatibility with lmod * Added error for None module_cmd * Add test for get_module_cmd_from_which() Add test for get_module_cmd_from_which(). Add -c argument to Popen call to typeset -f module in get_module_cmd_from_bash(). * Increased detection options Included BASH_FUNC_module() variable outside of typeset as a detection option This should work on bash even in restricted_shell mode Kept the typeset detection as an option in case the module function is not exported in bash Also added try statements to tests, with environment recreation in finally blocks. * More tests added; some hackiness * increased test coverage for util/module_cmd
2017-06-21mumps: fixed compilation issues due to scotch not found at link time (#4567)Massimiliano Culpo4-7/+38
2017-06-21refactor openfoam packages (#3669)Mark Olesen15-757/+1316
* Several improvements for the openfoam packages -- Refactor openfoam packages by adding an OpenfoamArch class Use separate configure, build, install phases. Provide FOAM_PROJECT_DIR dependent env for openfoam packages - easier way to locate Eliminate intermediate installation directories - unneeded clutter. - makes it less than easy to find the etc/bashrc file Add versioning for all openfoam patches - no certainty which parts (if any) will be needed in future versions, especially if we strive to ensure that the upstream version builds well with spack to begin with. Support build of develop branches - helps track build regressions for future openfoam releases STYLE: use common/ and assets/ to provide additional (build) resources ... * - adjust OpenFOAM provider Move openfoam-com up front since this is the one being used as a base for the others
2017-06-21Andi and libdivsufsort (#4559)Audrey Thoma2-0/+77
* andi: adding andi and libdivsufsort * andi: adding andi and dependency libdivsufsort * andi: adding andi and dependency libdivsufsort * andi: fixing autotool dependency types * andi: fixed whitespace to make flake8 compliant
2017-06-21Modified ipopt package to support build on ppc64le (#4561)Jonathan Wong2-0/+28
Added line in package.py to patch using ipopt_ppc_build.patch. The patch simply adds support in config.guess and Ipopt/config.guess to build ipopt on ppc64le.
2017-06-21adding H5Z-ZFP; updating zfp to use choice variant for bit stream word size ↵Mark C. Miller2-8/+77
(#4466) * adding H5Z-ZFP; updating zfp to use choice variant for bit stream word size * fixing homepage url * removed fortran error message...just build fortran if can, otherwise ignore
2017-06-21Fix for SAMRAI build debug spec bug (#4564) (#4565)Jim Eliot1-1/+1
2017-06-20FFTW: remove search for IBM XL threaded compiler when compiler is not gcc ↵serbanmaerean2-0/+122
(#4187) * Added magma package * Incorporated Serban's change * fftw: patch configuration file to remove search for xlc_r compiler when compiler not gcc FFTW assumes there are only 2 compilers: gcc and IBM XL. When building threaded fftw, the configuration file is looking for the threaded IBM XL's xlc_r compiler when the compiler is not gcc. The PGI compiler is not gcc.
2017-06-20Add abyss package (#4555)Audrey Thoma1-0/+54
* abyss * abyss: deleting attemped test from script * abyss: adding new package abyss * abyss: partially fixing mpi dependency issue * abyss: added mpi provider conflicts
2017-06-20Features/votca (#4556)Christoph Junghans3-2/+109
* votca-csg: needs non-mpi version of gromacs * votca-csg: fixed deps * votca-moo: new package * votca-ctp: new package * votca-ctp: make flake8 happy
2017-06-20fontconfig should depend on gperf (#4551)George Hartzell1-0/+1
* Include depends_on for gperf Sometime around 2.12.2 fontconfig acquired a build-time dependency on `gperf` (this commit, I think: 59fd9960bbb58fd6257adb13ec0f918882149332). This adds the dependency. `gperf` is called in the `src/Makefile`, see line 907 of `src/Makefile.in`. * Only depend_on gperf if @2.12.2: The gperf dependency *seems* to only be required when @2.12.2:. Earlier releases do not check the arg type of the gperf lookup function (which requires gperf) and are able to use pre-generated files so gperf is not required at build time.
2017-06-20Fix veclibfort for gcc (#4548)Mark C. Miller1-2/+10
* fixes #967 * Version bump to 0.9.1 - Bugfixes for spack find - 0.9.1 can read specs from current develop. * Don't assume spack is in the path when building docs. * fixing Makefile override of PREFIX and install w/gcc-6
2017-06-19added py-dxchange and its dependencies dxfile,edffile,spefile,tifffile (#4534)Stas Sergienko5-0/+203
* added py-dxchange and its dependencies dxfile,edffile,spefile,tifffile * fixed https in homepage of py-dxfile
2017-06-19Various updates to wget and dependencies (#4116)Adam J. Stewart4-39/+162
* Various updates to wget and dependencies * Add newer version of gnutls
2017-06-19Overhaul CONVERGE installation and concretization (#4397)Adam J. Stewart4-14/+178
2017-06-19fontconfig: Update to latest stable release (#4543)Diana Bite1-1/+2
2017-06-19Add Slack info to READMEmd (#4542)Todd Gamblin1-2/+12
- Added a badge to show who's online. - Added a section under "Get involved!"
2017-06-17Update README.md and add analytics. (#4537)Todd Gamblin1-31/+29
2017-06-17votca-csg: fixing develop url (#4536)Andrey Prokopenko1-1/+1
Fix #4525.
2017-06-16System config (#4518)becker335-20/+40
* Code changes to enable system config scope in /etc Files will go in either /etc/spack or /etc/spack/<platform> Required minor changes to conftest. * Updated documentation to match new config scope
2017-06-16Added py-pybtex package (#4507)Stas Sergienko1-0/+41
* Added py-pybtex package * added more dependencies to py-pybtex * added run to py-latexcodec dependency
2017-06-16Py ase (#4517)John Roberts1-0/+39
* py-ase: Adding python package py-ase. * py-ase: Adding Python package py-ase. * py-ase: Shortened package description. * py-ase: Splitting package description to multiple lines to avoid char count max. * py-ase: Removing trailing whitespace. Local flake8 tests passed now that flake8 is working for me.
2017-06-16added py-sphinxcontrib-bibtex and py-pybtex-docutils packages (#4520)Stas Sergienko2-0/+82
* added py-sphinxcontrib-bibtex and py-pybtex-docutils packages * added dpendency py-ordereddict
2017-06-16Update intel* packages (#4528)Kyle Fernandes, né Jacobs6-2/+24
* Update intel-* packages * Update intel package
2017-06-16Update Scalasca/Score-P/Cube/OTF2 (#4485)David Böhme3-30/+31
* Update Scalasca/Score-P/OTF2/Cube. Should fix #4349# * cube: Fix flake8 warnings * cube, scalasca: Fix version range syntax for deps * otf2: Fix version URL generation * cube: Remove static URLs
2017-06-16Fix OpenMPI CUDA support (#4323)Adam J. Stewart1-2/+20
* Fix OpenMPI CUDA support * Remove --with-cuda-libdir flag, not a real flag * Fix PGI and CUDA 7 support
2017-06-16py-pillow: ensure that RPATH includes graphics libraries (#4522)Milton Woods1-1/+3
2017-06-16oce changes for cgm (#4514)iulian7872-18/+31
* oce changes for cgm cgm can be configured with oce, but oce needs to have X11 enabled, because some libraries (like TKCAF in occ/oce) gets built only of X11 is NOT disabled so introduce a variant +X11 for oce, which is needed when configuring cgm with oce(+X11) * follow up review simplify by removing the patch and different url paths use append instead of extend, when necessary make mpi true by default X11 dependency is still to be addressed; it pulls in some opengl library (on laptop nvidia seem to work, on virtual linux machine mesa was good enough)
2017-06-16bugfix: support EDITOR values with spaces (#4523)Todd Gamblin1-8/+8
- previous code called `which` on $EDITOR, but that doesn't work for EDITORs like `emacs -nw` or `emacsclient -t -nw`. - This patch just trusts EDITOR if it is set (same as previous behavior), and only uses the defaults if it's not.
2017-06-16issue 4492: DependencyMap.concrete checks for unconditional dependencies (#4499)Massimiliano Culpo2-10/+96
* issue 4492: added xfailing test, added owner to DependencyMap * DependencyMap.concrete checks if we have unconditional dependencies This fixes #4492 and #4107 using some heuristics to avoid an infinite recursion among Spec.satisfies, Spec.concrete and DependencyMap.concrete The idea, as suggested by @becker33, is to check just for unconditional dependencies. This is not covering the whole space and a package with just conditional dependencies can still fail in the same way. It should cover though all the **real** packages we have in our repo so far.
2017-06-15Fix tests on cray (#4298)Mario Melara3-5/+4
* Check for CRAYPE_VERSION instead of path Architecture tests would fail on Cray since it would not find the expected path. To make the test correctly work on Cray search for the CRAYPE version instead. * Catch SystemExit error in case flake8 not in path On shared systems having flake8 can involve starting own virtual env. Skip the test if no flake8 is found to avoid failure reporting. * Add compatibility to 1.5 svnadmin create The flag added is needed to correctly create svn repos on NERSC systems. This could be unnecessary for other sites. I'd like to see others test before this change gets merged.
2017-06-15Added package py-oset (#4500)Stas Sergienko1-0/+37
* Added py-oset package * Added package py-oset * changed homepage url
2017-06-15added py-latexcodec package (#4509)Stas Sergienko1-0/+37
* Added py-latexcodec package * removed url line from the file
2017-06-15added py-counter package (#4510)Stas Sergienko1-0/+37
2017-06-15openblas: Fix build on aarch64. (#4487)Diana Bite1-1/+8
- invoke make with the correct TARGET for aarch64 - foforce PILERDRIVER as openblas cannot correctly detect CPU on aarch64 - update url to more recent version
2017-06-15Add latest version of JDK (#4317)Adam J. Stewart2-20/+15
* Add latest version of JDK * Use a more specific URL to get curl to work * Remove failing unit test
2017-06-15Add missing doc variant to fenics package (#4473)Adam J. Stewart1-15/+22
2017-06-15Adding initial AMReX package (#4467)Mark C. Miller1-0/+85
* adding initial amrex package * adding missing fortran variant predicate * adjusting description text * adjusting as per @tgamlin guidance
2017-06-15Added py-pywavelets package (#4496)Stas Sergienko1-0/+42
* Added py-pywt package * passes flake8 test * renamed py-pywt to py-pywavelets
2017-06-15Fix dashes in variant parsing (#4498)Todd Gamblin2-8/+8
- Skip spack flake8 test when flake8 is not installed. - Fix parsing of dashes in specs broken by new help parser. - use argparse.REMAINDER instead of narg='?' - don't interpret parts of specs like -mpi as arguments.
2017-06-15Nalu requires Trilinos with Exodus support (#4505)Jon Rood1-1/+1
* Disabling Exodus in Trilinos by default. * Returning default of Exodus to true in Trilinos.
2017-06-15Prefer vim to vi for default editor (#4230)Adam J. Stewart7-85/+97
* vim > vi * Allow which to accept multiple args * Update __init__ to use which with multiple args * Fix doc tests