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2017-08-18sbang support: add node-js and fix luahealther2-1/+10
This adds sbang hook support for node-js and fixes the sbang filter for lua (the character class exclusion was swallowing newlines and reporting a false positive if lua was mentioned anywhere in the file).
2017-08-18build boost with graph library even when +mpihealther1-1/+0
Previously, when +graph and +mpi were enabled, the graph library was replaced with the graph_parallel library. This alters the logic for +graph+mpi to build both libraries.
2017-08-18corset: new package (#5157)Audrey Thoma1-0/+44
2017-08-18parsimonator: new package (#5143)Audrey Thoma1-0/+65
* parsimonator: new package * adding variant conflict
2017-08-18vegas2: new package (#5150)Audrey Thoma4-1/+126
* vegas2: new package * small version things
2017-08-18Add info for nextflow@v0.25.6 (#5148)George Hartzell1-0/+2
2017-08-18add man-db package and friends (#4844)Stephen McDowell5-0/+212
* add man-db package and friends * fix groff, libpipeline, and man-db dependencies * remove parallel groff altogether, build-only deps
2017-08-17Add a new package for gaussian (#5149)zenln1-0/+71
* Gaussian: Gaussian install * Adding Patch to spack installed files * Adding extra environment variables for gaussian at run time * Adding provides linda * Adding linda as a provided package * Shortning vars and fixing flake8 indentation and spacings
2017-08-17pagit: new package (#5140)Audrey Thoma1-0/+68
* pagit: new package * removed unneeded env var
2017-08-17new package libfabric (#5146)Audrey Thoma1-0/+35
* pbmpi: new package * forgot about libfabric
2017-08-17pbmpi: new package (#5144)Audrey Thoma1-0/+48
2017-08-17Docs: Travis-CI Workflow (#5133)Axel Huebl1-0/+78
* Docs: Travis-CI Workflow Add a workflow how to use spack on Travis-CI. Future Work: depending if and how we can simplify 5101: add a multi-compiler, multi-C++-standard, multi-software build matrix example * Fix Typos
2017-08-17paml: new package (#5142)Audrey Thoma1-0/+52
2017-08-17Colorize spack info. Adds prominence to preferred version. (#4994)Massimiliano Culpo2-33/+117
* Colorize spack info. Adds prominence to preferred version. fixes #2708 This uses 'llnl.util.tty.color' to colorize the output of 'spack info'. It also displays versions in the order the concretizer would choose them and shows the preferred in a line on its own and in bold. * Modified output according to Adam and Denis reviews. Section titles are not bold + black, but bold + blue. Added a new section named "Preferred version", which prints the preferred version in bold characters. * Further modifications according to Adam and Denis reviews. After "Homepage:" we now have a single space. Removed newline after each variant. Preferred version is not in bold fonts anymore. Added a simple test that just runs the command.
2017-08-17microbiomeutil: new package (#5134)Audrey Thoma1-0/+53
* microbiomeutil: new package * got rid of unnecessary self * oops
2017-08-17Add new package for rhash, a cmake dependency (#5120)Adam J. Stewart2-40/+120
* Add new package for rhash, a cmake dependency * Add missing libuv dependency to cmake
2017-08-17py-faststructure: new package (#5131)Audrey Thoma1-0/+39
2017-08-17add libiconv dependency to libxslt (#5138)healther1-0/+1
this is a fix to an installation that failed due to configure for some reason not finding the libiconv shipped with glibc, but still trying to link against it see http://xmlsoft.org/FAQ.html
2017-08-17Improved error message for unsatisfiable specs (#5113)Massimiliano Culpo1-4/+13
* Improved error message for unsatisfiable specs. fixes #5066 This PR improves the error message for unsatisfiable specs by showing in tree format both the spec that cannot satisfy the constraint and the spec that asked for that constraint. After that follows a readable error message.
2017-08-17Relaxed constraints on config.yaml structure (#5115)Massimiliano Culpo1-1/+0
This PR allows additional unused properties at the top-level of the config.yaml file. Having these properties permits to use two different versions of Spack, one of which adds a new property, without receiving error messages due to the presence of this new property in a configuration cache stored in the user's home.
2017-08-16buildcache fixes: index.html & unsigned installsPatrick Gartung1-20/+21
This fixes a syntax error in the index.html file generated by the "spack buildcache" command when creating build caches. This also fixes support for installing unsigned binaries.
2017-08-16add missing dependencies to elfutils (#5135)sknigh1-2/+10
2017-08-16tppred: new package (#5091)Audrey Thoma2-1/+55
* tppred: new package * fixed url_for_version * fixed version spec on dependency * removing unneeded dependency
2017-08-16dialign-tx: new package (#5126)Audrey Thoma1-0/+50
* dialign-tx: new package * utilizing build_directory variable * forgot one
2017-08-16discovar: new package (#5129)Audrey Thoma1-0/+36
2017-08-16gapcloser: new package (#5130)Audrey Thoma1-0/+39
2017-08-16Add tab completion & update docs for buildcacheAdam J. Stewart3-67/+135
This adds tab completion and fixes some formatting issues in the documentation for the "spack buildcache" command.
2017-08-16py-misopy: new package (#5119)Audrey Thoma1-0/+46
* py-misopy: new package * waiting for link to be fixed * got correct url and checksum * specifying dependency version requirements
2017-08-16Add package rtags (#5111)healther2-0/+116
* Add package rtags * fixed license * transform to cmakepackage and add dependencies * add dependencies and patch for rtags * flake8 fix * clean up dependencies
2017-08-16Adding Thrift versions 0.10.0 and 0.9.3 (#5117)Cesare Cugnasco1-0/+2
* Adding Thrift version 0.10.0 and 0.9.3 Hi, I've added the versions 0.10.0 and 0.9.3 * fixed flake8 errors
2017-08-16phylip: new package (#5121)Audrey Thoma1-0/+45
2017-08-16preseq: new package (#5122)Audrey Thoma1-0/+44
2017-08-16Add better generator support to CMakePackage (#4988)Adam J. Stewart4-31/+71
* Add better generator support to CMakePackage * List valid CMake generators on error
2017-08-16Refactor IntelInstaller into IntelPackage base class (#4300)Adam J. Stewart17-614/+954
* Refactor IntelInstaller into IntelPackage base class * Move license attributes from __init__ to class-level * Flake8 fixes: remove unused imports * Fix logic that writes the silent.cfg file * More specific version numbers for Intel MPI * Rework logic that selects components to install * Final changes necessary to get intel package working * Various updates to intel-parallel-studio * Add latest version of every Intel package * Add environment variables for Intel packages * Update env vars for intel package * Finalize components for intel-parallel-studio package Adds a +tbb variant to intel-parallel-studio. The tbb package was renamed to intel-tbb. Now both intel-tbb and intel-parallel-studio+tbb provide tbb. * Overhaul environment variables set by intel-parallel-studio * Point dependent packages to the correct MPI wrappers * Never default to intel-parallel-studio * Gather env vars by sourcing setup scripts * Use mpiicc instead of mpicc when using Intel compiler * Undo change to ARCH * Add changes from intel-mpi to intel-parallel-studio * Add comment explaining mpicc vs mpiicc * Prepend env vars containing 'PATH' or separators * Flake8 fix * Fix bugs in from_sourcing_file * Indentation fix * Prepend, not set if contains separator * Fix license symlinking broken by changes to intel-parallel-studio * Use comments instead of docstrings to document attributes * Flake8 fixes * Use a set instead of a list to prevent duplicate components * Fix MKL and MPI library linking directories * Remove +all variant from intel-parallel-studio * It is not possible to build with MKL, GCC, and OpenMP at this time * Found a workaround for locating GCC libraries * Typos and variable names * Fix initialization of empty LibraryList
2017-08-16mpiblast: new package (#5106)Audrey Thoma2-0/+233
2017-08-16scorep: Fix build with GCC 7 (#5107)Michael Kuhn2-0/+44
2017-08-16otf2: Add 2.1 (#5108)Michael Kuhn1-0/+1
2017-08-16Fix future import in hdf5-blosc (#5010)Adam J. Stewart1-1/+0
2017-08-16Add package rr (#5105)healther1-0/+66
* Add package rr * Flake8 fixes * fix flake8 no2 * add future dependency stub, add hw dependency and clean up * add missing self
2017-08-16Add package PyPytestXdist and dependencies (#5095)healther3-0/+114
* Add py-pytest-xdist * fixed licenses * attempt to fix flake8 * added missing build dependency
2017-08-16Add package py-pybind11 (#5096)healther1-0/+51
* py-pybind11 package was missing * fixed license file * attempt to fix flake8 * use python3 compatible python detection
2017-08-16cdhit: new package (#5085)Audrey Thoma1-0/+49
2017-08-15fix reference to spec in apex package (#5076)Gregory Lee2-2/+3
* fix reference to spec in apex package * fixed md5 sums for ompt-openmp and apex packages
2017-08-15Openblas clang fix (#5065)Brian Van Essen1-6/+9
* Added a package for the MDAnalysis toolkit. * Openblas now builds with clang when using 0.2.20 * Fixed flake8 error * Added a guard to fail for openblas+openmp when on OSX systems * Changed the guard to look for Apple's build of clang and to improve the error messages. * Removed blank line.
2017-08-15Fix ffmpeg (add missing yasm dependency) (#5087)healther1-0/+2
2017-08-15nco: Add patch to fix invalid conversion from char to char* (#5102)Michael Kuhn2-0/+54
This patch is needed to be able to build nco with GCC 7.
2017-08-15ncview: Fix download URL (#5103)Michael Kuhn1-1/+1
2017-08-15add version 0.2.10 to py-lazyarray (#5093)healther1-1/+2
2017-08-15gcc: Add 7.2.0 (#5098)Michael Kuhn1-3/+4
2017-08-15Use correct variant syntax to build zfp (#5099)Mark C. Miller1-2/+1
`h5z-zfp` now builds zfp with correct bit stream word size; the syntax of the variant declaration did not work in previous versions of spack but does now
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