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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
2017-08-15add older versions to package folly (#5088)healther1-0/+5
2017-08-14Create, install and relocate tarballs of installed packagesPatrick Gartung7-0/+1467
Adds the "buildcache" command to spack. The buildcache command is used to create gpg signatures for archives of installed spack packages; the signatures and archives are placed together in a directory that can be added to a spack mirror. A user can retrieve the archives from a mirror and verify their integrity using the buildcache command. It is often the case that the user's Spack instance is located in a different path compared to the Spack instance used to generate the package archive and signature, so this includes logic to relocate the RPATHs generated by Spack.
2017-08-14Added a custom action for --clean and --dirty. (#5081)Massimiliano Culpo3-9/+52
The action `CleanOrDirtyAction` has been added. It sets the default value for `dest` to `spack.dirty`, and changes it according to the flags passed via command line. Added unit tests to check that the arguments are parsed correctly. Removed lines in `PackageBase` that were setting the default value of dirty according to what was in the configuration.
2017-08-14Decode process stream only for python3scheibelp1-2/+17
Popen.communicate outputs a str object for python2 and a bytes object for python3. This updates the Executable.__call__ function to call .decode on the output of Popen.communicate only for python3. This ensures that Executable.__call__ returns a str for python2 and python3.
2017-08-11Opencv update (#5079)Brian Van Essen1-0/+1
* Added a package for the MDAnalysis toolkit. * Added version 3.3.0
2017-08-11patch: get correct package directory for a given packageMassimiliano Culpo1-3/+15
fixes #4236 fixes #5002 When a package is defined in more than one repository, RepoPath.dirname_for_package_name may return the path to either definition. This sidesteps that ambiguity by accessing the module associated with the package definition.
2017-08-11adding falcon (#5057)snehring7-0/+293
* py-networkx: adding older version py-networkx * py-pypeflow: new package * falcon: adding new package pacbio-daligner: adding new package pacbio-damasker: adding new package pacbio-dazz-db: adding new package pacbio-dextractor: adding new package * py-networkx: modifying version order to be in line with convention * falcon: tweaking py-networkx dependency to satisfy setuptools py-pypeflow: adding missing dependency * pacbio-dextractor: changing hdf5 dependency * pacbio-daligner: adding gmake build dep pacbio-damasker: adding gmake build dep pacbio-dazz-db: adding gmake build dep pacbio-dextractor: adding gmake build dep
2017-08-11mpest: new package (#5064)Audrey Thoma1-0/+50
* mpest: new package * adding architecture env var and making more version-flexible * fixing environment * fixed build directory * getting rid of duplicated code
2017-08-11packages need to reference self.spec instead of spec (#5075)Gregory Lee4-5/+6
2017-08-11signalp: new package (#5054)Audrey Thoma1-0/+61
* signalp: new package * fixed homepage * fixed url and phases * refixed phase * improved readability * making path in execuatble adaptable to new versions
2017-08-11sspace-standard: new pacakge (#5071)Audrey Thoma1-0/+56
* sspace-standard: new pacakge * fixing install versioning * fixing description
2017-08-11sspace-longread: new package (#5072)Audrey Thoma1-0/+52
* sspace-longread: new package * fixing description * fixing order
2017-08-11gapfiller: new package (#5073)Audrey Thoma1-0/+52
2017-08-11More variants for MFEM (#4533)Mark C. Miller3-131/+205
* 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. * adding mfem variants; do not assume build defaults * adjusting format to clarify options * fixing some build issues * fixing mfem+sundials * removing mesquite variant...turns out it is obsolete * adding examples to mfem; fixing sundials darwin installs * adding some additional variants and setting some configure flags by fiat * switching most check_variants logic to conflicts() directives * adding comment about cmake config * fixing flake8 issues; thought I had already done that * moving func def into install method * switch yes_no to no_yes; fix miss-spelling of miniapps * switching make target all to lib * changing yes_no to function as requested; fix problem with same in sundials * fix missing import sys directive * adding master and develop versions to amrex
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