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2017-07-25trimgalore: new package (#4899)Audrey Thoma1-0/+44
2017-07-25fix config.guess patch for ppc64le (#4858)Gregory Lee1-15/+3
* fix config.guess patch for ppc64le * explicit patch for config.guess not required
2017-07-25cleaveland4: new package (#4894)Audrey Thoma3-0/+150
* cleaveland4: new package * fixing return line in viennarna url_for_version
2017-07-25tabix: new package (#4886)Audrey Thoma1-0/+50
* tabix: new package * fixed docs location
2017-07-25sumaclust: new package (#4884)Audrey Thoma1-0/+42
* sumaclust: new package * tweaking url and make specs
2017-07-25Update zstd version (#4873)Jimmy Tang1-4/+2
* Update zstd version * Change order of versions * Use MakefilePackage
2017-07-25Rename the gpu variant to cuda, this is to be consistent with other (#4890)Jimmy Tang1-4/+4
packages.
2017-07-24fix GobjectIntrospection on Darwin (#4872)Denis Davydov1-0/+3
* fix GobjectIntrospection on Darwin * minor
2017-07-24stacks: new package (#4875)Audrey Thoma1-0/+48
2017-07-24added new version of jdk 8u141-b15 (#4876)Stas Sergienko1-0/+2
2017-07-24swarm: new package (#4885)Audrey Thoma1-0/+41
2017-07-24structure: new package (#4879)Audrey Thoma1-0/+47
* structure: new pacakge * fixing package structure (not a pun)
2017-07-24subread: new package (#4882)Audrey Thoma1-0/+52
2017-07-24added new version of cdo (#4877)Stas Sergienko1-0/+2
2017-07-24stringtie: new package (#4878)Audrey Thoma1-0/+41
2017-07-24Change Version formatting properties and functions to return Version objects ↵Adam J. Stewart7-27/+138
(#4834) * Change version.up_to() to return Version() object * Add unit tests for Version.up_to() * Fix packages that expected up_to() to return a string * Ensure that up_to() preserves separator characters * Use version indexing instead of up_to * Make all Version formatting properties return Version objects * Update docs * Tests need to test string representation
2017-07-24Add a py-theano version from git repo (#4871)Jimmy Tang1-0/+1
2017-07-23Add cuda variant for mvapich2. (#4800)健美猫1-2/+13
* Add cuda variant for mvapich2. * Disable cuda for mvapich2 by default.
2017-07-23fix sphinx dependencies, add v1.6.3 (#4870)Stephen McDowell1-2/+13
2017-07-23Perl - allow package activation without PERL5LIB variable (#4540)Milton Woods1-9/+22
* perl: prepend default perl @INC path to support package activation * perl: remove stray comma from list of configure arguments * perl: final comma in configure arguments makes adding arguments safer This reverts commit fdc10cd611f525ebc31ca1953e048095b1c75350. * perl: add comment about modified @INC (thanks to George Hartzell) * perl: use self.prefix.lib and self.prefix.bin for clarity * perl: convert tabs added by editor to spaces for flake8 * perl: use new path syntax: prefix.lib.perl5 * perl: avoid line break before binary operator * perl: use compact spack syntax for perl executable
2017-07-23gBenchmark: Development Package (#4847)Axel Huebl2-51/+15
* gBenchmark: Development Package Add the development version (master branch) of `gBenchmark` * gBenchmark: Remove Duplicate Remove duplicate `gbenchmark` library and keep its patch to remove the shipped -Werror
2017-07-22Make testing spack commands simpler (#4868)Todd Gamblin13-398/+299
Adds SpackCommand class allowing Spack commands to be easily in Python Example usage: from spack.main import SpackCommand info = SpackCommand('info') out, err = info('mpich') print(info.returncode) This allows easier testing of Spack commands. Also: * Simplify command tests * Simplify mocking in command tests. * Simplify module command test * Simplify python command test * Simplify uninstall command test * Simplify url command test * SpackCommand uses more compatible output redirection
2017-07-21Savanna (#4856)Kshitij Mehta1-2/+3
Installing the stable version 0.5 through the checksummed tar.gz does not fetch the git submodule in the package. The submodule appears as an empty directory. Thus, clone the commit tagged as v0.5 using git to get around this issue * savanna: modified adios dependency spec * Replaced adios+staging with adios+flexpath+dataspaces * savanna: Enabling fortran support in adios by default * savanna: reverting to variant 'staging' for enabling all staging transports
2017-07-21sparta: new package (#4867)Audrey Thoma1-0/+46
* sparta: new package * fixing homepage
2017-07-21new package: miniGMG (#4849)jiseung1-0/+67
* new package: miniGMG * changed based on comments * removed cuda version
2017-07-21revbayes: trying this again (#4861)Audrey Thoma1-0/+62
2017-07-21sortmerna: new package (#4866)Audrey Thoma1-0/+44
2017-07-21added new pruners-ninja version (#4859)Gregory Lee1-0/+1
2017-07-21lmdb: Update to 0.9.21 (#4830)Michael Kuhn1-32/+30
Convert to MakefilePackage and add pkg-config file.
2017-07-21singularity: new package (#4852)Audrey Thoma1-0/+40
2017-07-21smalt: new package (#4853)Audrey Thoma1-0/+34
2017-07-21seqprep: new package (#4850)Audrey Thoma1-0/+39
2017-07-21sickle: new package (#4851)Audrey Thoma1-0/+43
2017-07-21New Package: C-Ares (#4840)Axel Huebl1-0/+41
Adds the c-ares library, a C library for asynchronous DNS requests. Required for the google gRPC library.
2017-07-21salmon: new package (#4833)Audrey Thoma1-0/+41
2017-07-21satsuma2: new package (#4838)Audrey Thoma1-0/+41
2017-07-20py-cdat-lite: ensure that RPATH includes netcdf (#4521)Milton Woods1-0/+11
2017-07-20add mesa +swrender variants (gallium software/off-screen rendering) (#4602)Mark Olesen1-13/+64
- +swrender variant lets you compile an off-screen only version for software rendering on clusters. - +swrender+llvm for using llvm for the software pipe - added newer versions (17.1 and 13.0) and corrected the url location to use the canonical location.
2017-07-20GTKorvo (#4657)Kshitij Mehta6-0/+266
* gtkorvo-atl: atl library from gtkorvo * gtkorvo-dill: dill library from gtkorvo * gtkorvo-cercs-env: cercs_env library from gtkorvo * gtkorvo-enet: Enet networking library from gtkorvo * libffs: FFS middleware communication library from GTKorvo * libevpath: EVPath high performance communication library from GTKorvo * gtkorvo-cercs-env: Added homepage and removed function configure_args * gtkorvo-cercs-env: Re-add of accidental removal of cmake_args function in previous commit * gtkorvo-enet: Removed configure_args since unused
2017-07-20New Package: SNbone. (#4754)pkondamudi1-0/+64
* removed the tags as per comment in PR# 4749 * addressed above comments * changed fortran compiler. * added proxy application tags. * added tags by removing them from description. * addressed comments * used join_path instead of path concat. * addressed comments * removed string formatting for LDFLAGS.
2017-07-20Spack updates to three Krell packages (#4765)Jim Galarowicz5-558/+242
* Update the krell institute products to use the latest features of spack for building on cluster platforms. * Address travis error messages and resubmit the pull request. * Update the contents of openspeedshop package.py so it passes the flake8 tests. * Fix flake8 error-whitespack issue in mrnet package.py file. * Add updates based on spack reviewer feedback. * More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH. * More review related changes. Update MPIOption.append lines and take out xercesc references. * Create a base options function for common openspeedshop base cmake options to reduce redundencies. * Add libxml2+python depends on to get around issues with the libxml2 package file. * Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build. * Fix bad syntax in specifying the boost version range. * Update the version numbers for the krell institute components and tools: cbtf and openspeedshop. * Do not build glib for qt3, it is not needed and causes build problems at this time anyway. * A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set. * Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH. * A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set. * Trim comments to fit more concisely. * Fix tabs versus spaces and swap if and else clause check from a negative to a positive check. * Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build. * Fix issues with the cbtf-argonavis package.py files related to comments. * Add changes for changing the krell packages from Package to CMakePackage. * Add better changes for changing the krell packages from Package to CMakePackage. * Add more modifications for changing the krell packages from Package to CMakePackage. * Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros * Fix new travis errors. * Fix new travis errors. * Add more changes for PR 4765. * Add more refinements to the conversion from Package to CMakePackage. * Fix new travis errors. * Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop. * Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue. * Fix more flake issues caused by last changes.
2017-07-20kentutils: new pacakge (#4831)Audrey Thoma1-0/+52
2017-07-20new package:SNAP (#4826)jiseung1-0/+62
2017-07-19Allow packages to control handling of compiler flags (#4421)becker3316-12/+203
* Initial work on flag trapping using functions called <flag>_handler and default_flag_handler * Update packages so they do not obliterate flags * Added append to EnvironmentModifications class * changed EnvironmentModifications to have append_flags method * changed flag_val to be a tuple * Increased test coverage * added documentation of flag handling
2017-07-19Add info for zsh@5.3.1 (#4827)George Hartzell1-0/+1
2017-07-19Add MPI support and tags to embs package (#4824)pkondamudi1-1/+24
2017-07-19Add tags to nekbone package (#4825)pkondamudi1-0/+3
2017-07-19new package: cns-nospec (#4806)jiseung1-0/+67
* new package: cns-nospec * made changes as suggested and added proxy-app tag * updated edit() * adjusted logic for '+debug'
2017-07-19new package: amr-exp-parabolic (#4821)jiseung1-0/+78
* new package: amr-exp-parabolic * removed boilerplate and added tag
2017-07-19Package/xsbench (#4822)pkondamudi1-4/+10
* removed the tags as per comment in PR# 4749 * addressed above comments * changed fortran compiler. * added proxy application tags. * added tags by removing them from description. * addressed comments * used join_path instead of path concat. * added tags and other minor changes. * removed tags from description.
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