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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
2017-08-11Elemental fix (#5067)Brian Van Essen2-2/+5
* Added a package for the MDAnalysis toolkit. * Added additional packages that Elemental depends on. * Changed LBANN to not ask for the scalapack variant in Elemental. * Removed variant control on scalapack
2017-08-10New package: qbox (#4711)EmreAtes3-3/+100
* New package: qbox * API changes * Use install instead of shutil for comd * Use any BLAS library * Fix typo * Python2 fix * python2 + fix backslashes * Modified to respond to ld_flags correctly * Modified to use ld_flags * Add ld_flags support
2017-08-10Add AMG2013 package (#4836)Akhil Reddy Patlolla1-0/+73
* Updated Changes * Updated AMG with required MPI * Updated AMG with Version ' changes' * Fixed Issues with flag's and variant checks * Updated with MPI Alone and Changes - NO Serial Variant * Updated with MPI Alone and Changes - NO Serial Variant * Fixed Flake 8 line length error * Updated Spack Issues
2017-08-10 Variants Serial MPI openmp (#4897)Akhil Reddy Patlolla2-79/+47
* Variants Serial MPI openmp * Fixed Flake8 Issue and remove Patch File * Fixed issues with openmp Flag * Edited Required Changes * Fixed issues with flake8 and Added Conditional GCC Flags * Fixed Flake 8 Issue * Fixed flag's issue with non GCC Compiler * Fixed condition and spacing issues
2017-08-10braker & genemark-et: new packages (#5058)Audrey Thoma3-0/+106
* braker & genemark-et: new packages * fixing install
2017-08-10fimpute: new package (#5060)Audrey Thoma1-0/+40
2017-08-10impute2: new package (#5062)Audrey Thoma1-0/+39
2017-08-10mothur: new package (#5055)Audrey Thoma1-0/+59
* mothur: new package * fixing mpi things
2017-08-10Update Krell products: Add new OpenSpeedShop gui package based on qt4/qt5 ↵Jim Galarowicz1-0/+97
gui toolkit. (#5056) * 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. * Add new OpenSpeedShop gui package based on qt4/qt5 gui toolkit. * Fix flake8 errors. * Fix flake8 errors.
2017-08-10gblocks: new package (#5061)Audrey Thoma1-0/+40
2017-08-10kallisto: new package (#5063)Audrey Thoma1-0/+39
2017-08-10fastphase: new package (#5059)Audrey Thoma1-0/+39
2017-08-10go: Fix cgo (#5052)Michael Kuhn1-0/+4
2017-08-09Add version 2.19.1.403 to bcl2fastq2 package (#5047)George Hartzell1-3/+10
* Update bcl2fastq2 with info for 2.19.1.403 Heads up, the download location changed (domain name AND protocol). * Flake8 fix What's one space between friends?
2017-08-09soapindel: new package (#5048)Audrey Thoma1-0/+53
* soapindel: new package * fixed versioning
2017-08-09Adding lower bound to pnetcdf conflict in Trilinos (#5039)Jon Rood1-1/+1
* Adding lower bound to pnetcdf conflict in Trilinos to allow for use of develop and master branch. * Using even lower bound for pnetcdf conflict in Trilinos.
2017-08-09soap2: new package (#5045)Audrey Thoma1-0/+42
2017-08-09haploview: new package (#5036)Audrey Thoma2-0/+57
2017-08-09soapsnp: new package (#5046)Audrey Thoma1-0/+42
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