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2016-09-22Fix sbang for perl (#1802)Eric2-7/+13
* Perform shebang fix for all files * Fix sbang for perl scripts Otherwise perl would look at the #! line and call sbang again, resulting in an infinite loop.
2016-09-22Remove SPACK_DIRTY env var (#1818)Elizabeth Fischer3-10/+6
* Removed SPACK_DIRTY env var support. * Finished removing SPACK_DIRTY support. * Minor changes.
2016-09-22fix : stops infinite recursion for python 2.6 (#1823)Massimiliano Culpo1-2/+3
2016-09-21Reworking of `lapack_shared_libs` and similar properties (#1682)Massimiliano Culpo33-244/+526
* Turned <provider>_libs into an iterable Modifications : - added class LibraryList + unit tests - added convenience functions `find_libraries` and `dedupe` - modifed non Intel blas/lapack providers - modified packages using blas_shared_libs and similar functions * atlas : added pthread variant * intel packages : added lapack_libs and blas_libs * find_library_path : removed unused function * PR review : fixed last issues * LibraryList : added test on __add__ return type * LibraryList : added __radd__ fixed unit tests fix : failing unit tests due to missing `self` * cp2k and dependecies : fixed blas-lapack related statements in package.py
2016-09-21Flake8 fixes.Todd Gamblin1-23/+23
2016-09-21Merge branch 'qt-osx' of git://github.com/mathstuf/spack into mathstuf-qt-osxTodd Gamblin7-12/+158
2016-09-21Add package for bedtools2 (#1572)George Hartzell1-0/+43
Add package for bedtools2, with support for v2.25.0 and v2.26.0.
2016-09-21Add package for bamtools (#1571)George Hartzell1-0/+45
bamtools provides a C++ API & command-line toolkit for working with BAM data.
2016-09-21Update espresso recipe to track change in spack internals (#1734)Mayeul d'Avezac1-1/+1
2016-09-21Add missing build dependencies to hdf package (#1812)Adam J. Stewart1-7/+7
2016-09-21Update to allow netlib-scalapack to build against netlib-lapack. (#1539)Kelly Thompson1-5/+7
2016-09-21Stop python from linking with system ncurses (#1672)Glenn Johnson2-0/+13
Python will look to link with libncursesw in preference to libncurses. Since ncurses in spack is built without suffixes there is no libncursesw and python will link to the system libncursesw for _curses.so and _curses_panel.so, as well as libpanelw for _curses_panel.so. This PR introduces a patch that simple removes the check for ncursesw in setup.py and therefore sets `curses_library` to `ncurses`.
2016-09-21Build pkg-config files for ncurses (#1673)Glenn Johnson1-1/+4
2016-09-21Fixed bug propagating --dirty flag to sub-installs. (#1625)Elizabeth Fischer4-5/+18
* Fixed bug propagating --dirty flag to sub-installs. * Fix syntax error * Allow --dirty flag to be set with SPACK_DIRTY env var. * Added dirty flag to `spack diy` and `spack setup`, as is currently in `spack install` * flake8
2016-09-21Rework libgd package (#1679)Glenn Johnson1-10/+25
* Added missing libtiff dependency * added dependency on fontconfig * Added version 2.2.3 * use autotools rather than cmake The cmake build was not producing a complete install. * There was no versioning of the installed libraries. * gdlib-config was missing * pkgconfig directory was missing These problems do not happen when built with autotools.
2016-09-21Adds all available CrayPE CPU targets to platform by default. (#1745)Matt Belhorn1-42/+67
2016-09-21Merge branch 'efischer/160914-FixBinutils226Question' of ↵Todd Gamblin3-4/+5
git://github.com/citibeth/spack into bugfix/efischer-160914-FixBinutils226Question
2016-09-21Close #1683 Apply ADIOS 1.10.0 Patch (HDF5 1.10+) (#1699)Axel Huebl2-9/+42
* Close #1683 Apply ADIOS 1.10.0 Patch Also correct version dependencies and comments. * Clean Up ADIOS - add develop - simplify HDF5 options (parallel only) - remove optional netCDF (not fully v4)
2016-09-21cp2k : added dependencies (#1724)Massimiliano Culpo4-7/+157
* wannier90 : added package (#24) * wannier90 : added package * cp2k : added dependency on wannier90 * elpa : updated package, added cp2k dependency (#26) Conflicts: var/spack/repos/builtin/packages/elpa/package.py
2016-09-21Set JAVA_HOME on module load and on dependent installs. (#1716)Alfredo Adolfo Gimenez2-0/+7
* Set JAVA_HOME on module load and on dependent installs. * Include environment setup from dependencies in dependee module (#1714)
2016-09-21grackle : added package (#1725)Massimiliano Culpo2-0/+160
Modifications : * grackle : added package * grackle : added version 2.2
2016-09-21Wrap yt package (#1751)Erik Schnetter1-0/+78
yt is a python package for analyzing and visualizing volumetric, multi-resolution data from astrophysical simulations, radio telescopes, and a burgeoning interdisciplinary community.
2016-09-21Qt library: added variant to enable/disable compilation of examples (#1763)Sergey Kosukhin1-1/+7
2016-09-20Compiling python with gnu c++ on macos fails with toolboxglue enabled.Patrick Gartung1-0/+2
2016-09-20fix MacOs class for Sierra (#1811)Denis Davydov1-1/+1
2016-09-20added STAT release 3.0.0Gregory L. Lee1-2/+2
2016-09-20Julia: Add version 0.5.0 (#1809)Erik Schnetter1-2/+3
2016-09-20Remove url_for_version as it breaks spack info (#1503)Adam J. Stewart1-6/+0
2016-09-20Update Package: Git-LFS (#1769)Joseph Ciurej3-27/+109
* Fixed a few small bugs in the 'git-lfs' install script. * Fixed a bug in the '(go|go-bootstrap)@1.4.2+test' install scripts. * Fixing a minor style issue in the 'git-lfs' install script.
2016-09-20PETSc: Explicitly point to cpp when configuring (#1807)Erik Schnetter1-0/+4
I encountered an HPC system where PETSc's configure stage does not find a valid `cpp` (C preprocessor). Explicitly pointing to Spack's `cpp` wrapper resolves the problem.
2016-09-20Remove lingering boilerplate FIXMEs (#1756)Adam J. Stewart5-9/+8
2016-09-20fix : failing unit tests due to missing `self` (#1806)Massimiliano Culpo1-2/+2
2016-09-20Update Package: Metis (#1783)Joseph Ciurej2-84/+91
* Fixed a bug that was causing post-install METIS tests to fail. * Improved the patching procedure used in the 'metis' install script. * Enabled patch skipping for the 'metis' and 'parmetis' packages. * Fixed some minor style issues in the 'parmetis' package. * Improved the 'metis' test fix and added 'run_tests' support.
2016-09-20Add UberFTP utility (#1780)Robert D. French1-0/+44
2016-09-20dealii: add 8.4.2 (#1782)Denis Davydov1-5/+6
2016-09-20Add Python support to gdb. (#1790)Bruno Turcksin1-1/+10
2016-09-20Update Package : Zoltan (#1793)Joseph Ciurej1-44/+71
* Refactored and reorganized the 'zoltan' install script. * Fixed a few bugs with the '+mpi' and '+fortan' variants of 'zoltan'. * Reintroduced and improved the '+shared' variant for the 'zoltan' package. * Improved compatibility with different MPI providers for 'zoltan'.
2016-09-20Fix format string (in class RemoveFailedError) (#1803)Eric1-1/+1
2016-09-20samtools could not find the ncurses library (#1785)Tom Merrick1-1/+2
2016-09-20lmod : added support for the creation of hierarchical lua module files (#1723)Massimiliano Culpo10-149/+560
Includes : - treatment of a generic hierarchy (i.e. lapack + mpi + compiler) - possibility to specify which compilers are to be considered Core - correct treatment of the 'family' directive - unit tests for most new features
2016-09-20Allow multi-user installations (#1804)Eric1-1/+1
When re-using previously downloaded tarballs, spack copies from `var/spack/stage/PACKAGE-VERSION-HASH/downloaded_file` to `var/spack/cache/PACKAGE/downloaded_file`. This fails if the source is owned by a different user (`shutil.copy` tries to retain all meta data including file ownership). Change to a non-meta-data copy function (`shutil.copyfile`).
2016-09-20Update Julia to 0.4.7 (#1805)Erik Schnetter1-1/+2
2016-09-20Make VisIt build again (#1762)Erik Schnetter1-1/+4
- add new version 2.10.3 - explicitly require hdf5 variant ~mpi, since we don't know how to build with mpicc - explicitly disable glew since it may not be installed
2016-09-20Work around cmake problems in VTK (#1761)Erik Schnetter2-0/+23
The cmake scripts can't handle the semicolons in gcc's version output. Filter them out before detecting the version.
2016-09-20Tighten HDF5 version requirements for Silo (#1760)Erik Schnetter1-1/+2
2016-09-20Make cmake @2.8 build again (#1759)Erik Schnetter1-5/+7
2016-09-20Update hwloc to 1.11.4 (#1752)Erik Schnetter1-0/+1
2016-09-20Declare py-beautifulsoup4's dependency on py-setuptools (#1748)Erik Schnetter1-0/+2
2016-09-20Update curl to 7.50.3 (#1747)Erik Schnetter1-0/+2
* Update curl to 7.50.2 * Update curl to 7.50.3
2016-09-20Update OpenMPI to 2.0.1 (#1721)Erik Schnetter1-0/+1
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