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2016-09-27Make graph_ascii support deptypes.Todd Gamblin6-27/+37
- fix deptype support - by default, graph command omits build depedencies - update docs to use deptype args
2016-09-27Fixes #1098: spack graph crashes for large graphs.Todd Gamblin1-6/+15
- Fixed logic for collapsing backward edges - Last collapse now depends on whether prior step in left collapse sequence alrady did the collapse.
2016-09-27Improvements to the Spack graph command.Todd Gamblin3-29/+103
- Distinguish between static (package) and dynamic (spec) graphs. - static graphs ignore conditions and multiple instances (hashes) and plot raw dependencies among packages. - dynamic graphs include information from particular specs (instances of packages) and can have multiple instances with hashes. - Allow graphing all packages in the install DB. - useful for debugging.
2016-09-27Factor out canonical_deptype function, cleanup spec.pyTodd Gamblin2-41/+100
2016-09-27Clean up Exceptions in `spec.py`Todd Gamblin2-63/+6
2016-09-26Make PETSc build on Darwin (#1835)Erik Schnetter1-4/+7
Don't set cpp when building on Darwin.
2016-09-26Update OpenSSL (#1853)Erik Schnetter1-0/+1
2016-09-26some fixes to blas/lapack usage in packages (#1852)Denis Davydov12-43/+29
* atlas: fix unit test * openblas: remove symlinks; use lapack_libs.ld_flags in the test * mkl: fix openmp variant of blas/lapack libs * intel-parallel-studio: fix openmp variant of blas/lapack libs * netlib-scalapack: fix blas/lapack for multilib case (e.g. mkl) * arpack-ng: fix blas/lapack for multilib case (e.g. mkl) * petsc: explicitly specify blas/lapack * minor * cantera: fix blas/lapack usage * ipopt: fix blas/lapack usage * netlib-lapack: fix external blas usage * mfem: fix lapack/blas usage * superlu-mt: fix blas usage * flake8 fixes
2016-09-23Fix doc bugs, widen columns in the package listTodd Gamblin2-2/+2
2016-09-23a few package used in HEP including ROOT6Patrick Gartung10-0/+607
2016-09-23Remove duplicate ICU package (#1837)Adam J. Stewart7-65/+17
* Remove duplicate ICU package * Ignore deleted files during flake8 tests * Rename Boost ICU variant
2016-09-23m4: fix compilation on Sierra with GCC (#1844)Denis Davydov1-0/+6
* m4: fix compilation on Sierra with GCC * m4: check macOS version
2016-09-23Add Trilinos 12.8.1 (#1843)Bruno Turcksin1-0/+1
2016-09-23Don't require git for Julia @0.5: (#1834)Erik Schnetter1-1/+2
2016-09-23Update jemalloc to 4.2.1 (#1839)Erik Schnetter1-0/+2
2016-09-23Add libmesh, needed for some FEM applications (#1846)Robert D. French1-0/+42
2016-09-23hypre: fix a bug with blas/lapack names (#1841)Denis Davydov1-7/+2
2016-09-23Update OpenSSL (#1836)Erik Schnetter1-0/+2
This is a security update with priority "HIGH".
2016-09-22boost: fix a bug which broke it on macOS with clang+gfortran (#1816)Denis Davydov2-4/+19
* dealii: add missing python dependency * boost: fix a bug which broke it on macOS with clang+gfortran Boost was using gcc compiler instead of clang++, which lead to cryptic Undefined symbols linking errors for boost::python::objects::function_object() when building other packages against boost+python. * boost: add exceptions for intel * boost: use spack_cxx
2016-09-22Updates to CGAL and ICU4C packages (#1828)Adam J. Stewart2-26/+42
2016-09-22package: fix variable name usage (#1829)Ben Boeckel1-1/+1
2016-09-22Fix spack checksum output indentation (#1826)Adam J. Stewart1-1/+1
2016-09-22suitesparse: Added +fpic (for linking with shared libraries) (#1542)Elizabeth Fischer1-0/+3
2016-09-22New package "charm" for the Charm++ parallel programming framework (#1766)Erik Schnetter2-0/+191
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
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