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2017-04-22add Intel mpi package and add MPI wrappers to Intel parallel studio (#3905)Denis Davydov2-0/+89
* intel-mpi: add new package * fix hashes * fix typo * flake8 * add install * blank line * error * add bin64 * fix MPI wrappers in intel-parallel-studio * add missing I_MPI_FC * use shorter hashes
2017-04-21more fixes for use of setuptools in python packagesMatthew Krafczyk3-1/+37
- py-setuptools is required by py-yt for importing yt in jupyter notebooks. - add two dependencies needed for python 2.7 - add the py-subprocess32 package
2017-04-21Fix setuptools handling in Python packages.Paul Hopkins12-5/+8
- add setuptools dependencies to packages that need it. - remove setuptools from packages that do not need it.
2017-04-21PythonPackage builds flat installs instead of egg directories.Todd Gamblin18-26/+45
- Spack doesn't need eggs -- it manages its own directories - Simplify install layout and reduce sys.path searches by installing all packages flat (eggs are deprecated for wheels, and this is also what wheels do). - We now supply the --single-version-externally-managed argument to `setup.py install` for setuptools packages and setuptools. - modify packages to only use setuptools args if setuptools is an immediate dependency - Remove setuptools from packages that do not need it. - Some packages use setuptools *only* when certain args (likeb 'develop' or 'bdist') are supplied to setup.py, and they specifically do not use setuptools for installation. - Spack never calls setup.py this way, so just removing the setuptools dependency works for these packages.
2017-04-21Convert LLVM to CMakePackage, update cmake dependency version (#3940)Adam J. Stewart1-26/+27
* Convert LLVM to CMakePackage, update cmake dependency version * Remove unused import
2017-04-21Add info for nextflow@0.17.3 (#3947)George Hartzell1-0/+2
2017-04-21Fix checksumming in Python3; add more fetch tests (#3941)Todd Gamblin1-0/+35
* Checksum code wasn't opening binary files as binary. - Fixes Python 3 issue where files are opened as unicode text by default, and decoding fails for binary blobs. * Simplify fetch test parametrization. * - add tests for URL fetching and checksumming. - fix coverage on interface functions in FetchStrategy superclass - add some extra crypto tests.
2017-04-21Remove all test variants (#3923)Todd Gamblin8-23/+17
2017-04-21netcdf: fix missing CC = mpicc ; this makes it work with Intel MPI (#3942)Denis Davydov1-1/+2
2017-04-21add cppcheck new version (#3935)Jeffrey Salmond1-1/+2
2017-04-21Ensure that tests are optional (#3922)Adam J. Stewart13-14/+24
2017-04-21Fix HPL build, convert to MakefilePackage (#3777)Adam J. Stewart3-41/+69
* Fix HPL build, convert to MakefilePackage * Flake8 fix * Fix: spec -> self.spec * Properly query for system libraries * Update Intel-MKL as well * Recurse in system libs, fix MKL path, fixes lapack_libs
2017-04-21Adding new python package: py-python-gitlab (#3936)Javier1-0/+41
2017-04-21Fix for llvm 4.0.0 on centos (#3904)Jimmy Tang1-0/+3
* Fix for llvm 4.0.0 on centos This addresses https://github.com/LLNL/spack/issues/3791 * Only enable this option if on linux * Change condition to satisfy standard
2017-04-21Add boost 1.64.0 (#3934)Bruno Turcksin1-0/+1
2017-04-20Keras 2.0.3 (#3927)Brian Van Essen1-0/+1
* Added a package for the MDAnalysis toolkit. * Added has for Keras version 2.0.3
2017-04-20Add vampirtrace (#3911)Michael Kuhn1-0/+73
Since scorep does not support all use cases yet, vampirtrace is still useful in some circumstances.
2017-04-20Gettext test suite fails when run in parallel (#3921)Adam J. Stewart1-0/+10
2017-04-20Flake8Adam J. Stewart1-1/+1
2017-04-20Remove all test variantsAdam J. Stewart8-22/+16
2017-04-20Revert "Override partial installs by default" (#3918)Todd Gamblin1-41/+0
* Revert "Override partial installs by default (#3530)" This reverts commit a65c37f15dff4b4d60784fd4fcc55874ce9d6d11.
2017-04-19Override partial installs by default (#3530)scheibelp1-0/+41
* Package install remove prior unfinished installs Depending on how spack is terminated in the middle of building a package it may leave a partially installed package in the install prefix. Originally Spack treated the package as being installed if the prefix was present, in which case the user would have to manually remove the installation prefix before restarting an install. This commit adds a more thorough check to ensure that a package is actually installed. If the installation prefix is present but Spack determines that the install did not complete, it removes the installation prefix and starts a new install; if the user has enabled --keep-prefix, then Spack reverts to its old behavior. * Added test for partial install handling * Added test for restoring DB * Style fixes * Restoring 2.6 compatibility * Relocated repair logic to separate function * If --keep-prefix is set, package installs will continue an install from an existing prefix if one is present * check metadata consistency when continuing partial install * Added --force option to make spack reinstall a package (and all dependencies) from scratch * Updated bash completion; removed '-f' shorthand for '--force' for install command * dont use multiple write modes for completion file
2017-04-19Add variant to mvapich2 to set size of rank bits (#3886)Adam J. Stewart1-0/+7
2017-04-19binutils should link to Spack zlib installation (#3914)Adam J. Stewart1-7/+10
2017-04-19Add latest version of HOOMD-blue (#3889)Adam J. Stewart1-21/+40
2017-04-19Rework Spack's Mercurial support (#3834)Adam J. Stewart11-44/+117
* Add tests to mercurial package * Add support for --insecure with mercurial fetching * Install man pages and tab-completion scripts * Add tests and latest version for all deps * Flake8 fix * Use certifi module to find CA certificate * Flake8 fix * Unset PYTHONPATH when running hg * svn_fetch should use to svn-test, not hg-test * Drop Python 3 support in Mercurial Python 3 support is a work in progress and isn't currently recommended: https://www.mercurial-scm.org/wiki/SupportedPythonVersions * Test both secure and insecure hg fetching * Test both secure and insecure git and svn fetching
2017-04-19Sox (#3908)Jimmy Tang5-0/+276
* Initial add of flac * Initial add of id3lib * Initial add of the opus codec * Initial add of sox audio processing tools * Cleanup spec files to be inline with current standard * Fix pep8 compliance * Remove un-needed configuration
2017-04-19Add info for sqlite@3.18.0 (#3913)George Hartzell1-0/+2
2017-04-19add lines missed in rebase (adios +bzip2) (#3907)Mark Olesen1-0/+2
2017-04-19ncl: capture more dependencies (#3902)Milton Woods1-0/+6
* ncl: add depends_on statements for bison, flex and libiconv * ncl: depends on flex for building and linking * ncl: links with -ll, so requires flex with variant '+lex' * ncl: depends on szip; external hdf5 may not provide it
2017-04-19pango: depends on libxft when +X, disable libxft support when ~X (#3899)Milton Woods1-0/+9
2017-04-19Ensure sbin is prepended to PATH in modulefiles (#3843)George Hartzell1-0/+4
2017-04-19espresso: add 6.1.0 (#3881)Denis Davydov2-6/+38
* espresso: fix missing dependency on elpa, add 6.1.0 * override default libs of elpa to get shared always
2017-04-19gdbm: GNU dbm package for manipulating hashed databases (#3895)Milton Woods1-0/+46
2017-04-18Disable parallel builds for vim (#3893)George Hartzell1-0/+6
* Disable parallel builds The install step creates a bunch of links to the vim binary, e.g. `view`. When run with -j greater than 1 there are silent failures. Running w/out parallelism seems to fix it. * Only constrain the install phase to be -j 1 Thanks @adamjstewart!
2017-04-18Adding new python package: py-simplejson (#3883)Javier1-0/+41
* Adding new python package: py-simplejson * Adding setuptools dependency * Fixing typo
2017-04-18charm: set sane default (#3865)Christoph Junghans1-33/+5
see https://github.com/LLNL/spack/pull/3852#pullrequestreview-32996651 for details
2017-04-18ocotpus and arpack-ng: fix arpack bug and add libs to arpack-ng (#3875)Denis Davydov2-11/+27
* ocotpus and arpack-ng: fix arpack bug and add libs to arpack-ng also rename the variant to be consistent with other packages * fix a bug * flake8
2017-04-18Add version info for git-lfs v2.0.2 (#3885)George Hartzell1-0/+1
2017-04-18Provide version 3.8.0 of CMake. (#3882)Kelly (KT) Thompson1-0/+1
2017-04-18Adding new package: sas (#3877)Javier1-0/+56
2017-04-18ape: constrain libxc version (#3876)Denis Davydov1-1/+1
2017-04-18ADIOS - add bzip2 transport, python patch not applicable to adios 1.9.0 (#3874)Mark Olesen1-2/+4
2017-04-18Added expat dependency to apr-util (#3871)sknigh1-0/+2
2017-04-18Add patched openfst-1.4.1 and kaldi@c024e8 required by CNTK. (#3806)健美猫5-9/+321
2017-04-18octave: add 4.2.1 (#3872)Denis Davydov2-3/+21
Also switch to arpack-ng, which is maintained and has bugfixes, whereas the original arpack code is abandoned.
2017-04-18gmsh: add 3.0.1 (#3873)Denis Davydov1-0/+1
2017-04-17Add a py-fiscalyear package (#3864)Adam J. Stewart5-6/+155
* Add a py-fiscalyear package * Declare supported Python versions
2017-04-17Add latest numpy release (#3869)Adam J. Stewart1-0/+2
2017-04-17opneblas: fix compilation with clang (#3862)Denis Davydov2-6/+851
* opneblas: fix compilation with clang * indentation