Commit graph

6301 commits

Author SHA1 Message Date
Brian Van Essen
011442fd37 Keras 2.0.3 (#3927)
* Added a package for the MDAnalysis toolkit.

* Added has for Keras version 2.0.3
2017-04-20 17:48:30 -05:00
Michael Kuhn
f520c0dd8d Add vampirtrace (#3911)
Since scorep does not support all use cases yet, vampirtrace is still
useful in some circumstances.
2017-04-20 15:01:06 -05:00
Adam J. Stewart
e2e6dea9b3 Gettext test suite fails when run in parallel (#3921) 2017-04-20 13:06:11 -05:00
Adam J. Stewart
f0a6ead19c Flake8 2017-04-20 12:48:02 -05:00
Adam J. Stewart
9ca0d1f5f0 Remove all test variants 2017-04-20 12:13:11 -05:00
Adam J. Stewart
21e4a81de0 Add Napoleon extension to support Google docstrings (#3920) 2017-04-20 08:32:21 -07:00
Todd Gamblin
beeca6bb54 Revert "Override partial installs by default" (#3918)
* Revert "Override partial installs by default (#3530)"

This reverts commit a65c37f15d.
2017-04-20 03:53:41 -07:00
Todd Gamblin
fa3e91bf2a Revert "Add lmod files to MODULEPATH" (#3917)
* Revert "Add lmod files to MODULEPATH (#3912)"

This reverts commit 186d1f4511.
2017-04-20 03:05:44 -07:00
Massimiliano Culpo
50d7b33563 test/python_version.py: ported to pytest (#3438) 2017-04-20 01:18:52 -07:00
scheibelp
a65c37f15d Override partial installs by default (#3530)
* 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
2017-04-19 21:59:18 -07:00
Adam J. Stewart
e12f2c1855 Set proper deptypes for certain build systems (#3866)
* Set proper deptypes for certain build systems

* Add depends_on to namespace
2017-04-19 21:33:14 -07:00
Adam J. Stewart
9bd6d21322 Add variant to mvapich2 to set size of rank bits (#3886) 2017-04-19 21:31:21 -07:00
Adam J. Stewart
186d1f4511 Add lmod files to MODULEPATH (#3912) 2017-04-19 21:30:08 -07:00
Adam J. Stewart
3c0c0f3457 binutils should link to Spack zlib installation (#3914) 2017-04-19 21:29:27 -07:00
Adam J. Stewart
f51af42bc6 Add latest version of HOOMD-blue (#3889) 2017-04-19 21:24:32 -07:00
Adam J. Stewart
f4858cb7a7 Rework Spack's Mercurial support (#3834)
* 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
2017-04-19 18:59:04 -07:00
Jimmy Tang
53763f7698 Sox (#3908)
* 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
2017-04-19 16:21:13 -05:00
George Hartzell
a3dff31b07 Add info for sqlite@3.18.0 (#3913) 2017-04-19 16:15:21 -05:00
Mark Olesen
22a966d010 add lines missed in rebase (adios +bzip2) (#3907) 2017-04-19 09:36:46 -05:00
Milton Woods
9b6b91b0b9 ncl: capture more dependencies (#3902)
* 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
2017-04-19 06:55:22 -05:00
Milton Woods
b00a12565c pango: depends on libxft when +X, disable libxft support when ~X (#3899) 2017-04-19 06:54:06 -05:00
George Hartzell
13fef18244 Ensure sbin is prepended to PATH in modulefiles (#3843) 2017-04-19 06:51:04 -05:00
Denis Davydov
eaefaaba5b espresso: add 6.1.0 (#3881)
* espresso: fix missing dependency on elpa, add 6.1.0

* override default libs of elpa to get shared always
2017-04-19 12:34:42 +02:00
Milton Woods
13911f1b46 gdbm: GNU dbm package for manipulating hashed databases (#3895) 2017-04-19 09:32:00 +02:00
George Hartzell
a0b19d50c5 Disable parallel builds for vim (#3893)
* 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!
2017-04-18 20:46:09 -05:00
Javier
687f5e78ae Adding new python package: py-simplejson (#3883)
* Adding new python package: py-simplejson

* Adding setuptools dependency

* Fixing typo
2017-04-18 12:02:55 -05:00
Christoph Junghans
2a3fc6c404 charm: set sane default (#3865)
see https://github.com/LLNL/spack/pull/3852#pullrequestreview-32996651
for details
2017-04-18 12:02:41 -05:00
Denis Davydov
ce714b5641 ocotpus and arpack-ng: fix arpack bug and add libs to arpack-ng (#3875)
* 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
2017-04-18 11:50:10 -05:00
George Hartzell
afbe81b455 Add version info for git-lfs v2.0.2 (#3885) 2017-04-18 11:48:53 -05:00
Kelly (KT) Thompson
fad4ce21cc Provide version 3.8.0 of CMake. (#3882) 2017-04-18 10:59:59 -05:00
Javier
7ed99a4c86 Adding new package: sas (#3877) 2017-04-18 07:07:07 -05:00
Denis Davydov
5558bec14e ape: constrain libxc version (#3876) 2017-04-18 07:03:48 -05:00
Mark Olesen
c65d0775cf ADIOS - add bzip2 transport, python patch not applicable to adios 1.9.0 (#3874) 2017-04-18 07:00:39 -05:00
sknigh
d17b5eb2b9 Added expat dependency to apr-util (#3871) 2017-04-18 06:57:49 -05:00
健美猫
4e95525280 Add patched openfst-1.4.1 and kaldi@c024e8 required by CNTK. (#3806) 2017-04-18 06:56:18 -05:00
Denis Davydov
fc938962fa octave: add 4.2.1 (#3872)
Also switch to arpack-ng, which is maintained and has bugfixes,
whereas the original arpack code is abandoned.
2017-04-18 06:55:11 -05:00
Denis Davydov
89f531c18a gmsh: add 3.0.1 (#3873) 2017-04-18 11:30:17 +02:00
Adam J. Stewart
6d7b386199 Add a py-fiscalyear package (#3864)
* Add a py-fiscalyear package

* Declare supported Python versions
2017-04-17 16:46:52 -05:00
Adam J. Stewart
ebf30d95cd Add latest numpy release (#3869) 2017-04-17 15:45:52 -05:00
Denis Davydov
0ed18de836 opneblas: fix compilation with clang (#3862)
* opneblas: fix compilation with clang

* indentation
2017-04-17 09:16:18 -05:00
Michael Kuhn
3331c042af Fix udunits2 (#3809) 2017-04-17 09:15:02 -05:00
Adam J. Stewart
cc747d6b6f Remove redundant cmake dependencies (#3860) 2017-04-16 12:23:26 -05:00
Christoph Junghans
675a67e2ca random123: put uniform.hpp in right subfolder (#3858) 2017-04-16 08:47:46 -05:00
Christoph Junghans
a3378ccd3d charm: add support for shared linking (#3859) 2017-04-16 08:47:00 -05:00
Christoph Junghans
fdc8f71a5c trilinos: allow to compile exodus (#3857) 2017-04-15 21:57:44 -05:00
Christoph Junghans
1d514f48bc random123: install uniform.hpp as well (#3856) 2017-04-15 21:57:19 -05:00
Adam J. Stewart
5aa273b319 Fix flake8 changed files detection (#3855) 2017-04-15 11:46:28 -05:00
Adam J. Stewart
bd1beedaf5 Allow users to set parallel jobs in config.yaml (#3812)
* Allow users to set parallel jobs in config.yaml

* Undo change from endash to emdash

* Remove parallel config, rename jobs to build_jobs
2017-04-15 08:31:00 -07:00
Erik Schnetter
62fb1ad990 hpx5: Add patch to select Spack compiler on Cray (#3798) 2017-04-14 22:38:22 -05:00
Christoph Junghans
caad110757 New package: flecsi (#3780)
* New package: flecsi

* make fetch independent of #3779
2017-04-14 17:56:36 -05:00